Earth History databases and visualization - the TimeScale Creator system

NASA Astrophysics Data System (ADS)

Ogg, James; Lugowski, Adam; Gradstein, Felix

2010-05-01

The "TimeScale Creator" team (www.tscreator.org) and the Subcommission on Stratigraphic Information (stratigraphy.science.purdue.edu) of the International Commission on Stratigraphy (www.stratigraphy.org) has worked with numerous geoscientists and geological surveys to prepare reference datasets for global and regional stratigraphy. All events are currently calibrated to Geologic Time Scale 2004 (Gradstein et al., 2004, Cambridge Univ. Press) and Concise Geologic Time Scale (Ogg et al., 2008, Cambridge Univ. Press); but the array of intercalibrations enable dynamic adjustment to future numerical age scales and interpolation methods. The main "global" database contains over 25,000 events/zones from paleontology, geomagnetics, sea-level and sequence stratigraphy, igneous provinces, bolide impacts, plus several stable isotope curves and image sets. Several regional datasets are provided in conjunction with geological surveys, with numerical ages interpolated using a similar flexible inter-calibration procedure. For example, a joint program with Geoscience Australia has compiled an extensive Australian regional biostratigraphy and a full array of basin lithologic columns with each formation linked to public lexicons of all Proterozoic through Phanerozoic basins - nearly 500 columns of over 9,000 data lines plus hot-curser links to oil-gas reference wells. Other datapacks include New Zealand biostratigraphy and basin transects (ca. 200 columns), Russian biostratigraphy, British Isles regional stratigraphy, Gulf of Mexico biostratigraphy and lithostratigraphy, high-resolution Neogene stable isotope curves and ice-core data, human cultural episodes, and Circum-Arctic stratigraphy sets. The growing library of datasets is designed for viewing and chart-making in the free "TimeScale Creator" JAVA package. This visualization system produces a screen display of the user-selected time-span and the selected columns of geologic time scale information. The user can change the vertical-scale, column widths, fonts, colors, titles, ordering, range chart options and many other features. Mouse-activated pop-ups provide additional information on columns and events; including links to external Internet sites. The graphics can be saved as SVG (scalable vector graphics) or PDF files for direct import into Adobe Illustrator or other common drafting software. Users can load additional regional datapacks, and create and upload their own datasets. The "Pro" version has additional dataset-creation tools, output options and the ability to edit and re-save merged datasets. The databases and visualization package are envisioned as a convenient reference tool, chart-production assistant, and a window into the geologic history of our planet.

Alkylaminopyridine-Modified Aluminum Aminoterephthalate Metal-Organic Frameworks as Components of Reactive Self-Detoxifying Materials

DTIC Science & Technology

2012-08-07

was obtained from the Cambridge Structural Database (ref code OCUNAC). Chromium was substituted with aluminum in the reference crystal structure and the...structure when starting from similar synthesis compositions;30 as a result, the MIL-53 structure is encountered with a broader variety of trivalent metals

Copy-Editing: The Cambridge Handbook.

ERIC Educational Resources Information Center

Butcher, Judith

This handbook is designed as a reference manual for copy editors who prepare typescript for printing. It deals with the following topics: the copy editor's function; the work to be done at each stage in the production process; some difficult points of spelling, capitalization, and other features collectively known as "house style"; the parts of a…

A Comparison of Keyword Subject Searching on Six British University OPACs Online Public Access Catalogs.

ERIC Educational Resources Information Center

Aanonson, John

1987-01-01

Compares features of online public access catalogs (OPACs) at six British universities: (1) Cambridge; (2) Hull; (3) Newcastle; (4) Surrey; (5) Sussex; and (6) York. Results of keyword subject searches on two topics performed on each of the OPACs are reported and compared. Six references are listed. (MES)

Neutral evolution of proteins: The superfunnel in sequence space and its relation to mutational robustness

NASA Astrophysics Data System (ADS)

Noirel, Josselin; Simonson, Thomas

2008-11-01

Following Kimura's neutral theory of molecular evolution [M. Kimura, The Neutral Theory of Molecular Evolution (Cambridge University Press, Cambridge, 1983) (reprinted in 1986)], it has become common to assume that the vast majority of viable mutations of a gene confer little or no functional advantage. Yet, in silico models of protein evolution have shown that mutational robustness of sequences could be selected for, even in the context of neutral evolution. The evolution of a biological population can be seen as a diffusion on the network of viable sequences. This network is called a "neutral network." Depending on the mutation rate μ and the population size N, the biological population can evolve purely randomly (μN ≪1) or it can evolve in such a way as to select for sequences of higher mutational robustness (μN ≫1). The stringency of the selection depends not only on the product μN but also on the exact topology of the neutral network, the special arrangement of which was named "superfunnel." Even though the relation between mutation rate, population size, and selection was thoroughly investigated, a study of the salient topological features of the superfunnel that could affect the strength of the selection was wanting. This question is addressed in this study. We use two different models of proteins: on lattice and off lattice. We compare neutral networks computed using these models to random networks. From this, we identify two important factors of the topology that determine the stringency of the selection for mutationally robust sequences. First, the presence of highly connected nodes ("hubs") in the network increases the selection for mutationally robust sequences. Second, the stringency of the selection increases when the correlation between a sequence's mutational robustness and its neighbors' increases. The latter finding relates a global characteristic of the neutral network to a local one, which is attainable through experiments or molecular modeling.

Neutral evolution of proteins: The superfunnel in sequence space and its relation to mutational robustness.

PubMed

Noirel, Josselin; Simonson, Thomas

2008-11-14

Following Kimura's neutral theory of molecular evolution [M. Kimura, The Neutral Theory of Molecular Evolution (Cambridge University Press, Cambridge, 1983) (reprinted in 1986)], it has become common to assume that the vast majority of viable mutations of a gene confer little or no functional advantage. Yet, in silico models of protein evolution have shown that mutational robustness of sequences could be selected for, even in the context of neutral evolution. The evolution of a biological population can be seen as a diffusion on the network of viable sequences. This network is called a "neutral network." Depending on the mutation rate mu and the population size N, the biological population can evolve purely randomly (muN<1) or it can evolve in such a way as to select for sequences of higher mutational robustness (muN>1). The stringency of the selection depends not only on the product muN but also on the exact topology of the neutral network, the special arrangement of which was named "superfunnel." Even though the relation between mutation rate, population size, and selection was thoroughly investigated, a study of the salient topological features of the superfunnel that could affect the strength of the selection was wanting. This question is addressed in this study. We use two different models of proteins: on lattice and off lattice. We compare neutral networks computed using these models to random networks. From this, we identify two important factors of the topology that determine the stringency of the selection for mutationally robust sequences. First, the presence of highly connected nodes ("hubs") in the network increases the selection for mutationally robust sequences. Second, the stringency of the selection increases when the correlation between a sequence's mutational robustness and its neighbors' increases. The latter finding relates a global characteristic of the neutral network to a local one, which is attainable through experiments or molecular modeling.

Sapientia: accelerating rare disease diagnosis and treatment.

PubMed

Furness, Mike

2016-09-01

Congenica (Cambridge, UK) is a world leading developer of genome-based discovery and diagnostic technologies. The UK company is a spin-out from the Wellcome Trust Sanger Institute (Cambridge, UK) and was founded by scientists and clinicians at the leading edge of genomic analysis. Congenica's Sapientia™ technology platform allows whole-genome sequence analysis to be easily interpreted and presented within a clinically actionable diagnostic report. It is based on pioneering research from Wellcome Trust Sanger Institute, National Health Service clinicians and regional genetic testing laboratories and validated by Genomics England Ltd (London, UK). Sapientia used for medical diagnosis in hospitals including Great Ormond Street Hospital (London, UK), Manchester Centre for Genomic Medicine (Manchester, UK), Birmingham Women's Hospital (Birmingham, UK) and for new drug development by pharmaceutical companies. This profile follows the journey from proof of concept to clinical diagnosis.

Hamming's "open doors" and group creativity as keys to scientific excellence: the example of Cambridge.

PubMed

Erren, Thomas C

2008-01-01

Dr. Charlton used diverse approaches to identify research institutions which provided home to outstanding scientists and work. One intriguing example of long-lasting scientific excellence is Cambridge with 19 Nobel laureates who worked at the University or at the MRC Molecular Biology Unit when they received the prize between 1947 and 2006. With specific reference to Cambridge, I would like to complement the primarily quantitative assessment and offer considerations as to why and how research achievements may have clustered in space and time. Indeed, observations voiced by the mathematician Richard Hamming as to how great research can be pursued offer explanations for the series of great science in the UK. In my view, the most important determinant of the clustering may be illustrated by Hamming's fitting picture of "open doors": working in environments with the doors open allows constant interactions with peers with various disciplinary backgrounds, and thus fast avoidance of detours or dead ends in science and, ultimately, a focus on and the solution of problems of paramount, rather than of tangential, importance. Narrative insights into a strong argumentative tradition at Cambridge provided by Drs. Watson and Magueijo between 1968 and 2003 are in line with Hamming's suggestion and the value of group creativity. In the internet age with abundant interactions beyond home institutions we should not be surprised if clusters of great science were no longer confined to the usual suspect institutions which were awarded disproportionally with Nobel prizes in the past.

Advanced distributed simulation technology: Digital Voice Gateway Reference Guide

NASA Astrophysics Data System (ADS)

Vanhook, Dan; Stadler, Ed

1994-01-01

The Digital Voice Gateway (referred to as the 'DVG' in this document) transmits and receives four full duplex encoded speech channels over the Ethernet. The information in this document applies only to DVG's running firmware of the version listed on the title page. This document, previously named Digital Voice Gateway Reference Guide, BBN Systems and Technologies Corporation, Cambridge, MA 02138, was revised for revision 2.00. This new revision changes the network protocol used by the DVG, to comply with the SINCGARS radio simulation (For SIMNET 6.6.1). Because of the extensive changes to revision 2.00 a separate document was created rather than supplying change pages.

Identical mitochondrial somatic mutations unique to chronic periodontitis and coronary artery disease

PubMed Central

Pallavi, Tokala; Chandra, Rampalli Viswa; Reddy, Aileni Amarender; Reddy, Bavigadda Harish; Naveen, Anumala

2016-01-01

Context: The inflammatory processes involved in chronic periodontitis and coronary artery diseases (CADs) are similar and produce reactive oxygen species that may result in similar somatic mutations in mitochondrial deoxyribonucleic acid (mtDNA). Aims: The aims of the present study were to identify somatic mtDNA mutations in periodontal and cardiac tissues from subjects undergoing coronary artery bypass surgery and determine what fraction was identical and unique to these tissues. Settings and Design: The study population consisted of 30 chronic periodontitis subjects who underwent coronary artery surgery after an angiogram had indicated CAD. Materials and Methods: Gingival tissue samples were taken from the site with deepest probing depth; coronary artery tissue samples were taken during the coronary artery bypass grafting procedures, and blood samples were drawn during this surgical procedure. These samples were stored under aseptic conditions and later transported for mtDNA analysis. Statistical Analysis Used: Complete mtDNA sequences were obtained and aligned with the revised Cambridge reference sequence (NC_012920) using sequence analysis and auto assembler tools. Results: Among the complete mtDNA sequences, a total of 162 variations were spread across the whole mitochondrial genome and present only in the coronary artery and the gingival tissue samples but not in the blood samples. Among the 162 variations, 12 were novel and four of the 12 novel variations were found in mitochondrial NADH dehydrogenase subunit 5 complex I gene (33.3%). Conclusions: Analysis of mtDNA mutations indicated 162 variants unique to periodontitis and CAD. Of these, 12 were novel and may have resulted from destructive oxidative forces common to these two diseases. PMID:27041832

Comparability: manufacturing, characterization and controls, report of a UK Regenerative Medicine Platform Pluripotent Stem Cell Platform Workshop, Trinity Hall, Cambridge, 14–15 September 2015

PubMed Central

Williams, David J; Archer, Richard; Archibald, Peter; Bantounas, Ioannis; Baptista, Ricardo; Barker, Roger; Barry, Jacqueline; Bietrix, Florence; Blair, Nicholas; Braybrook, Julian; Campbell, Jonathan; Canham, Maurice; Chandra, Amit; Foldes, Gabor; Gilmanshin, Rudy; Girard, Mathilde; Gorjup, Erwin; Hewitt, Zöe; Hourd, Paul; Hyllner, Johan; Jesson, Helen; Kee, Jasmin; Kerby, Julie; Kotsopoulou, Nina; Kowalski, Stanley; Leidel, Chris; Marshall, Damian; Masi, Louis; McCall, Mark; McCann, Conor; Medcalf, Nicholas; Moore, Harry; Ozawa, Hiroki; Pan, David; Parmar, Malin; Plant, Anne L; Reinwald, Yvonne; Sebastian, Sujith; Stacey, Glyn; Thomas, Robert J; Thomas, Dave; Thurman-Newell, Jamie; Turner, Marc; Vitillo, Loriana; Wall, Ivan; Wilson, Alison; Wolfrum, Jacqueline; Yang, Ying; Zimmerman, Heiko

2016-01-01

This paper summarizes the proceedings of a workshop held at Trinity Hall, Cambridge to discuss comparability and includes additional information and references to related information added subsequently to the workshop. Comparability is the need to demonstrate equivalence of product after a process change; a recent publication states that this ‘may be difficult for cell-based medicinal products’. Therefore a well-managed change process is required which needs access to good science and regulatory advice and developers are encouraged to seek help early. The workshop shared current thinking and best practice and allowed the definition of key research questions. The intent of this report is to summarize the key issues and the consensus reached on each of these by the expert delegates. PMID:27404768

Comparability: manufacturing, characterization and controls, report of a UK Regenerative Medicine Platform Pluripotent Stem Cell Platform Workshop, Trinity Hall, Cambridge, 14-15 September 2015.

