High-resolution mapping of cancer cell networks using co-functional interactions.

Powerful new technologies for perturbing genetic elements have recently expanded the study of genetic interactions in model systems ranging from yeast to human cell lines. However, technical artifacts can confound signal across genetic screens and limit the immense potential of parallel screening approaches. To address this problem, we devised a novel PCA-based method for correcting genome-wide screening data, bolstering the sensitivity and specificity of detection for genetic interactions. Applying this strategy to a set of 436 whole genome CRISPR screens, we report more than 1.5 million pairs of correlated "co-functional" genes that provide finer-scale information about cell compartments, biological pathways, and protein complexes than traditional gene sets. Lastly, we employed a gene community detection approach to implicate core genes for cancer growth and compress signal from functionally related genes in the same community into a single score. This work establishes new algorithms for probing cancer cell networks and motivates the acquisition of further CRISPR screen data across diverse genotypes and cell types to further resolve complex cellular processes

Detecting the signatures of helium in type Iax supernovae

Recent studies have argued that the progenitor system of type Iax supernovae must consist of a carbon-oxygen white dwarf accreting from a helium star companion. Based on existing explosion models invoking the pure deflagration of carbon-oxygen white dwarfs, we investigate the likelihood of producing spectral features due to helium in type Iax supernovae. From this scenario, we select those explosion models producing ejecta and $^{56}$Ni masses that are broadly consistent with those estimated for type Iax supernovae (0.014 - 0.478~$M_{\odot}$ and $\sim0.003$ - 0.183~$M_{\odot}$, respectively). To this end, we present a series of models of varying luminosities ($-18.4 \lesssim M_{\rm{V}} \lesssim -14.5$~mag) with helium abundances accounting for up to $\sim$36\% of the ejecta mass, and covering a range of epochs beginning a few days before B$-$band maximum to approximately two weeks after maximum. We find that the best opportunity for detecting \ion{He}{i} features is at near-infrared wavelengths, and in the post-maximum spectra of the fainter members of this class. We show that the optical spectrum of SN~2007J is potentially consistent with a large helium content (a few 10$^{-2}~M_{\odot}$), but argue that current models of accretion and material stripping from a companion struggle to produce compatible scenarios. We also investigate the presence of helium in all objects with near-infrared spectra. We show that SNe~2005hk, 2012Z, and 2015H contain either no helium or their helium abundances are constrained to much lower values ($\lesssim$10$^{-3}~M_{\odot}$). Our results demonstrate the differences in helium content among type Iax supernovae, perhaps pointing to different progenitor channels. Either SN~2007J is an outlier in terms of its progenitor system, or it is not a true member of the type Iax supernova class.Comment: 15 pages, 12 figures, 2 tables. Accepted for publication in Astronomy and Astrophysic

The Major Sources of the Cosmic Reionizing Background at z ~ 6

In this paper, we address which sources contributed most of the reionizing photons. Our argument assumes that the reionization ended around z ~ 6 and that it was a relatively quick process, i.e., that there was a non-negligible fraction of neutral hydrogen in the Universe at somewhat earlier epochs. Starting from our earlier estimate of the luminosity function (LF) of galaxies at z ~ 6, we quantitatively show that the major sources of reionization are most likely galaxies with L < L*. Our approach allows us to put stronger constraints to the LF of galaxies at z ~ 6. To have the Universe completely ionized at this redshift, the faint-end slope of the LF should be steeper than $\alpha=-1.6$, which is the value measured at lower redshifts (z ~ 3), unless either the normalization (Phi*) of the LF or the clumping factor of the ionized hydrogen has been significantly underestimated. If Phi* is actually lower than what we assumed by a factor of two, a steep slope close to $\alpha=-2.0$ is required. Our LF predicts a total of 50 -- 80 z ~ 6 galaxies in the HST Ultra Deep Field (UDF) to a depth of AB=28.4 mag, which can be used to constraint both Phi* and $\alpha$. We conclude that the least luminous galaxies existing at this redshift should reach as low as some critical luminosity in order to accumulate the entire reionizing photon budget. On the other hand, the existence of significant amounts of neutral hydrogen at slightly earlier epochs, e.g. z ~ 7, requires that the least luminous galaxies should not be fainter than another critical value (i.e., the LF should cut-off at this point).Comment: ApJL in press (Jan 1, 2004 issue

