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Book
1 online resource (76 p. ) : digital, PDF file.
This report provides a status of the markets and technology development involved in growing a domestic bioenergy economy as it existed at the end of 2013. It compiles and integrates information to provide a snapshot of the current state and historical trends influencing the development of bioenergy markets. This information is intended for policy-makers as well as technology developers and investors tracking bioenergy developments. It also highlights some of the key energy and regulatory drivers of bioenergy markets.
Book
1 online resource (33 p. ) : digital, PDF file.
In order to understand the anticipated status of the industry for non-starch ethanol and renewable hydrocarbon biofuels as of the end of calendar year 2015, the National Renewable Energy Laboratory (NREL) conducted its first annual survey update of U.S. non-starch ethanol and renewable hydrocarbon biofuels producers. This report presents the results of this survey, describes the survey methodology, and documents important changes since the 2013 survey.
Book
p. 1049-1062 : digital, PDF file.
Switchgrass is a relatively high-yielding and environmentally sustainable biomass crop, but further genetic gains in biomass yield must be achieved to make it an economically viable bioenergy feedstock. Genomic selection (GS) is an attractive technology to generate rapid genetic gains in switchgrass, and meet the goals of a substantial displacement of petroleum use with biofuels in the near future. In this study, we empirically assessed prediction procedures for genomic selection in two different populations, consisting of 137 and 110 half-sib families of switchgrass, tested in two locations in the United States for three agronomic traits: dry matter yield, plant height, and heading date. Marker data were produced for the families’ parents by exome capture sequencing, generating up to 141,030 polymorphic markers with available genomic-location and annotation information. We evaluated prediction procedures that varied not only by learning schemes and prediction models, but also by the way the data were preprocessed to account for redundancy in marker information. More complex genomic prediction procedures were generally not significantly more accurate than the simplest procedure, likely due to limited population sizes. Nevertheless, a highly significant gain in prediction accuracy was achieved by transforming the marker data through a marker correlation matrix. Our results suggest that marker-data transformations and, more generally, the account of linkage disequilibrium among markers, offer valuable opportunities for improving prediction procedures in GS. Furthermore, some of the achieved prediction accuracies should motivate implementation of GS in switchgrass breeding programs.
Book
13 p. : digital, PDF file.
CouR, a MarR-type transcriptional repressor, regulates the cou genes, encoding p-hydroxycinnamate catabolism in the soil bacterium Rhodococcus jostii RHA1. The CouR dimer bound two molecules of the catabolite p-coumaroyl-CoA (K<sub>d</sub> = 11 ± 1 μM). The presence of p-coumaroyl-CoA, but neither p-coumarate nor CoASH, abrogated CouR's binding to its operator DNA <i>in vitro</i>. The crystal structures of ligand-free CouR and its p-coumaroyl-CoA-bound form showed no significant conformational differences, in contrast to other MarR regulators. The CouR-p-coumaroyl-CoA structure revealed two ligand molecules bound to the CouR dimer with their phenolic moieties occupying equivalent hydrophobic pockets in each protomer and their CoA moieties adopting non-equivalent positions to mask the regulator's predicted DNA-binding surface. More specifically, the CoA phosphates formed salt bridges with predicted DNA-binding residues Arg36 and Arg38, changing the overall charge of the DNA-binding surface. The substitution of either arginine with alanine completely abrogated the ability of CouR to bind DNA. By contrast, the R36A/R38A double variant retained a relatively high affinity for p-coumaroyl-CoA (K<sub>d</sub> = 89 ± 6 μM). Altogether, our data point to a novel mechanism of action in which the ligand abrogates the repressor's ability to bind DNA by steric occlusion of key DNA-binding residues and charge repulsion of the DNA backbone.
Book
1 online resource (p. 1-7 ) : digital, PDF file.
