Environmental Science

A new method for determining nucleotide sequences in DNA is described. It is similar to the "plus and minus" method [Sanger, F. & Coulson, A. R. (1975) J. Mol. Biol. 94, 441-448] but makes use of the 2',3'-dideoxy and arabinonucleoside analogues of the normal deoxynucleoside triphosphates, which act as specific chain-terminating inhibitors of DNA polymerase. The technique has been applied to the DNA of bacteriophage varphiX174 and is more rapid and more accurate than either the plus or the minus method.

We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applicati

We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying mi

SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for hi

Abstract Within the Copernicus Climate Change Service (C3S), ECMWF is producing the ERA5 reanalysis which, once completed, will embody a detailed record of the global atmosphere, land surface and ocean waves from 1950 onwards. This new reanalysis replaces the ERA‐Interim reanalysis (spanning 1979 onwards) which was started in 2006. ERA5 is based on the Integrated Forecasting System (IFS) Cy41r2 which was operational in 2016. ERA5 thus benefits from a decade of developments in model physics, core dynamics and data assimilation. In addition to a significantly enhanced horizontal resolution of 31 km, compared to 80 km for ERA‐Interim, ERA5 has hourly output throughout, and an uncertainty estimate from an ensemble (3‐hourly at half the horizontal resolution). This paper describes the general s

The NCEP and NCAR are cooperating in a project (denoted “reanalysis”) to produce a 40-year record of global analyses of atmospheric fields in support of the needs of the research and climate monitoring communities. This effort involves the recovery of land surface, ship, rawinsonde, pibal, aircraft, satellite, and other data; quality controlling and assimilating these data with a data assimilation system that is kept unchanged over the reanalysis period 1957–96. This eliminates perceived climate jumps associated with changes in the data assimilation system. The NCEP/NCAR 40-yr reanalysis uses a frozen state-of-the-art global data assimilation system and a database as complete as possible. The data assimilation and the model used are identical to the global system implemented operationally

Abstract A new and relatively simple equation for the soil‐water content‐pressure head curve, θ( h ), is described in this paper. The particular form of the equation enables one to derive closed‐form analytical expressions for the relative hydraulic conductivity, K r , when substituted in the predictive conductivity models of N.T. Burdine or Y. Mualem. The resulting expressions for K r ( h ) contain three independent parameters which may be obtained by fitting the proposed soil‐water retention model to experimental data. Results obtained with the closed‐form analytical expressions based on the Mualem theory are compared with observed hydraulic conductivity data for five soils with a wide range of hydraulic properties. The unsaturated hydraulic conductivity is predicted well in four out of

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncult

Abstract ERA‐Interim is the latest global atmospheric reanalysis produced by the European Centre for Medium‐Range Weather Forecasts (ECMWF). The ERA‐Interim project was conducted in part to prepare for a new atmospheric reanalysis to replace ERA‐40, which will extend back to the early part of the twentieth century. This article describes the forecast model, data assimilation method, and input datasets used to produce ERA‐Interim, and discusses the performance of the system. Special emphasis is placed on various difficulties encountered in the production of ERA‐40, including the representation of the hydrological cycle, the quality of the stratospheric circulation, and the consistency in time of the reanalysed fields. We provide evidence for substantial improvements in each of these aspects

Cuando la deserción es producto de la ruptura de la conexión de intereses que unen a un estudiante con una institución educativa o por la ausencia de políticas que favorezcan la permanencia de estudiantes en las instituciones, el costo económico y social de una deserción es mayor porque se deteriora la calidad de vida del estudiante y por ende afecta el crecimiento de un país, más cuando la educación es considerada como un factor esencial en el crecimiento económico y la reducción de la pobreza. El proyecto analiza el fenómeno de la deserción en el Centro de Servicios Empresariales y Turísticos del SENA Regional Santander CSET, teniendo en cuenta que esta regional se ubica en cuarto lugar entre las 33 regionales del país por los altos niveles de deserción que presenta en los últimos period

The methodology used to construct tree structured rules is the focus of this monograph. Unlike many other statistical procedures, which moved from pencil and paper to calculators, this text's use of trees was unthinkable before computers. Both the practical and theoretical sides have been developed in the authors' study of tree methods. Classification and Regression Trees reflects these two sides, covering the use of trees as a data analysis method, and in a more mathematical framework, proving some of their fundamental properties.

