Geometry of the faithfulness assumption in causal inference

Many algorithms for inferring causality rely heavily on the faithfulness assumption. The main justification for imposing this assumption is that the set of unfaithful distributions has Lebesgue measure zero, since it can be seen as a collection of hypersurfaces in a hypercube. However, due to sampling error the faithfulness condition alone is not sufficient for statistical estimation, and strong-faithfulness has been proposed and assumed to achieve uniform or high-dimensional consistency. In contrast to the plain faithfulness assumption, the set of distributions that is not strong-faithful has nonzero Lebesgue measure and in fact, can be surprisingly large as we show in this paper. We study the strong-faithfulness condition from a geometric and combinatorial point of view and give upper and lower bounds on the Lebesgue measure of strong-faithful distributions for various classes of directed acyclic graphs. Our results imply fundamental limitations for the PC-algorithm and potentially also for other algorithms based on partial correlation testing in the Gaussian case.Comment: Published in at http://dx.doi.org/10.1214/12-AOS1080 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Scalable Privacy-Preserving Data Sharing Methodology for Genome-Wide Association Studies

The protection of privacy of individual-level information in genome-wide association study (GWAS) databases has been a major concern of researchers following the publication of "an attack" on GWAS data by Homer et al. (2008) Traditional statistical methods for confidentiality and privacy protection of statistical databases do not scale well to deal with GWAS data, especially in terms of guarantees regarding protection from linkage to external information. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach that provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information, although the guarantees may come at a serious price in terms of data utility. Building on such notions, Uhler et al. (2013) proposed new methods to release aggregate GWAS data without compromising an individual's privacy. We extend the methods developed in Uhler et al. (2013) for releasing differentially-private $\chi^2$-statistics by allowing for arbitrary number of cases and controls, and for releasing differentially-private allelic test statistics. We also provide a new interpretation by assuming the controls' data are known, which is a realistic assumption because some GWAS use publicly available data as controls. We assess the performance of the proposed methods through a risk-utility analysis on a real data set consisting of DNA samples collected by the Wellcome Trust Case Control Consortium and compare the methods with the differentially-private release mechanism proposed by Johnson and Shmatikov (2013).Comment: 28 pages, 2 figures, source code available upon reques

Dynamic deformability of individual PbSe nanocrystals during superlattice phase transitions

The behavior of individual nanocrystals during superlattice phase transitions can profoundly affect the structural perfection and electronic properties of the resulting superlattices. However, details of nanocrystal morphological changes during superlattice phase transitions are largely unknown due to the lack of direct observation. Here, we report the dynamic deformability of PbSe semiconductor nanocrystals during superlattice phase transitions that are driven by ligand displacement. Real-time high-resolution imaging with liquid-phase transmission electron microscopy reveals that following ligand removal, the individual PbSe nanocrystals experience drastic directional shape deformation when the spacing between nanocrystals reaches 2 to 4 nm. The deformation can be completely recovered when two nanocrystals move apart or it can be retained when they attach. The large deformation, which is responsible for the structural defects in the epitaxially fused nanocrystal superlattice, may arise from internanocrystal dipole-dipole interactions

A 'reality of return': the case of the Sarawakian-Chinese visiting China

Using an interpretive ethnographic framework, this paper focuses on how travel to the homeland informs the identity of the Sarawakian-Chinese, a diaspora that contains a composite of subcultures. The data collection is based upon 35 semi-structured interviews and participant observation of a Sarawakian-Chinese tour group to China. Whilst emotional connections with China are universally significant in constructing the diaspora's ethnic identity, the strength of association is influenced by characteristics of education, religion and language, as identity becomes re-defined and plural. The findings suggest that the influence of tourism to the homeland may not necessarily be significant in enhancing emotional and cultural connections with China. Instead, ambivalent connections to homeland become established during tourism experiences. Visits to the homeland could play a significant role in forging new and hybrid identities of ethnic communities outside the homeland, thereby bringing a new vital dimension to identity formation and communication of the Sarawakian-Chinese in the future

Angiogenesis and Its Role in the Tumour Microenvironment: A Target for Cancer Therapy

The process of angiogenesis refers to the growth of new blood vessels from existing ones. Tumours can produce factors in the micro-environment which act on blood vessels to promote angiogenesis. It is therefore considered to be fundamental in tumour progression and metastatic dissemination. This neovascularization can be regulated by numerous endogenous factors in the tumour micro-environment. As a result, anti-angiogenic therapies have been developed in the hope of targeting this process to reduce tumour growth and progression. However, only a proportion of patients respond to therapy, indicating the presence of treatment resistance in some. In this chapter, we aim to highlight the process of angiogenesis and to review pivotal evidence for the use of anti-angiogenic therapies thus far (alone and in combination with other agents). Finally, we will illustrate recent evidence for the discovery of biomarkers for anti-angiogenic therapies and potential mechanisms of resistance to such agents

Use of AR to Bring Medical Simulation to Life

Use of simulation facilities and equipment in medical training has become the fabric of curricula across nearly all professions, most notably medical school, nursing, and related medical sciences programs. The gold standard for simulators is SimMan3G, Laerdal Inc., which offers a static electronic mannequin that affords the opportunity to create disease states, signs/symptoms, and real physiological/vital sign data complemented by voice interactions between faculty (within the control room) and student. All sessions are videotaped and, through a 15-30 minute debriefing, students exchange thoughts and impressions with faculty and engage in a deep reflective learning experience. The other option for medical simulation training is the use of “standardized patients”; people who serve as mock patients to mimic signs and symptoms but, clearly, cannot mimic real disease states or physiological changes. To bridge the gap between static mannequin and real human as patient, we have begun work on the utilization of AR to bring our SimMan3G mannequin to life

In Situ TEM Study of the Degradation of PbSe Nanocrystals in Air

PbSe nanocrystals have attracted widespread attention due to a variety of potential applications. However, the practical utility of these nanocrystals has been hindered by their poor air stability, which induces undesired changes in the optical and electronic properties. An understanding of the degradation of PbSe nanocrystals when they are exposed to air is critical for improving the stability and enhancing their applications. Here, we use in situ transmission electron microscopy (TEM) with an environmental cell connected to air to study PbSe nanocrystal degradation triggered by air exposure. We have also conducted a series of complementary studies, including in situ environmental TEM study of PbSe nanocrystals exposed to pure oxygen and PbSe nanocrystals in H2O using a liquid cell, and ex situ experiments, such as O2 plasma treatment and thermal heating of PbSe nanocrystals under different air exposure. Our in situ observations reveal that when PbSe nanocrystals are exposed to air (or oxygen) under electron beam irradiation, they experience a series of changes, including shape evolution of individual nanocrystals with the cuboid intermediates, coalescence between nanocrystals, and formation of PbSe thin films through drastic solid-state fusion. Further studies show that the PbSe thin films transform into an amorphous Pb rich phase or eventually pure Pb, which suggest that Se reacts with oxygen and can be evaporated under electron beam illumination. These various in situ and ex situ experimental results indicate that PbSe nanocrystal degradation in air is initiated by the dissociation and removal of ligands from the PbSe nanocrystal surface