Transit Analysis Package (TAP and autoKep): IDL Graphical User Interfaces for Extrasolar Planet Transit Photometry

We present an IDL graphical user interface-driven software package designed for the analysis of extrasolar planet transit light curves. The Transit Analysis Package (TAP) software uses Markov Chain Monte Carlo (MCMC) techniques to fit light curves using the analytic model of Mandel and Agol (2002). The package incorporates a wavelet based likelihood function developed by Carter and Winn (2009) which allows the MCMC to assess parameter uncertainties more robustly than classic chi-squared methods by parameterizing uncorrelated "white" and correlated "red" noise. The software is able to simultaneously analyze multiple transits observed in different conditions (instrument, filter, weather, etc). The graphical interface allows for the simple execution and interpretation of Bayesian MCMC analysis tailored to a user's specific data set and has been thoroughly tested on ground-based and Kepler photometry. AutoKep provides a similar GUI for the preparation of Kepler MAST archive data for analysis by TAP or any other analysis software. This paper describes the software release and provides instructions for its use.Comment: 8 pages, 2 figure

The Disputed Quality of Software Patents

We analyze the characteristics of the patents held by firms in the software industry. Unlike prior researchers, we rely on the examination of individual patents to determine which patents involve software inventions. This method of identifying the relevant patents is more laborious than the methods that previous scholars have used, but it produces a data set from which we can learn more about the role of patents in the software industry. In general, we find that patents the computer technology firms obtain on software inventions have more prior art references, claims, and forward citations than the patents that the same firms obtain on nonsoftware inventions. We also find that the patents that pure software firms (those producing only software) obtain on software inventions have more prior art references, claims, and forward citations than the software patents obtained by the firms that derive revenues from other product lines. Finally, we conclude that the patents of the largest firms are no better (or worse) than the patents of the smallest firms, belying the idea that large firms are plagued by challenges based on the worthless patents of their smaller competitors. The Article closes with a brief discussion of the implications of our empirical analysis. The findings undermine the strongest criticisms about the low quality of software patents. It is simply not accurate to say that software patents as a group have remarkably low numbers of prior art references and forward citations. Thus, these findings cut against technology-based patent reforms designed to make it more difficult to obtain software patents. On the other hand, the evidence that small firms are no less capable than large firms of producing quality patents undermines concerns that higher hurdles at the early stage of the patenting process would disadvantage smaller inventors

Evidence for the intense exchange of MazG in marine cyanophages by horizontal gene transfer

Background: S-PM2 is a phage capable of infecting strains of unicellular cyanobacteria belonging to the genus Synechococcus. S-PM2, like other myoviruses infecting marine cyanobacteria, encodes a number of bacterial-like genes. Amongst these genes is one encoding a MazG homologue that is hypothesized to be involved in the adaption of the infected host for production of progeny phage. Methodology/Principal Findings: This study focuses on establishing the occurrence of mazG homologues in other cyanophages isolated from different oceanic locations. Degenerate PCR primers were designed using the mazG gene of S-PM2. The mazG gene was found to be widely distributed and highly conserved among Synechococcus myoviruses and podoviruses from diverse oceanic provinces. Conclusions/Significance: This study provides evidence of a globally connected cyanophage gene pool, the cyanophage mazG gene having a small effective population size indicative of rapid lateral gene transfer despite being present in a substantial fraction of cyanophage. The Prochlorococcus and Synechococcus phage mazG genes do not cluster with the host mazG gene, suggesting that their primary hosts are not the source of the mazG gene

The Disputed Quality of Software Patents

We analyze the characteristics of the patents held by firms in the software industry. Unlike prior researchers, we rely on the examination of individual patents to determine which patents involve software inventions. This method of identifying the relevant patents is more laborious than the methods that previous scholars have used, but it produces a data set from which we can learn more about the role of patents in the software industry. In general, we find that patents the computer technology firms obtain on software inventions have more prior art references, claims, and forward citations than the patents that the same firms obtain on nonsoftware inventions. We also find that the patents that “pure” software firms (those producing only software) obtain on software inventions have more prior art references, claims, and forward citations than the software patents obtained by the firms that derive revenues from other product lines. Finally, we conclude that the patents of the largest firms are no better (or worse) than the patents of the smallest firms, belying the idea that large firms are plagued by challenges based on the worthless patents of their smaller competitors. The Article closes with a brief discussion of the implications of our empirical analysis. The findings undermine the strongest criticisms about the low quality of software patents. It is simply not accurate to say that software patents as a group have remarkably low numbers of prior art references and forward citations. Thus, these findings cut against technology-based patent reforms designed to make it more difficult to obtain software patents. On the other hand, the evidence that small firms are no less capable than large firms of producing quality patents undermines concerns that higher hurdles at the early stage of the patenting process would disadvantage smaller inventors

A physically motivated and empirically calibrated method to measure effective temperature, metallicity, and Ti abundance of M dwarfs

