Causal inference for complex data: randomization inference for treatment effect heterogeneity, network outcomes, and subgroup specific effects

This dissertation presents three new methodologies for analyzing randomized controlled trials using the researcher controlled randomization mechanism as the basis for inference. The first method extends inference for the ``attributable effect'', the total of the difference of outcomes if the treatment group had instead been assigned to the control condition, to count and continuous data using a fast approximation algorithm. Alternative approaches are limited to binary data, require asymptotic approximations, or are computationally expensive. A refinement of the method to allow for including additional information is also included. The second method extends randomization inference to the study of network formation. Previous approaches either required strong parametric assumptions or only allowed for pre-treatment networks to be used. This approach develops several test statistics that can be used to test against common network formation models, based purely on the randomization of treatment. The final method improves inference in cluster randomized trials, where collections of individuals are assigned to treatment conditions simultaneously. Under the appealing assumption that larger clusters will have larger outcomes, on average, the method provides efficient, unbiased estimation of average treatment effects requiring minimal additional assumptions. All three of these methods demonstrate the relevance of randomized controlled trials to key areas of science and statistical development as well as the advantages of carefully crafting study design to fit the problem of interest. Data examples include a large scale field experiment involving health insurance, a gene-wide association study involving high dimensional outcomes, and a policy relevant study of parental social capital and student achievement in schools

Shear Alignment and Instability of Smectic Phases

We consider the shear flow of well-aligned one-component smectic phases, such as thermotropic smectics and lamellar diblock copolymers, below the critical region. We show that, as a result of thermal fluctuations of the layers, parallel ($c$) alignment is generically unstable and perpendicular ($a$) alignment is stable against long-wavelength undulations. We also find, surprisingly, that both $a$ and $c$ are stable for a narrow window of values for the anisotropic viscosity.Comment: To appear in PRL. Revtex, 1 figure

Field-theoretic simulation of block copolymers at experimentally-relevant molecular weights

Field-theoretic simulation (FTS) offers an efficient means of predicting the equilibrium behavior of high-molecular-weight structured polymers, provided one is able to deal with the strong ultraviolet (UV) divergence that occurs at realistic molecular weights. Here melts of lamellar-forming diblock copolymer are studied using a Monte Carlo version (MC-FTS), where the composition field fluctuates while the pressure field follows the mean-field approximation. We are able to control the UV divergence by introducing a new effective Flory-Huggins interaction parameter, $\chi_e$, thereby permitting MC-FTS for molecular weights extending down to values characteristic of experiment. Results for the disordered-state structure function, the layer spacing and compressibility of the ordered lamellar phase, and the position of the order-disorder transition (ODT) show excellent agreement with recent particle-based simulation. Given the immense versatility of FTS, this opens up the opportunity for quantitative studies on a wide range of more complicated block copolymer systems

Facial expressions depicting compassionate and critical emotions: the development and validation of a new emotional face stimulus set

Attachment with altruistic others requires the ability to appropriately process affiliative and kind facial cues. Yet there is no stimulus set available to investigate such processes. Here, we developed a stimulus set depicting compassionate and critical facial expressions, and validated its effectiveness using well-established visual-probe methodology. In Study 1, 62 participants rated photographs of actors displaying compassionate/kind and critical faces on strength of emotion type. This produced a new stimulus set based on N = 31 actors, whose facial expressions were reliably distinguished as compassionate, critical and neutral. In Study 2, 70 participants completed a visual-probe task measuring attentional orientation to critical and compassionate/kind faces. This revealed that participants lower in self-criticism demonstrated enhanced attention to compassionate/kind faces whereas those higher in self-criticism showed no bias. To sum, the new stimulus set produced interpretable findings using visual-probe methodology and is the first to include higher order, complex positive affect displays

Positive Affect Predicts Cerebral Glucose Metabolism in Late Middle-aged Adults.