This report is the first volume of the IPCC's Fourth Assessment Report. It covers several topics including the extensive range of observations now available for the atmosphere and surface, changes in sea level, assesses the paleoclimatic perspective, climate change causes both natural and anthropogenic, and climate models for projections of global climate.

Methods of evaluating and comparing the performance of diagnostic tests are of increasing importance as new tests are developed and marketed. When a test is based on an observed variable that lies on a continuous or graded scale, an assessment of the overall value of the test can be made through the use of a receiver operating characteristic (ROC) curve. The curve is constructed by varying the cutpoint used to determine which values of the observed variable will be considered abnormal and then plotting the resulting sensitivities against the corresponding false positive rates. When two or more empirical curves are constructed based on tests performed on the same individuals, statistical analysis on differences between curves must take into account the correlated nature of the data. This pa

The <i>Journal of Electronic Imaging</i> (JEI), copublished bimonthly with the Society for Imaging Science and Technology, publishes peer-reviewed papers that cover research and applications in all areas of electronic imaging science and technology.

mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the alpha and beta diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

(First edition: 1998, this reprint: 2004). This publication presents an updated procedure for calculating reference and crop evapotranspiration from meteorological data and crop coefficients. The procedure, first presented in FAO Irrigation and Drainage Paper No. 24, Crop water requirements, in 1977, allows estimation of the amount of water used by a crop, taking into account the effect of the climate and the crop characteristics. The publication incorporates advances in research and more accurate procedures for determining crop water use as recommended by a panel of high-level experts organised by FAO in May 1990. The first part of the guidelines includes procedures for determining reference crop evapotranspiration according to the FAO Penman-Monteith method. These are followed by updated

Two new two-equation eddy-viscosity turbulence models will be presented.They combine different elements of existing models that are considered superior to their alternatives.The first model, referred to as the baseline (BSL) model, utilizes the original k-u model of Wilcox in the inner region of the boundary layer and switches to the standard A>e model in the outer region and in free shear flows.It has a performance similar to the Wilcox model, but avoids that model's strong freestream sensitivity.The second model results from a modification to the definition of the eddy-viscosity in the BSL model, which accounts for the effect of the transport of the principal turbulent shear stress.The new model is called the shear-stress transport-model and leads to major improvements in the prediction

The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The majority of classifications (98%) were of high estimated confidence (> or = 95%) and high accuracy (98%). In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. The results from leave-one-out testing on both corpor

We developed interpolated climate surfaces for global land areas (excluding Antarctica) at a spatial resolution of 30 arc s (often referred to as 1-km spatial resolution). The climate elements considered were monthly precipitation and mean, minimum, and maximum temperature. Input data were gathered from a variety of sources and, where possible, were restricted to records from the 1950–2000 period. We used the thin-plate smoothing spline algorithm implemented in the ANUSPLIN package for interpolation, using latitude, longitude, and elevation as independent variables. We quantified uncertainty arising from the input data and the interpolation by mapping weather station density, elevation bias in the weather stations, and elevation variation within grid cells and through data partitioning and

Computer Program Abstracts The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and significant updates to existing ones. Following normal submission, a Computer Program Abstract will be reviewed by one or two members of the IUCr Commission on Crystallographic Computing. It should not exceed 500 words in length and should follow the standard format given on page 189 of the June 1985 issue of the Journal [J. Appl. CrysL (1985). 18, 189190] and on the World Wide Web at http://www.iucr. ac. uk/journals/jac/software/. Lists of software presented and~or reviewed in the Journal of Applied Crystallography are available on the World Wide Web at the above address, together with information about the availabili