PubMed

Williams, David J; Archer, Richard; Archibald, Peter; Bantounas, Ioannis; Baptista, Ricardo; Barker, Roger; Barry, Jacqueline; Bietrix, Florence; Blair, Nicholas; Braybrook, Julian; Campbell, Jonathan; Canham, Maurice; Chandra, Amit; Foldes, Gabor; Gilmanshin, Rudy; Girard, Mathilde; Gorjup, Erwin; Hewitt, Zöe; Hourd, Paul; Hyllner, Johan; Jesson, Helen; Kee, Jasmin; Kerby, Julie; Kotsopoulou, Nina; Kowalski, Stanley; Leidel, Chris; Marshall, Damian; Masi, Louis; McCall, Mark; McCann, Conor; Medcalf, Nicholas; Moore, Harry; Ozawa, Hiroki; Pan, David; Parmar, Malin; Plant, Anne L; Reinwald, Yvonne; Sebastian, Sujith; Stacey, Glyn; Thomas, Robert J; Thomas, Dave; Thurman-Newell, Jamie; Turner, Marc; Vitillo, Loriana; Wall, Ivan; Wilson, Alison; Wolfrum, Jacqueline; Yang, Ying; Zimmerman, Heiko

2016-07-01

This paper summarizes the proceedings of a workshop held at Trinity Hall, Cambridge to discuss comparability and includes additional information and references to related information added subsequently to the workshop. Comparability is the need to demonstrate equivalence of product after a process change; a recent publication states that this 'may be difficult for cell-based medicinal products'. Therefore a well-managed change process is required which needs access to good science and regulatory advice and developers are encouraged to seek help early. The workshop shared current thinking and best practice and allowed the definition of key research questions. The intent of this report is to summarize the key issues and the consensus reached on each of these by the expert delegates.

Cognitive impairment in patients clinically recovered from central nervous system depressant drug overdose.

PubMed

Dassanayake, Tharaka L; Michie, Patricia T; Jones, Alison; Carter, Gregory; Mallard, Trevor; Whyte, Ian

2012-08-01

Central nervous system depressant drugs (CNS-Ds) are known to impair cognitive functions. Overdose of these drugs is common, and most of the hospital-treated patients are discharged within 24 to 48 hours. No previous studies have examined whether they have residual impairment at the time of discharge. Our aim was to evaluate whether patients with CNS-D overdose are impaired in cognitive domains important in daily activities at that time. We compared visuomotor skills (Trail-Making Test A and Choice Reaction Time), executive functions (viz attentional set-shifting: Trail-Making Test B; and planning: Stockings of Cambridge Task from the Cambridge Neuropsychological Test Automated Battery), working memory (Letter-Number Sequencing), and impulsivity and decision making (Cambridge Neuropsychological Test Automated Battery Information Sampling) in 107 patients with CNS-D overdose (benzodiazepines, opioids, or antipsychotics) with a control group of 68 with non-CNS-D overdose (acetaminophen, selective serotonin reuptake inhibitors, and serotonin noradrenaline reuptake inhibitors) on discharge from hospital. Outcome measures were adjusted for demographic and clinical covariates in multivariate regression models. Compared with the controls, patients in the CNS-D group were significantly impaired in all domains: they had prolonged Trail-Making completion times and reaction times, poorer working memory and planning and were more impulsive in decision making. Their Stockings of Cambridge Task performance was comparable to that of the control group for simple problems but worsened with increasing task complexity. The results show that patients with CNS-D overdose could be impaired in multiple cognitive domains underlying everyday functioning even at the time they are deemed medically fit to be discharged. Such impairments could adversely affect social and professional lives of this relatively young population during the immediate postdischarge period.

Reginald Crundall Punnett: First Arthur Balfour Professor of Genetics, Cambridge, 1912

PubMed Central

Edwards, A. W. F.

2012-01-01

R. C. Punnett, the codiscoverer of linkage with W. Bateson in 1904, had the good fortune to be invited to be the first Arthur Balfour Professor of Genetics at Cambridge University, United Kingdom, in 1912 when Bateson, for whom it had been intended, declined to leave his new appointment as first Director of the John Innes Horticultural Institute. We here celebrate the centenary of the first professorship dedicated to genetics, outlining Punnett’s career and his scientific contributions, with special reference to the discovery of “partial coupling” in the sweet pea (later “linkage”) and to the diagram known as Punnett’s square. His seeming reluctance as coauthor with Bateson to promote the reduplication hypothesis to explain the statistical evidence for linkage is stressed, as is his relationship with his successor as Arthur Balfour Professor, R. A. Fisher. The background to the establishment of the Professorship is also described. PMID:22964834

Does the Cambridge Automated Neuropsychological Test Battery (CANTAB) Distinguish Between Cognitive Domains in Healthy Older Adults?

PubMed

Lenehan, Megan E; Summers, Mathew J; Saunders, Nichole L; Summers, Jeffery J; Vickers, James C

2016-04-01

The Cambridge Neuropsychological Test Automated Battery (CANTAB) is a semiautomated computer interface for assessing cognitive function. We examined whether CANTAB tests measured specific cognitive functions, using established neuropsychological tests as a reference point. A sample of 500 healthy older (M = 60.28 years, SD = 6.75) participants in the Tasmanian Healthy Brain Project completed battery of CANTAB subtests and standard paper-based neuropsychological tests. Confirmatory factor analysis identified four factors: processing speed, verbal ability, episodic memory, and working memory. However, CANTAB tests did not consistently load onto the cognitive domain factors derived from traditional measures of the same function. These results indicate that five of the six CANTAB subtests examined did not load onto single cognitive functions. These CANTAB tests may lack the sensitivity to measure discrete cognitive functions in healthy populations or may measure other cognitive domains not included in the traditional neuropsychological battery. © The Author(s) 2015.

Reginald Crundall Punnett: first Arthur Balfour Professor of Genetics, Cambridge, 1912.

PubMed

Edwards, A W F

2012-09-01

R. C. Punnett, the codiscoverer of linkage with W. Bateson in 1904, had the good fortune to be invited to be the first Arthur Balfour Professor of Genetics at Cambridge University, United Kingdom, in 1912 when Bateson, for whom it had been intended, declined to leave his new appointment as first Director of the John Innes Horticultural Institute. We here celebrate the centenary of the first professorship dedicated to genetics, outlining Punnett's career and his scientific contributions, with special reference to the discovery of "partial coupling" in the sweet pea (later "linkage") and to the diagram known as Punnett's square. His seeming reluctance as coauthor with Bateson to promote the reduplication hypothesis to explain the statistical evidence for linkage is stressed, as is his relationship with his successor as Arthur Balfour Professor, R. A. Fisher. The background to the establishment of the Professorship is also described.

Ted Hall and the science of biological microprobe X-ray analysis: a historical perspective of methodology and biological dividends.

PubMed

Gupta, B L

1991-06-01

This review surveys the emergence of electron probe X-ray microanalysis as a quantitative method for measuring the chemical elements in situ. The extension of the method to the biological sciences under the influence of Ted Hall is reviewed. Some classical experiments by Hall and his colleagues in Cambridge, UK, previously unpublished, are described; as are some of the earliest quantitative results from the cryo-sections obtained in Cambridge and elsewhere. The progress of the methodology is critically evaluated from the earliest starts to the present state of the art. Particular attention has been focused on the application of the method in providing fresh insights into the role of ions in cell and tissue physiology and pathology. A comprehensive list of references is included for a further pursuit of the topics by the interested reader.

Applications of the Cambridge Structural Database in organic chemistry and crystal chemistry.

PubMed

Allen, Frank H; Motherwell, W D Samuel

2002-06-01

The Cambridge Structural Database (CSD) and its associated software systems have formed the basis for more than 800 research applications in structural chemistry, crystallography and the life sciences. Relevant references, dating from the mid-1970s, and brief synopses of these papers are collected in a database, DBUse, which is freely available via the CCDC website. This database has been used to review research applications of the CSD in organic chemistry, including supramolecular applications, and in organic crystal chemistry. The review concentrates on applications that have been published since 1990 and covers a wide range of topics, including structure correlation, conformational analysis, hydrogen bonding and other intermolecular interactions, studies of crystal packing, extended structural motifs, crystal engineering and polymorphism, and crystal structure prediction. Applications of CSD information in studies of crystal structure precision, the determination of crystal structures from powder diffraction data, together with applications in chemical informatics, are also discussed.

Summary Proceedings of the Congress of International Physicians for the Prevention of Nuclear War (2nd, Cambridge, England, April, 1982).

ERIC Educational Resources Information Center

International Physicians for the Prevention of Nuclear War, Inc., Boston, MA.

This conference was held to alert physicians worldwide of the mortal peril of nuclear war to public health, with the hope that they will help educate their communities about the effects of nuclear war. Summary papers prepared during the conference include: medical consequences of nuclear war with special reference to Europe--immediate problems for…

The Delphi Method and Its Applications: A Bibliography

DTIC Science & Technology

1976-06-01

Quality of Life ," The Quality of Life " Connept, chapter, 5p: Environmental Protection Agency4 Jantsch, Erich, Perspectives of’ PLanning, Paris...develop measures of effectiveness in evaluating new governmental organizations or reorganizations, with particular reference to the Army...Controlled Environment. Cambridge, Mass.: M.I.To Press, 1968. 340p. Ansolf, L.I. and Brandenburg, R.G., A Language for Organization Design. Perspectives

Measurement of nitrogen dioxide in cigarette smoke using quantum cascade tunable infrared laser differential absorption spectroscopy (TILDAS)

NASA Astrophysics Data System (ADS)

Shorter, Joanne H.; Nelson, David D.; Zahniser, Mark S.; Parrish, Milton E.; Crawford, Danielle R.; Gee, Diane L.

2006-04-01

Although nitrogen dioxide (NO 2) has been previously reported to be present in cigarette smoke, the concentration estimates were derived from kinetic calculations or from measurements of aged smoke, where NO 2 was formed some time after the puff was taken. The objective of this work was to use tunable infrared laser differential absorption spectroscopy (TILDAS) equipped with a quantum cascade (QC) laser to determine if NO 2 could be detected and quantified in a fresh puff of cigarette smoke. A temporal resolution of ˜0.16 s allowed measurements to be taken directly as the NO 2 was formed during the puff. Sidestream cigarette smoke was sampled to determine if NO 2 could be detected using TILDAS. Experiments were conducted using 2R4F Kentucky Reference cigarettes with and without a Cambridge filter pad. NO 2 was detected only in the lighting puff of whole mainstream smoke (without a Cambridge filter pad), with no NO 2 detected in the subsequent puffs. The measurement precision was ˜1.0 ppbV Hz -1/2, which allows a detection limit of ˜0.2 ng in a 35 ml puff volume. More NO 2 was generated in the lighting puff using a match or blue flame lighter (29 ± 21 ng) than when using an electric lighter (9 ± 3 ng). In the presence of a Cambridge filter pad, NO 2 was observed in the gas phase mainstream smoke for every puff (total of 200 ± 30 ng/cigarette) and is most likely due to smoke chemistry taking place on the Cambridge filter pad during the smoke collection process. Nitrogen dioxide was observed continuously in the sidestream smoke starting with the lighting puff.

Variance to mean ratio, R(t), for poisson processes on phylogenetic trees.

PubMed

Goldman, N

1994-09-01

The ratio of expected variance to mean, R(t), of numbers of DNA base substitutions for contemporary sequences related by a "star" phylogeny is widely seen as a measure of the adherence of the sequences' evolution to a Poisson process with a molecular clock, as predicted by the "neutral theory" of molecular evolution under certain conditions. A number of estimators of R(t) have been proposed, all predicted to have mean 1 and distributions based on the chi 2. Various genes have previously been analyzed and found to have values of R(t) far in excess of 1, calling into question important aspects of the neutral theory. In this paper, I use Monte Carlo simulation to show that the previously suggested means and distributions of estimators of R(t) are highly inaccurate. The analysis is applied to star phylogenies and to general phylogenetic trees, and well-known gene sequences are reanalyzed. For star phylogenies the results show that Kimura's estimators ("The Neutral Theory of Molecular Evolution," Cambridge Univ. Press, Cambridge, 1983) are unsatisfactory for statistical testing of R(t), but confirm the accuracy of Bulmer's correction factor (Genetics 123: 615-619, 1989). For all three nonstar phylogenies studied, attained values of all three estimators of R(t), although larger than 1, are within their true confidence limits under simple Poisson process models. This shows that lineage effects can be responsible for high estimates of R(t), restoring some limited confidence in the molecular clock and showing that the distinction between lineage and molecular clock effects is vital.(ABSTRACT TRUNCATED AT 250 WORDS)

Photo-Activated Synthesis of Functional Oxide Thin Films

DTIC Science & Technology

2010-03-01

Sponsored Research 1350 Massachusetts Ave. Holyoke 727 Cambridge, MA 02138 - REPORT DOCUMENTATION PAGE b . ABSTRACT UU c. THIS PAGE UU 2. REPORT TYPE...including journal references, in the following categories: ( b ) Papers published in non-peer-reviewed journals or in conference proceedings (N/A for...minimize the roughness. Figure 1 ( b ) shows the XRR spectra of ~ 100 Å YDZ film grown on Ge. Interestingly, the effect of UV irradiation was more

Viewing brain processes as Critical State Transitions across levels of organization: Neural events in Cognition and Consciousness, and general principles.

PubMed

Werner, Gerhard

2009-04-01

In this theoretical and speculative essay, I propose that insights into certain aspects of neural system functions can be gained from viewing brain function in terms of the branch of Statistical Mechanics currently referred to as "Modern Critical Theory" [Stanley, H.E., 1987. Introduction to Phase Transitions and Critical Phenomena. Oxford University Press; Marro, J., Dickman, R., 1999. Nonequilibrium Phase Transitions in Lattice Models. Cambridge University Press, Cambridge, UK]. The application of this framework is here explored in two stages: in the first place, its principles are applied to state transitions in global brain dynamics, with benchmarks of Cognitive Neuroscience providing the relevant empirical reference points. The second stage generalizes to suggest in more detail how the same principles could also apply to the relation between other levels of the structural-functional hierarchy of the nervous system and between neural assemblies. In this view, state transitions resulting from the processing at one level are the input to the next, in the image of a 'bucket brigade', with the content of each bucket being passed on along the chain, after having undergone a state transition. The unique features of a process of this kind will be discussed and illustrated.

Undergraduate/Postgraduate Astronomy in Cambridge--A Student's Perspective.

