lassopack: Model selection and prediction with regularized regression in Stata

This article introduces lassopack, a suite of programs for regularized regression in Stata. lassopack implements lasso, square-root lasso, elastic net, ridge regression, adaptive lasso and post-estimation OLS. The methods are suitable for the high-dimensional setting where the number of predictors $p$ may be large and possibly greater than the number of observations, $n$. We offer three different approaches for selecting the penalization (`tuning') parameters: information criteria (implemented in lasso2), $K$-fold cross-validation and $h$-step ahead rolling cross-validation for cross-section, panel and time-series data (cvlasso), and theory-driven (`rigorous') penalization for the lasso and square-root lasso for cross-section and panel data (rlasso). We discuss the theoretical framework and practical considerations for each approach. We also present Monte Carlo results to compare the performance of the penalization approaches.Comment: 52 pages, 6 figures, 6 tables; submitted to Stata Journal; for more information see https://statalasso.github.io

Unified translation repression mechanism for microRNAs and upstream AUGs

Abstract Background MicroRNAs (miRNAs) are endogenous small RNAs that modulate gene expression at the post-transcriptional level by binding complementary sites in the 3'-UTR. In a recent genome-wide study reporting a new miRNA target class (miBridge), we identified and validated interactions between 5'-UTRs and miRNAs. Separately, upstream AUGs (uAUGs) in 5'-UTRs are known to regulate genes translationally without affecting mRNA levels, one of the mechanisms for miRNA-mediated repression. Results Using sequence data from whole-genome cDNA alignments we identified 1418 uAUG sequences on the 5'-UTR that specifically interact with 3'-ends of conserved miRNAs. We computationally identified miRNAs that can target six genes through their uAUGs that were previously reported to suppress translation. We extended this meta-analysis by confirming expression of these miRNAs in cell-lines used in the uAUG studies. Similarly, seven members of the KLF family of genes containing uAUGs were computationally identified as interacting with several miRNAs. Using KLF9 as an example (whose protein expression is limited to brain tissue despite the mRNA being expressed ubiquitously), we show computationally that miRNAs expressed only in HeLa cells and not in neuroblastoma (N2A) cells can bind the uAUGs responsible for translation inhibition. Our computed results demonstrate that tissue- or cell-line specific repression of protein translation by uAUGs can be explained by the presence or absence of miRNAs that target these uAUG sequences. We propose that these uAUGs represent a subset of miRNA interaction sites on 5'-UTRs in miBridge, whereby a miRNA binding a uAUG hinders the progression of ribosome scanning the mRNA before it reaches the open reading frame (ORF). Conclusions While both miRNAs and uAUGs are separately known to down-regulate protein expression, we show that they may be functionally related by identifying potential interactions through a sequence-specific binding mechanism. Using prior experimental evidence that shows uAUG effects on translation repression together with miRNA expression data specific to cell lines, we demonstrate through computational analysis that cell-specific down-regulation of protein expression (while maintaining mRNA levels) correlates well with the simultaneous presence of miRNA and target uAUG sequences in one cell type and not others, suggesting tissue-specific translation repression by miRNAs through uAUGs.http://deepblue.lib.umich.edu/bitstream/2027.42/112383/1/12864_2009_Article_2749.pd

Estimating Heterogeneous Consumer Preferences for Restaurants and Travel Time Using Mobile Location Data

