The Calculus of M-estimation in R with geex

M-estimation, or estimating equation, methods are widely applicable for point estimation and asymptotic inference. In this paper, we present an R package that can find roots and compute the empirical sandwich variance estimator for any set of user-specified, unbiased estimating equations. Examples from the M-estimation primer by Stefanski and Boos (2002) demonstrate use of the software. The package also includes a framework for finite sample variance corrections and a website with an extensive collection of tutorials

Thick Slice Clarity for Localization of Novel Neuroactive Target Gene Products

This poster describes the Thick Slice CLARITY technique, an alternative to the whole tissue or whole body clarity technique. The CLARITY technique is a tissue clearing method allowing for both structural and molecular analysis of a tissue sample, but the method applied to whole tissue or body is very expensive and time consuming. Thick Slice CLARITY applies the same principles but to a 200 micrometer slice of brain tissue. This method, used in conjunction wit standard fluorescent staining methods and imaging via confocal microscopy, has allowed for the colocalization of GPR3 with neurons in the mouse striatum

A Study of the Shortest-Period Planets Found With Kepler

We present the results of a survey aimed at discovering and studying transiting planets with orbital periods shorter than one day (ultra--short-period, or USP, planets), using data from the {\em Kepler} spacecraft. We computed Fourier transforms of the photometric time series for all 200,000 target stars, and detected transit signals based on the presence of regularly spaced sharp peaks in the Fourier spectrum. We present a list of 106 USP candidates, of which 18 have not previously been described in the literature. In addition, among the objects we studied, there are 26 USP candidates that had been previously reported in the literature which do not pass our various tests. All 106 of our candidates have passed several standard tests to rule out false positives due to eclipsing stellar systems. A low false positive rate is also implied by the relatively high fraction of candidates for which more than one transiting planet signal was detected. By assuming these multi-transit candidates represent coplanar multi-planet systems, we are able to infer that the USP planets are typically accompanied by other planets with periods in the range 1-50 days, in contrast with hot Jupiters which very rarely have companions in that same period range. Another clear pattern is that almost all USP planets are smaller than 2 $R_\oplus$, possibly because gas giants in very tight orbits would lose their atmospheres by photoevaporation when subject to extremely strong stellar irradiation. Based on our survey statistics, USP planets exist around approximately $(0.51\pm 0.07)\%$ of G-dwarf stars, and $(0.83\pm 0.18)\%$ of K-dwarf stars.Comment: 20 pages, 10 figures. Submitted to ApJ. This version has been reviewed by a refere

Gene Expression Changes in the Septum: Possible Implications for MicroRNAs in Sculpting the Maternal Brain

The transition from the non-maternal to the maternal state is characterized by a variety of CNS alterations that support the care of offspring. The septum (including lateral and medial portions) is a brain region previously linked to various emotional and motivational processes, including maternal care. In this study, we used microarrays (PLIER algorithm) to examine gene expression changes in the septum of postpartum mice and employed gene set enrichment analysis (GSEA) to identify possible regulators of altered gene expression. Genes of interest identified as differentially regulated with microarray analysis were validated with quantitative real-time PCR. We found that fatty acid binding protein 7 (Fabp7) and galanin (Gal) were downregulated, whereas insulin-like growth factor binding protein 3 (Igfbp3) was upregulated in postpartum mice compared to virgin females. These genes were previously found to be differentially regulated in other brain regions during lactation. We also identified altered expression of novel genes not previously linked to maternal behavior, but that could play a role in postpartum processes, including glutamate-ammonia ligase (Glul) and somatostatin receptor 1 (Sstr1) (both upregulated in postpartum). Genes implicated in metabolism, cell differentiation, or proliferation also exhibited altered expression. Unexpectedly, enrichment analysis revealed a high number of microRNAs, transcription factors, or conserved binding sites (177 with corrected P-value <0.05) that were significantly linked to maternal upregulated genes, while none were linked to downregulated genes. MicroRNAs have been linked to placenta and mammary gland development, but this is the first indication they may also play a key role in sculpting the maternal brain. Together, this study provides new insights into genes (along with possible mechanisms for their regulation) that are involved in septum-mediated adaptations during the postpartum period

Transits and Occultations of an Earth-Sized Planet in an 8.5-Hour Orbit

We report the discovery of an Earth-sized planet ($1.16\pm 0.19 R_\oplus$) in an 8.5-hour orbit around a late G-type star (KIC 8435766, Kepler-78). The object was identified in a search for short-period planets in the {\it Kepler} database and confirmed to be a transiting planet (as opposed to an eclipsing stellar system) through the absence of ellipsoidal light variations or substantial radial-velocity variations. The unusually short orbital period and the relative brightness of the host star ($m_{\rm Kep}$ = 11.5) enable robust detections of the changing illumination of the visible hemisphere of the planet, as well as the occultations of the planet by the star. We interpret these signals as representing a combination of reflected and reprocessed light, with the highest planet dayside temperature in the range of 2300 K to 3100 K. Follow-up spectroscopy combined with finer sampling photometric observations will further pin down the system parameters and may even yield the mass of the planet.Comment: Accepted for publication, ApJ, 10 pages and 6 figure

Lattice study of ChPT beyond QCD

We describe initial results by the Lattice Strong Dynamics (LSD) collaboration of a study into the variation of chiral properties of chiral properties of SU(3) Yang-Mills gauge theory as the number of massless flavors changes from $N_f = 2$ to $N_f = 6$, with a focus on the use of chiral perturbation theory.Comment: 9 pages, 3 figures. Presented at the 6th International Workshop on Chiral Dynamics, University of Bern, Switzerland, July 6-10 200

Toward TeV Conformality

We study the chiral condensate $$ for an SU(3) gauge theory with $N_f$ massless Dirac fermions in the fundamental representation when $N_f$ is increased from 2 to 6. For $N_f=2$, our lattice simulations of $<\bar{\psi} \psi >/F^3$, where $F$ is the Nambu-Goldstone-boson decay constant, agree with the measured QCD value. For $N_f = 6$, this ratio shows significant enhancement, presaging an even larger enhancement anticipated as $N_f$ increases further, toward the critical value for transition from confinement to infrared conformality.Comment: 4 pages, 4 figures. v2: revised version for PR

A Recipe for inferference: Start with Causal Inference. Add Interference. Mix Well with R.

In causal inference, interference occurs when the treatment of one subject affects the outcome of other subjects. Interference can distort research conclusions about causal effects when not accounted for properly. In the absence of interference, inverse probability weighted (IPW) estimators are commonly used to estimate causal effects from observational data. Recently, IPW estimators have been extended to handle interference. Tchetgen Tchetgen and VanderWeele (2012) proposed IPW methods to estimate direct and indirect (or spillover) effects that allow for interference between individuals within groups. In this paper, we present inferference, an R package that computes these IPW causal effect estimates when interference may be present within groups. We illustrate use of the package with examples from political science and infectious disease