MPRAnalyze: statistical framework for massively parallel reporter assays.

Massively parallel reporter assays (MPRAs) can measure the regulatory function of thousands of DNA sequences in a single experiment. Despite growing popularity, MPRA studies are limited by a lack of a unified framework for analyzing the resulting data. Here we present MPRAnalyze: a statistical framework for analyzing MPRA count data. Our model leverages the unique structure of MPRA data to quantify the function of regulatory sequences, compare sequences' activity across different conditions, and provide necessary flexibility in an evolving field. We demonstrate the accuracy and applicability of MPRAnalyze on simulated and published data and compare it with existing methods

Stellar Dynamics of Extreme-Mass-Ratio Inspirals

Inspiral of compact stellar remnants into massive black holes (MBHs) is accompanied by the emission of gravitational waves at frequencies that are potentially detectable by space-based interferometers. Event rates computed from statistical (Fokker-Planck, Monte-Carlo) approaches span a wide range due to uncertaintities about the rate coefficients. Here we present results from direct integration of the post-Newtonian N-body equations of motion descrbing dense clusters of compact stars around Schwarzschild MBHs. These simulations embody an essentially exact (at the post-Newtonian level) treatment of the interplay between stellar dynamical relaxation, relativistic precession, and gravitational-wave energy loss. The rate of capture of stars by the MBH is found to be greatly reduced by relativistic precession, which limits the ability of torques from the stellar potential to change orbital angular momenta. Penetration of this "Schwarzschild barrier" does occasionally occur, resulting in capture of stars onto orbits that gradually inspiral due to gravitational wave emission; we discuss two mechanisms for barrier penetration and find evidence for both in the simulations. We derive an approximate formula for the capture rate, which predicts that captures would be strongly disfavored from orbits with semi-major axes below a certain value; this prediction, as well as the predicted rate, are verified in the N-body integrations. We discuss the implications of our results for the detection of extreme-mass-ratio inspirals from galactic nuclei with a range of physical properties.Comment: 28 pages, 16 figures. Version 2 is significantly revised to reflect new insights into J and Q effects, to be published late

Charge transport across metal/molecular (alkyl) monolayer-Si junctions is dominated by the LUMO level

We compare the charge transport characteristics of heavy doped p- and n-Si-alkyl chain/Hg junctions. Photoelectron spectroscopy (UPS, IPES and XPS) results for the molecule-Si band alignment at equilibrium show the Fermi level to LUMO energy difference to be much smaller than the corresponding Fermi level to HOMO one. This result supports the conclusion we reach, based on negative differential resistance in an analogous semiconductor-inorganic insulator/metal junction, that for both p- and n-type junctions the energy difference between the Fermi level and LUMO, i.e., electron tunneling, controls charge transport. The Fermi level-LUMO energy difference, experimentally determined by IPES, agrees with the non-resonant tunneling barrier height deduced from the exponential length-attenuation of the current

Precursors prior to Type IIn supernova explosions are common: precursor rates, properties, and correlations

There is a growing number of supernovae (SNe), mainly of Type IIn, which present an outburst prior to their presumably final explosion. These precursors may affect the SN display, and are likely related to some poorly charted phenomena in the final stages of stellar evolution. Here we present a sample of 16 SNe IIn for which we have Palomar Transient Factory (PTF) observations obtained prior to the SN explosion. By coadding these images taken prior to the explosion in time bins, we search for precursor events. We find five Type IIn SNe that likely have at least one possible precursor event, three of which are reported here for the first time. For each SN we calculate the control time. Based on this analysis we find that precursor events among SNe IIn are common: at the one-sided 99% confidence level, more than 50% of SNe IIn have at least one pre-explosion outburst that is brighter than absolute magnitude -14, taking place up to 1/3 yr prior to the SN explosion. The average rate of such precursor events during the year prior to the SN explosion is likely larger than one per year, and fainter precursors are possibly even more common. We also find possible correlations between the integrated luminosity of the precursor, and the SN total radiated energy, peak luminosity, and rise time. These correlations are expected if the precursors are mass-ejection events, and the early-time light curve of these SNe is powered by interaction of the SN shock and ejecta with optically thick circumstellar material.Comment: 15 pages, 20 figures, submitted to Ap

iPTF13beo: The Double-Peaked Light Curve of a Type Ibn Supernova Discovered Shortly after Explosion

