Cytoscape: the network visualization tool for GenomeSpace workflows.

Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013

A Democratic Art

This is a report on my creative research and it is written in support of my thesis exhibition entitled A Democratic Art. This thesis is an investigation into the ways printmaking is celebrated within the printmaking community, with particular attention given to the notion that printmaking is the most democratic of all art forms. In exploring the concept of a democratic art, I will consider democratic participation that has taken place throughout the history of the United States. This work is the result of my experience working as a collaborative fine art printer and the satisfaction I have derived from my involvement in these endeavors, coupled with my concern for the relationship between this specialized labor and the constant struggle for social justice within the broader political economy to which it is inevitably tied.  M.F.A

Diphenhydramine as an adjunct to conscious sedation in bronchoscopy

Intravenous benzodiazepines are commonly used to achieve conscious sedation in outpatient bronchoscopy. Though effective, dose-dependent-adverse events may be encountered with the use of these sedatives. Diphenhydramine, a hypnotic, is sometimes used as an adjunctive agent in bronchoscopy to decrease sedative usage. However, data to support this practice is lacking. Our goal was to determine if adjunctive diphenhydramine significantly decreases doses of benzodiazepine in outpatient bronchoscopy. METHODS: We conducted a single-center retrospective analysis of all outpatient bronchoscopies from November 2013 to February 2016. Subjects included were those who each had two bronchoscopies: no diphenhydramine used (control) versus diphenhydramine used (intervention). The procedure time, total doses of midazolam and opiates (in morphine equivalence) for each procedure were collected. A multiple regression analysis was used to compare differences between bronchoscopy groups in midazolam and opiate use. RESULTS: Of 1164 patients with greater than 1 outpatient bronchoscopies, 61 unique subjects (female 56%) fulfilled the primary inclusion criteria thus resulting to 122 procedures. Mean body mass index was 32 kg/m2. Procedure time was 22.9 ± 16 mins in diphenhydramine group and 23.2 ± 17.8 mins in control group. Mean morphine equivalents administered was 5.6 ± 2.6 mg in diphenhydramine group and 6.2 ± 2.4 mg in control group. Mean midazolam use was 8.4 ± 3.2 mg in diphenhydramine group and 10.2 ± 3.8 mg in control group (difference: -1.795, p-value = 0.005). The mean dose of diphenhydramine used was 38.32 ± 15.12 mg. In a multivariate model, mean midazolam use remained less in the diphenhydramine group after adjusting for procedure time and morphine equivalents, (difference -1.28 mg, p-value = 0.005). CONCLUSIONS: Intravenous administration of diphenhydramine during outpatient bronchoscopy reduces midazolam usage, however, the absolute amount of dose reduction may not be clinically significant

Versatile and open software for comparing large genomes

The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes. Two new graphical viewing tools provide alternative ways to analyze genome alignments. The new system is the first version of MUMmer to be released as open-source software. This allows other developers to contribute to the code base and freely redistribute the code. The MUMmer sources are available at

On Perturbations in Warm Inflation

Warm inflation is an interesting possibility of describing the early universe, whose basic feature is the absence, at least in principle, of a preheating or reheating phase. Here we analyze the dynamics of warm inflation generalizing the usual slow-roll parameters that are useful for characterizing the inflationary phase. We study the evolution of entropy and adiabatic perturbations, where the main result is that for a very small amount of dissipation the entropy perturbations can be neglected and the purely adiabatic perturbations will be responsible for the primordial spectrum of inhomogeneities. Taking into account the COBE-DMR data of the cosmic microwave background anisotropy as well as the fact that the interval of inflation for which the scales of astrophysical interest cross outside the Hubble radius is about 50 e-folds before the end of inflation, we could estimate the magnitude of the dissipation term. It was also possible to show that at the end of inflation the universe is hot enough to provide a smooth transition to the radiation era.Comment: 12 pages, no figures, requires revtex4. Further explanation on the origin of the entropy perturbation, reference added and minor notation change. Version accepted for publication in Phys. Rev.