Hadronic contribution to the muon g-2: a theoretical determination

The leading order hadronic contribution to the muon g-2, $a_{\mu}^{HAD}$, is determined entirely from theory using an approach based on Cauchy's theorem in the complex squared energy s-plane. This is possible after fitting the integration kernel in $a_{\mu}^{HAD}$ with a simpler function of $s$. The integral determining $a_{\mu}^{HAD}$ in the light-quark region is then split into a low energy and a high energy part, the latter given by perturbative QCD (PQCD). The low energy integral involving the fit function to the integration kernel is determined by derivatives of the vector correlator at the origin, plus a contour integral around a circle calculable in PQCD. These derivatives are calculated using hadronic models in the light-quark sector. A similar procedure is used in the heavy-quark sector, except that now everything is calculable in PQCD, thus becoming the first entirely theoretical calculation of this contribution. Using the dual resonance model realization of Large $N_{c}$ QCD to compute the derivatives of the correlator leads to agreement with the experimental value of $a_\mu$. Accuracy, though, is currently limited by the model dependent calculation of derivatives of the vector correlator at the origin. Future improvements should come from more accurate chiral perturbation theory and/or lattice QCD information on these derivatives, allowing for this method to be used to determine $a_{\mu}^{HAD}$ accurately entirely from theory, independently of any hadronic model.Comment: Several additional clarifying paragraphs have been added. 1/N_c corrections have been estimated. No change in result

The Adjudication and Enforcement of Rights After Brexit

This report records the inaugural meeting and roundtable of the Brexit and Rights Engagement Network (BREN) on Tuesday 3rd July 2018 at Edinburgh Law School. Attendees at the roundtable included network members, fellow academics, representatives of the Scottish Parliament, the Scottish Government, the Scottish Human Rights Commission, the Equality and Human Rights Commission, the legal professions, and NGOs. Two years after the EU Referendum and only a few days after the European Union (Withdrawal) Act 2018 (the 2018 Act) receiving Royal Assent, the Brexit and Rights Engagement Network met for the first time. The purpose of the roundtable was to ignite debate amongst legal scholars and policy makers, and others working in a rights environment relating to interpretation, adjudication and enforcement of rights in the lead up to, and following “Brexit Day,” (March 29, 2019). This report is split into two sections, Part A will consider the adjudication of EU rights, but also their enforcement under the 2018 Act and the Withdrawal Agreement, whilst ‘options for the future’ will be broached in Part B

Hardware and software status of QCDOC

QCDOC is a massively parallel supercomputer whose processing nodes are based on an application-specific integrated circuit (ASIC). This ASIC was custom-designed so that crucial lattice QCD kernels achieve an overall sustained performance of 50% on machines with several 10,000 nodes. This strong scalability, together with low power consumption and a price/performance ratio of $1 per sustained MFlops, enable QCDOC to attack the most demanding lattice QCD problems. The first ASICs became available in June of 2003, and the testing performed so far has shown all systems functioning according to specification. We review the hardware and software status of QCDOC and present performance figures obtained in real hardware as well as in simulation.Comment: Lattice2003(machine), 6 pages, 5 figure

Electron heating mechanisms in dual frequency capacitive discharges

We discuss electron heating mechanisms in the sheath regions of dual-frequency capacitive discharges, with the twin aims of identifying the dominant mechanisms and supplying closed-form expressions from which the heating power can be estimated. We show that the heating effect produced by either Ohmic or collisionless heating is much larger when the discharge is excited by a superposition of currents at two frequencies than if either current had acted alone. This coupling effect occurs because the lower frequency current, while not directly heating the electrons to any great extent, strongly affects the spatial structure of the discharge in the sheath regions

The static potential: lattice versus perturbation theory in a renormalon-based approach

We compare, for the static potential and at short distances, perturbation theory with the results of lattice simulations. We show that a renormalon-dominance picture explains why in the literature sometimes agreement, and another disagreement, is found between lattice simulations and perturbation theory depending on the different implementations of the latter. We also show that, within a renormalon-based scheme, perturbation theory agrees with lattice simulations.Comment: 18 pages, 11 figures, lattice data of Necco and Sommer introduced, references added, some lengthier explanations given, physical results unchange