Positive affect is associated with a number of health benefits; however, few studies have examined the relationship between positive affect and cerebral glucose metabolism, a key energy source for neuronal function and a possible index of brain health. We sought to determine if positive affect was associated with cerebral glucose metabolism in late middle-aged adults (n = 133). Participants completed the positive affect subscale of the Center for Epidemiological Studies Depression Scale at two time points over a two-year period and underwent 18F-fluorodeoxyglucose-positron emission tomography scanning. After controlling for age, sex, perceived health status, depressive symptoms, anti-depressant use, family history of Alzheimer’s disease, APOE ε4 status and interval between visits, positive affect was associated with greater cerebral glucose metabolism across para-/limbic, frontal, temporal and parietal regions. Our findings provide evidence that positive affect in late midlife is associated with greater brain health in regions involved in affective processing and also known to be susceptible to early neuropathological processes. The current findings may have implications for interventions aimed at increasing positive affect to attenuate early neuropathological changes in at-risk individuals

First-in-human phase I study of pictilisib (GDC-0941), a potent pan-class I phosphatidylinositol-3-kinase (PI3K) inhibitor, in patients with advanced solid tumors.

PURPOSE: This first-in-human dose-escalation trial evaluated the safety, tolerability, maximal-tolerated dose (MTD), dose-limiting toxicities (DLT), pharmacokinetics, pharmacodynamics, and preliminary clinical activity of pictilisib (GDC-0941), an oral, potent, and selective inhibitor of the class I phosphatidylinositol-3-kinases (PI3K). PATIENTS AND METHODS: Sixty patients with solid tumors received pictilisib at 14 dose levels from 15 to 450 mg once-daily, initially on days 1 to 21 every 28 days and later, using continuous dosing for selected dose levels. Pharmacodynamic studies incorporated (18)F-FDG-PET, and assessment of phosphorylated AKT and S6 ribosomal protein in platelet-rich plasma (PRP) and tumor tissue. RESULTS: Pictilisib was well tolerated. The most common toxicities were grade 1-2 nausea, rash, and fatigue, whereas the DLT was grade 3 maculopapular rash (450 mg, 2 of 3 patients; 330 mg, 1 of 7 patients). The pharmacokinetic profile was dose-proportional and supported once-daily dosing. Levels of phosphorylated serine-473 AKT were suppressed >90% in PRP at 3 hours after dose at the MTD and in tumor at pictilisib doses associated with AUC >20 h·μmol/L. Significant increase in plasma insulin and glucose levels, and >25% decrease in (18)F-FDG uptake by PET in 7 of 32 evaluable patients confirmed target modulation. A patient with V600E BRAF-mutant melanoma and another with platinum-refractory epithelial ovarian cancer exhibiting PTEN loss and PIK3CA amplification demonstrated partial response by RECIST and GCIG-CA125 criteria, respectively. CONCLUSION: Pictilisib was safely administered with a dose-proportional pharmacokinetic profile, on-target pharmacodynamic activity at dose levels ≥100 mg and signs of antitumor activity. The recommended phase II dose was continuous dosing at 330 mg once-daily.This study was supported by Genentech Inc. The Drug Development Unit, The Royal Marsden NHS Foundation Trust, and The Institute of Cancer Research (London) is supported in part by programme grants from Cancer Research UK. Support was also provided by Experimental Cancer Medicine Center grants (to The Institute of Cancer Research and the Cancer Research UK Center), the National Institute for Health Research Biomedical Research Center (jointly to The Royal Marsden NHS Foundation Trust and The Institute of Cancer Research) and the Wellcome Trust (grant 090952/Z/09/Z to Dr. Ang). Paul Workman is a Cancer Research UK Life Fellow.Originally published by the American Association for Cancer Research in Clinical Cancer Research January 1, 2015 21; 77 http://dx.doi.org/10.1158/1078-0432.CCR-14-094

Multi-Scale Mass Transfer Processes Controlling Natural Attenuation and Engineered Remediation: An IFRC Focused on Hanford?s 300 Area Uranium Plume January 2010 to January 2011