Illumina is the most widely used next generation sequencing technology and produces millions of short reads that contain errors. These sequencing errors constitute a major problem in applications such as de novo genome assembly, metagenomics analysis and single nucleotide polymorphism discovery. In this study, we present ADEPT, a dynamic error detection method, based on the quality scores of each nucleotide and its neighboring nucleotides, together with their positions within the read and compares this to the position-specific quality score distribution of all bases within the sequencing run. This method greatly improves upon other available methods in terms of the true positive rate of error discovery without affecting the false positive rate, particularly within the middle of reads. We conclude that ADEPT is the only tool to date that dynamically assesses errors within reads by comparing position-specific and neighboring base quality scores with the distribution of quality scores for the dataset being analyzed. The result is a method that is less prone to position-dependent under-prediction, which is one of the most prominent issues in error prediction. The outcome is that ADEPT improves upon prior efforts in identifying true errors, primarily within the middle of reads, while reducing the false positive rate.
Book
8 p. : digital, PDF file.
<i>Escherichia coli</i> plays an important role as a member of the gut microbiota; however, pathogenic strains also exist, including various diarrheagenic <i>E. coli</i> pathotypes and extraintestinal pathogenic <i>E. coli</i> that cause illness outside of the GI-tract. <i>E. coli</i> have traditionally been serotyped using antisera against the ca. 186 O-antigens and 53 H-flagellar antigens. Phenotypic methods, including bacteriophage typing and O- and H- serotyping for differentiating and characterizing <i>E. coli</i> have been used for many years; however, these methods are generally time consuming and not always accurate. Advances in next generation sequencing technologies have made it possible to develop genetic-based subtyping and molecular serotyping methods for <i>E. coli</i>, which are more discriminatory compared to phenotypic typing methods. Furthermore, whole genome sequencing (WGS) of <i>E. coli</i> is replacing established subtyping methods such as pulsedfield gel electrophoresis, providing a major advancement in the ability to investigate food-borne disease outbreaks and for trace-back to sources. Furthermore, a variety of sequence analysis tools and bioinformatic pipelines are being developed to analyze the vast amount of data generated by WGS and to obtain specific information such as O- and H-group determination and the presence of virulence genes and other genetic markers.
Book
1 online resource.
Embodiments of the invention include methods of altering the enzymatic activity or solubility of an extremophilic enzyme or post-translationally modifying a protein of interest via using isolated or partially purified glycosyltransferases and/or post-translational modification proteins, extracts of cells comprising glycosyltransferases and/or post-translational modification proteins, and/or in cells comprising one or more glycosyltransferases and/or post-translational modification proteins.
Book
254 p. ; 21x28 cm
El programa de la OCDE sobre Análisis de los resultados medioambientales proporciona una evaluación independiente del progreso de los países para cumplir los compromisos nacionales e internacionales en materia de políticas ambientales junto con recomendaciones relevantes a dichas políticas. Las evaluaciones están dirigidas para promover el aprendizaje entre pares, estimular una mayor rendición de cuentas entre países y ante la opinión pública y para que los países mejoren su comportamiento individual y colectivo en la gestión del medio ambiente. Los análisis están avalados por un amplio espectro de datos económicos y ambientales. Cada ciclo de Análisis de los resultados medioambientales cubre todos los países miembros de la OCDE y algunos países socios. Entre las más recientes evaluaciones se encuentran: Islandia (2014), Suecia (2014) y Colombia (2014). Este informe es el tercer análisis de los resultados medioambientales de España. Evalúa el progreso hacia el desarrollo sostenible y el crecimiento verde y se centra en políticas sobre biodiversidad y resultados medioambientales del sector industrial. Contenido: Parte I. Progreso hacia el desarrollo sostenible Capítulo 1. Principales tendencias medioambientales Capítulo 2. Entorno decisorio Capítulo 3. Hacia el crecimiento verde Parte II. Progreso hacia objetivos medioambientales seleccionados Capítulo 4. Conservación y uso sostenible del medio ambiente marino y terrestre Capítulo 5. Resultados medioambientales del sector industrial
Book
Article No. e1607 : digital, PDF file.
