Sublinear Algorithms for Approximating String Compressibility

We raise the question of approximating the compressibility of a string with respect to a fixed compression scheme, in sublinear time. We study this question in detail for two popular lossless compression schemes: run-length encoding (RLE) and a variant of Lempel-Ziv (LZ77), and present sublinear algorithms for approximating compressibility with respect to both schemes. We also give several lower bounds that show that our algorithms for both schemes cannot be improved significantly. Our investigation of LZ77 yields results whose interest goes beyond the initial questions we set out to study. In particular, we prove combinatorial structural lemmas that relate the compressibility of a string with respect to LZ77 to the number of distinct short substrings contained in it (its ℓth subword complexity , for small ℓ). In addition, we show that approximating the compressibility with respect to LZ77 is related to approximating the support size of a distribution.National Science Foundation (U.S.) (Award CCF-1065125)National Science Foundation (U.S.) (Award CCF-0728645)Marie Curie International Reintegration Grant PIRG03-GA-2008-231077Israel Science Foundation (Grant 1147/09)Israel Science Foundation (Grant 1675/09

A comprehensive analysis of autocorrelation and bias in home range estimation

Home range estimation is routine practice in ecological research. While advances in animal tracking technology have increased our capacity to collect data to support home range analysis, these same advances have also resulted in increasingly autocorrelated data. Consequently, the question of which home range estimator to use on modern, highly autocorrelated tracking data remains open. This question is particularly relevant given that most estimators assume independently sampled data. Here, we provide a comprehensive evaluation of the effects of autocorrelation on home range estimation. We base our study on an extensive data set of GPS locations from 369 individuals representing 27 species distributed across five continents. We first assemble a broad array of home range estimators, including Kernel Density Estimation (KDE) with four bandwidth optimizers (Gaussian reference function, autocorrelated-Gaussian reference function [AKDE], Silverman´s rule of thumb, and least squares cross-validation), Minimum Convex Polygon, and Local Convex Hull methods. Notably, all of these estimators except AKDE assume independent and identically distributed (IID) data. We then employ half-sample cross-validation to objectively quantify estimator performance, and the recently introduced effective sample size for home range area estimation ((Formula presented.)) to quantify the information content of each data set. We found that AKDE 95% area estimates were larger than conventional IID-based estimates by a mean factor of 2. The median number of cross-validated locations included in the hold-out sets by AKDE 95% (or 50%) estimates was 95.3% (or 50.1%), confirming the larger AKDE ranges were appropriately selective at the specified quantile. Conversely, conventional estimates exhibited negative bias that increased with decreasing (Formula presented.). To contextualize our empirical results, we performed a detailed simulation study to tease apart how sampling frequency, sampling duration, and the focal animal´s movement conspire to affect range estimates. Paralleling our empirical results, the simulation study demonstrated that AKDE was generally more accurate than conventional methods, particularly for small (Formula presented.). While 72% of the 369 empirical data sets had >1,000 total observations, only 4% had an (Formula presented.) >1,000, where 30% had an (Formula presented.) <30. In this frequently encountered scenario of small (Formula presented.), AKDE was the only estimator capable of