Incrementally Computing Minimal Unsatisfiable Cores of QBFs via a Clause Group Solver API

We consider the incremental computation of minimal unsatisfiable cores (MUCs) of QBFs. To this end, we equipped our incremental QBF solver DepQBF with a novel API to allow for incremental solving based on clause groups. A clause group is a set of clauses which is incrementally added to or removed from a previously solved QBF. Our implementation of the novel API is related to incremental SAT solving based on selector variables and assumptions. However, the API entirely hides selector variables and assumptions from the user, which facilitates the integration of DepQBF in other tools. We present implementation details and, for the first time, report on experiments related to the computation of MUCs of QBFs using DepQBF's novel clause group API.Comment: (fixed typo), camera-ready version, 6-page tool paper, to appear in proceedings of SAT 2015, LNCS, Springe

Genetic recombination is targeted towards gene promoter regions in dogs

The identification of the H3K4 trimethylase, PRDM9, as the gene responsible for recombination hotspot localization has provided considerable insight into the mechanisms by which recombination is initiated in mammals. However, uniquely amongst mammals, canids appear to lack a functional version of PRDM9 and may therefore provide a model for understanding recombination that occurs in the absence of PRDM9, and thus how PRDM9 functions to shape the recombination landscape. We have constructed a fine-scale genetic map from patterns of linkage disequilibrium assessed using high-throughput sequence data from 51 free-ranging dogs, Canis lupus familiaris. While broad-scale properties of recombination appear similar to other mammalian species, our fine-scale estimates indicate that canine highly elevated recombination rates are observed in the vicinity of CpG rich regions including gene promoter regions, but show little association with H3K4 trimethylation marks identified in spermatocytes. By comparison to genomic data from the Andean fox, Lycalopex culpaeus, we show that biased gene conversion is a plausible mechanism by which the high CpG content of the dog genome could have occurred.Comment: Updated version, with significant revision

Measurement of the Absolute Differential Cross Section for np Elastic Scattering at 194 MeV

A tagged medium-energy neutron beam has been used in a precise measurement of the absolute differential cross section for np back-scattering. The results resolve significant discrepancies within the np database concerning the angular dependence in this regime. The experiment has determined the absolute normalization with 1.5% uncertainty, suitable to verify constraints of supposedly comparable precision that arise from the rest of the database in partial wave analyses. The analysis procedures, especially those associated with evaluation of systematic errors in the experiment, are described in detail so that systematic uncertainties may be included in a reasonable way in subsequent partial wave analysis fits incorporating the present results.Comment: 22 pages, 21 figures, submitted for publication in Physical Review

Measurement of the Absolute np Scattering Differential Cross Section at 194 MeV

We describe a double-scattering experiment with a novel tagged neutron beam to measure differential cross sections for np back-scattering to better than 2% absolute precision. The measurement focuses on angles and energies where the cross section magnitude and angle-dependence constrain the charged pion-nucleon coupling constant, but existing data show serious discrepancies among themselves and with energy-dependent partial wave analyses (PWA). The present results are in good accord with the PWA, but deviate systematically from other recent measurements.Comment: 4 pages, 4 figure

Eliciting imitation in early infancy

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Airway hyperresponsiveness, but not airway remodeling, is attenuated during chronic pulmonary allergic responses to Aspergillus in CCR4‐/‐ mice

The role of CC chemokine receptor 4 (CCR4) during the development and maintenance of Th2type allergic airway disease is controversial. In this study, we examined the role of CCR4 in the chronic allergic airway response to live Aspergillus fumigatus spores, or conidia, in A. fumigatussensitized mice. After the conidia challenge, mice lacking CCR4 (CCR4‐/‐ mice) exhibited significantly increased numbers of airway neutrophils and macrophages, and conidia were more rapidly eliminated from these mice compared with control CCR4 wild‐type (CCR4+/+) mice. Significant airway hyperresponsiveness to intravenous methacholine was observed at day 3 in CCR4‐/‐ mice, whereas at days 7 and 30, airway hyperresponsiveness was attenuated in these mice compared with control mice. A major reduction in peribronchial and airway eosinophilia was observed in CCR4‐/‐ mice at all times after conidia challenge in contrast to CCR4+/+ mice. Further, whole lung levels of interleukin (IL) 4 and IL‐5 were significantly increased in CCR4‐/‐ mice at day 3, whereas these Th2 cytokines and IL‐13 were significantly decreased at day 30 in CCR4‐/‐ mice compared with their wild‐type counterparts. Peribronchial fibrosis and goblet cell hyperplasia were similar in both groups of mice throughout the course of this model. In summary, CCR4 modulates both innate and acquired immune responses associated with chronic fungal asthma.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154441/1/fsb2fasebj16100193-sup-0001.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154441/2/fsb2fasebj16100193.pd

