Locating regions in a sequence under density constraints

Several biological problems require the identification of regions in a sequence where some feature occurs within a target density range: examples including the location of GC-rich regions, identification of CpG islands, and sequence matching. Mathematically, this corresponds to searching a string of 0s and 1s for a substring whose relative proportion of 1s lies between given lower and upper bounds. We consider the algorithmic problem of locating the longest such substring, as well as other related problems (such as finding the shortest substring or a maximal set of disjoint substrings). For locating the longest such substring, we develop an algorithm that runs in O(n) time, improving upon the previous best-known O(n log n) result. For the related problems we develop O(n log log n) algorithms, again improving upon the best-known O(n log n) results. Practical testing verifies that our new algorithms enjoy significantly smaller time and memory footprints, and can process sequences that are orders of magnitude longer as a result.Comment: 17 pages, 8 figures; v2: minor revisions, additional explanations; to appear in SIAM Journal on Computin

Summary for policymakers

This Summary for Policymakers presents key findings from the Special Report on Managing the Risks of Extreme Events and Disasters to Advance Climate Change Adaptation (SREX). The SREX approaches the topic by assessing the scientific literature on issues that range from the relationship between climate change and extreme weather and climate events ("climate extremes") to the implications of these events for society and sustainable development. The assessment concerns the interaction of climatic, environmental, and human factors that can lead to impacts and disasters, options for managing the risks posed by impacts and disasters, and the important role that non-climatic factors play in determining impacts. The character and severity of impacts from climate extremes depend not only on the extremes themselves but also on exposure and vulnerability. In this report, adverse impacts are considered disasters when they produce widespread damage and cause severe alterations in the normal functioning of communities or societies. Climate extremes, exposure, and vulnerability are influenced by a wide range of factors, including anthropogenic climate change, natural climate variability, and socioeconomic development. Disaster risk management and adaptation to climate change focus on reducing exposure and vulnerability and increasing resilience to the potential adverse impacts of climate extremes, even though risks cannot fully be eliminated. Although mitigation of climate change is not the focus of this report, adaptation and mitigation can complement each other and together can significantly reduce the risks of climate change. This report integrates perspectives from several historically distinct research communities studying climate science, climate impacts, adaptation to climate change, and disaster risk management. Each community brings different viewpoints, vocabularies, approaches, and goals, and all provide important insights into the status of the knowledge base and its gaps. Many of the key assessment findings come from the interfaces among these communities

Physicochemical Properties and Catalytic Behavior of the Molecular Sieve SSZ-70

SSZ-70 is synthesized using 1,3-bis(isobutyl)imidazolium, 1,3-bis(cyclohexyl)imidazolium, and 1,3-bis(cycloheptyl)imidazolium structure directing agents (SDAs), and the solids obtained are characterized by powder X-ray diffraction (XRD), ^(29)Si magic angle spinning nuclear magnetic resonance (MAS NMR), electron microscopy, nitrogen and hydrocarbon adsorption, and thermogravimetric analyses. The physicochemical properties of SSZ-70 show that it is a new molecular sieve that has similarities to MWW-type materials. The catalytic behavior of SSZ-70 is evaluated through the use of the constraint index (CI) test. Distinct differences in the reactivity between Al-SSZ-70 and SSZ-25 (MWW) are observed and are the consequences of the structural differences between these two molecular sieves

XMM-Newton observations of the supernova remnant IC443: I. soft X-ray emission from shocked interstellar medium

The shocked interstellar medium around IC443 produces strong X-ray emission in the soft energy band (E<1.5 keV). We present an analysis of such emission as observed with the EPIC MOS cameras on board the XMM-Newotn observatory, with the purpose to find clear signatures of the interactions with the interstellar medium (ISM) in the X-ray band, which may complement results obtained in other wavelenghts. We found that the giant molecular cloud mapped in CO emission is located in the foreground and gives an evident signature in the absorption of X-rays. This cloud may have a torus shape and the part of torus interacting with the IC443 shock gives rise to 2MASS-K emission in the southeast. The measured density of emitting X-ray shocked plasma increases toward the northeastern limb, where the remnant is interacting with an atomic cloud. We found an excellent correlation between emission in the 0.3-0.5 keV band and bright optical/radio filament on large spatial scales. The partial shell structure seen in this band therefore traces the encounter with the atomic cloud.Comment: 10 pages, 10 figures, accepted for publication in ApJ (20 September 2006, v649). For hi-res figures, see http://www.astropa.unipa.it/Library/OAPA_preprints/ic443ele1.ps.g

Lattice Effects in Crystal Evaporation

We study the dynamics of a stepped crystal surface during evaporation, using the classical model of Burton, Cabrera and Frank, in which the dynamics of the surface is represented as a motion of parallel, monoatomic steps. The validity of the continuum approximation treated by Frank is checked against numerical calculations and simple, qualitative arguments. The continuum approximation is found to suffer from limitations related, in particular, to the existence of angular points. These limitations are often related to an adatom detachment rate of adatoms which is higher on the lower side of each step than on the upper side ("Schwoebel effect").Comment: DRFMC/SPSMS/MDN, Centre d'Etudes Nucleaires de Grenoble, 25 pages, LaTex, revtex style. 8 Figures, available upon request, report# UBFF30119

