On Bijective Variants of the Burrows-Wheeler Transform

The sort transform (ST) is a modification of the Burrows-Wheeler transform (BWT). Both transformations map an arbitrary word of length n to a pair consisting of a word of length n and an index between 1 and n. The BWT sorts all rotation conjugates of the input word, whereas the ST of order k only uses the first k letters for sorting all such conjugates. If two conjugates start with the same prefix of length k, then the indices of the rotations are used for tie-breaking. Both transforms output the sequence of the last letters of the sorted list and the index of the input within the sorted list. In this paper, we discuss a bijective variant of the BWT (due to Scott), proving its correctness and relations to other results due to Gessel and Reutenauer (1993) and Crochemore, Desarmenien, and Perrin (2005). Further, we present a novel bijective variant of the ST.Comment: 15 pages, presented at the Prague Stringology Conference 2009 (PSC 2009

Scalable succinct indexing for large text collections

Self-indexes save space by emulating operations of traditional data structures using basic operations on bitvectors. Succinct text indexes provide full-text search functionality which is traditionally provided by suffix trees and suffix arrays for a given text, while using space equivalent to the compressed representation of the text. Succinct text indexes can therefore provide full-text search functionality over inputs much larger than what is viable using traditional uncompressed suffix-based data structures. Fields such as Information Retrieval involve the processing of massive text collections. However, the in-memory space requirements of succinct text indexes during construction have hampered their adoption for large text collections. One promising approach to support larger data sets is to avoid constructing the full suffix array by using alternative indexing representations. This thesis focuses on several aspects related to the scalability of text indexes to larger data sets. We identify practical improvements in the core building blocks of all succinct text indexing algorithms, and subsequently improve the index performance on large data sets. We evaluate our findings using several standard text collections and demonstrate: (1) the practical applications of our improved indexing techniques; and (2) that succinct text indexes are a practical alternative to inverted indexes for a variety of top-k ranked document retrieval problems

Preliminary proceedings of the 2001 ACM SIGPLAN Haskell workshop

This volume contains the preliminary proceedings of the 2001 ACM SIGPLAN Haskell Workshop, which was held on 2nd September 2001 in Firenze, Italy. The final proceedings will published by Elsevier Science as an issue of Electronic Notes in Theoretical Computer Science (Volume 59). The HaskellWorkshop was sponsored by ACM SIGPLAN and formed part of the PLI 2001 colloquium on Principles, Logics, and Implementations of high-level programming languages, which comprised the ICFP/PPDP conferences and associated workshops. Previous Haskell Workshops have been held in La Jolla (1995), Amsterdam (1997), Paris (1999), and Montr´eal (2000). The purpose of the Haskell Workshop was to discuss experience with Haskell, and possible future developments for the language. The scope of the workshop included all aspects of the design, semantics, theory, application, implementation, and teaching of Haskell. Submissions that discussed limitations of Haskell at present and/or proposed new ideas for future versions of Haskell were particularly encouraged. Adopting an idea from ICFP 2000, the workshop also solicited two special classes of submissions, application letters and functional pearls, described below

The impacts of biotic and abiotic factors on resource subsidy processes - leaf litter breakdown in freshwaters