ERIC Educational Resources Information Center

Williams, Robin

1991-01-01

Described is the undergraduate curriculum in physics and its relationship to astronomy at Cambridge University. Discussed are the astronomical research and research establishments at Cambridge. Personal views of a student on the postgraduate research being done at Cambridge are also included. (KR)

Brain Region-Specific Expression of Genes Mapped within Quantitative Trait Loci for Behavioral Responsiveness to Acute Stress in Fisher 344 and Wistar Kyoto Male Rats (Postprint)

DTIC Science & Technology

2018-03-12

Integrative Genomics Viewer (Broad Institute, Cambridge, Massachusetts), we iden- tified the coding sequence variations between the F344 and WKY... abnormalities and disturbances in brain metabolism resem- bling those in depressive states [74]. Ifna2 is also known to induce memory, concentration, and...Variant and Chronic Interpersonal Stress Prospectively Predicts Social Anxiety and Depression Symptoms Over Six Years. Clinical psychological science

The Cambridge Guide to the Solar System

NASA Astrophysics Data System (ADS)

Lang, Kenneth R.

2003-10-01

The Cambridge Guide to the Solar System provides a comprehensive, funamental, and up-to-date description of the solar system. It is written in a concise, light and uniform style, without being unnecessarily weighted down with specialized materials or the variable writing of multiple authors. It is filled with vital facts and information for astronomers of all types and for anyone with a scientific interest in the Earth, our Moon, all the other planets and their satellites, and related topics such as asteroids, comets, meteorites and meteors. The language, style, ideas and profuse illustrations will attract the general reader as well as professionals. A thorough report for general readers, it includes much compact reference data. Metaphors, similes and analogies will be of immense help to the lay person or non-science student, and they add to the enjoyment of the material. Vignettes containing historical, literary and even artistic material make this book unusual and interesting, and enhance its scientific content. Kenneth Lang is professor of astronomy in the Physics and Astronomy Department at Tufts University. He is the author of several astrophysics books, including The Sun from Space (Springer Verlag, 2000), Astrophysical Formulae: Radiation, Gas Processes, and High Energy Physics (Springer Verlag, 1999), Sun, Earth and Sky (Copernicus Books, 1997), Astrophysical Data: Planets and Stars (Springer Verlag, 1993), and Wanderers in Space: Exploration and Discovery in the Solar System (Cambridge, 1991),

Unstable Behavior of Lasers and Other Optical Systems.

DTIC Science & Technology

1987-11-27

Isaacs, R.S. Gioggia, S.P. Adams, L.M. Narducci, L.A. Lugiato, Optical Instabilities, R.W. Boyd, M.G. Raymer , L.M. Narducci, Eds. (Cambridge...Instabilities, R.W. Boyd, M.G. Raymer , L.M. Narducci, Eds. (Cambridge University" Press, Cambridge, 1986), p. 34. "The Effect of Modulation in a Bistable System...Books "* " "OPTICAL INSTABILITIES", edited by R.W. Boyd, M.G. Raymer , and L.M. Narducci, Cambridge University Press, Cambridge, 1986. S P.-• 58

Integrated Software Development System/Higher Order Software Conceptual Description (ISDS/HOS)

DTIC Science & Technology

1976-11-01

Structured Flowchart Conventions 270 6.3.5.3 Design Diagram Notation 273 xii HIGHER ORDER SOFTWARE, INC. 843 MASSACHUSETTS AVENUE. CAMBRIDGE, MASSACHUSETTS...associated with the process steps. They also reference other HIPO diagrams as well an non-HIPO documentation such as flowcharts or decision tables of...syntax that is easy to learn and must provide the novice with some prompting to help him avoid classic beginner errors. Desirable editing capabilities

U.S. Army Research Laboratory Directed Energy Visiting Scholars Program 2012

DTIC Science & Technology

2013-03-01

area under each peak was found and matched to its corresponding manifold. 48 5. References Gruber, J.; Nijar, A.; Sarder, D. K .; Yow, R...Electronics. Cambridge University Press, 1989. 8. Satyan, Naresh . Optoelectronic Control of the Phase and Frequency of Semiconductor Lasers. PhD...1 GOVT PRINTG OFC (PDF) A MALHOTRA 732 N CAPITOL ST NW WASHINGTON DC 20401 ADELPHI LABORATORY CENTER 1 DIR USARL (PDF) RDRL SEE M J WHITE

77 FR 64143 - Manufacturer of Controlled Substances; Notice of Registration; Cambridge Isotope Lab

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-18

...; Notice of Registration; Cambridge Isotope Lab By Notice dated June 18, 2012, and published in the Federal Register on June 26, 2012, 77 FR 38086, Cambridge Isotope Lab, 50 Frontage Road, Andover, Massachusetts....C. 823(a) and determined that the registration of Cambridge Isotope Lab to manufacture the listed...

Depersonalization: An exploratory factor analysis of the Italian version of the Cambridge Depersonalization Scale.

PubMed

Fagioli, F; Telesforo, L; Dell'Erba, A; Consolazione, M; Migliorini, V; Patanè, M; Boldrini, T; Graziani, R; Nicoletti, F; Fiori-Nastro, P

2015-07-01

"Depersonalization" (DP) is a common symptom in the general population and psychiatric patients (Michal et al., 2011 [1]). DP is characterized by an alteration in the experience of the self, so that one feels detached from his or her own mental processes or body (or from the world), feeling as being an outside observer of his or her own self, and loosing the experience of unity and identity (American Psychiatric Association, 2013 [2]). We performed an exploratory factor analysis of the Cambridge Depersonalization Scale Italian version (CDS-IV). We enrolled 149 inpatients and outpatients of psychiatric services located in two Italian regions, Lazio and Campania. Patients were aged between 15 and 65 and diagnosed with schizophrenic, depressive or anxiety disorders. Four factors accounted for 97.4% of the variance. Factor 1 (10, 24, 26, 1, 13, 23, 9, 2, 5, and 11), called "Detachment from the Self", captures experiences of detachment from actions and thoughts. Factor 2 (19, 20, 27, 3, 12, 23, 22, and 11), called "Anomalous bodily experiences", refers to unusual bodily experiences. Factor 3 (7, 28, 25, 6, 9, and 2), named "Numbing", describes the dampening of affects. Factor 4 (14, 17, and 16), named "Temporal blunting", refers to the subjective experience of time. We did not find any specific factor that refers to derealization; this suggests that the constructs of depersonalization/derealization (DP/DR) were strongly related to each other. Our results show that the constructs of DP/DR subsume several psychopathological dimensions; moreover, the above mentioned factors were broadly consistent with prior literature. Copyright © 2015. Published by Elsevier Inc.

Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes.

PubMed

Behura, Susanta K; Severson, David W

2013-02-01

Codon usage bias refers to the phenomenon where specific codons are used more often than other synonymous codons during translation of genes, the extent of which varies within and among species. Molecular evolutionary investigations suggest that codon bias is manifested as a result of balance between mutational and translational selection of such genes and that this phenomenon is widespread across species and may contribute to genome evolution in a significant manner. With the advent of whole-genome sequencing of numerous species, both prokaryotes and eukaryotes, genome-wide patterns of codon bias are emerging in different organisms. Various factors such as expression level, GC content, recombination rates, RNA stability, codon position, gene length and others (including environmental stress and population size) can influence codon usage bias within and among species. Moreover, there has been a continuous quest towards developing new concepts and tools to measure the extent of codon usage bias of genes. In this review, we outline the fundamental concepts of evolution of the genetic code, discuss various factors that may influence biased usage of synonymous codons and then outline different principles and methods of measurement of codon usage bias. Finally, we discuss selected studies performed using whole-genome sequences of different insect species to show how codon bias patterns vary within and among genomes. We conclude with generalized remarks on specific emerging aspects of codon bias studies and highlight the recent explosion of genome-sequencing efforts on arthropods (such as twelve Drosophila species, species of ants, honeybee, Nasonia and Anopheles mosquitoes as well as the recent launch of a genome-sequencing project involving 5000 insects and other arthropods) that may help us to understand better the evolution of codon bias and its biological significance. © 2012 The Authors. Biological Reviews © 2012 Cambridge Philosophical Society.

Reflective scientific sense-making dialogue in two languages: The science in the dialogue and the dialogue in the science

NASA Astrophysics Data System (ADS)

Ash, Doris

2004-11-01

In this paper I focus on the transition from everyday to scientific ways of reasoning, and on the intertwined roles of meaning-making dialogue and science content as they contribute to scientific literacy. I refer to views of science, and how scientific understanding is advanced dialogically, by Hurd (Science Education, 1998, 82, 402-416), Brown (The Journal of Learning Sciences, 1992, 2(2), 141-178), Bruner (Acts of Meaning, Cambridge, MA: Harvard University Press, 1990), Roth (In J. Brophy (Ed.), Social Constructivist Teaching: Affordances and Constraints (Advances in Research on Teaching Series, Vol. 9), New York: Elsevier/JAI, 2003), and Wells (Dialogic Inquiry: Towards a Sociocultural Practice and Theory of Education, New York: Cambridge University Press, 1999). I argue that family collaborative dialogues in nonschool settings can be the foundations for scientific ways of thinking. I focus on the particular reflective family dialogues at the Monterey Bay Aquarium, when family members remembered and synthesized essential biological themes, centering on adaptation, from one visit to the next, in both Spanish and English. My approach is informed by sociocultural theory, with emphasis on the negotiations of meaning in the zone of proximal development (Vygotsky, 1978), as learners engage in joint productive activity (Tharp & Gallimore, Rousing Minds to Life: Teaching, Learning and Schooling in Social Context, New York: Cambridge University Press, 1988). Over the past decades, researchers have discovered that observing social activity, conversation, and meaning-making in informal settings (Crowley & Callanan, 1997; Guberman, 2002; Rogoff, 2001; Vasquez, Pease-Alvarez, & Shannon, Pushing Boundaries: Language and Culture in a Mexicano Community, New York: Cambridge University Press, 1994) has much to teach us regarding learning in general. To date there has been little research with Spanish-speaking families in informal learning settings and virtually none that integrates the home with both formal and informal learning.

Freyinae, a major new subfamily of Neotropical jumping spiders (Araneae: Salticidae).

PubMed

Edwards, G B

2015-11-02

Freyinae, new subfamily, is described for a group of genera of Neotropical jumping spiders that can be distinguished from other non-ant mimic salticoid Neotropical salticids by having the following three morphological features: a slightly more elongate carapace, a distinctive prolateral tibial macrosetae arrangement (medially placed subdistal and subproximal macrosetae, with a subdorsal medial macroseta in some males), and an unusual dorsoventrally thick tegulum basal division (although one or two of these features are sometimes lost). It includes 20 genera previously considered valid, of which 19 are retained: Akela Peckham & Peckham, 1896, Aphirape C.L. Koch, 1850, Asaracus C.L. Koch, 1846, Capidava Simon, 1902, Chira Peckham & Peckham, 1896, Edilemma Ruiz & Brescovit, 2006, Eustiromastix Simon, 1902, Freya C.L. Koch, 1850, Frigga C.L. Koch, 1850, Kalcerrytus Galiano, 2000, Nycerella Galiano, 1982, Onofre Ruiz & Brescovit, 2007, Pachomius Peckham & Peckham, 1896, Phiale C.L. Koch, 1846, Rishaschia Makhan, 2006, Sumampattus Galiano, 1983, Trydarssus Galiano, 1995, Tullgrenella Mello‑Leitão, 1941, and Wedoquella Galiano, 1984. Romitia Caporiacco, 1947 (and its synonym Uspachus Galiano, 1995) is synonymized with Pachomius, new synonymy. New genera described in the subfamily are: Drizztius, Leptofreya, Megafreya, Philira, Tarkas, Triggella, and Xanthofreya. The following nomenclatorial changes are made: New synonyms: Freya demarcata Chamberlin & Ivie, 1936 = Freya (sub Cyrene) albosignata (F.O.P.-Cambridge, 1901); Freya (sub Cyrene) grisea (F.O.P.-Cambridge, 1901) = Freya (sub Cyrene) infuscata (F.O.P.-Cambridge, 1901); Freya (sub Cyrene) emarginata (F.O.P.-Cambridge, 1901) and Nycerella (sub Heraclea) sanguinea paradoxa (Peckham & Peckham, 1896) = Nycerella (sub Heraclea) sanguinea (Peckham & Peckham, 1896); Pachomius (sub Phiale) maculosus (Chickering, 1946) = Phiale (sub Cyrene) bilobata (F.O.P.-Cambridge, 1901); Phiale (sub Cyrene) mediocava (F.O.P.-Cambridge, 1901) = Freya (sub Cyrene) maculatipes (F.O.P.-Cambridge, 1901); Phiale (sub Cyrene) simplicicava (F.O.P.-Cambridge, 1901) = Freya (sub Cyrene) bifurcata (F.O.P.-Cambridge, 1901). New combinations: Capidava rufithorax Simon, 1902 = Drizztius rufithorax; Freya frontalis Banks, 1929 = Eustiromastix frontalis; Chira (sub Attus) spinipes (Taczanowski, 1872) = Eustiromastix spinipes; Freya (sub Euophrys) ambigua (C.L. Koch, 1846) = Leptofreya ambigua; Freya (sub Cyrene) bifurcata (F.O.P.-Cambridge, 1901) = Leptofreya bifurcata; Freya (sub Cyrene) laticava (F.O.P.-Cambridge, 1901) = Leptofreya laticava; Freya (sub Cyrene) longispina (F.O.P.-Cambridge, 1901) = Leptofreya longispina; Phiale (sub Cyrene) bilobata (F.O.P.-Cambridge, 1901) = Pachomius bilo-batus; Phiale (sub Cyrene) hieroglyphica (F.O.P.-Cambridge, 1901) = Pachomius hieroglyphicus; Phiale (sub Cyrene) niveoguttata (F.O.P.-Cambridge, 1901) = Pachomius niveoguttatus; Romitia (sub Euophrys) albipalpis (Taczanowski, 1878) = Pachomius albipalpis; Romitia (sub Euophrys) andina (Taczanowski, 1878) = Pachomius andinus; Romitia (sub Uspachus) bahiensis (Galiano, 1995) = Pachomius bahiensis; Romitia (sub Uspachus) columbiana (Galiano, 1995) = Pachomius columbianus; Romitia (sub Uspachus) juquiaensis (Galiano, 1995) = Pachomius juquiaensis; Romitia (sub Phiale) ministerialis (C.L. Koch, 1846) = Pachomius ministerialis; Romitia (sub Uspachus) misionensis (Galiano, 1995) = Pachomius misionensis; Romitia nigra Caporiacco, 1947 = Pachomius nigrus; Romitia (sub Uspachus) patellaris (Galiano, 1995) = Pachomius patellaris; Chira (sub Diagondas) micans (Simon, 1902) = Philira micans; Chira superba Caporiacco, 1947 = Philira superba; Freya (sub Cyrene) maculatipes (F.O.P.-Cambridge, 1901) = Tarkas maculatipes; Freya (sub Cyrene) bifida (F.O.P.-Cambridge, 1901) = Triggella bifida; Freya infuscata (F.O.P.-Cambridge, 1901) = Triggella infuscata; Freya (sub Cyrene) minuta (F.O.P.-Cambridge, 1901) = Triggella minuta; Freya (sub Cyrene) albosignata (F.O.P.-Cambridge, 1901) = Xanthofreya albosignata; Freya arraijanica Chickering, 1946 = Xanthofreya arraijanica; Phiale (sub Cyrene) bicuspidata (F.O.P.-Cambridge, 1901) = Xantho-freya bicuspidata; Freya chionopogon Simon, 1902 = Xanthofreya chionopogon; Freya (sub Heraclea) rustica (Peckham & Peckham, 1896) = Xanthofreya rustica. Combinations restored: Phiale (sub Pachomius) flavescens (Peckham & Peckham, 1896) = Pachomius flavescens; Phiale (sub Pachomius) similis (Peckham & Peckham, 1896) = Pachomius similis. Invalid name: Freya dyali Roewer 1951 is an invalid replacement name for Euophrys trifasciata "Dyal 1935", which was a redescription of Euophrys trifasciata C.L. Koch, 1846, not a homonym. New species: Drizztius geminensis. First female descriptions and transfers of mismatched females: First descriptions for Asaracus megacephalus C.L. Koch, 1846, Capidava biuncata Simon, 1902, and Phiale formosa (Banks, 1909); the true female of Eustiromastix spinipes is described, and its mismatched female is identified as the female of Eustiromastix falcatus Galiano, 1981; the mismatched female of Freya (sub Cyrene) prominens (F.O.P.-Cambridge, 1901) is identified as the female of Xanthofreya rustica; the misidentified female of X. rustica is identified as the female of Leptofreya bifurcata. Lectotypes: designated for Cyrene bifida F.O.P.-Cambridge, 1901 and Cyrene formosa Banks, 1909. New synapomorphy: a constricted proximal end of the cymbium of the male palp is an apparent new synapomorphy for Salticoida.