<p>Five closely related populations of bacteria from the Candidate Phylum (CP) Peregrinibacteria, part of the bacterial Candidate Phyla Radiation (CPR), were sampled from filtered groundwater obtained from an aquifer adjacent to the Colorado River near the town of Rifle, CO, USA. Here, we present the first complete genome sequences for organisms from this phylum. These bacteria have small genomes and, unlike most organisms from other lineages in the CPR, have the capacity for nucleotide synthesis. They invest significantly in biosynthesis of cell wall and cell envelope components, including peptidoglycan, isoprenoids via the mevalonate pathway, and a variety of amino sugars including perosamine and rhamnose. The genomes encode an intriguing set of large extracellular proteins, some of which are very cysteine-rich and may function in attachment, possibly to other cells. Strain variation in these proteins is an important source of genotypic variety. Overall, the cell envelope features, combined with the lack of biosynthesis capacities for many required cofactors, fatty acids, and most amino acids point to a symbiotic lifestyle. Furthermore, phylogenetic analyses indicate that these bacteria likely represent a new class within the Peregrinibacteria phylum, although they ultimately may be recognized as members of a separate phylum. In conclusion, we propose the provisional taxonomic assignment as ‘<i>Candidatus</i> Peribacter riflensis’, Genus Peribacter, Family Peribacteraceae, Order Peribacterales, Class Peribacteria in the phylum Peregrinibacteria.</p>
Video
1 online resource (1 streaming video file (43 min.) : color, sound).
  • Contents: Anesthesia in lab animals sciences: reasons and concerns
  • Different stages and components of general anesthesia
  • Groups of drugs and side effects
  • Injectable vs. inhalational agents
  • Equipment
  • Choosing the best practice.
This report summarizes the persistence of bacterial strains and their resistance to antibacterial drugs, as well as how they have emerged.
Book
1 online resource.
Switchgrass is an increasingly important biofuel crop, but knowledge of switchgrass fungal pathogens is not extensive. The purpose of this research was to identify the fungal pathogens that decrease crop yield of switchgrass grown in Tennessee and to investigate a potential sustainable disease management strategy from a value-added by-product of the switchgrass biofuel conversion process. The specific objectives were 1) to identify and characterize prevalent fungal pathogens of switchgrass in Tennessee, 2) assess switchgrass seed produced in the United States for seedborne fungal pathogens, and 3) evaluate switchgrass extractives for antimicrobial activity against plant pathogens.
Book
Article No. 27930 : digital, PDF file.
The emergence and spread of antimicrobial resistance (AMR) mechanisms in bacterial pathogens, coupled with the dwindling number of effective antibiotics, has created a global health crisis. Being able to identify the genetic mechanisms of AMR and predict the resistance phenotypes of bacterial pathogens prior to culturing could inform clinical decision-making and improve reaction time. At PATRIC (http://patricbrc.org/), we have been collecting bacterial genomes with AMR metadata for several years. In order to advance phenotype prediction and the identification of genomic regions relating to AMR, we have updated the PATRIC FTP server to enable access to genomes that are binned by their AMR phenotypes, as well as metadata including minimum inhibitory concentrations. Using this infrastructure, we custom built AdaBoost (adaptive boosting) machine learning classifiers for identifying carbapenem resistance in <i>Acinetobacter baumannii</i>, methicillin resistance in <i>Staphylococcus aureus</i>, and beta-lactam and co-trimoxazole resistance in <i>Streptococcus pneumoniae</i> with accuracies ranging from 88–99%. We also did this for isoniazid, kanamycin, ofloxacin, rifampicin, and streptomycin resistance in <i>Mycobacterium tuberculosis</i>, achieving accuracies ranging from 71–88%. Lastly, this set of classifiers has been used to provide an initial framework for species-specific AMR phenotype and genomic feature prediction in the RAST and PATRIC annotation services.
Book
1 online resource.
The present invention, in part, relates to an apparatus having a single-use, normally-closed fluidic valve that is initially maintained in the closed position by a valve element bonded to an adhesive coating. The valve is opened using a magnetic force. The valve element includes a magnetic material or metal. In some examples, the valve is opened by bringing a magnet in proximity to the valve element to provide a magnetic force that delaminates the valve element from the adhesive coating. In particular, the apparatus can be useful for on-chip amplification and/or detection of various targets, including biological targets and any amplifiable targets. Such apparatuses and methods are useful for in-field or real-time detection of targets, especially in limited resource settings.