Freshwaters are closely linked with adjacent terrestrial ecosystems through reciprocal resource subsidies, which are fluxes of nutrients, organisms, and materials between ecosystems. Terrestrial ecosystems provide many resource subsidies to freshwaters including leaf litter, one of the most prevalent terrestrial-derived subsidies. Inputs of leaf litter fuel detritivores food web, as food resources and refuges, and affect nutrients cycling in freshwaters. The decomposition of leaf litter is subjected to many biotic and abiotic factors, which makes it a good indicator of freshwater ecosystem functioning. Yet, this ecosystem process has been affected by anthropogenic disturbances that alter abiotic and biotic factors in the nature. Therefore, this thesis aimed to investigate some previously under-investigated or unclear but important factors that may affect the decomposition of leaf litter in streams. First, I reviewed the importance of resource subsidy fluxes between riparian zones and freshwaters and how these subsidies can influence recipient ecosystems. Then, I conducted a field experiment exploring the effects of anthropogenic carrion subsidy (chicken meat) and environmental-relevant concentration of glyphosate (the most widely applied herbicides worldwide) on leaf litter decomposition and invertebrate communities colonizing in the leaf-litter bags deploying in streams with different types of land use. Next, I conducted a mesocosm experiment nearby an urban stream to investigate the effects of water temperature (~ 8 oC above vs ambient), consumer - snails (presence vs absence), and leaf-litter quality (intact vs >40 % leaf area was consumed by terrestrial insects) on litter decomposition. Finally, I explored the global patterns of riparian leaf litter C, N, P, and their stoichiometric ratios to gradients of climatic (mean annual temperature and precipitation) and geographic (absolute latitude and altitude) factors, and the differences between biotic factors (phylogeny, leaf habit, N-fixing function, invasion status, and life form). The results of field experiment indicated that: in coarse mesh bags, glyphosate, carrion subsidy, and the addition of both decreased litter breakdown rates by 6.3 %, 22.6 %, and 24.3 % respectively; in fine mesh bags, glyphosate and the addition of both retarded litter breakdown rates by 8.3 % and 12.5 % respectively. Litter decomposition also differed among streams, with the highest breakdown rates in village streams and lowest in urban/suburban streams. Invertebrates were significantly different among streams, with biodiversity index and total taxon richness were highest in village streams and lowest in suburban stream. However, overall effects of carrion subsidy and glyphosate on macroinvertebrates were not significant. The results of mesocosm experiment indicated that warming and the presence of snails accelerated litter decomposition by 60.2 % and 34.9 % respectively, while litter breakdown rates of terrestrial insect damaged leaves were 5.1 % slower than intact leaves because of lower leaf litter quality. The results of meta-analysis study demonstrated that global riparian leaf litter had higher N and P, while lower C, C:N, and C:P ratios than terrestrial leaf litter in general. Riparian leaf litter quality changed with gradients of climatic and geographic predictors, and these patterns differed between leaf habits (evergreen or deciduous) and climate zones (tropical or non-tropical area). In general, my research provides important information on resource subsidy processes, which will benefit freshwater ecosystem management to support biodiversity and maintain ecosystem services

Microbe-Mineral Interactions During Exceptional Fossil Preservation, Stromatolite Formation, and Desert Varnish Growth

The Ediacaran to Cambrian Deep Spring Formation consists of mixed carbonate-siliciclastic strata which contain an increasingly complex and biogeographically important biota. Past investigations of the Deep Spring Formation at Mt. Dunfee, Nevada, explored the highly diverse microbialite reefs consisting of a wide range of stromatolite morphologies which exerted significant control on local sedimentation and topography. Early investigations also documented the biomineralizing metazoan Cloudina (an Ediacaran index fossil). However, recent exploration of the area has resulted in the discovery of several new metazoan fossil communities consisting of a diverse assemblage of Ediacaran soft-tissue tubicolous vermiforms (tube fossils) similar to Cloudina. The focus of this dissertation is on the geomicrobiological processes at work in the Deep Spring Formation and elsewhere which result in the preservation of soft-tissues (Ch. 2), the dissolution/precipitation of feldspars within stromatolites (Ch. 3), and the early formation of modern desert varnish (Ch. 4). Chapter 1 of my dissertation examines the stratigraphic and paleontologic context of the Deep Spring Formation. In this chapter, I summarize the current understanding of the paleontological transition at the Ediacaran-Cambrian boundary in the western United States. The Death Valley and White-Inyo-Esmeralda regions of California and Nevada contain some of the most fossiliferous terminal Neoproterozoic to early Phanerozoic strata in the world. Within these strata, the Cambrian explosion is in full display, resplendent with diverse trace and body fossils. The Wood Canyon and Deep Spring Formations, within which the boundary is contained, are comprised of mixed carbonate and siliciclastic lithologies—allowing for a more in-depth understanding of this critical transition in the history of life. Here, I briefly review our current state of understanding of life contained within these rocks. This chapter has been published (Strange and Rowland, 2017) Chapter 2 consists of a manuscript I submitted to the journal Geobiology describing the microbial-related mineralization pathways responsible for preserving the upper fossil horizon in the Deep Spring Formation at Mt. Dunfee, Nevada. The manuscript was recently rejected, with an offer to resubmit after reviewers’ comments have been addressed. In this manuscript, I describe a new mineralization pathway to exceptional fossil preservation which involves the metabolic activities of an iron-oxidizing bacterial community. This model expands on previous microbial/redox zonation models of exceptional preservation and requires rapid emplacement of organic matter into the microaerophilic sedimentary environment. Within these redox conditions, iron-oxidation by bacteria produce abundant Fe (III) from porewater sourced Fe (II), resulting in the precipitation of early Fe (III) mineral phases with the quick stabilization in the form of goethite and iron-rich aluminosilicates. I have named this taphonomic pathway “ferrumation”. Ferrumation incorporates well into the microbial/redox zonation model of Schiffbauer et al. (2014) due to the occurrence of pyritization within the fossil assemblage. Chapter 3 moves away from iron-oxidizing bacteria to the mineral producing capabilities of the consortia of microbes involved in stromatolite formation. Feldspar assemblages found within stromatolite laminae differ between stromatolite localities and from the surrounding interstromatolite zone between columnar stromatolites. This suggests that microbial activities may be influencing their dissolution and precipitation. Textural associations between feldspars, quartz, and calcite are similar to the micrographic textures seen in some igneous rocks which result from the co-stability of feldspar and quartz in a magma chamber. These highly unusual feldspar textures within Deep Spring stromatolites led to the hypothesis that microbial activity resulted in the dissolution of detrital feldspars (mostly orthoclase) captured by the sticky surface of the stromatolite. The capture of dissolved ions from detrital orthoclase by organic molecules become released into the closed system of a mineralizing microbialite and precipitate out as authigenic albite, quartz, Ca-plagioclase, and a K-rich aluminosilicate, or their poorly crystalline precursors. This pattern of feldspar-quartz-calcite associations has been found at the Ediacaran-Cambrian Mount Dunfee section and the Molly Gibson Mine section of the Deep Spring Formation, in Miocene stromatolites from the Duero Basin, Spain, and also in a stromatolite from the Flinders Range, Australia. This research is significant because it could lead to the ability to isolate and date authigenic albite grains using the Ar/Ar method, potentially opening the utilization of stromatolites as abundant repositories of syndepositional authigenic minerals for geochronology. Chapter four departs from the Ediacaran-Cambrian boundary but continues with the theme of microbe-mineral interactions. This chapter details the earliest phases of desert varnish formation on ephemeral wash sediments from Nelson, Nevada. I show that the early development of incipient desert varnish occurs through small “microdots”. These are likely associated with Fe- and Mn-oxidizing microbial communities on the surface of the sediment grains. The Fe-oxide composition of some microdots and the mixed-composition of more advanced desert varnish suggests that desert varnish may accumulate through the cyclic deposition of layers during periods of habitability of each microbial community. Desert varnish microdots are shown to have progressive mineralization from smooth surfaces to micronodules, while advanced development becomes botryoidal. The previously reported “microstromatolitic” growth habit of some desert varnish seems to correspond with the microdot morphology of the incipient varnish found on these grains