BOOK REVIEW Exact Space-Times in Einstein's General Relativity Exact Space-Times in Einstein's General Relativity

NASA Astrophysics Data System (ADS)

Lake, Kayll

2010-12-01

The title immediately brings to mind a standard reference of almost the same title [1]. The authors are quick to point out the relationship between these two works: they are complementary. The purpose of this work is to explain what is known about a selection of exact solutions. As the authors state, it is often much easier to find a new solution of Einstein's equations than it is to understand it. Even at first glance it is very clear that great effort went into the production of this reference. The book is replete with beautifully detailed diagrams that reflect deep geometric intuition. In many parts of the text there are detailed calculations that are not readily available elsewhere. The book begins with a review of basic tools that allows the authors to set the notation. Then follows a discussion of Minkowski space with an emphasis on the conformal structure and applications such as simple cosmic strings. The next two chapters give an in-depth review of de Sitter space and then anti-de Sitter space. Both chapters contain a remarkable collection of useful diagrams. The standard model in cosmology these days is the ICDM model and whereas the chapter on the Friedmann-Lemaître-Robertson-Walker space-times contains much useful information, I found the discussion of the currently popular a representation rather too brief. After a brief but interesting excursion into electrovacuum, the authors consider the Schwarzschild space-time. This chapter does mention the Swiss cheese model but the discussion is too brief and certainly dated. Space-times related to Schwarzschild are covered in some detail and include not only the addition of charge and the cosmological constant but also the addition of radiation (the Vaidya solution). Just prior to a discussion of the Kerr space-time, static axially symmetric space-times are reviewed. Here one can find a very interesting discussion of the Curzon-Chazy space-time. The chapter on rotating black holes is rather brief and, for example, does not contain reference to the insights found by Pretorius and Israel [2]. This is perhaps justifiable in view of the many specialized texts devoted to the Kerr space-time (e.g. [3]). The large clear diagrams that one becomes accustomed to in this book show off the Taub-NUT (and related) space-times in the next chapter. After perhaps a somewhat standard discussion of stationary axially symmetric space-times, there is a very informative discussion of accelerating black holes. For example, the global structure of the C-metric is considered in detail. This is followed by a brief discussion of solutions for uniformly accelerating particles. The discussion of the Plebański-Demiański solutions contains two very useful flow charts that help to systematize two rather complex families of solutions. After a somewhat brief discussion of plane and pp-waves, the authors give an extensive discussion of the Kunt solutions. I note here that after this text was in production the importance of the Kunt space-times as regards the characterization of space-times by scalar curvature invariants was made clear [4]. The discussion of the Robinson-Trautman solutions that follows is extensive, containing, for example, details of the singularity structure and of the global structure. The final formal chapter in this text covers colliding plane waves. This contains, for example, discussions of the Khan-Penrose, Ferrari-Ibañez and Chandrasekhar-Xanthopoulos solutions. The text ends with a `final miscellany'. This covers a number of interesting topics, but I found the discussion of the Lemaître-Tolman solutions rather weak (compare e.g. [5]). The book has two quite useful appendices covering 2-spaces and 3-spaces of constant curvature. To conclude, I will quote from the dust jacket: `The book is an invaluable resource for both graduate students and academic researchers working in gravitational physics'. I highly recommend it. References [1] Stephani H, Kramer D, MacCallum M, Hoenselaers C and Herlt E 2003 Exact Solutions of Einstein's Field Equations (Second Edition) (Cambridge: Cambridge University Press) [2] Pretorius F and Israel W 1998 Class. Quantum Grav.15 2289 [3] Wiltshire D, Visser M and Scott S (ed) 2008 The Kerr Spacetime: Rotating Black Holes in General Relativity (Cambridge: Cambridge University Press) [4] Coley A, Hervik S and Pelavas N 2009 Class. Quantum Grav. 26 025013 [5] Plebański J and Krasiński A 2006 An Introduction to General Relativity and Cosmology (Cambridge: Cambridge University Press)

Oral Histories in Meteoritics and Planetary Science - XV: John Wood

NASA Astrophysics Data System (ADS)

Sears, Derek W. G.

2012-05-01

John Wood (Fig. 1) was trained in Geology at Virginia Tech and M.I.T. To fulfill a minor subject requirement at M.I.T., he studied astronomy at Harvard, taking courses with Fred Whipple and others. Disappointed at how little was known in the 1950s about the origin of the earth, he seized an opportunity to study a set of thin sections of stony meteorites, on the understanding that these might shed light on the topic. This study became his Ph.D. thesis. He recognized that chondrites form a metamorphic sequence, and that idea proved surprisingly hard to sell. After brief service in the Army and a year at Cambridge University, John served for 3 years as a research associate with Ed Anders at the University of Chicago. He then returned to the Smithsonian Astrophysical Observatory in Cambridge, Massachusetts, where he spent the remainder of his career. At Chicago, he investigated the formation of the Widmanstätten structure, and found that the process informs us of the cooling rates of iron meteorites. Back in Cambridge, he collaborated with W. R. Van Schmus on a chondrite classification that incorporates metamorphic grade, and published on metal grains in chondrites, before becoming absorbed by preparations for the return of lunar samples by the Apollo astronauts. His group's work on Apollo samples helped to establish the character of the lunar crust, and the need for a magma ocean to form it. Wood served as President of the Meteoritical Society in 1971-72 and received the Leonard Medal in 1978.

Reply to L.M. Brown et al. "Brief history of the Cambridge STEM aberration correction project and its progeny" in Ultramicroscopy 157, 88 (2015).

PubMed

Urban, K W; Rose, H

2016-02-01

We comment on a Short Communication recently published in Ultramicroscopy in which Brown et al. criticize our description of the time sequence of events in the development of aberration correction systems in electron optics during the 1990s put forward in the introduction to the Ultramicroscopy April 2015 Special Issue. We present an analysis of the published literature furnishing evidence that our description is correct. Copyright © 2015 Elsevier B.V. All rights reserved.

Brain Region-Specific Expression of Genes Mapped within Quantitative Trait Loci for Behavioral Responsiveness to Acute Stress in Fisher 344 and Wistar Kyoto Male Rats (Open Access Postprint)

DTIC Science & Technology

2018-03-12

RGSC_3.4. Using the Integrative Genomics Viewer (Broad Institute, Cambridge, Massachusetts), we iden- tified the coding sequence variations between the...adrenal axis abnormalities and disturbances in brain metabolism resem- bling those in depressive states [74]. Ifna2 is also known to induce memory... psychological science a journal of the Association for Psychological Science. 2016; 4(1):17–27. https://doi.org/10.1177/2167702615577470 PMID: 26958455

Findings from the Harvard Medical School Cambridge Integrated Clerkship, a Year-Long Longitudinal Psychiatry Experience.

PubMed

Cheng, Elisa; Hirsh, David; Gaufberg, Elizabeth; Griswold, Todd; Wesley Boyd, J

2018-06-01

The Harvard Medical School Cambridge Integrated Clerkship is a longitudinal integrated clerkship that has provided an alternative clinical model for medical education in psychiatry since its inception in 2004. This study was undertaken in an effort to better understand the student experience of the Cambridge Integrated Clerkship and how it may have impacted students' perceptions of and interest in psychiatry, as well as performance. Qualitative surveys were sent via e-mail to the first 11 student cohorts who had completed the Cambridge Integrated Clerkship (from 2004 to 2014) and for whom we had e-mail addresses (N = 100), and the free-text responses were coded thematically. All available standardized scoring data and residency match data for Cambridge Integrated Clerkship graduates were obtained. From 2006 to 2014, 12 out of 73 Cambridge Integrated Clerkship students who entered the match chose a psychiatry residency (16.4%), four times more than students in traditional clerkships at Harvard Medical School (3.8% of 1355 students) or the national average (4.1% of 146,066 US applicants). Thirty of the 100 surveyed Cambridge Integrated Clerkship graduates (30%) responded to the qualitative survey with free-text remarks on a number of themes. Cambridge Integrated Clerkship students compared positively to their classmates in terms of standardized test performance. Their fourfold higher match rate into psychiatry compared to other students raises intriguing questions as to what role a longitudinal clerkship might have played in developing interest in psychiatry as a career.

Revision Planned for the Cambridge Latin Course.

ERIC Educational Resources Information Center

Sebesta, Judith Lynn

1980-01-01

Summarizes a discussion on the revision of the Cambridge Latin Course (CLC) held during the 1980 ACL Institute at the University of New Hampshire by CLC users and Cambridge University Press representatives. Emphasizes suggestions by users on grammar instruction strategies better suited to American students' needs. (MES)

Teachers Learning: Professional Development and Education. Cambridge Education Research Series

ERIC Educational Resources Information Center

McLaughlin, Colleen, Ed.

2012-01-01

"Teachers Learning: Professional Development and Education" is part of The Cambridge Education Research series, edited by senior colleagues at the University of Cambridge Faculty of Education, which has a longstanding tradition of involvement in high quality, innovative teacher education and continuing professional development.…

Large-scale sequencing trials begin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roberts, L.

1990-12-07

As genome sequencing gets under way, investigators are grappling not just with new techniques but also with questions about what is acceptable accuracy and when data should be released. Four groups are embarking on projects that could make or break the human genome project. They are setting out to sequence the longest stretches of DNA ever tackled-several million bases each-and to do it faster and cheaper than anyone has before. If these groups can't pull it off, then prospects for knocking off the entire human genome, all 3 billion bases, in 15 years and for $3 billion will look increasinglymore » unlikely. Harvard's Walter Gilbert, is first tackling the genome of Mycoplasma capricolum. At Stanford, David Botstein and Ron Davis are sequencing Saccharomyces cerevisiae. In a collaborative effort, Robert Waterson at Washington University and John Sulston at the Medical Research Council lab in Cambridge, England, have already started on the nematode Caenorhabditis elegans. And in the only longstanding project of the bunch, University of Wisconsin geneticist Fred Blattner is already several hundred kilobases into the Escherichia coli genome.« less

Ottoman Turkish in the High School Curriculum: Current Language Planning Discussions in Turkey

ERIC Educational Resources Information Center

Yazan, Bedrettin; Üzüm, Melike

2017-01-01

This paper explores the recent policy decision about the teaching of Ottoman Turkish at high schools in Turkey and unpacks its historical, political, and social undercurrents. It theoretically rests upon Spolsky's [2004. "Language policy". Cambridge: Cambridge University Press, 2009. "Language management." Cambridge: Cambridge…

76 FR 77257 - Manufacturer of Controlled Substances; Notice of Registration

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-12

... 18, 2011, 76 FR 51400, Cambridge Isotope Lab, 50 Frontage Road, Andover, Massachusetts 01810, made... determined that the registration of Cambridge Isotope Lab to manufacture the listed basic class of controlled substance is consistent with the public interest at this time. DEA has investigated Cambridge Isotope Lab to...

RNA-based molecular survey of biodiversity of limestone tombstone microbiota in response to atmospheric sulphur pollution.