This paper analyzes consumer choices over lunchtime restaurants using data from a sample of several thousand anonymous mobile phone users in the San Francisco Bay Area. The data is used to identify users' approximate typical morning location, as well as their choices of lunchtime restaurants. We build a model where restaurants have latent characteristics (whose distribution may depend on restaurant observables, such as star ratings, food category, and price range), each user has preferences for these latent characteristics, and these preferences are heterogeneous across users. Similarly, each item has latent characteristics that describe users' willingness to travel to the restaurant, and each user has individual-specific preferences for those latent characteristics. Thus, both users' willingness to travel and their base utility for each restaurant vary across user-restaurant pairs. We use a Bayesian approach to estimation. To make the estimation computationally feasible, we rely on variational inference to approximate the posterior distribution, as well as stochastic gradient descent as a computational approach. Our model performs better than more standard competing models such as multinomial logit and nested logit models, in part due to the personalization of the estimates. We analyze how consumers re-allocate their demand after a restaurant closes to nearby restaurants versus more distant restaurants with similar characteristics, and we compare our predictions to actual outcomes. Finally, we show how the model can be used to analyze counterfactual questions such as what type of restaurant would attract the most consumers in a given location.Marie Curie Fellowship from the European Commission (H2020 programme, grant agreement 706760)

Photometry Results for the Globular Clusters M10 and M12: Extinction Maps, Color-Magnitude Diagrams, and Variable Star Candidates

We report on photometry results of the equatorial globular clusters (GCs) M10 and M12. These two clusters are part of our sample of GCs which we are probing for the existence of photometrically varying eclipsing binary stars. During the search for binaries in M10 and M12, we discovered the signature of differential reddening across the fields of the clusters. The effect is stronger for M10 than for M12. Using our previously described dereddening technique, we create differential extinction maps for the clusters which dramatically improve the appearance of the color-magnitude diagrams (CMDs). Comparison of our maps with the dust emissivity maps of Schlegel, Finkbeiner, & Davis (SFD) shows good agreement in terms of spatial extinction features. Several methods of adding an E_{V-I} zero point to our differential maps are presented of which isochrone fitting proved to be the most successful. Our E_{V-I} values fall within the range of widely varying literature values. More specifically, our reddening zero point estimate for M12 agrees well with the SFD estimate, whereas the one for M10 falls below the SFD value. Our search for variable stars in the clusters produced a total of five variables: three in M10 and two in M12. The M10 variables include a binary system of the W Ursa Majoris (W UMa) type, a background RR Lyrae star, and an SX Phoenicis pulsator, none of which is physically associated with M10. M12's variables are two W UMa binaries, one of which is most likely a member of the cluster. We present the phased photometry lightcurves for the variable stars, estimate their distances, and show their locations in the fields and the CMDs of the GCs.Comment: 22 pages, 21 figures, to be published in AJ October 2002. For a higher-resolution version of this paper, please visit http://www.astro.lsa.umich.edu/~kaspar/M10_M12_photometry.ps.gz (gzipped postscript) or http://www.astro.lsa.umich.edu/~kaspar/M10_M12_photometry.pdf (pdf file

Natural disasters and university enrolment: Evidence from L’Aquila earthquake

Although there are several studies looking at the effect of natural disasters on economic growth, less attention has been dedicated to their impact on educational outcomes, especially in more developed countries. We use the synthetic control method to examine how the L’Aquila earthquake affected subsequent enrolment at the local university. This issue has wide economic implications as the University of L’Aquila made a large contribution to the local economy before the earthquake. Our results indicate that the earthquake had no statistically significant effect on first-year enrolment at the University of L’Aquila in the three academic years after the disaster. This natural disaster, however, caused a compositional change in the first-year student population, with a substantial increase in the number of students aged 21 or above. This is likely to have been driven by post-disaster measures adopted in order to mitigate the expected negative effects on enrolment triggered by the earthquake