The Integrated Field Research Challenge (IFRC) at the Hanford Site 300 Area uranium (U) plume addresses multi-scale mass transfer processes in a complex subsurface biogeochemical setting where groundwater and riverwater interact. A series of forefront science questions on reactive mass transfer motivates research. These questions relate to the effect of spatial heterogeneities; the importance of scale; coupled interactions between biogeochemical, hydrologic, and mass transfer processes; and measurements and approaches needed to characterize and model a mass-transfer dominated biogeochemical system. The project was initiated in February 2007, with CY 2007, CY 2008, CY 2009, and CY 2010 progress summarized in preceding reports. A project peer review was held in March 2010, and the IFRC project acted upon all suggestions and recommendations made in consequence by reviewers and SBR/DOE. These responses have included the development of 'Modeling' and 'Well-Field Mitigation' plans that are now posted on the Hanford IFRC web-site, and modifications to the IFRC well-field completed in CY 2011. The site has 35 instrumented wells, and an extensive monitoring system. It includes a deep borehole for microbiologic and biogeochemical research that sampled the entire thickness of the unconfined 300 A aquifer. Significant, impactful progress has been made in CY 2011 including: (i) well modifications to eliminate well-bore flows, (ii) hydrologic testing of the modified well-field and upper aquifer, (iii) geophysical monitoring of winter precipitation infiltration through the U-contaminated vadose zone and spring river water intrusion to the IFRC, (iv) injection experimentation to probe the lower vadose zone and to evaluate the transport behavior of high U concentrations, (v) extended passive monitoring during the period of water table rise and fall, and (vi) collaborative down-hole experimentation with the PNNL SFA on the biogeochemistry of the 300 A Hanford-Ringold contact and the underlying redox transition zone. The modified well-field has functioned superbly without any evidence for well-bore flows. Beyond these experimental efforts, our site-wide reactive transport models (PFLOTRAN and eSTOMP) have been updated to include site geostatistical models of both hydrologic properties and adsorbed U distribution; and new hydrologic characterization measurements of the upper aquifer. These increasingly robust models are being used to simulate past and recent U desorption-adsorption experiments performed under different hydrologic conditions, and heuristic modeling to understand the complex functioning of the smear zone. We continued efforts to assimilate geophysical logging and 3D ERT characterization data into our site wide geophysical model, with significant and positive progress in 2011 that will enable publication in 2012. Our increasingly comprehensive field experimental results and robust reactive transport simulators, along with the field and laboratory characterization, are leading to a new conceptual model of U(VI) flow and transport in the IFRC footprint and the 300 Area in general, and insights on the microbiological community and associated biogeochemical processes influencing N, S, C, Mn, and Fe. Collectively these findings and higher scale models are providing a unique and unparalleled system-scale understanding of the biogeochemical function of the groundwater-river interaction zone

The fallibility of memory in judicial processes: Lessons from the past and their modern consequences

The capability of adult and child witnesses to accurately recollect events from the past and provide reliable testimony has been hotly debated for more than one hundred years (Binet, 1900). Prominent legal cases of the 1980s and 1990s sparked lengthy debates and important research questions surrounding the fallibility and general reliability of memory. But what lessons have we learned, some forty years later, about the role of memory in the judicial system? In this review, we focus on what we now know about the consequences of the fallibility of memory for legal proceedings. We present a brief historical overview of false memories that focuses on three critical forensic areas that changed memory research: Children as eyewitnesses, historic sexual abuse, and eyewitness (mis)identification. We revisit some of the prominent trials of the 1980s and 1990s to not only consider the role false memories have played, but also to see how this has helped us understand memory today. Finally, we consider the way in which the research on memory (true and false) has been successfully integrated into some courtroom procedures

Functional Assessment of EnvZ/OmpR Two-Component System in Shewanella oneidensis

EnvZ and OmpR constitute the bacterial two-component signal transduction system known to mediate osmotic stress response in a number of Gram-negative bacteria. In an effort to understand the mechanism through which Shewanella oneidensis senses and responds to environmental osmolarity changes, structure of the ompR-envZ operon was determined with Northern blotting assay and roles of the EnvZ/OmpR two-component system in response to various stresses were investigated with mutational analysis, quantitative reverse transcriptase PCR (qRT-PCR), and phenotype microarrays. Results from the mutational analysis and qRT-PCR suggested that the EnvZ/OmpR system contributed to osmotic stress response of S. oneidensis and very likely engaged a similar strategy employed by E. coli, which involved reciprocal regulation of two major porin coding genes. Additionally, the ompR-envZ system was also found related to cell motility. We further showed that the ompR-envZ dependent regulation of porin genes and motility resided almost completely on ompR and only partially on envZ, indicating additional mechanisms for OmpR phosphorylation. In contrast to E. coli lacking ompR-envZ, however, growth of S. oneidensis did not show a significant dependence on ompR-envZ even under osmotic stress. Further analysis with phenotype microarrays revealed that the S. oneidensis strains lacking a complete ompR-envZ system displayed hypersensitivities to a number of agents, especially in alkaline environment. Taken together, our results suggest that the function of the ompR-envZ system in S. oneidensis, although still connected with osmoregulation, has diverged considerably from that of E. coli. Additional mechanism must exist to support growth of S. oneidensis under osmotic stress