Multiple Sclerosis

The book “Multiple Sclerosis: Diagnosis and Treatment” provides a collection of selected articles published in Biomedicines as part of Volume II addressing current issues on this major inflammatory demyelinating neurological disorder. The articles describe recent advances and discoveries in the molecular and cell microenvironment contributing to neuro-inflammation in the brain and spinal cord. The role of the neurofilaments light chain as a serological biomarker of axonal and neuronal degeneration of the CNS is presented not just as a sensitive diagnostic tool, but also as an indicator of treatment responses. The new generation of therapeutic molecules belonging to the sphingosine-1-phosphate class are discussed, and their potential as disease-modifying treatment is considered. Investigations into the intimate molecular mechanisms of highly active MS, disclosed clinically and by MRI, are discussed by researchers proposing that the expression of RNAs in peripheral blood cells is a biomarker of highly active disease. The book also addresses important clinical and epidemiological aspects of pediatric MS and that in multi-ethnic cohorts

LSST Science Book, Version 2.0

A survey that can cover the sky in optical bands over wide fields to faint magnitudes with a fast cadence will enable many of the exciting science opportunities of the next decade. The Large Synoptic Survey Telescope (LSST) will have an effective aperture of 6.7 meters and an imaging camera with field of view of 9.6 deg^2, and will be devoted to a ten-year imaging survey over 20,000 deg^2 south of +15 deg. Each pointing will be imaged 2000 times with fifteen second exposures in six broad bands from 0.35 to 1.1 microns, to a total point-source depth of r~27.5. The LSST Science Book describes the basic parameters of the LSST hardware, software, and observing plans. The book discusses educational and outreach opportunities, then goes on to describe a broad range of science that LSST will revolutionize: mapping the inner and outer Solar System, stellar populations in the Milky Way and nearby galaxies, the structure of the Milky Way disk and halo and other objects in the Local Volume, transient and variable objects both at low and high redshift, and the properties of normal and active galaxies at low and high redshift. It then turns to far-field cosmological topics, exploring properties of supernovae to z~1, strong and weak lensing, the large-scale distribution of galaxies and baryon oscillations, and how these different probes may be combined to constrain cosmological models and the physics of dark energy.Comment: 596 pages. Also available at full resolution at http://www.lsst.org/lsst/sciboo