X-ray Spectral Properties of Low-Mass X-ray Binaries in Nearby Galaxies

We investigated the X-ray spectral properties of a collection of low-mass X-ray binaries (LMXBs) within a sample of 15 nearby early-type galaxies observed with Chandra. We find that the spectrum of the sum of the sources in a given galaxy is remarkably similar from galaxy to galaxy when only sources with X-ray luminosities less than 10^39 ergs/s (0.3-10 keV) are considered. Fitting these lower luminosity sources in all galaxies simultaneously yielded a best-fit power law exponent of Gamma = 1.56 +/- 0.02 (or kT_brem = 7.3 +/- 0.3 keV). This is the tightest constraint to date on the spectral properties of LMXBs in external galaxies. There is no apparent difference in the spectral properties of LMXBs that reside inside and outside globular clusters. We demonstrate how the uniformity of the spectral properties of LMXBs can lead to more accurate determinations of the temperature and metallicity of the hot gas in galaxies. Although few in number in any given galaxy, sources with luminosities of 1-2 x 10^39 ergs/s are present in 10 of the galaxies. The spectra of these luminous sources are softer than the spectra of the rest of the sources, and are consistent with the spectra of Galactic black hole X-ray binary candidates when they are in their very high state. The spectra of these sources are very different than those of ultraluminous X-ray sources (ULXs) found within spiral galaxies, suggesting that the two populations of X-ray luminous objects have different formation mechanisms. The number of sources with apparent luminosities above 2 x 10^39 ergs/s is equal to the number of expected background AGN and thus appear to not be associated with the galaxy, indicating that very luminous sources are absent or very rare in early-type galaxies. (Abridged)Comment: 11 pages in emulateapj5 style with 4 embedded Postscript figures; to be accepted by Ap

The signalling effect of eco-labels in modern coastal tourism

As the demand for environmentally sustainable tourism grows, eco-labels are becoming increasingly popular as a signal of environmental quality. However, the existence of a causal link between awarding a seaside eco-label and the increase in tourism flows is still under discussion in the literature. In this article, we gauge the signalling impact of a specific eco-label, the Blue Flag award, using detailed data on tourism flows to seaside Italian destinations during the period 2008-2012. We adopt a recent econometric modelling strategy - the synthetic control method - in shaping estimation results and testing the sensitivity and robustness of our results. We find that being awarded the Blue Flag increases the flow of domestic tourists for up to three seasons after assignment. However, we find no effect for the flow of international tourists. Investigating the mechanisms driving the results, we find that the award of a Blue Flag only positively affects the flow of domestic tourists when it is used as a driver of organisation, coordination and integrated management of the tourism supply

The optimal degree of discretion in monetary policy

How much discretion should the monetary authority have in setting its policy? This question is analyzed in an economy with an agreed-upon social welfare function that depends on the economy’s randomly fluctuating state. The monetary authority has private information about that state. Well designed rules trade off society’s desire to give the monetary authority discretion to react to its private information against society’s need to prevent that authority from giving in to the temptation to stimulate the economy with unexpected inflation, the time inconsistency problem. Although this dynamic mechanism design problem seems complex, its solution is simple: legislate an inflation cap. The optimal degree of monetary policy discretion turns out to shrink as the severity of the time inconsistency problem increases relative to the importance of private information. In an economy with a severe time inconsistency problem and unimportant private information, the optimal degree of discretion is none

Molecular gut content analysis of different spider body parts

Molecular gut-content analysis has revolutionized the study of food webs and feeding interactions, allowing the detection of prey DNA within the gut of many organisms. However, successful prey detection is a challenging procedure in which many factors affect every step, starting from the DNA extraction process. Spiders are liquid feeders with branched gut diverticula extending into their legs and throughout the prosoma, thus digestion takes places in different parts of the body and simple gut dissection is not possible. In this study, we investigated differences in prey detectability in DNA extracts from different parts of the spider's body: legs, prosoma and opisthosoma, using prey-specific PCR and metabarcoding approaches. We performed feeding trials with the woodlouse hunter spider Dysdera verneaui Simon, 1883 (Dysderidae) to estimate the time at which prey DNA is detectable within the predator after feeding. Although we found that all parts of the spider body are suitable for gut-content analysis when using prey-specific PCR approach, results based on metabarcoding suggested the opisthosoma is optimal for detection of predation in spiders because it contained the highest concentration of prey DNA for longer post feeding periods. Other spiders may show different results compared to D. verneaui, but given similarities in the physiology and digestion in different families, it is reasonable to assume this to be common across species and this approach having broad utility across spiders.Peer reviewe