Isolated X-ray -- infrared sources in the region of interaction of the supernova remnant IC 443 with a molecular cloud

The nature of the extended hard X-ray source XMMU J061804.3+222732 and its surroundings is investigated using XMM-Newton, Chandra, and Spitzer observations. This source is located in an interaction region of the IC 443 supernova remnant with a neighboring molecular cloud. The X-ray emission consists of a number of bright clumps embedded in an extended structured non-thermal X-ray nebula larger than 30" in size. Some clumps show evidence for line emission at ~1.9 keV and ~3.7 keV at the 99% confidence level. Large-scale diffuse radio emission of IC 443 passes over the source region, with an enhancement near the source. An IR source of about 14" x 7" size is prominent in the 24 um, 70 um, and 2.2 um bands, adjacent to a putative Si K-shell X-ray line emission region. The observed IR/X-ray morphology and spectra are consistent with those expected for J/C-type shocks of different velocities driven by fragmented supernova ejecta colliding with the dense medium of a molecular cloud. The IR emission of the source detected by Spitzer can be attributed to both continuum emission from an HII region created by the ejecta fragment and line emission excited by shocks. This source region in IC 443 may be an example of a rather numerous population of hard X-ray/IR sources created by supernova explosions in the dense environment of star-forming regions. Alternative Galactic and extragalactic interpretations of the observed source are also discussed.Comment: The Astrophysical Journal, v. 677 (April 2008), in pres

Impact of elosulfase alfa in patients with morquio A syndrome who have limited ambulation: An open-label, phase 2 study.

Efficacy and safety of elosulfase alfa enzyme replacement therapy (ERT) were assessed in an open-label, phase 2, multi-national study in Morquio A patients aged ≥5 years unable to walk ≥30 meters in the 6-min walk test. Patients received elosulfase alfa 2.0 mg/kg/week intravenously for 48 weeks. Efficacy measures were functional dexterity, pinch/grip strength, mobility in a modified timed 25-foot walk, pain, quality of life, respiratory function, and urine keratan sulfate (KS). Safety/tolerability was also assessed. Fifteen patients received elosulfase alfa, three patients discontinued ERT due to adverse events (two were grade 3 drug-related adverse events, the other was not drug-related), and two patients missed &gt;20% of planned infusions; 10 completed treatment through 48 weeks and received ≥80% of planned infusions (Modified Per Protocol [MPP] population). The study population had more advanced disease than that enrolled in other trials. From baseline to week 48, MPP data showed biochemical efficacy (urine KS decreased 52.4%). The remaining efficacy results were highly variable due to challenges in test execution because of severe skeletal and joint abnormalities, small sample sizes, and clinical heterogeneity among patients. Eight patients showed improvements in one or more outcome measures; several patients indicated improvements not captured by the study assessments (e.g., increased energy, functional ability). The nature of adverse events was similar to other elosulfase alfa studies. This study illustrates the considerable challenges in objectively measuring impact of ERT in very disabled Morquio A patients and highlights the need to examine results on an individual basis. © 2016 The Authors. American Journal of Medical Genetics Part A Published by Wiley Periodicals, Inc

Quantifying the Direct Radiative Effect of Absorbing Aerosols for Numerical Weather Prediction: A Case Study

We conceptualize aerosol radiative transfer processes arising from the hypothetical coupling of a global aerosol transport model and a global numerical weather prediction model by applying the US Naval Research Laboratory Navy Aerosol Analysis and Prediction System (NAAPS) and the Navy Global Environmental Model (NAVGEM) meteorological and surface reflectance fields. A unique experimental design during the 2013 NASA Studies of Emissions and Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS) field mission allowed for collocated airborne sampling by the high spectral resolution Lidar (HSRL), the Airborne Multi-angle SpectroPolarimetric Imager (AirMSPI), up/down shortwave (SW) and infrared (IR) broadband radiometers, as well as NASA A-Train support from the Moderate Resolution Imaging Spectroradiometer (MODIS), to attempt direct aerosol forcing closure. The results demonstrate the sensitivity of modeled fields to aerosol radiative fluxes and heating rates, specifically in the SW, as induced in this event from transported smoke and regional urban aerosols. Limitations are identified with respect to aerosol attribution, vertical distribution, and the choice of optical and surface polarimetric properties, which are discussed within the context of their influence on numerical weather prediction output that is particularly important as the community propels forward towards inline aerosol modeling within global forecast systems

Using network-flow techniques to solve an optimization problem from surface-physics

The solid-on-solid model provides a commonly used framework for the description of surfaces. In the last years it has been extended in order to investigate the effect of defects in the bulk on the roughness of the surface. The determination of the ground state of this model leads to a combinatorial problem, which is reduced to an uncapacitated, convex minimum-circulation problem. We will show that the successive shortest path algorithm solves the problem in polynomial time.Comment: 8 Pages LaTeX, using Elsevier preprint style (macros included