We present optical photometric and spectroscopic observations of the Type Ibn (SN 2006jc-like) supernova iPTF13beo. Detected by the intermediate Palomar Transient Factory ~3 hours after the estimated first light, iPTF13beo is the youngest and the most distant (~430 Mpc) Type Ibn event ever observed. The iPTF13beo light curve is consistent with light curves of other Type Ibn SNe and with light curves of fast Type Ic events, but with a slightly faster rise-time of two days. In addition, the iPTF13beo R-band light curve exhibits a double-peak structure separated by ~9 days, not observed before in any Type Ibn SN. A low-resolution spectrum taken during the iPTF13beo rising stage is featureless, while a late-time spectrum obtained during the declining stage exhibits narrow and intermediate-width He I and Si II features with FWHM ~ 2000-5000 km/s and is remarkably similar to the prototypical SN Ibn 2006jc spectrum. We suggest that our observations support a model of a massive star exploding in a dense He-rich circumstellar medium (CSM). A shock breakout in a CSM model requires an eruption releasing a total mass of ~0.1 Msun over a time scale of couple of weeks prior to the SN explosion.Comment: 8 pages, 5 figures, submitted to MNRA

Worth the risk? Terrorism-induced fear of flying

We conducted two bi-national experiments regarding emotional and behavioral responses to a terrorist plot against commercial flights, examining both feelings and projected action. The studies employed hypothetical scenarios in which terrorists attacked airplanes with shoulder-fired missiles as they were landing or taking off from an international airport. The scenarios were built around two factorially crossed manipulated variables, each with three levels: (1) government announcements or actions (2) social norm, expressed as variation in airline ticket sales. Each respondent read a questionnaire containing only one of the nine scenarios. Experiment 1 was conducted in Spain and California (n = 360, 50% female), Experiment 2 in Israel and California (n = 504, 50% female). In both studies, fear and flight plans were not differentially affected by governmental response or social norm. Women expressed more fear than men. Experiment 1 examined the purpose of the trip. Most respondents would not change a planned flight to attend a close friend’s wedding or important job interview, but a substantial number would postpone a vacation or drive to a different location. Experiment 2 featured escalating attacks. These yielded increased fear and more canceled trips. Within both studies, responses were similar across countries despite national differences in direct experience with terrorism

Clinical Features and Outcomes of Paediatric Patients With Isolated Colonic Crohn Disease

Objectives: Adult studies suggest that patients with isolated colonic Crohn disease (L2 CD) exhibit unique characteristics differentiating them from patients with ileo-caecal (L1) CD and ulcerative colitis (UC). We aimed to characterize clinical features and outcomes of paediatric patients with L2. Methods: Retrospective data was collected through the Porto Inflammatory Bowel Disease group of the European Society for Paediatric Gastroenterology Hepatology and Nutrition (ESPGHAN) on Paediatric patients with L2, L1 or UC at different time-points. Outcome measures included time to first flare, hospital admissions, initiation of anti-tumor necrosis factor-alpha (TNF alpha) drug, stricture and surgery. Results: Three hundred patients were included: 102 L1, 94 L2 and 104 UC. Rates of hematochezia at presentation were 14.7%, 44.7% and 95.2%, while rates of fever were 12.7%, 26.6% and 2.9%, for patients with L1, L2 and UC, respectively (P < 0.001 for all comparisons). Skip lesions were identified in 65% of patients with L2, and granulomas in 36%, similar to L1 patients. Rates of anti-Saccharomyces cerevisiae antibodies (ASCA) and perinuclear antineutrophil cytoplasmic (pANCA) positivity significantly differed between the three groups: 25.4% and 16.7% for patients with L2, compared with 55.2% and 2.3%, and 1.8% and 52.9% for patients with L1 and UC, respectively. Response rates to exclusive enteral nutrition were comparable between L1 and L2 (78.3-82.4%), as was the response to oral steroids (70.4-76.5%) in the three groups. While times to first flare and admission were similar between groups, patients with L1 were commenced on anti-TNF alpha earlier. Moreover, stricturing phenotype and need for colectomy were very rare in patients with L2. Conclusions: Significant differences are observed in the clinical presentation and outcomes of Paediatric patients with L2, compared to patients with L1 and UC.Peer reviewe