producing an accurate home range estimate on autocorrelated data.Fil: Noonan, Michael J.. National Zoological Park; Estados Unidos. University of Maryland; Estados UnidosFil: Tucker, Marlee A.. Senckenberg Gesellschaft Für Naturforschung; . Goethe Universitat Frankfurt; AlemaniaFil: Fleming, Christen H.. University of Maryland; Estados Unidos. National Zoological Park; Estados UnidosFil: Akre, Thomas S.. National Zoological Park; Estados UnidosFil: Alberts, Susan C.. University of Duke; Estados UnidosFil: Ali, Abdullahi H.. Hirola Conservation Programme. Garissa; KeniaFil: Altmann, Jeanne. University of Princeton; Estados UnidosFil: Antunes, Pamela Castro. Universidade Federal do Mato Grosso do Sul; BrasilFil: Belant, Jerrold L.. State University of New York; Estados UnidosFil: Beyer, Dean. Universitat Phillips; AlemaniaFil: Blaum, Niels. Universitat Potsdam; AlemaniaFil: Böhning Gaese, Katrin. Senckenberg Gesellschaft Für Naturforschung; Alemania. Goethe Universitat Frankfurt; AlemaniaFil: Cullen Jr., Laury. Instituto de Pesquisas Ecológicas; BrasilFil: de Paula, Rogerio Cunha. National Research Center For Carnivores Conservation; BrasilFil: Dekker, Jasja. Jasja Dekker Dierecologie; Países BajosFil: Drescher Lehman, Jonathan. George Mason University; Estados Unidos. National Zoological Park; Estados UnidosFil: Farwig, Nina. Michigan State University; Estados UnidosFil: Fichtel, Claudia. German Primate Center; AlemaniaFil: Fischer, Christina. Universitat Technical Zu Munich; AlemaniaFil: Ford, Adam T.. University of British Columbia; CanadáFil: Goheen, Jacob R.. University of Wyoming; Estados UnidosFil: Janssen, René. Bionet Natuuronderzoek; Países BajosFil: Jeltsch, Florian. Universitat Potsdam; AlemaniaFil: Kauffman, Matthew. University Of Wyoming; Estados UnidosFil: Kappeler, Peter M.. German Primate Center; AlemaniaFil: Koch, Flávia. German Primate Center; AlemaniaFil: LaPoint, Scott. Max Planck Institute für Ornithologie; Alemania. Columbia University; Estados UnidosFil: Markham, A. Catherine. Stony Brook University; Estados UnidosFil: Medici, Emilia Patricia. Instituto de Pesquisas Ecológicas (IPE) ; BrasilFil: Morato, Ronaldo G.. Institute For Conservation of The Neotropical Carnivores; Brasil. National Research Center For Carnivores Conservation; BrasilFil: Nathan, Ran. The Hebrew University of Jerusalem; IsraelFil: Oliveira Santos, Luiz Gustavo R.. Universidade Federal do Mato Grosso do Sul; BrasilFil: Olson, Kirk A.. Wildlife Conservation Society; Estados Unidos. National Zoological Park; Estados UnidosFil: Patterson, Bruce. Field Museum of National History; Estados UnidosFil: Paviolo, Agustin Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste; ArgentinaFil: Ramalho, Emiliano Esterci. Institute For Conservation of The Neotropical Carnivores; Brasil. Instituto de Desenvolvimento Sustentavel Mamirauá; BrasilFil: Rösner, Sascha. Michigan State University; Estados UnidosFil: Schabo, Dana G.. Michigan State University; Estados UnidosFil: Selva, Nuria. Institute of Nature Conservation of The Polish Academy of Sciences; PoloniaFil: Sergiel, Agnieszka. Institute of Nature Conservation of The Polish Academy of Sciences; PoloniaFil: Xavier da Silva, Marina. Parque Nacional do Iguaçu; BrasilFil: Spiegel, Orr. Universitat Tel Aviv; IsraelFil: Thompson, Peter. University of Maryland; Estados UnidosFil: Ullmann, Wiebke. Universitat Potsdam; AlemaniaFil: Ziḝba, Filip. Tatra National Park; PoloniaFil: Zwijacz Kozica, Tomasz. Tatra National Park; PoloniaFil: Fagan, William F.. University of Maryland; Estados UnidosFil: Mueller, Thomas. Senckenberg Gesellschaft Für Naturforschung; . Goethe Universitat Frankfurt; AlemaniaFil: Calabrese, Justin M.. National Zoological Park; Estados Unidos. University of Maryland; Estados Unido

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Cleantech insinöörikoulutuksessa