PubMed

Villa, F; Vasanthakumar, A; Mitchell, R; Cappitelli, F

2015-01-01

Outdoor stoneworks sustain biofilm formation and are constantly at risk of deterioration by micro-organisms. In this study, the biofilm microflora of historic limestone tombstones located in a highly polluted urban environment (Cambridge, MA) and in a less polluted location (Lexington, MA) were compared using comprehensive RNA-based molecular analyses of 16S rRNA gene sequences as well as sequences of genes for different pathways of sulphur metabolism (soxB, apsA, dsrA). The metabolically active micro-organisms detected by denaturing gradient gel electrophoresis analysis of 16S rRNA fragments were predominantly represented by cyanobacteria (belonging to the family Nostocaceae and to the genus Chroococcidiopsis) in both polluted and unpolluted environments. The investigation of soxB, apsA, dsrA transcripts reflected the abundance and the diversity of sulphur-oxidizing and sulphate-reducing bacteria in the Cambridge samples in comparison with the Lexington samples. The investigation revealed that in addition to phototrophic sulphur bacteria belonging to the genera Thiocapsa, Halochromatium, Allochromatium, Thiococcus and Thermochromatium, other sulphate-oxidizing prokaryotes (e.g. the genus Thiobacillus) as well as sequences of Deltaproteobacteria from the genus Desulfovibrio occurred at the polluted urban site. The interactions between the main functional groups retrieved from the limestone tombstones were discussed. The biofilm microflora inhabiting historic limestones are a multi-component open ecosystem sensitively reacting to all environmental factors including air pollutants. Little is known about specific target groups that are active in the biofilm and their physiological functions. For the first time, transcripts involved in important energy-yielding processes were investigated to reveal the metabolic capabilities of the microflora in response to atmospheric sulphur pollution. This work provides novel and important information about the ecology of limestone tombstone microbiota and its complex interaction with the external environment. © 2014 The Society for Applied Microbiology.

Partners | Office of Cancer Clinical Proteomics Research

Cancer.gov

Awardees and Affiliated Institutions Agilent Technologies, Inc., Cambridge, MA Baylor College of Medicine, Houston, TX Biomedical Hosting LLC, Arlington, MA Brigham and Women’s Hospital, Cambridge, MA Brown University, Providence, RI Cell Signaling Technology, Danvers, MA Chang Gung University, Molecular Medicine Research Center, Taoyuan City, Taiwan Dana-Farber Cancer Institute, Boston, MA Fluidigm Corp., Cambridge, MA

Geometry Report; Cambridge Conference on School Mathematics Feasibility Study No. 39.

ERIC Educational Resources Information Center

Stolzenberg, Gabriel

These materials were written with the aim of reflecting the thinking of the Cambridge Conference on School Mathematics (CCSM) regarding the goals and objectives for school mathematics. This report deals with some seventh grade mathematical concepts taught at Cambridge Friends' School. The discovery approach was utilized by the teacher in order to…

Astronomy in the College Curriculum for Preservice Elementary Teachers

NASA Astrophysics Data System (ADS)

French, L. M.; MacCormack, A.; Winokur, J.

1997-05-01

Astronomy, astrophysics, and space science play a major role in courses being developed at Wheelock College. The majority of the students are preparing for careers as elementary and early childhood teachers; they will thus be among the first teachers of science a child meets. Wheelock's introductory course in astronomy is based around key topics in the new national science frameworks such as size and scale, our place in the Universe, and light and color. Astrophysics, an intermediate level course, provides a more quantitative survey for those with a background in physical science. An interdisciplinary sequence of two courses, "The Physical Universe" and "The Living World", introduces students to key concepts such as motion and energy. Applications are studied from all of the sciences, including crater formation and the conversion of light to chemical energy in photosynthesis. The interdisciplinary courses have been developed and taught by an astrophysicist, an ecologist, and an early childhood educator. This work has been done under the auspices of TEAMS-BC (Teacher Education Addressing Math and Science in Boston and Cambridge), a Collaborative for Excellence in Teacher Preparation involving Harvard University, MIT, the University of Massachusetts-Boston, Wheelock College, and the Boston and Cambridge Public School Systems.

Investigating the Impact of Cambridge International Assessments on U.S. Stakeholders: Student and Teacher Perceptions

ERIC Educational Resources Information Center

Shaw, Stuart

2011-01-01

As part of the continuing program to study the impact of its international assessments, the University of Cambridge International Examinations ("Cambridge") has undertaken a series of studies investigating the impact on a range of US stakeholders. This paper reports on research designed to respond to a series of washback and impact…

Assessing the Impact of Arts and Humanities Research at the University of Cambridge. Technical Report

ERIC Educational Resources Information Center

Levitt, Ruth; Celia, Claire; Diepeveen, Stephanie; Chonaill, Siobhan Ni; Rabinovich, Lila; Tiessen, Jan

2010-01-01

This project for the University of Cambridge and the Arts and Humanities Research Council (AHRC) assesses the impacts of arts and humanities research at the University of Cambridge. Evidence from interviews, a survey of research staff and detailed case studies indicates that these disciplines already have a broad range of impacts. Many of these…

EDUCATION: Gates Gives Cambridge a Rival to Rhodes.

PubMed

Cohen, J

2000-10-20

Thanks to a new $210 million trust announced on 11 October by the Bill & Melinda Gates Foundation, Cambridge University is launching a new high-visibility scholars' program, which each year will fund at least 225 students from outside the United Kingdom. The university will select Gates Cambridge Scholars based on merit, not need, focusing on academic ability and leadership potential.

The Search for Suitable Strategy: Threat-Based and Capabilities-Based Strategies in a Complex World

DTIC Science & Technology

2016-05-26

subject to copyright, however further publication or sale of copyrighted images is not permissible. ii...Williamson Murray and Richard Hart Sinnreich, eds., Successful Strategies: Triumphing in War and Peace from Antiquity to the Present (Cambridge, United...Sinnreich, eds. Successful Strategies: Triumphing in War and Peace from Antiquity to the Present. Cambridge, United Kingdom: Cambridge University Press

A single-molecule diode

NASA Astrophysics Data System (ADS)

Elbing, Mark; Ochs, Rolf; Koentopp, Max; Fischer, Matthias; von Hänisch, Carsten; Weigend, Florian; Evers, Ferdinand; Weber, Heiko B.; Mayor, Marcel

2005-06-01

We have designed and synthesized a molecular rod that consists of two weakly coupled electronic π -systems with mutually shifted energy levels. The asymmetry thus implied manifests itself in a current-voltage characteristic with pronounced dependence on the sign of the bias voltage, which makes the molecule a prototype for a molecular diode. The individual molecules were immobilized by sulfur-gold bonds between both electrodes of a mechanically controlled break junction, and their electronic transport properties have been investigated. The results indeed show diode-like current-voltage characteristics. In contrast to that, control experiments with symmetric molecular rods consisting of two identical π -systems did not show significant asymmetries in the transport properties. To investigate the underlying transport mechanism, phenomenological arguments are combined with calculations based on density functional theory. The theoretical analysis suggests that the bias dependence of the polarizability of the molecule feeds back into the current leading to an asymmetric shape of the current-voltage characteristics, similar to the phenomena in a semiconductor diode. Author contributions: F.E., H.B.W., and M.M. designed research; M.E., R.O., M.K., M.F., F.E., H.B.W., and M.M. performed research; M.E., R.O., M.K., M.F., C.v.H., F.W., F.E., H.B.W., and M.M. contributed new reagents/analytic tools; M.E., R.O., M.K., C.v.H., F.E., H.B.W., and M.M. analyzed data; and F.E., H.B.W., and M.M. wrote the paper.This paper was submitted directly (Track II) to the PNAS office.Abbreviations: A, acceptor; D, donor; MCB, mechanically controlled break junction.Data deposition: The atomic coordinates have been deposited in the Cambridge Structural Database, Cambridge Crystallographic Data Centre, Cambridge CB2 1EZ, United Kingdom (CSD reference no. 241632).

Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows.

PubMed

Siebert, Stefan; Robinson, Mark D; Tintori, Sophia C; Goetz, Freya; Helm, Rebecca R; Smith, Stephen A; Shaner, Nathan; Haddock, Steven H D; Dunn, Casey W

2011-01-01

We investigated differential gene expression between functionally specialized feeding polyps and swimming medusae in the siphonophore Nanomia bijuga (Cnidaria) with a hybrid long-read/short-read sequencing strategy. We assembled a set of partial gene reference sequences from long-read data (Roche 454), and generated short-read sequences from replicated tissue samples that were mapped to the references to quantify expression. We collected and compared expression data with three short-read expression workflows that differ in sample preparation, sequencing technology, and mapping tools. These workflows were Illumina mRNA-Seq, which generates sequence reads from random locations along each transcript, and two tag-based approaches, SOLiD SAGE and Helicos DGE, which generate reads from particular tag sites. Differences in expression results across workflows were mostly due to the differential impact of missing data in the partial reference sequences. When all 454-derived gene reference sequences were considered, Illumina mRNA-Seq detected more than twice as many differentially expressed (DE) reference sequences as the tag-based workflows. This discrepancy was largely due to missing tag sites in the partial reference that led to false negatives in the tag-based workflows. When only the subset of reference sequences that unambiguously have tag sites was considered, we found broad congruence across workflows, and they all identified a similar set of DE sequences. Our results are promising in several regards for gene expression studies in non-model organisms. First, we demonstrate that a hybrid long-read/short-read sequencing strategy is an effective way to collect gene expression data when an annotated genome sequence is not available. Second, our replicated sampling indicates that expression profiles are highly consistent across field-collected animals in this case. Third, the impacts of partial reference sequences on the ability to detect DE can be mitigated through workflow choice and deeper reference sequencing.

Differential Gene Expression in the Siphonophore Nanomia bijuga (Cnidaria) Assessed with Multiple Next-Generation Sequencing Workflows

PubMed Central

Siebert, Stefan; Robinson, Mark D.; Tintori, Sophia C.; Goetz, Freya; Helm, Rebecca R.; Smith, Stephen A.; Shaner, Nathan; Haddock, Steven H. D.; Dunn, Casey W.

2011-01-01

We investigated differential gene expression between functionally specialized feeding polyps and swimming medusae in the siphonophore Nanomia bijuga (Cnidaria) with a hybrid long-read/short-read sequencing strategy. We assembled a set of partial gene reference sequences from long-read data (Roche 454), and generated short-read sequences from replicated tissue samples that were mapped to the references to quantify expression. We collected and compared expression data with three short-read expression workflows that differ in sample preparation, sequencing technology, and mapping tools. These workflows were Illumina mRNA-Seq, which generates sequence reads from random locations along each transcript, and two tag-based approaches, SOLiD SAGE and Helicos DGE, which generate reads from particular tag sites. Differences in expression results across workflows were mostly due to the differential impact of missing data in the partial reference sequences. When all 454-derived gene reference sequences were considered, Illumina mRNA-Seq detected more than twice as many differentially expressed (DE) reference sequences as the tag-based workflows. This discrepancy was largely due to missing tag sites in the partial reference that led to false negatives in the tag-based workflows. When only the subset of reference sequences that unambiguously have tag sites was considered, we found broad congruence across workflows, and they all identified a similar set of DE sequences. Our results are promising in several regards for gene expression studies in non-model organisms. First, we demonstrate that a hybrid long-read/short-read sequencing strategy is an effective way to collect gene expression data when an annotated genome sequence is not available. Second, our replicated sampling indicates that expression profiles are highly consistent across field-collected animals in this case. Third, the impacts of partial reference sequences on the ability to detect DE can be mitigated through workflow choice and deeper reference sequencing. PMID:21829563

Dissipative behavior of some fully non-linear KdV-type equations

NASA Astrophysics Data System (ADS)

Brenier, Yann; Levy, Doron

2000-03-01

The KdV equation can be considered as a special case of the general equation u t+f(u) x-δg(u xx) x=0, δ>0, where f is non-linear and g is linear, namely f( u)= u2/2 and g( v)= v. As the parameter δ tends to 0, the dispersive behavior of the KdV equation has been throughly investigated (see, e.g., [P.G. Drazin, Solitons, London Math. Soc. Lect. Note Ser. 85, Cambridge University Press, Cambridge, 1983; P.D. Lax, C.D. Levermore, The small dispersion limit of the Korteweg-de Vries equation, III, Commun. Pure Appl. Math. 36 (1983) 809-829; G.B. Whitham, Linear and Nonlinear Waves, Wiley/Interscience, New York, 1974] and the references therein). We show through numerical evidence that a completely different, dissipative behavior occurs when g is non-linear, namely when g is an even concave function such as g( v)=-∣ v∣ or g( v)=- v2. In particular, our numerical results hint that as δ→0 the solutions strongly converge to the unique entropy solution of the formal limit equation, in total contrast with the solutions of the KdV equation.

Microscopy of semiconducting materials

NASA Astrophysics Data System (ADS)

Pennycook, S. J.

1991-04-01

The purpose of the trip was to present an invited talk at the 7th Oxford Conference on Microscopy of Semiconducting Materials entitled, High-Resolution Z-Contrast Imaging of Heterostructures and Superlattices, (Oxford, United Kingdom) and to visit VG Microscopes, East Grinstead, for discussions on the progress of the Oak Ridge National Laboratory (ORNL) 300-kV high-resolution scanning transmission electron microscope (STEM), which is currently on order. The traveler also visited three other institutions with 100-kV STEMs that either have or intend to purchase the necessary modifications to provide Z-contrast capability similar to that of the existing ORNL machine. Specifically, Max-Planck Institut fuer Metallforschung (Stuttgart, Germany); Cambridge University, Department of Materials Science and Metallurgy (Cambridge, United Kingdom); and Cavendish Laboratory, Cambridge University (Cambridge, United Kingdom) were visited. In addition, discussions were held with C. Humphreys on the possibility of obtaining joint funding for collaborative research involving electron beam writing and Z-contrast imaging in the Cambridge and Oak Ridge STEMs, respectively.

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology.