Drotrecogin alfa (activated) in patients with severe sepsis presenting with purpura fulminans, meningitis, or meningococcal disease: a retrospective analysis of patients enrolled in recent clinical studies

INTRODUCTION: We report data from adult and pediatric patients with severe sepsis from studies evaluating drotrecogin alfa (activated) (DrotAA) and presenting with purpura fulminans (PF), meningitis (MEN), or meningococcal disease (MD) (PF/MEN/MD). Such conditions may be associated with an increased bleeding risk but occur in a relatively small proportion of patients presenting with severe sepsis; pooling data across clinical trials provides an opportunity for improving the characterization of outcomes. METHODS: A retrospective analysis of placebo-controlled, open-label, and compassionate-use trials was conducted. Adult patients received infusions of either DrotAA or placebo. All pediatric patients (<18 years old) received DrotAA. 189 adult and 121 pediatric patients presented with PF/MEN/MD. RESULTS: Fewer adult patients with PF/MEN/MD met cardiovascular (68.3% versus 78.8%) or respiratory (57.8% versus 80.5%) organ dysfunction entry criteria than those without. DrotAA-treated adult patients with PF/MEN/MD (n = 163) had an observed 28-day mortality rate of 19.0%, a 28-day serious bleeding event (SBE) rate of 6.1%, and an intracranial hemorrhage (ICH) rate of 4.3%. Six of the seven ICHs occurred in patients with MEN (three of whom were more than 65 years old with a history of hypertension). DrotAA-treated adult patients without PF/MEN/MD (n = 3,088) had an observed 28-day mortality rate of 25.5%, a 28-day SBE rate of 5.8%, and an ICH rate of 1.0%. In contrast, a greater number of pediatric patients with PF/MEN/MD met the cardiovascular organ dysfunction entry criterion (93.5% versus 82.5%) than those without. DrotAA-treated PF/MEN/MD pediatric patients (n = 119) had a 14-day mortality rate of 10.1%, an SBE rate of 5.9%, and an ICH rate of 2.5%. DrotAA-treated pediatric patients without PF/MEN/MD (n = 142) had a 14-day mortality rate of 14.1%, an SBE rate of 9.2%, and an ICH rate of 3.5%. CONCLUSION: DrotAA-treated adult patients with severe sepsis presenting with PF/MEN/MD had a similar SBE rate, a lower observed 28-day mortality rate, and a higher observed rate of ICH than DrotAA-treated patients without PF/MEN/MD. DrotAA-treated pediatric patients with severe sepsis with PF/MEN/MD may differ from adults, because all three outcome rates (SBE, mortality, and ICH) were lower in pediatric patients with PF/MEN/MD

Measurement of the Differential and Total Cross Sections of the ᵧd→KºɅ(p) Reaction Within the Resonance Region

We report the first measurement of differential and total cross sections for the γd →K0 Λ(p)reaction, using data from the CLAS detector at the Thomas Jefferson National Accelerator Facility. Data collected during two separate experimental runs were studied with photon-energy coverage 0.8-3.6 GeV and 0.5-2.6 GeV, respectively. The two measurements are consistent giving confidence in the method and determination of systematic uncertainties. The cross sections are compared with predictions from the KAON-MAID theoretical model (without kaon exchange), which deviate from the data at higher W and at forward kaon angles. These data, along with previously published cross sections for K+Λ photoproduction, provide essential constraints on the nucleon resonance spectrum. A first partial wave analysis was performed that describes the data without the introduction of new resonances