The ability to perform detailed chemical analysis of Sun-like F-, G-, and K-type stars is a powerful tool with many applications including studying the chemical evolution of the Galaxy and constraining planet formation theories. Unfortunately, complications in modeling cooler stellar atmospheres hinders similar analysis of M-dwarf stars. Empirically-calibrated methods to measure M dwarf metallicity from moderate-resolution spectra are currently limited to measuring overall metallicity and rely on astrophysical abundance correlations in stellar populations. We present a new, empirical calibration of synthetic M dwarf spectra that can be used to infer effective temperature, Fe abundance, and Ti abundance. We obtained high-resolution (R~25,000), Y-band (~1 micron) spectra of 29 M dwarfs with NIRSPEC on Keck II. Using the PHOENIX stellar atmosphere modeling code (version 15.5), we generated a grid of synthetic spectra covering a range of temperatures, metallicities, and alpha-enhancements. From our observed and synthetic spectra, we measured the equivalent widths of multiple Fe I and Ti I lines and a temperature-sensitive index based on the FeH bandhead. We used abundances measured from widely-separated solar-type companions to empirically calibrate transformations to the observed indices and equivalent widths that force agreement with the models. Our calibration achieves precisions in Teff, [Fe/H], and [Ti/Fe] of 60 K, 0.1 dex, and 0.05 dex, respectively and is calibrated for 3200 K < Teff < 4100 K, -0.7 < [Fe/H] < +0.3, and -0.05 < [Ti/Fe] < +0.3. This work is a step toward detailed chemical analysis of M dwarfs at a similar precision achieved for FGK stars.Comment: accepted for publication in ApJ, all synthetic spectra available at http://people.bu.edu/mveyette/phoenix

Temporal Trends in Suicidal Ideation and Attempts among US Adolescents by Sex and Race/Ethnicity, 1991-2019

Importance: Disparities by sex and racial/ethnic group in suicide death rates are present in US adolescents. Whether disparities in suicide death extend to groups targeted for suicide prevention efforts, namely, those with suicidal ideation or nonfatal suicide attempts, is unknown. Objective: To examine differences in temporal trends between suicidal ideation and suicide attempts in US adolescents from 1991 through 2019 by sex and race/ethnicity subgroups. Design, Setting, and Participants: A cross-sectional analysis of the national Youth Risk Behavior Survey, weighted to represent US adolescents from 1991 to 2019, included 183 563 US high-school students in grades 9 to 12. Data were analyzed from September 16, 2020, through April 12, 2021. Exposures: Calendar year, sex, race/ethnicity, and interactions of sex and race/ethnicity. Main Outcomes and Measures: Survey-weighted prevalence estimates, annual percentage changes (APCs) and average APC in the survey-weighted prevalence of suicidal ideation and nonfatal suicide attempts, constructed from self-reported suicidal ideation, plan, and attempts in each survey year, by sex, race/ethnicity (non-Hispanic White, non-Hispanic Black, Hispanic, non-Hispanic Asian or Pacific Islander and Native Hawaiian, American Indian/Alaska Native), and their interactions (sex × race/ethnicity). Results: In 183 563 (unweighted) included adolescents (mean [SD] age, 16.07 [1.23] years; 94 282 females [weighted percentage, 49.4%; 95% CI, 48.8%-50.1%]), the prevalence of suicidal ideation decreased from 1991 to 2019 (from 19.4% to 15.8%; 95% CI, 0.7%-0.9%), whereas the prevalence of nonfatal suicide attempts increased from 1991 to 2019 (from 7.3% to 8.9%; 95% CI, 1.0%-1.4%). Joinpoint regression indicated a -3.1% (95% CI, -3.7% to -2.6%) annual decrease in suicidal ideation between 1991 and 2009, followed by a 3.4% annual increase (95% CI, 1.9% -4.8%) between 2009 and 2019. Decreasing followed by increasing trends in suicidal ideation showed modestly different turning points in female (1991-2009, 2009-2019), White (1991-2009, 2009-2019), Hispanic (1991-2007, 2007-2019), and Black (1991-2005, 2005-2019) adolescents. Although no significant trends were observed in suicide attempts from 1991 through 2019, male (68.4% increase; 95% CI, 0.2% -1.2%) and Black (79.7% increase; 95% CI, 0.1%-1.5%) adolescents had greater increases in the prevalence of suicide attempts. Interaction of sex and race/ethnicity revealed increases in suicidal ideation in White females from 2009 to 2019 (APC, 4.3%; 95% CI, 1.5%-7.1%), Black females from 2005 to 2019 (APC, 3.4%; 95% CI, 1.4%-5.4%), and Hispanic females from 2009 to 2019 (APC, 3.3%; 95% CI, 1.0%-5.6%) and suicide attempts in White females from 2009 to 2019 (APC, 3.1%; 95% CI, 0.3%-6.0%). Conclusions and Relevance: The findings of this study show apparent sex and racial/ethnic differences in trends in suicidal ideation and suicide attempts. Increases in suicidal ideation since 2009 were observed in female individuals; changes in male and Black adolescents represented the largest increase in the prevalence of suicide attempts between 1991 and 2019. Evidence-based suicide prevention programs need to be tailored by sex and race/ethnicity, calling for greater diversification of health care system, school, and community prevention approaches

Evidence of complex involvement of serotonergic genes with restrictive and binge purge subtypes of anorexia nervosa

Peer reviewedPreprin