PubMed

Otto, Thomas D; Sanders, Mandy; Berriman, Matthew; Newbold, Chris

2010-07-15

The accuracy of reference genomes is important for downstream analysis but a low error rate requires expensive manual interrogation of the sequence. Here, we describe a novel algorithm (Iterative Correction of Reference Nucleotides) that iteratively aligns deep coverage of short sequencing reads to correct errors in reference genome sequences and evaluate their accuracy. Using Plasmodium falciparum (81% A + T content) as an extreme example, we show that the algorithm is highly accurate and corrects over 2000 errors in the reference sequence. We give examples of its application to numerous other eukaryotic and prokaryotic genomes and suggest additional applications. The software is available at http://icorn.sourceforge.net

Report from the second cytomegalovirus and immunosenescence workshop

PubMed Central

2011-01-01

The Second International Workshop on CMV & Immunosenescence was held in Cambridge, UK, 2-4th December, 2010. The presentations covered four separate sessions: cytomegalovirus and T cell phenotypes; T cell memory frequency, inflation and immunosenescence; cytomegalovirus in aging, mortality and disease states; and the immunobiology of cytomegalovirus-specific T cells and effects of the virus on vaccination. This commentary summarizes the major findings of these presentations and references subsequently published work from the presenter laboratory where appropriate and draws together major themes that were subsequently discussed along with new areas of interest that were highlighted by this discussion. PMID:22035114

WebCSD: the online portal to the Cambridge Structural Database

PubMed Central

Thomas, Ian R.; Bruno, Ian J.; Cole, Jason C.; Macrae, Clare F.; Pidcock, Elna; Wood, Peter A.

2010-01-01

WebCSD, a new web-based application developed by the Cambridge Crystallographic Data Centre, offers fast searching of the Cambridge Structural Database using only a standard internet browser. Search facilities include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching. Text, chemical diagrams and three-dimensional structural information can all be studied in the results browser using the efficient entry summaries and embedded three-dimensional viewer. PMID:22477776

Usage of mitochondrial D-loop variation to predict risk for Huntington disease.

PubMed

Mousavizadeh, Kazem; Rajabi, Peyman; Alaee, Mahsa; Dadgar, Sepideh; Houshmand, Massoud

2015-08-01

Huntington's disease (HD) is an inherited autosomal neurodegenerative disease caused by the abnormal expansion of the CAG repeats in the Huntingtin (Htt) gene. It has been proven that mitochondrial dysfunction is contributed to the pathogenesis of Huntington's disease. The mitochondrial displacement loop (D-loop) is proven to accumulate mutations at a higher rate than other regions of mtDNA. Thus, we hypothesized that specific SNPs in the D-loop may contribute to the pathogenesis of Huntington's disease. In the present study, 30 patients with Huntington's disease and 463 healthy controls were evaluated for mitochondrial mutation sites within the D-loop region using PCR-sequencing method. Sequence analysis revealed 35 variations in HD group from Cambridge Mitochondrial Sequences. A significant difference (p < 0.05) was seen between patients and control group in eight SNPs. Polymorphisms at C16069T, T16126C, T16189C, T16519C and C16223T were correlated with an increased risk of HD while SNPs at C16150T, T16086C and T16195C were associated with a decreased risk of Huntington's disease.

Ten years experience of Salmonella infections in Cambridge, UK.

PubMed

Matheson, Nicholas; Kingsley, Robert A; Sturgess, Katherine; Aliyu, Sani H; Wain, John; Dougan, Gordon; Cooke, Fiona J

2010-01-01

Review of all Salmonella infections diagnosed in the Cambridge area over 10 years. All Salmonella enterica isolated in the Clinical Microbiology Laboratory, Addenbrooke's Hospital between 1.1.1999 and 31.12.2008 were included. Patient demographics, serotype and additional relevant details (travel history, resistance-type, phage-type) were recorded. 1003 episodes of Salmonella gastroenteritis were confirmed by stool culture, representing 88 serotypes. Serotypes Enteritidis (59%), Typhimurium (4.7%), Virchow (2.6%), Newport (1.8%) and Braenderup (1.7%) were the 5 most common isolates. There were an additional 37 invasive Salmonella infections (32 blood cultures, 4 tissue samples, 1 CSF). 13/15 patients with Salmonella Typhi or Salmonella Paratyphi isolated from blood or faeces with an available travel history had returned from the Indian subcontinent. 8/10 S. Typhi or Paratyphi isolates tested had reduced susceptibility to fluoroquinolones (MIC > or = 0.125 mg/L). 7/21 patients with non-typhoidal Salmonella bacteraemia were known to be immunosuppressed. This study describes Salmonella serotypes circulating within a defined geographical area over a decade. Prospective molecular analysis of isolates of S. enterica by multi-locus sequence typing (MLST) and single nucleotide polymorphism (SNP) detection will determine the geo-phylogenetic relationship of isolates within our region. 2009 The British Infection Society. Published by Elsevier Ltd. All rights reserved.

Bericht uber den 2. Internationalen Kongress fur Angewandte Linguistik. Cambridge 8.-12. IX. 1969. [Report on the Second International Congress for Applied Linguistics, Cambridge, Dec. 8-12, 1969.

ERIC Educational Resources Information Center

Mohr, Peter

This paper is a summary report on the Second International Congress of Applied Linguistics held in Cambridge, England in September 1969. Because of the large number of papers delivered, only a selection of the papers delivered in any one section of the Congress are considered, and the author attempts to identify current interests and trends in…

Titan's Impact Cratering Record: Erosion of Ganymedean (and other) Craters on a Wet Icy Landscape

NASA Astrophysics Data System (ADS)

Schenk, P.; Moore, J.; Howard, A.

2012-04-01

We examine the cratering record of Titan from the perspective of icy satellites undergoing persistent landscape erosion. First we evaluate whether Ganymede (and Callisto) or the smaller low-gravity neighboring icy satellites of Saturn are the proper reference standard for evaluating Titan’s impact crater morphologies, using topographic and morphometric measurements (Schenk, 2002; Schenk et al. (2004) and unpublished data). The special case of Titan’s largest crater, Minrva, is addressed through analysis of large impact basins such as Gilgamesh, Lofn, Odysseus and Turgis. Second, we employ a sophisticated landscape evolution and modification model developed for study of martian and other planetary landforms (e.g., Howard, 2007). This technique applies mass redistribution principles due to erosion by impact, fluvial and hydrological processes to a planetary landscape. The primary advantage of our technique is the possession of a limited but crucial body of areal digital elevation models (DEMs) of Ganymede (and Callisto) impact craters as well as global DEM mapping of Saturn’s midsize icy satellites, in combination with the ability to simulate rainfall and redeposition of granular material to determine whether Ganymede craters can be eroded to resemble Titan craters and the degree of erosion required. References: Howard, A. D., “Simulating the development of martian highland landscapes through the interaction of impact cratering, fluvial erosion, and variable hydrologic forcing”, Geomorphology, 91, 332-363, 2007. Schenk, P. "Thickness constraints on the icy shells of the galilean satellites from impact crater shapes". Nature, 417, 419-421, 2002. Schenk, P.M., et al. "Ages and interiors: the cratering record of the Galilean satellites". In: Jupiter: The Planet, Satellites, and Magnetosphere, Cambridge University Press, Cambridge, UK, pp. 427-456, 2004.

The Douglas-fir genome sequence reveals specialization of the photosynthetic apparatus in Pinaceae

Treesearch

David B. Neale; Patrick E. McGuire; Nicholas C. Wheeler; Kristian A. Stevens; Marc W. Crepeau; Charis Cardeno; Aleksey V. Zimin; Daniela Puiu; Geo M. Pertea; U. Uzay Sezen; Claudio Casola; Tomasz E. Koralewski; Robin Paul; Daniel Gonzalez-Ibeas; Sumaira Zaman; Richard Cronn; Mark Yandell; Carson Holt; Charles H. Langley; James A. Yorke; Steven L. Salzberg; Jill L. Wegrzyn

2017-01-01

A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50...

Implications of Societal Fragmentation for State Formation: Can Democracy Succeed in Afghanistan

DTIC Science & Technology

2006-03-01

Conflict,” in Nationalism and Ethnic Conflict, Eds. Michael E. Brown, Owen R. Cote Jr., Sean M . Lynn-Jones, and Steven E. Miller (Cambridge and London: The...Cote Jr., Sean M . Lynn-Jones, and Steven E. Miller (Cambridge and London: The MIT Press, 1997), 49. 21 conceptions of legitimacy, they are...and Ethnic Conflict, Eds. Michael E. Brown, Owen R. Cote Jr., Sean M . Lynn-Jones, and Steven E. Miller (Cambridge and London: The MIT Press, 1997

The U.S., Japan, and Asia: Challenges to U.S. Policy

DTIC Science & Technology

1993-10-01

1945-1990. Cambridge: Cambridge UP, 1992. (E 183.8 .J3 B78 1992) Burks , Ardath W. Japan: A Postindustrial Power. 3rd ed. Boulder: Westview, 1991. (DS 806...1988) Anchordoguy, Marie . Computers Inc.: Japan’s Challenge to IB4. Cambridge: Harvard UP, 1989. (HD 9696 .C63 J29 1989) Arrison, Thomas S., et. al...Strategv towards the East. London: International Institute for Strategic Studies, 1984. (U 162 .A23 no.192) Burke , Patrick, ed. Nuclear Weapons World

Loads and yields of deicing compounds and total phosphorus in the Cambridge drinking-water source area, Massachusetts, water years 2009–15

USGS Publications Warehouse

Smith, Kirk P.

2017-09-12

The source water area for the drinking-water supply of the city of Cambridge, Massachusetts, encompasses major transportation corridors, as well as large areas of light industrial, commercial, and residential land use. Because of the large amount of roadway in the drinking-water source area, the Cambridge water supply is affected by the usage of deicing compounds and by other constituents that are flushed from such impervious areas. The U.S. Geological Survey (USGS) has monitored surface-water quality in the Cambridge Reservoir and Stony Brook Reservoir Basins, which compose the drinking-water source area, since 1997 (water year 1998) through continuous monitoring and the collection of stream-flow samples.In a study conducted by the USGS, in cooperation with the City of Cambridge Water Department, concentrations and loads of calcium (Ca), chloride (Cl), magnesium (Mg), sodium (Na), and sulfate (SO4) were estimated from continuous records of specific conductance and streamflow for streams and tributaries at 10 continuous water-quality monitoring stations. These data were used to characterize current (2015) water-quality conditions, estimate loads and yields, and describe trends in Cl and Na in the tributaries and main-stem streams in the Cambridge Reservoir and Stony Brook Reservoir Basins. These data also were used to describe how stream-water quality is related to various basin characteristics and provide information to guide future management of the drinking-water source area.Water samples from 2009–15 were analyzed for physical properties and concentrations of Ca, Cl, Mg, Na, potassium (K), SO4, and total phosphorus (TP). Values of physical properties and constituent concentrations varied widely, particularly in composite samples of stormflow from tributaries that have high percentages of constructed impervious areas. Median concentrations of Ca, Cl, Mg, Na, and K in samples collected from the tributaries in the Cambridge Reservoir Basin (27.2, 273, 4.7, 154.5, and 2.8 milligrams per liter (mg/L), respectively) were higher than those for the Stony Brook Reservoir Basin (22.2, 128, 4.3, 77.1, and 2.5, respectively). Differences between tributary samples for concentrations of Cl and Na were related to the percentage of developed land and constructed impervious area in the drinking-water source area. Median concentrations of SO4 in samples collected from the tributaries in the Cambridge Reservoir Basin (10.7 mg/L) were lower than those for the Stony Brook Reservoir Basin (18.0 mg/L).Concentrations of dissolved Cl and Na in samples and those concentrations estimated from continuous records of specific conductance (particularly during base flow) often were greater than the U.S. Environmental Protection Agency (EPA) secondary drinking-water standard for Cl (250 mg/L), the chronic aquatic-life guideline for Cl (230 mg/L), and the Massachusetts Department of Environmental Protection drinking-water guideline for Na (20 mg/L). Concentrations of TP (range from 0.008 to 0.69 mg/L in all subbasins) in tributary samples did not differ substantially between the Cambridge Reservoir and Stony Brook Reservoir Basins. About one-half of the concentrations of TP in samples collected during water years 2013–15 exceeded the EPA proposed reference concentration of 0.024 mg/L.For most tributaries, about 70 percent of the annual loads of Ca, Cl, Mg, Na, and SO4 were associated with base flow. Concentrations of major ions were negatively correlated with streamflow, indicating that these constituents were diluted during stormflow and tend to increase during the summer when streamflow is low. In contrast, between 57 and 92 percent of the annual load for TP was transported during stormflows.Mean annual yields of Ca, Cl, Mg, Na, and SO4 in the drinking-water source area were 13, 75, 2.6, 40, and 6.9 metric tons per square kilometer, respectively, for water years 2009–15. The mean annual yield of TP in the drinking-water source area for water years 2013–15 was 0.012 metric tons per square kilometer. Yields for major ions and TP were highest in tributary subbasins adjacent to Interstate 95.Temporal trends in mean annual concentrations for Cl and Na were not significant for water years 1998‒2015 (period of record by the USGS) for the outlet of the Cambridge Reservoir and for the main stem of Stony Brook downstream from the reservoir. Median values of base-flow concentrations of TP at three stations were higher for samples collected during base-flow conditions during water years 2005–7 than for samples collected during water years 2013–15. However, the results were not significant for statistical tests between concentrations in samples collected during storms for the same periods, indicating that the quality of stormwater remains similar.

Liquid chromatographic determination of benzo(a)pyrene in total particulate matter of cigarette smoke

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tomkins, B.A.; Jenkins, R.A.; Griest, W.H.

The benzo(a)pyrene (BaP) delivery of reference and commercially available tobacco cigarettes, as well as reference and placebo marijuana cigarettes, is determined using a sequential liquid chromatographic/liquid chromatographic procedure. The total particulate matter of sample cigarette smoke is collected using a Cambridge filter pad, which is ultrasonically extracted with acetone. The resulting extract is filtered, then fractionated using semipreparative-scale normal phase liquid chromatography (LC). Quantitative determination is achieved using analytical-scale reverse phase LC equipped with a fluorescence detector. The method is precise (+/- 10-15% relative standard deviation) and yields 85% or better BaP recovery at the ng/cig. level. A single padmore » may be analyzed in 8 person-hours, while a more typical lot of 12 pads (6 pads each for 2 cigarette brands) may be analyzed in 10 person-days.« less

Training Metacognitive Skills for Situation Assessment

DTIC Science & Technology

1994-06-01

see Toulmin , 1978). The initial recognitional response to a cue provides its normal meaning. For example, the absence of enemy artillery within...Holland. Toulmin , S. (1958). The uses of argument. Cambridge, UK: Cambridge University Press.