Rotifer adaptation to environmental unpredictability

Environmental unpredictability is a phenomenon that occurs in any habitat, and is an important selection pressure for the evolution of adaptive responses in the organisms. Interestingly, the ponds located in the Mediterranean region are characterized by having a high degree of seasonality and uncertainty at various temporal scales. Unpredictability in natural populations can act on several organism traits, especially in those species with complex life histories. The rotifer Brachionus plicatilis is a zooplankton species that frequently inhabits the salt ponds of the Mediterranean region. It has a type of reproduction in which proliferation by parthenogenesis (asexual phase) combines with occasional bouts of male production and sexual reproduction; the latter resulting in diapausing egg production (sexual phase). This makes B. plicatilis populations inhabiting Mediterranean ponds a good model system to study the adaptation to environmental unpredictability. In this thesis the first objective was to quantify the degree of environmental unpredictability of the studied Mediterranean ponds. In order to do that the variation in water-surface area during 27 years of a group of twenty saline water bodies was obtained from the scenes from the satellites Landsat 5 and 7. Different models for predictability estimation were developed here by considering how the variation in water-surface area could be relevant for the focus organism. The group of Mediterranean ponds studied were found to have a wide range of predictability values. A posteriori classification of the models for predictability estimation showed that some assumptions had negligible effects, while others can be associated with the species assemblages for which predictability needs to be assessed. The second objective was to study variation in diapause-related life-history traits in B. plicatilis. To do this, nine populations from a set of Mediterranean saline ponds were studied and showed significant levels of within-population genetic variation for the following life-history traits: propensity for sex and for hatching fraction of diapausing eggs. The propensity for sex in rotifer populations, and hence the early investment in diapause, decreased with environmental predictability. This suggests a conservative, bet-hedging strategy. Diapausing egg hatching fractions showed intermediate values (from 44 to 88%) in all the studied populations, but this trait was not related to the level of environmental predictability. Rotifer populations are able to locally diverge in diapause-related traits within a small geographical range (240 km2) despite their potential for widespread genetic exchange through the passive dispersal of diapausing eggs. The third objective was to unveil, at a genome wide scale, genotypes correlated to adaptation to local environmental unpredictability. The B. plicatilis genome was assembled in this thesis and its structural annotation yielded 54,725 predicted genes. Functions were tentatively assigned to 30% of them. Genotyping by sequencing (GBS), and the subsequent bioinformatics analyses in the 30 clones for each of the nine saline ponds studied provided a large number (4,543) of high quality single nucleotide polymorphisms (SNPs). A number of SNPs —most of them located within genes– showed higher between-population differentiation than expected by chance and were correlated with life-history traits and environmental parameters, so that they are candidates for diversifying selection for local adaptation. Unexpectedly, a large set of SNPs, more than half of them located within genes were found to present signatures of balancing/purifying selection in B. plicatilis. A number of genes were identified as strong candidates to be part of the genomic basis of local adaptation to fluctuating environments and constitute a database for future studies. Overall this thesis supports the expectation that wild populations of B. plicatilis can develop evolutionary responses to face environmental unpredictability and contribute to the empirical evidence of bet hedging strategies

Study of genetic factors in treatment-related complications in patients with childhood acute lymphoblastic leukemia and post transplantation of hematopoietic stem cells

