Do Read Errors Matter for Genome Assembly?

While most current high-throughput DNA sequencing technologies generate short reads with low error rates, emerging sequencing technologies generate long reads with high error rates. A basic question of interest is the tradeoff between read length and error rate in terms of the information needed for the perfect assembly of the genome. Using an adversarial erasure error model, we make progress on this problem by establishing a critical read length, as a function of the genome and the error rate, above which perfect assembly is guaranteed. For several real genomes, including those from the GAGE dataset, we verify that this critical read length is not significantly greater than the read length required for perfect assembly from reads without errors.Comment: Submitted to ISIT 201

Organizational Scope and Investment: Evidence from the Drug Development Strategies and Performance of Biopharmaceutical Firms

This paper compares the clinical trial strategies and performance of large, established ("mature") biopharmaceutical firms to those of smaller ("early stage") firms that have not yet successfully developed a drug. We study a sample of 235 cancer drug candidates that entered clinical trials during the period 1990-2002 and were sponsored by public firms. Early stage firms are more likely than mature firms to advance drug candidates from Phase I to Phase II clinical trials. However, early stage firms have much less promising clinical results in their Phase II trials and their Phase II drug candidates are also less likely to advance to Phase III and to receive Food and Drug Administration approval. This pattern is more pronounced for early stage firms with large cash reserves. The evidence points to an agency problem between shareholders and managers of single-product early stage firms who are reluctant to abandon development of their only viable drug candidates. By contrast, the managers of mature firms with multiple products in development are more willing to drop unpromising drug candidates. The findings appear to be consistent with the benefits of internal capital markets identified by Stein (1997).

Optimizing plug-in electric vehicle charging in interaction with a small office building

This paper considers the integration of plug-in electric vehicles (PEVs) in micro-grids. Extending a theoretical framework for mobile storage connection, the economic analysis here turns to the interactions of commuters and their driving behavior with office buildings. An illustrative example for a real office building is reported. The chosen system includes solar thermal, photovoltaic, combined heat and power generation as well as an array of plug-in electric vehicles with a combined aggregated capaci-ty of 864 kWh. With the benefit-sharing mechanism proposed here and idea-lized circumstances, estimated cost savings of 5% are possible. Different pricing schemes were applied which include flat rates, demand charges, as well as hourly variable final customer tariffs and their effects on the operation of intermittent storage were revealed and examined in detail. Because the plug-in electric vehicle connection coincides with peak heat and electricity loads as well as solar radiation, it is possible to shift energy demand as desired in order to realize cost savings. --Battery storage,building management systems,dispersed storage and generation,electric vehicles,load management,microgrid,optimization methods,power system economics,road vehicle electric propulsion

Syncrip/hnRNP Q is required for activity-induced Msp300/Nesprin-1 expression and new synapse formation.

Memory and learning involve activity-driven expression of proteins and cytoskeletal reorganization at new synapses, requiring posttranscriptional regulation of localized mRNA a long distance from corresponding nuclei. A key factor expressed early in synapse formation is Msp300/Nesprin-1, which organizes actin filaments around the new synapse. How Msp300 expression is regulated during synaptic plasticity is poorly understood. Here, we show that activity-dependent accumulation of Msp300 in the postsynaptic compartment of the Drosophila larval neuromuscular junction is regulated by the conserved RNA binding protein Syncrip/hnRNP Q. Syncrip (Syp) binds to msp300 transcripts and is essential for plasticity. Single-molecule imaging shows that msp300 is associated with Syp in vivo and forms ribosome-rich granules that contain the translation factor eIF4E. Elevated neural activity alters the dynamics of Syp and the number of msp300:Syp:eIF4E RNP granules at the synapse, suggesting that these particles facilitate translation. These results introduce Syp as an important early acting activity-dependent regulator of a plasticity gene that is strongly associated with human ataxias

The Qualitative Interview in Psychology and the Study of Social Change: Sexual Identity Development, Minority Stress, and Health in the Generations Study.