The Life of James Clerk Maxwell

NASA Astrophysics Data System (ADS)

Campbell, Lewis; Garnett, William

2010-06-01

Preface; Part I. Biographical Outline: 1. Birth and parentage; 2. Glenlair - childhood, 1831-1841; 3. Boyhood, 1841-1844; 4. Adolescence, 1844-1847; 5. Opening manhood, 1847-1850; 6. Undergraduate life at Cambridge, 1850-1854; 7. Bachelor-scholar and fellow of Trinity, 1854-1856; 8. Essays at Cambridge, 1853-1856; 9. Death of his father. Professorship at Aberdeen, 1856-1857; 10. Aberdeen. Marriage, 1857-1860; 11. King's College, London. Glenair, 1860-1870; 12. Cambridge, 1871-1879; 13. Illness and death, 1879; 14. Last essays at Cambridge; Part II. Contributions to Science: 1. Experiments on colour vision, and other contributions to optics; 2. Investigations respecting elastic solids; 3. Pure geometry; 4. Mechanics; 5. Saturn's rings; 6. Faraday's lines of force, and Maxwell's theory of the electromagnetic field; 7. Molecular physics; Part III. Poems: 1. Juvenile verses and translations; 2. Occasional pieces; 3. Serio-comic verse; Index.

Dynamic crack propagation in a 2D elastic body: The out-of-plane case

NASA Astrophysics Data System (ADS)

Nicaise, Serge; Sandig, Anna-Margarete

2007-05-01

Already in 1920 Griffith has formulated an energy balance criterion for quasistatic crack propagation in brittle elastic materials. Nowadays, a generalized energy balance law is used in mechanics [F. Erdogan, Crack propagation theories, in: H. Liebowitz (Ed.), Fracture, vol. 2, Academic Press, New York, 1968, pp. 498-586; L.B. Freund, Dynamic Fracture Mechanics, Cambridge Univ. Press, Cambridge, 1990; D. Gross, Bruchmechanik, Springer-Verlag, Berlin, 1996] in order to predict how a running crack will grow. We discuss this situation in a rigorous mathematical way for the out-of-plane state. This model is described by two coupled equations in the reference configuration: a two-dimensional scalar wave equation for the displacement fields in a cracked bounded domain and an ordinary differential equation for the crack position derived from the energy balance law. We handle both equations separately, assuming at first that the crack position is known. Then the weak and strong solvability of the wave equation will be studied and the crack tip singularities will be derived under the assumption that the crack is straight and moves tangentially. Using the energy balance law and the crack tip behavior of the displacement fields we finally arrive at an ordinary differential equation for the motion of the crack tip.

NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

PubMed Central

Pruitt, Kim D.; Tatusova, Tatiana; Maglott, Donna R.

2005-01-01

The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) provides a non-redundant collection of sequences representing genomic data, transcripts and proteins. Although the goal is to provide a comprehensive dataset representing the complete sequence information for any given species, the database pragmatically includes sequence data that are currently publicly available in the archival databases. The database incorporates data from over 2400 organisms and includes over one million proteins representing significant taxonomic diversity spanning prokaryotes, eukaryotes and viruses. Nucleotide and protein sequences are explicitly linked, and the sequences are linked to other resources including the NCBI Map Viewer and Gene. Sequences are annotated to include coding regions, conserved domains, variation, references, names, database cross-references, and other features using a combined approach of collaboration and other input from the scientific community, automated annotation, propagation from GenBank and curation by NCBI staff. PMID:15608248

Reliable Detection of Herpes Simplex Virus Sequence Variation by High-Throughput Resequencing.

PubMed

Morse, Alison M; Calabro, Kaitlyn R; Fear, Justin M; Bloom, David C; McIntyre, Lauren M

2017-08-16

High-throughput sequencing (HTS) has resulted in data for a number of herpes simplex virus (HSV) laboratory strains and clinical isolates. The knowledge of these sequences has been critical for investigating viral pathogenicity. However, the assembly of complete herpesviral genomes, including HSV, is complicated due to the existence of large repeat regions and arrays of smaller reiterated sequences that are commonly found in these genomes. In addition, the inherent genetic variation in populations of isolates for viruses and other microorganisms presents an additional challenge to many existing HTS sequence assembly pipelines. Here, we evaluate two approaches for the identification of genetic variants in HSV1 strains using Illumina short read sequencing data. The first, a reference-based approach, identifies variants from reads aligned to a reference sequence and the second, a de novo assembly approach, identifies variants from reads aligned to de novo assembled consensus sequences. Of critical importance for both approaches is the reduction in the number of low complexity regions through the construction of a non-redundant reference genome. We compared variants identified in the two methods. Our results indicate that approximately 85% of variants are identified regardless of the approach. The reference-based approach to variant discovery captures an additional 15% representing variants divergent from the HSV1 reference possibly due to viral passage. Reference-based approaches are significantly less labor-intensive and identify variants across the genome where de novo assembly-based approaches are limited to regions where contigs have been successfully assembled. In addition, regions of poor quality assembly can lead to false variant identification in de novo consensus sequences. For viruses with a well-assembled reference genome, a reference-based approach is recommended.

Mantle convection and the distribution of geochemical reservoirs in the silicate shell of the Earth

NASA Astrophysics Data System (ADS)

Walzer, Uwe; Hendel, Roland

2010-05-01

We present a dynamic 3-D spherical-shell model of mantle convection and the evolution of the chemical reservoirs of the Earth`s silicate shell. Chemical differentiation, convection, stirring and thermal evolution constitute an inseparable dynamic system. Our model is based on the solution of the balance equations of mass, momentum, energy, angular momentum, and four sums of the number of atoms of the pairs 238U-206Pb, 235U-207Pb, 232Th-208Pb, and 40K-40Ar. Similar to the present model, the continental crust of the real Earth was not produced entirely at the start of the evolution but developed episodically in batches [1-7]. The details of the continental distribution of the model are largely stochastic, but the spectral properties are quite similar to the present real Earth. The calculated Figures reveal that the modeled present-day mantle has no chemical stratification but we find a marble-cake structure. If we compare the observational results of the present-day proportion of depleted MORB mantle with the model then we find a similar order of magnitude. The MORB source dominates under the lithosphere. In our model, there are nowhere pure unblended reservoirs in the mantle. It is, however, remarkable that, in spite of 4500 Ma of solid-state mantle convection, certain strong concentrations of distributed chemical reservoirs continue to persist in certain volumes, although without sharp abundance boundaries. We deal with the question of predictable and stochastic portions of the phenomena. Although the convective flow patterns and the chemical differentiation of oceanic plateaus are coupled, the evolution of time-dependent Rayleigh number, Rat , is relatively well predictable and the stochastic parts of the Rat(t)-curves are small. Regarding the juvenile growth rates of the total mass of the continents, predictions are possible only in the first epoch of the evolution. Later on, the distribution of the continental-growth episodes is increasingly stochastic. Independently of the varying individual runs, our model shows that the total mass of the present-day continents is not generated in a single process at the beginning of the thermal evolution of the Earth but in episodically distributed processes in the course of geological time. This is in accord with observation. Finally, we present results regarding the numerical method, implementation, scalability and performance. References [1] Condie, K. C., Episodie continental growth models: Afterthoughts and extensions, Tectonophysics, 322 (2000), 153-162. [2] Davidson, J. P. and Arculus, R. J., The significance of Phanerozoic arc magmatism in generating continental crust, in Evolution and Differentiation of the Continental Crust, edited by M. Brown and T. Rushmer (2006), 135-172, Cambridge Univ. Press, Cambridge, UK. [3] Hofmann, A. W., Sampling mantle heterogeneity through oceanic basalts: Isotopes and trace elements, in Treatise on Geochemistry, Vol. 2: The Mantle and the Core, edited by R. W. Carlson (2003), 61-101, Elsevier, Amsterdam. [4] Rollinson, H., Crustal generation in the Archean, in Evolution and Differentiation of the Continental Crust, edited by M. Brown and T. Rushmer (2006), 173-230, Cambridge Univ. Press, Cambridge, UK: [5] Taylor, S. R. and McLennan, S. M., Planetary Crusts. Their Composition, Origin and Evolution. (2009), 1-378, Cambridge Univ. Press, Cambridge, UK. [6] Walzer, U. and Hendel, R., Mantle convection and evolution with growing continents. J. Geophys. Res. 113 (2008), B09405, doi: 10.1029/2007JB005459 [7] http://www.igw.uni-jena.de/geodyn

Development of a reference material of a single DNA molecule for the quality control of PCR testing.

PubMed

Mano, Junichi; Hatano, Shuko; Futo, Satoshi; Yoshii, Junji; Nakae, Hiroki; Naito, Shigehiro; Takabatake, Reona; Kitta, Kazumi

2014-09-02

We developed a reference material of a single DNA molecule with a specific nucleotide sequence. The double-strand linear DNA which has PCR target sequences at the both ends was prepared as a reference DNA molecule, and we named the PCR targets on each side as confirmation sequence and standard sequence. The highly diluted solution of the reference molecule was dispensed into 96 wells of a plastic PCR plate to make the average number of molecules in a well below one. Subsequently, the presence or absence of the reference molecule in each well was checked by real-time PCR targeting for the confirmation sequence. After an enzymatic treatment of the reaction mixture in the positive wells for the digestion of PCR products, the resultant solution was used as the reference material of a single DNA molecule with the standard sequence. PCR analyses revealed that the prepared samples included only one reference molecule with high probability. The single-molecule reference material developed in this study will be useful for the absolute evaluation of a detection limit of PCR-based testing methods, the quality control of PCR analyses, performance evaluations of PCR reagents and instruments, and the preparation of an accurate calibration curve for real-time PCR quantitation.

Searching the Cambridge Structural Database for polymorphs.

PubMed

van de Streek, Jacco; Motherwell, Sam

2005-10-01

In order to identify all pairs of polymorphs in the Cambridge Structural Database (CSD), a method was devised to automatically compare two crystal structures. The comparison is based on simulated powder diffraction patterns, but with special provisions to deal with differences in unit-cell volumes caused by temperature or pressure. Among the 325,000 crystal structures in the Cambridge Structural Database, 35,000 pairs of crystal structures of the same chemical compound were identified and compared. A total of 7300 pairs of polymorphs were identified, of which 154 previously were unknown.

New in-depth rainbow trout transcriptome reference and digital atlas of gene expression

USDA-ARS?s Scientific Manuscript database

Sequencing the rainbow trout genome is underway and a transcriptome reference sequence is required to help in genome assembly and gene discovery. Previously, we reported a transcriptome reference sequence using a 19X coverage of 454-pyrosequencing data. Although this work added a great wealth of ann...

Exploiting long read sequencing technologies to establish high quality highly contiguous pig reference genome assemblies

USDA-ARS?s Scientific Manuscript database

The current pig reference genome sequence (Sscrofa10.2) was established using Sanger sequencing and following the clone-by-clone hierarchical shotgun sequencing approach used in the public human genome project. However, as sequence coverage was low (4-6x) the resulting assembly was only of draft qua...

75 FR 11197 - Notice Pursuant to the National Cooperative Research and Production Act of 1993-Pistoia Alliance...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-10

...; CambridgeSoft, San Diego, CA; Merck, Boston, MA; Collaborative Drug Discovery, Burlingame, CA; Royal Society of Chemistry, Cambridge, UNITED KINGDOM; Thomson Reuters HealthCare and Science, Philadelphia, PA...

76 FR 57757 - Endangered Species; Receipt of Applications for Permit

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-16

....) held in zoos in the United States to the Department of Anthropology, University of Cambridge, Cambridge... activities to be conducted by the applicant over a 5-year period. Applicant: Los Angeles Zoo and Botanical...

Validity of a short questionnaire to assess physical activity in 10 European countries.

PubMed

Peters, Tricia; Brage, Soren; Westgate, Kate; Franks, Paul W; Gradmark, Anna; Tormo Diaz, Maria Jose; Huerta, Jose Maria; Bendinelli, Benedetta; Vigl, Mattheaus; Boeing, Heiner; Wendel-Vos, Wanda; Spijkerman, Annemieke; Benjaminsen-Borch, Kristin; Valanou, Elisavet; de Lauzon Guillain, Blandine; Clavel-Chapelon, Françoise; Sharp, Stephen; Kerrison, Nicola; Langenberg, Claudia; Arriola, Larraitz; Barricarte, Aurelio; Gonzales, Carlos; Grioni, Sara; Kaaks, Rudolf; Key, Timothy; Khaw, Kay Tee; May, Anne; Nilsson, Peter; Norat, Teresa; Overvad, Kim; Palli, Domenico; Panico, Salvatore; Ramón Quirós, Jose; Ricceri, Fulvio; Sanchez, Maria-Jose; Slimani, Nadia; Tjonneland, Anne; Tumino, Rosario; Feskins, Edith; Riboli, Elio; Ekelund, Ulf; Wareham, Nick

2012-01-01

To accurately examine associations of physical activity (PA) with disease outcomes, a valid method of assessing free-living activity is required. We examined the validity of a brief PA questionnaire (PAQ) used in the European Prospective Investigation into Cancer and Nutrition (EPIC). PA energy expenditure (PAEE) and time spent in moderate and vigorous physical activity (MVPA) was measured in 1,941 healthy individuals from 10 European countries using individually-calibrated combined heart-rate and movement sensing. Participants also completed the short EPIC-PAQ, which refers to past year's activity. Pearson (r) and Spearman (σ) correlation coefficients were calculated for each country, and random effects meta-analysis was used to calculate the combined correlation across countries to estimate the validity of two previously- and one newly-derived ordered, categorical PA indices ("Cambridge index", "total PA index", and "recreational index") that categorized individuals as inactive, moderately inactive, moderately active, or active. The strongest associations with PAEE and MVPA were observed for the Cambridge index (r = 0.33 and r = 0.25, respectively). No significant heterogeneity by country was observed for this index (I(2) = 36.3%, P = 0.12; I(2) = 0.0%, P = 0.85), whereas heterogeneity was suggested for other indices (I(2) > 48%, P < 0.05, I(2) > 47%, P < 0.05). PAEE increased linearly across self-reported PA categories (P for trend <0.001), with an average difference of approximately 460 kJ/d for men and 365 kJ/d for women, between categories of the Cambridge index. The EPIC-PAQ is suitable for categorizing European men and women into four distinct categories of overall physical activity. The difference in PAEE between categories may be useful when estimating effect sizes from observational research.