¿Vale la pena el riesgo? Miedo inducido por el terrorismo a volar

We conducted two bi-national experiments regarding emotional and behavioral responses to a terrorist plot against commercial flights, examining both feelings and projected action. The studies employed hypothetical scenarios in which terrorists attacked airplanes with shoulder-fired missiles as they were landing or taking off from an international airport. The scenarios were built around two factorially crossed manipulated variables, each with three levels: (1) government announcements or actions (2) social norm, expressed as variation in airline ticket sales. Each respondent read a questionnaire containing only one of the nine scenarios. Experiment 1 was conducted in Spain and California (n = 360, 50% female), Experiment 2 in Israel and California (n = 504, 50% female). In both studies, fear and flight plans were not differentially affected by governmental response or social norm. Women expressed more fear than men. Experiment 1 examined the purpose of the trip. Most respondents would not change a planned flight to attend a close friend’s wedding or important job interview, but a substantial number would postpone a vacation or drive to a different location. Experiment 2 featured escalating attacks. These yielded increased fear and more canceled trips. Within both studies, responses were similar across countries despite national differences in direct experience with terrorism.Se realizaron dos experimentos bi-nacionales con respecto a las respuestas emocionales y conductuales a un plan terrorista contra vuelos comerciales, examinando ambas cosas: sentimientos y proyectos de acción. Los estudios emplearon escenarios hipotéticos en los que los terroristas atacaron los aviones con misiles disparados desde el hombro, ya que estaban aterrizando o despegando desde un aeropuerto internacional. Los escenarios fueron construidos alrededor de dos variables factoriales cruzadas, cada uno con tres niveles: (1) los anuncios o acciones del gobierno (2) norma social, expresada como la variación en la venta de billetes de avión. Cada encuestado leyó un cuestionario que contenía sólo uno de los nueve escenarios. El experimento 1 se realizó en España y California (n = 360, 50% mujeres), el experimento 2 en Israel y California (n = 504, 50% mujeres). En ambos estudios, el miedo y los planes de vuelo no fueron diferencialmente afectados por la respuesta gubernamental o la norma social. Las mujeres expresaron más miedo que los hombres. El experimento 1 examinó el propósito del viaje. La mayoría de los encuestados no cambiarían un vuelo planeado para asistir a la boda de un amigo cercano o para una importante entrevista de trabajo, pero un número considerable de participantes podrían posponer unas vacaciones o ir en coche a un lugar diferente. El experimento 2 contó con la escalada de los ataques. Estas aumentaron el temor y la cantidad de viajes cancelados. En ambos estudios, las respuestas fueron similares en todos los países a pesar de las diferencias nacionales y la experiencia directa con el terrorismo.Depto. de Economía Aplicada, Estructura e HistoriaFac. de Ciencias Económicas y EmpresarialesTRUEpu

Robustness and Generalization

We derive generalization bounds for learning algorithms based on their robustness: the property that if a testing sample is "similar" to a training sample, then the testing error is close to the training error. This provides a novel approach, different from the complexity or stability arguments, to study generalization of learning algorithms. We further show that a weak notion of robustness is both sufficient and necessary for generalizability, which implies that robustness is a fundamental property for learning algorithms to work