Cleantech-insinoorit -projekti on Lahden ammattikorkeakoulun tekniikan alan hallinnoima ja Hameen ELY-keskuksen osarahoittama Euroopan Sosiaalirahaston hanke, jonka tavoitteena on parantaa Paijat-Hameen cleantech-osaamista seka insinoorikoulutuksen tyoelamavastaavuutta. Projektin tavoitteena on tuottaa uudenlainen koulutuksen toimintamalli, joka luo aitoja edellytyksia cleantech-innovaatioiden syntymiselle seka uusille tuotteille ja palveluille ymparistoliiketoiminnan alueella. Uuden yhteistyo- ja toimintamallin kehittaminen tekniikan alan koulutukseen perustuu yhteistyohon yrityselaman ja muiden toimijoiden kanssa. Yhteistyota on toteutettu erilaisissa opiskelija- ja T&K-projekteissa, opinnaytetoissa, koulutuksissa, tyopajoissa, seminaareissa, opintomatkoilla ja benchmarkkaamalla erilaisia kaytantoja koti- ja ulkomailla. Uusi yhteistyo- ja toimintamalli kasittaa lisaksi CDIO-/PBL-pedagogiikkaan (CDIO = Conceive – Design – Implement – Operate- / PBL = Problem Based Learning) perustuvan oppimismallin tuomisen tekniikan alan koulutukseen perinteisten insinooritietojen ja -taitojen ohella seka cleantech-osaamisen sisallyttamisen opintosuunnitelmiin. Myos tyoelamalta saadut tiedot tyoelamaosaamisen osaamis- ja muista tarpeista sisallytetaan opintosuunnitelmiin. Lahden ammattikorkeakoulu haluaa osaltaan seka kehittaa insinoorikoulutusta vastaamaan alueen cleantech-yritysten osaamistarpeita etta osallistua alueen yritysten tuotteiden, palvelujen ja prosessien kehittamiseen. Cleantech-insinoorit -projektin tarkoituksena on tunnistaa puhtaan teknologian suunnittelemisessa ja hyodyntamisessa tarvittavia tietoja ja taitoja ja integroida ne insinoorien koulutukseen. Lahden ammattikorkeakoulun tekniikan alalla on viisi koulutusohjelmaa, joista jokaisen cleantech-tarpeita on projektissa tarkasteltu. Lisaksi projektissa selvitettiin olemassa olevan tiedon avulla cleantech-sektorin tarpeita. Cleantech-osaamisen koulutustarvekartoitus tehtiin syksylla 2011, josta tarkempi koulutussuunnitelma cleantech-osaamisen parantamiseksi Paijat-Hameessa valmistui joulukuussa 2011. Kartoituksen ja yritysten haastattelujen pohjalta projektissa toteutettiin cleantech-osaamisen parantamiseksi koulutuksia vuosina 2012 – 2013. Koulutukset pureutuivat ajankohtaisiin teemoihin, kuten vihreaan ICT:hen, energia- ja materiaalitehokkuuteen, kestaviin hankintoihin seka ajankohtaisiin lainsaadannon vaatimuksiin. Tassa artikkelikokoelmassa kerrotaan Lahden ammattikorkeakoulun tekniikan alan koulutusohjelmien toimenpiteista, joilla alueen ja insinoorikoulutuksen cleantech-osaamista ja tyoelamavastaavuutta on parannettu. Raportin suomenkielisessa osassa on tarkasteltu cleantech-liiketoiminnan globaaleja markkinoita ja tulevaisuuden nakymia seka Suomen ja Lahden seudun cleantech-osaamista ja osaamistarpeita. Materiaalitekniikan koulutusohjelman artikkeleissa on kasitelty opintosuunnitelman muutostyota, joka kasittaa myos cleantech-nakokulman ja CDIO- / PBL-pedagogiikan sisallyttamisen opintosuunnitelmaan. Mekatroniikan koulutusohjelman artikkelissa on kasitelty CDIO- / PBL-pedagogiikan lahestymistapaa ja toteutumista kone- ja tuotantotekniikan koulutusohjelmassa. Raportin englanninkielinen osuus kasittelee ymparistoteknologian koulutusohjelman opintosuunnitelman muutosta, joka sisaltaa myos englanninkielisen ylemman ammattikorkeakoulututkinnon. Lisaksi englanninkieliset artikkelit kasittelevat tietotekniikan koulutusohjelman cleantech-nakokulmaa Green ICT -moduuleissa