La leucémie lymphoblastique aiguë (LLA) est le cancer le plus fréquent chez les enfants. Malgré le fait que plus de 80% des enfants atteints de LLA sont aujourd'hui guéris de leur maladie, ce succès a toutefois un prix élevé, car l’exposition aux médicaments cytotoxique et/ou à l’irradiation pendant une période vulnérable du développement de l’enfant peut entraîner des conséquences à long terme. En effet, environ 60% des enfants ayant survécu à une LLA devront vivre avec des problèmes de santé liés au traitement, également appelés effets indésirables tardifs (late-adverse effects, LAEs). Parmi ces derniers, on notera des problèmes métaboliques, l’ostéoporose, une altération des fonctions cognitives ou cardiaques, ainsi que la dépression et l’anxiété. Si certains survivants ne présentent aucune de ces complications, d'autres peuvent en avoir plusieurs. Différents facteurs peuvent contribuer à cette variabilité, notamment le traitement reçu, les caractéristiques de la maladie, les habitudes de vie et, surtout, la constitution génétique du patient. Ce projet s'est concentré sur les biomarqueurs génétiques permettant d'identifier les individus les plus susceptibles de souffrir de LAEs. Récemment, une étude exhaustive (évaluations cliniques, psychosociales et biochimiques) s’est déroulée au CHU Sainte-Justine pour caractériser chacune de ces morbidités chez 250 survivants de la LLA de l'enfant (cohorte PETALE). De plus, on a obtenu le profil génétique de chaque participant. Nous avons utilisé cet ensemble de données et des outils statistiques et bio-informatiques pour réaliser des études d'association comparant la fréquence des variants génétiques chez les survivants ayant développé ou non des LAEs; en particulier, les complications cardiovasculaires et neurocognitives, ainsi que les troubles de l'humeur tels que l'anxiété et la dépression. D'autres facteurs de risque tels que les caractéristiques de traitement et/ou de la leucémie ont été pris en compte lors de l'analyse pour dériver les meilleurs prédicteurs génétiques. Ainsi, en utilisant l'approche des gènes candidats, nous avons identifié les variants communs des gènes MTR, PPARA, ABCC3, CALML5, CACNB2 et PCDHB10 qui étaient associés à des déficits de performance des tests neurocognitifs, tandis que les variants des gènes SLCO1B1 et EPHA5 étaient associés à l'anxiété et à la dépression. Deux variants, rs1805087 dans le gène MTR et rs58225473 dans le gène CACNB2 sont particulièrement intéressants, car ces associations ont été validées dans la cohorte de réplication SJLIFE (St. Jude Children's Research Hospital, Memphis, USA). Les analyses d'association ont été complémentées par une étude d'association à l'échelle de l'exome, qui a identifié plusieurs gènes supplémentaires comme des modulateurs potentiels du risque de développer des complications neurocognitives liées au traitement (gènes AK8 et ZNF382), ainsi que l'anxiété et la dépression (gènes PTPRZ1, MUC16, TNRC6C-AS1, APOL2, C6orf165, EXO5, CYP2W1 et PCMTD1). Le variant rs61732180 du gène ZNF382 a ensuite été validé dans la cohorte de réplication SJLIFE. Également, nous avons effectué des analyses d’association concernant les complications cardiaques liées au traitement qui ont identifié plusieurs nouveaux marqueurs associés à ces complications dans les gènes TTN, NOS1, ABCG2, CBR1, ABCC5, AKR1C3, NOD2 et ZNF267. De plus, nous avons résumé les connaissances actuelles sur les marqueurs pharmacogénomiques qui ont été associés aux effets de cardiotoxicités, induites par les anthracyclines, qui affectent les patients atteints de cancer pédiatrique. Nous avons également inclus un aperçu de l'applicabilité des résultats rapportés, notamment ceux qui ont été validés dans la cohorte PETALE. Par ailleurs, nous nous sommes intéressés aux complications qui surviennent après une greffe de cellules souches hématopoïétiques. Nous avons appliqué des approches bio-informatiques et statistiques similaires pour obtenir un profil plus complet de la composante génétique derrière ces complications potentiellement mortelles. Ainsi, une étude d'association à l'échelle de l'exome a été réalisée dans une cohorte de patients pédiatriques subissant une greffe de cellules souches hématopoïétiques après un régime de conditionnement contenant du busulfan. Nous avons identifié de nouvelles variations génétiques conférant un risque plus élevé de syndrome d'obstruction sinusoïdale (notamment dans les gènes UGT2B10, BHLHE22, et KIAA1715) et de maladie aiguë du greffon contre l'hôte (dans les gènes ERC1, PLEK, NOP9 et SPRED1), qui pourraient être utiles pour des stratégies personnalisées de prévention et de traitement. Ces travaux contribuent à la compréhension de l'influence des facteurs génétiques sur le risque de développer des complications liées au traitement, tant au cours du traitement qu'à long terme. De plus, les marqueurs génétiques signalés ainsi que d'autres facteurs de risque connus peuvent conduire à des modèles de prédiction identifiant les patients à risque accru de ces complications.Acute lymphoblastic leukemia (ALL) is the most common cancer in children. Even though more than 80% of children with ALL are now cured of their disease, this success comes at a high price as exposure to cytotoxic drugs and/or radiation during a vulnerable period of child development may have long-term consequences. In fact, approximately 60% of children who survive ALL will have to live with treatment-related health