Interviewing is considered a key form of qualitative inquiry in psychology that yields rich data on lived experience and meaning making of life events. Interviews that contain multiple components informed by specific epistemologies have the potential to provide particularly nuanced perspectives on psychological experience. We offer a methodological model for a multi-component interview that draws upon both pragmatic and constructivist epistemologies to examine generational differences in the experience of identity development, stress, and health among contemporary sexual minorities in the United States. Grounded in theories of life course, narrative, and intersectionality, we designed and implemented a multi-component protocol that was administered among a diverse sample of three generations of sexual minority individuals. For each component, we describe the purpose and utility, underlying epistemology, foundational psychological approach, and procedure, and we provide illustrative data from interviewees. We discuss procedures undertaken to ensure methodological integrity in process of data collection, illustrating the implementation of recent guidelines for qualitative inquiry in psychology. We highlight the utility of this qualitative multi-component interview to examine the way in which sexual minorities of distinct generations have made meaning of significant social change over the past half-century

Partial DNA Assembly: A Rate-Distortion Perspective

Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is very often the case that the read data is not sufficiently rich to permit unambiguous reconstruction of the original sequence. While a natural generalization of the perfect assembly formulation to these cases would be to consider a rate-distortion framework, partial assemblies are usually represented in terms of an assembly graph, making the definition of a distortion measure challenging. In this work, we introduce a distortion function for assembly graphs that can be understood as the logarithm of the number of Eulerian cycles in the assembly graph, each of which correspond to a candidate assembly that could have generated the observed reads. We also introduce an algorithm for the construction of an assembly graph and analyze its performance on real genomes.Comment: To be published at ISIT-2016. 11 pages, 10 figure

State-space based mass event-history model I: many decision-making agents with one target

A dynamic decision-making system that includes a mass of indistinguishable agents could manifest impressive heterogeneity. This kind of nonhomogeneity is postulated to result from macroscopic behavioral tactics employed by almost all involved agents. A State-Space Based (SSB) mass event-history model is developed here to explore the potential existence of such macroscopic behaviors. By imposing an unobserved internal state-space variable into the system, each individual's event-history is made into a composition of a common state duration and an individual specific time to action. With the common state modeling of the macroscopic behavior, parametric statistical inferences are derived under the current-status data structure and conditional independence assumptions. Identifiability and computation related problems are also addressed. From the dynamic perspectives of system-wise heterogeneity, this SSB mass event-history model is shown to be very distinct from a random effect model via the Principle Component Analysis (PCA) in a numerical experiment. Real data showing the mass invasion by two species of parasitic nematode into two species of host larvae are also analyzed. The analysis results not only are found coherent in the context of the biology of the nematode as a parasite, but also include new quantitative interpretations.Comment: Published in at http://dx.doi.org/10.1214/08-AOAS189 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

The employment consequences of SMEs’ credit constraints in the wake of the great recession. National Bank of Belgium Working Paper No. 333

This article takes advantage of access to confidential matched bank-firm data relative to the Belgian economy to investigate whether and how employment decisions of small- and medium-sized enterprises (SMEs) have been affected by credit constraints in the wake of the Great Recession. Variability in banks’ financial health following the Great Recession is used as an exogenous determinant of firms’ access to credit. Two-stage least squares and bivariate probit estimates suggest that SMEs borrowing money from pre-crisis less healthy banks were significantly more likely to be affected by a credit constraint and, in turn, to adjust their labour input downwards than pre-crisis clients of more healthy banks. More precisely, estimates show that credit-constrained SMEs were ceteris paribus between 40 and 65% more likely to reduce their workforce than their counterparts not facing such constraints. Yet, findings also indicate that employment consequences of credit shortages depend heavily on the environment in which SMEs operate. Results indeed indicate that credit constraints have been essentially detrimental for employment among SMEs experiencing a negative demand shock or facing severe product market competition. Finally, in terms of adjustment channels, results show that credit-constrained SMEs adjusted their workforce significantly more at the extensive margin (through individual layoffs, reduction of temporary employment and early retirement) than their non-constrained counterparts, but also that they relied more intensively on temporary layoff schemes (for economic reasons)