Provided herein are methods and apparatus for detecting a target nucleic acid in a sample and related methods and apparatus for diagnosing a condition in an individual. The condition is associated with presence of nucleic acid produced by certain pathogens in the individual.
Book
1 online resource.
An apparatus for separating particles from a medium includes a capillary defining a flow path therein that is in fluid communication with a medium source. The medium source includes engineered acoustic contrast capture particle having a predetermined acoustic contrast. The apparatus includes a vibration generator that is operable to produce at least one acoustic field within the flow path. The acoustic field produces a force potential minima for positive acoustic contrast particles and a force potential minima for negative acoustic contrast particles in the flow path and drives the engineered acoustic contrast capture particles to either the force potential minima for positive acoustic contrast particles or the force potential minima for negative acoustic contrast particles.
Book
1 online resource (vi, 398 p.) : ill. (some col.). Digital: text file; PDF.
  • The Era of Big Data: From Data-driven Research to Data-driven Clinical Care.- Biostatistics, data mining and computational modeling.- Gene expression and profiling.- The next generation sequencing and applications in clinical research.- Clinical epigenetics and epigenomics.- Proteomic profiling: Data mining and analyses.- Targeted metabolomics: the next generation of clinical chemistry!?.- Clinical bioinformatics for biomarker discovery in targeted metabolomics.- Metagenomic Profiling, Interaction of Genomics with Meta-genomics.- Clinical Epigenetics and Epigenomics.- Integrative Biological Databases.- Standards and Regulations for (Bio)Medical Software.- Clinical applications and systems biomedicine.- Key Law and Policy Considerations for Clinical Bioinformaticians.- Challenges and Opportunities in Clinical Bioinformatics.- Heterogeneity of Hepatocellular Carcinoma.
  • (source: Nielsen Book Data)9789401775410 20160619
This book elucidates how genetic, biological and medical information can be applied to the development of personalized healthcare, medication and therapies. Focusing on aspects of the development of evidence-based approaches in bioinformatics and computational medicine, including data integration, methodologies, tools and models for clinical and translational medicine, it offers an essential introduction to clinical bioinformatics for clinical researchers and physicians, medical students and teachers, and scientists working with human disease-based omics and bioinformatics. Dr. Xiangdong Wang is a distinguished Professor of Medicine. He is Director of Shanghai Institute of Clinical Bioinformatics, Director of Fudan University Center for Clinical Bioinformatics, Deputy Director of Shanghai Respiratory Research Institute, Director of Biomedical Research Center, Fudan University Zhongshan Hospital, Shanghai, China; Dr. Christian Baumgartner is a Professor of Health Care and Biomedical Engineering at Institute of Health Care Engineering with European Notified Body of Medical Devices, Graz University of Technology, Graz, Austria; Dr. Denis Shields is a Professor of Clinical Bioinformatics at Conway Institute, Belfield, Dublin, Ireland; Dr. Hong-Wen Deng is a Professor at Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, USA; Dr. Jacques S Beckmann is a Professor and Director of Section of Clinical Bioinformatics, Swiss Institute of Bioinformatics, Switzerland.
(source: Nielsen Book Data)9789401775410 20160619
Book
48 p. ; 21 x 30 cm.
This paper presents a review of existing approaches to estimate the costs of inaction, as well as the benefits of policy action, for air pollution. It focuses primarily on health impacts from air pollution. The paper presents the "impact pathway approach", which includes various steps in the analysis of the costs of air pollution. These include quantifying emissions, calculating the concentrations of the pollutants, applying epidemiologic studies to calculate the physical health effects and applying valuation methods to calculate the economic costs of the health impacts. The report also reviews applications of the impact pathway approach to applied economic studies that aim at calculating the macroeconomic costs of air pollution. It proposes possible approaches for including the feedbacks from the health impacts of air pollution in an applied economic framework. While ideally this requires serious modifications of the modelling frameworks and an improvement of the available empirical results, some impacts, such as changes in health expenditures and labour productivity, can easily been incorporated, following the literature on the economic costs of the health impacts of climate change.