problems, also called late-adverse effects (LAEs). These include metabolic problems, osteoporosis, impaired cardiac or cognitive functions, as well as depression and anxiety. While some survivors do not have any of these complications, others may have more than one. Different factors can contribute to this variability, in particular, the treatment received, the characteristics of the disease, the lifestyle, and, above all, the genetic makeup of the patient. This project focused on genetic biomarkers capable of identifying the individuals most likely to suffer from LAEs. Recently, an exhaustive study (clinical, psychosocial, and biochemical evaluations) took place at Sainte-Justine University Health Center (Montreal, Canada), with the goal to characterize each of these morbidities in 250 survivors of childhood ALL (PETALE cohort). In addition, the genetic profile of each participant was obtained, and we used statistical and bioinformatics tools to perform association studies on this dataset in order to compare the frequency of genetic variants in survivors with or without LAEs. We evaluated cardiovascular and neurocognitive complications, as well as mood disorders such as anxiety and depression. Other risk factors, such as treatment and/or leukemia characteristics were also considered during the analysis to derive the best genetic predictors. Thus, using the candidate gene approach, we identified common variants in the MTR, PPARA, ABCC3, CALML5, CACNB2, and PCDHB10 genes that were associated with deficits in neurocognitive tests performance, whereas variants in the SLCO1B1 and EPHA5 genes were associated with anxiety and depression. Two variants, rs1805087 in the MTR gene and rs58225473 in the CACNB2 gene, are of particular interest since these associations were validated in an independent SJLIFE replication cohort (St. Jude Children's Research Hospital, Memphis, USA). The association analyses were complemented by an exome-wide association study, which identified several additional genes as potential modulators of the risk of developing treatment-related neurocognitive complications (genes AK8 and ZNF382), as well as anxiety and depression (genes PTPRZ1, MUC16, TNRC6C-AS1, APOL2, C6orf165, EXO5, CYP2W1, and PCMTD1). Variant rs61732180 in the ZNF382 gene was further validated in the replication SJLIFE cohort. To a great extent, we performed association analyses regarding treatment-related cardiac complications which identified several novel markers associated with these toxicities in the TTN, NOS1, ABCG2, CBR1, ABCC5, AKR1C3, NOD2, and ZNF267 genes in survivors of childhood ALL. In addition, we summarized the current knowledge on pharmacogenomic markers related to anthracycline-induced cardiotoxicity affecting pediatric cancer patients. We also included a brief overview of the applicability of reported findings to the PETALE cohort, validating several of them. Besides, we were interested in the complications that arise after a hematopoietic stem cell transplantation. We applied similar bioinformatics and statistical approaches to gain a more complete insight into the genetic component behind these life-threatening complications. Thus, an exome-wide association study was performed in a cohort of pediatric patients undergoing hematopoietic stem cell transplantation following a conditioning regimen containing busulfan. Our results identified new genetic variations conferring a higher risk of sinusoidal obstruction syndrome (notably in the UGT2B10, BHLHE22, and KIAA1715 genes) and acute graft-versus-host disease (ERC1, PLEK, NOP9, and SPRED1 genes), which could be useful for personalized prevention and treatment strategies. This work contributes to the understanding of the influence of genetic factors on the risk of developing treatment-related complications, both during treatment and in the long term. Furthermore, the reported genetic markers along with other known risk factors can lead to prediction models identifying patients at increased risk for these complications

LSST Science Book, Version 2.0

A survey that can cover the sky in optical bands over wide fields to faint magnitudes with a fast cadence will enable many of the exciting science opportunities of the next decade. The Large Synoptic Survey Telescope (LSST) will have an effective aperture of 6.7 meters and an imaging camera with field of view of 9.6 deg^2, and will be devoted to a ten-year imaging survey over 20,000 deg^2 south of +15 deg. Each pointing will be imaged 2000 times with fifteen second exposures in six broad bands from 0.35 to 1.1 microns, to a total point-source depth of r~27.5. The LSST Science Book describes the basic parameters of the LSST hardware, software, and observing plans. The book discusses educational and outreach opportunities, then goes on to describe a broad range of science that LSST will revolutionize: mapping the inner and outer Solar System, stellar populations in the Milky Way and nearby galaxies, the structure of the Milky Way disk and halo and other objects in the Local Volume, transient and variable objects both at low and high redshift, and the properties of normal and active galaxies at low and high redshift. It then turns to far-field cosmological topics, exploring properties of supernovae to z~1, strong and weak lensing, the large-scale distribution of galaxies and baryon oscillations, and how these different probes may be combined to constrain cosmological models and the physics of dark energy