Recovering the Inflationary Potential

A procedure is developed for the recovery of the inflationary potential over the interval that affects astrophysical scales (\approx 1\Mpc - 10^4\Mpc). The amplitudes of the scalar and tensor metric perturbations and their power-spectrum indices, which can in principle be inferred from large-angle CBR anisotropy experiments and other cosmological data, determine the value of the inflationary potential and its first two derivatives. From these, the inflationary potential can be reconstructed in a Taylor series and the consistency of the inflationary hypothesis tested. A number of examples are presented, and the effect of observational uncertainties is discussed.Comment: 13 pages LaTeX, 6 Figs. available on request, FNAL-Pub-93/182-

Inflation at the Electroweak Scale

We present a simple model for slow-rollover inflation where the vacuum energy that drives inflation is of the order of $G_F^{-2}$; unlike most models, the conversion of vacuum energy to radiation (``reheating'') is moderately efficient. The scalar field responsible for inflation is a standard-model singlet, develops a vacuum expectation value of the order of 4\times 10^6\GeV, has a mass of order 1\GeV, and can play a role in electroweak phenomena.Comment: 14 page

Perception versus reality: A National Cohort Analysis of the surgery-first approach for resectable pancreatic cancer

INTRODUCTION: Although surgical resection is necessary, it is not sufficient for long-term survival in pancreatic ductal adenocarcinoma (PDAC). We sought to evaluate survival after up-front surgery (UFS) in anatomically resectable PDAC in the context of three critical factors: (A) margin status; (B) CA19-9; and (C) receipt of adjuvant chemotherapy. METHODS: The National Cancer Data Base (2010-2015) was reviewed for clinically resectable (stage 0/I/II) PDAC patients. Surgical margins, pre-operative CA19-9, and receipt of adjuvant chemotherapy were evaluated. Patient overall survival was stratified based on these factors and their respective combinations. Outcomes after UFS were compared to equivalently staged patients after neoadjuvant chemotherapy on an intention-to-treat (ITT) basis. RESULTS: Twelve thousand and eighty-nine patients were included (n = 9197 UFS, n = 2892 ITT neoadjuvant). In the UFS cohort, only 20.4% had all three factors (median OS = 31.2 months). Nearly 1/3rd (32.7%) of UFS patients had none or only one factor with concomitant worst survival (median OS = 14.7 months). Survival after UFS decreased with each failing factor (two factors: 23 months, one factor: 15.5 months, no factors: 7.9 months) and this persisted after adjustment. Overall survival was superior in the ITT-neoadjuvant cohort (27.9 vs. 22 months) to UFS. CONCLUSION: Despite the perceived benefit of UFS, only 1-in-5 UFS patients actually realize maximal survival when known factors highly associated with outcomes are assessed. Patients are proportionally more likely to do worst, rather than best after UFS treatment. Similarly staged patients undergoing ITT-neoadjuvant therapy achieve survival superior to the majority of UFS patients. Patients and providers should be aware of the false perception of \u27optimal\u27 survival benefit with UFS in anatomically resectable PDAC

Cosmological parameter estimation using Very Small Array data out to l=1500

We estimate cosmological parameters using data obtained by the Very Small Array (VSA) in its extended configuration, in conjunction with a variety of other CMB data and external priors. Within the flat $\Lambda$CDM model, we find that the inclusion of high resolution data from the VSA modifies the limits on the cosmological parameters as compared to those suggested by WMAP alone, while still remaining compatible with their estimates. We find that $\Omega_{\rm b}h^2=0.0234^{+0.0012}_{-0.0014}$, $\Omega_{\rm dm}h^2=0.111^{+0.014}_{-0.016}$, $h=0.73^{+0.09}_{-0.05}$, $n_{\rm S}=0.97^{+0.06}_{-0.03}$, $10^{10}A_{\rm S}=23^{+7}_{-3}$ and $\tau=0.14^{+0.14}_{-0.07}$ for WMAP and VSA when no external prior is included.On extending the model to include a running spectral index of density fluctuations, we find that the inclusion of VSA data leads to a negative running at a level of more than 95% confidence ($n_{\rm run}=-0.069\pm 0.032$), something which is not significantly changed by the inclusion of a stringent prior on the Hubble constant. Inclusion of prior information from the 2dF galaxy redshift survey reduces the significance of the result by constraining the value of $\Omega_{\rm m}$. We discuss the veracity of this result in the context of various systematic effects and also a broken spectral index model. We also constrain the fraction of neutrinos and find that $f_{\nu}< 0.087$ at 95% confidence which corresponds to $m_\nu<0.32{\rm eV}$ when all neutrino masses are the equal. Finally, we consider the global best fit within a general cosmological model with 12 parameters and find consistency with other analyses available in the literature. The evidence for $n_{\rm run}<0$ is only marginal within this model