On the rationality of cycling in the Theory of Moves framework

NASA Astrophysics Data System (ADS)

Olsen, Jolie; Sen, Sandip

2014-04-01

Theory of Moves (TOM) is a novel approach to game theory for determining rational strategies during the play of dynamic games [Brams, S J. (1994). Theory of moves. Cambridge, UK: Cambridge University Press]. While alternate models such as normal form games exist, players of these games are limited to single shot interactions with each other, but within TOM, sequences of moves and counter moves are allowed. As a consequence of this framework potential cyclic behaviour may arise. Unfortunately, standard TOM framework suggests that players do not move from the initial state if the possibility of cyclic behaviour is detected. However, in a plethora of real life scenarios, cycling can benefit a player over time. We first extend the TOM framework by allowing players to choose how much time to stay in each state while specifying time limits for moves. This generalisation allows for cycling behaviour in addition to normal, acyclic TOM play. We present additional rationality rules to handle the choice of move time and cyclic play and identify conditions for the existence of solutions that involve cycles. Moreover, if solutions do exist, equilibrium are determined so a player can predict the rational outcome upon engaging a cycle. A variety of time constraints on move times are investigated and the effects of these contrasts on the solution space and equilibrium are analysed.

Cambridge Safer Truck Initiative : Vehicle-Based Strategies to Protect Pedestrians and Bicyclists

DOT National Transportation Integrated Search

2016-03-01

This report summarizes Volpe, The National Transportation Systems Centers (Volpes) research and recommendations for the City of Cambridge for implementing a number of proven vehicle safety strategies, including truck side guards, blind spot mir...

Theory of Effectiveness Measurement

DTIC Science & Technology

2006-09-01

features, or properties). These attributes can be either directly or indirectly observable ( Cropley , 1998:238). Additionally, a system embodies a set...John Shawe-Taylor, An Introduction to Support Vector Machines, Cambridge University Press, Cambridge, 2000. Cropley , D. H., “Towards Formulating a

Quark enables semi-reference-based compression of RNA-seq data.

PubMed

Sarkar, Hirak; Patro, Rob

2017-11-01

The past decade has seen an exponential increase in biological sequencing capacity, and there has been a simultaneous effort to help organize and archive some of the vast quantities of sequencing data that are being generated. Although these developments are tremendous from the perspective of maximizing the scientific utility of available data, they come with heavy costs. The storage and transmission of such vast amounts of sequencing data is expensive. We present Quark, a semi-reference-based compression tool designed for RNA-seq data. Quark makes use of a reference sequence when encoding reads, but produces a representation that can be decoded independently, without the need for a reference. This allows Quark to achieve markedly better compression rates than existing reference-free schemes, while still relieving the burden of assuming a specific, shared reference sequence between the encoder and decoder. We demonstrate that Quark achieves state-of-the-art compression rates, and that, typically, only a small fraction of the reference sequence must be encoded along with the reads to allow reference-free decompression. Quark is implemented in C ++11, and is available under a GPLv3 license at www.github.com/COMBINE-lab/quark. rob.patro@cs.stonybrook.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

The Release 6 reference sequence of the Drosophila melanogaster genome

DOE PAGES

Hoskins, Roger A.; Carlson, Joseph W.; Wan, Kenneth H.; ...

2015-01-14

Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy andmore » middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. In conclusion, further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.« less

The Release 6 reference sequence of the Drosophila melanogaster genome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoskins, Roger A.; Carlson, Joseph W.; Wan, Kenneth H.

Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy andmore » middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. In conclusion, further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.« less

A tree island approach to inferring phylogeny in the ant subfamily Formicinae, with especial reference to the evolution of weaving.

PubMed

Johnson, Rebecca N; Agapow, Paul-Michael; Crozier, Ross H

2003-11-01

The ant subfamily Formicinae is a large assemblage (2458 species (J. Nat. Hist. 29 (1995) 1037), including species that weave leaf nests together with larval silk and in which the metapleural gland-the ancestrally defining ant character-has been secondarily lost. We used sequences from two mitochondrial genes (cytochrome b and cytochrome oxidase 2) from 18 formicine and 4 outgroup taxa to derive a robust phylogeny, employing a search for tree islands using 10000 randomly constructed trees as starting points and deriving a maximum likelihood consensus tree from the ML tree and those not significantly different from it. Non-parametric bootstrapping showed that the ML consensus tree fit the data significantly better than three scenarios based on morphology, with that of Bolton (Identification Guide to the Ant Genera of the World, Harvard University Press, Cambridge, MA) being the best among these alternative trees. Trait mapping showed that weaving had arisen at least four times and possibly been lost once. A maximum likelihood analysis showed that loss of the metapleural gland is significantly associated with the weaver life-pattern. The graph of the frequencies with which trees were discovered versus their likelihood indicates that trees with high likelihoods have much larger basins of attraction than those with lower likelihoods. While this result indicates that single searches are more likely to find high- than low-likelihood tree islands, it also indicates that searching only for the single best tree may lose important information.

12. Historic American Buildings Survey Photocopy of ink on linen ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

12. Historic American Buildings Survey Photocopy of ink on linen drawing dated 1878, Longfellow & Clark, in possession of owner, 70 Sparks Street, Cambridge Street, Massachusetts ATTIC PLAN - Edward S. Dodge House, 70 Sparks Street, Cambridge, Middlesex County, MA

11. Historic American Buildings Survey Photocopy of ink on linen ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

11. Historic American Buildings Survey Photocopy of ink on linen drawing dated 1878, Longfellow & Clark, in possession of owner, 70 Sparks Street, Cambridge Street, Massachusetts SECOND FLOOR PLAN - Edward S. Dodge House, 70 Sparks Street, Cambridge, Middlesex County, MA

9. Historic American Buildings Survey Photocopy of ink on linen ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

9. Historic American Buildings Survey Photocopy of ink on linen drawing dated 1878, Longfellow & Clark, in possession of owner, 70 Sparks Street, Cambridge Street, Massachusetts BASEMENT PLAN - Edward S. Dodge House, 70 Sparks Street, Cambridge, Middlesex County, MA

10. Historic American Buildings Survey Photocopy of ink on linen ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

10. Historic American Buildings Survey Photocopy of ink on linen drawing dated 1878, Longfellow & Clark, in possession of owner, 70 Sparks Street, Cambridge Street, Massachusetts FIRST FLOOR PLAN - Edward S. Dodge House, 70 Sparks Street, Cambridge, Middlesex County, MA

6. Historic American Buildings Survey Photocopy of ink on linen ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

6. Historic American Buildings Survey Photocopy of ink on linen drawing dated 1878, Longfellow & Clark, in possession of owner, 70 Sparks Street, Cambridge Street, Massachusetts SOUTH ELEVATION DRAWING - Edward S. Dodge House, 70 Sparks Street, Cambridge, Middlesex County, MA

7. Historic American Buildings Survey Photocopy of ink on linen ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

7. Historic American Buildings Survey Photocopy of ink on linen drawing dated 1878, Longfellow & Clark, in possession of owner, 70 Sparks Street, Cambridge Street, Massachusetts EAST ELEVATION DRAWING - Edward S. Dodge House, 70 Sparks Street, Cambridge, Middlesex County, MA

8. Historic American Buildings Survey Photocopy of ink on linen ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

8. Historic American Buildings Survey Photocopy of ink on linen drawing dated 1878, Longfellow & Clark, in possession of owner, 70 Sparks Street, Cambridge Street, Massachusetts NORTH ELEVATION DRAWING - Edward S. Dodge House, 70 Sparks Street, Cambridge, Middlesex County, MA

5. Historic American Buildings Survey Photocopy of ink on linen ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

5. Historic American Buildings Survey Photocopy of ink on linen drawing dated 1878, Longfellow & Clark, in possession of owner, 70 Sparks Street, Cambridge Street, Massachusetts WEST ELEVATION DRAWING - Edward S. Dodge House, 70 Sparks Street, Cambridge, Middlesex County, MA

Some reminiscences about my early career

NASA Astrophysics Data System (ADS)

Domb, Cyril

1990-09-01

The author recalls some of the highlights of his scientific career before he took up a professional appointment at King's College, London in 1954. The periods covered are: High School and undergraduate studies at Cambridge University 1932-1941; radar research for the British Admiralty 1941-1946; graduate studies at Cambridge University 1946-1949; post-doctoral research at the Clarendon Laboratory, Oxford University 1949-1952; faculty appointment at Cambridge University 1952-1954. A brief description is given of the personalities with whom the author was associated, the research problems in which he was involved, and of the early post world war 2 scientific conferences.

Water quality in the Cambridge, Massachusetts, drinking-water source area, 2005-8

USGS Publications Warehouse

Smith, Kirk P.; Waldron, Marcus C.

2015-01-01

During 2005-8, the U.S. Geological Survey, in cooperation with the Cambridge, Massachusetts, Water Department, measured concentrations of sodium and chloride, plant nutrients, commonly used pesticides, and caffeine in base-flow and stormwater samples collected from 11 tributaries in the Cambridge drinking-water source area. These data were used to characterize current water-quality conditions, to establish a baseline for future comparisons, and to describe trends in surface-water quality. The data also were used to assess the effects of watershed characteristics on surface-water quality and to inform future watershed management.

Reconstructing the History of Mesoamerican Populations through the Study of the Mitochondrial DNA Control Region

PubMed Central

Gorostiza, Amaya; Acunha-Alonzo, Víctor; Regalado-Liu, Lucía; Tirado, Sergio; Granados, Julio; Sámano, David; Rangel-Villalobos, Héctor; González-Martín, Antonio

2012-01-01

The study of genetic information can reveal a reconstruction of human population’s history. We sequenced the entire mtDNA control region (positions 16.024 to 576 following Cambridge Reference Sequence, CRS) of 605 individuals from seven Mesoamerican indigenous groups and one Aridoamerican from the Greater Southwest previously defined, all of them in present Mexico. Samples were collected directly from the indigenous populations, the application of an individual survey made it possible to remove related or with other origins samples. Diversity indices and demographic estimates were calculated. Also AMOVAs were calculated according to different criteria. An MDS plot, based on FST distances, was also built. We carried out the construction of individual networks for the four Amerindian haplogroups detected. Finally, barrier software was applied to detect genetic boundaries among populations. The results suggest: a common origin of the indigenous groups; a small degree of European admixture; and inter-ethnic gene flow. The process of Mesoamerica’s human settlement took place quickly influenced by the region’s orography, which development of genetic and cultural differences facilitated. We find the existence of genetic structure is related to the region’s geography, rather than to cultural parameters, such as language. The human population gradually became fragmented, though they remained relatively isolated, and differentiated due to small population sizes and different survival strategies. Genetic differences were detected between Aridoamerica and Mesoamerica, which can be subdivided into “East”, “Center”, “West” and “Southeast”. The fragmentation process occurred mainly during the Mesoamerican Pre-Classic period, with the Otomí being one of the oldest groups. With an increased number of populations studied adding previously published data, there is no change in the conclusions, although significant genetic heterogeneity can be detected in Pima and Huichol groups. This result may be explained because populations historically assigned as belonging to the same group were, in fact, different indigenous populations. PMID:23028577

Mitochondrial DNA mutation screening of male patients with obstructive sleep apnea-hypopnea syndrome.

PubMed

Huang, Xiao-Ying; Li, Hong; Xu, Xiao-Mei; Wang, Liang-Xing

2014-08-01

The aim of the present study was to analyze the differences between the genes of the mitochondrial DNA (mtDNA) displacement loop (D-loop) region and the Cambridge Reference sequence, in order to screen the mutation sites and investigate the correlation between mutations, clinical parameters and complications associated with obstructive sleep apnea-hypopnea syndrome (OSAHS). mtDNA was obtained from male patients with OSAHS in the Zhejiang Province. In total, 60 male patients with OSAHS and 102 healthy adults were assessed to determine the levels of fasting blood glucose, total cholesterol, triglyceride (TG) and high-density and low-density lipoproteins (LDL). Furthermore, peripheral mtDNA was extracted and bidirectional sequencing was conducted to enable mutation screening. In the mtDNA D-loop region, 178 mutation sites were identified, of which 115 sites were present in the two groups. The number of non-common sites in the OSAHS group was significantly higher compared with the control group (P<0.05). No statistically significant difference was observed in the mutations among the mild, moderate and severe OSAHS groups (P>0.05). A total of 21 cases in the severe OSAHS group exhibited mutation rates of >10%. In the control group, there were 24 cases where the np73A-G and np263A-G mutations were predominant. The np303-np315 region was identified to be the highly variable region and various mutation forms were observed. Statistically significant differences were observed in the neck perimeter, TG and LDL levels among the OSAHS-no-mutation subgroups (P<0.05) and LDL was shown to be associated with an mtDNA mutation in the OSAHS group. Numerous polymorphic mutation sites were identified in the mtDNA D-loop region of the OSAHS group. Therefore, mtDNA mutation sites may be closely associated with the clinical manifestations and complications of OSAHS.

4. July 1971. AERIAL RECONNAISSANCE II, ERIE RAILWAY SURVEY. ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

4. July 1971. AERIAL RECONNAISSANCE II, ERIE RAILWAY SURVEY. - Erie Railway, Parallel French Creek Bridges, 100 feet South of Millers Station Road, 0.4 mile Northeast of State Route 408, 0.9 mile East of Cambridge Springs, Cambridge Springs, Crawford County, PA

2. July 1971. AERIAL RECONNAISSANCE II, ERIE RAILWAY SURVEY. ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

2. July 1971. AERIAL RECONNAISSANCE II, ERIE RAILWAY SURVEY. - Erie Railway, Parallel French Creek Bridges, 100 feet South of Millers Station Road, 0.4 mile Northeast of State Route 408, 0.9 mile East of Cambridge Springs, Cambridge Springs, Crawford County, PA

3. July 1971. AERIAL RECONNAISSANCE II, ERIE RAILWAY SURVEY. ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

3. July 1971. AERIAL RECONNAISSANCE II, ERIE RAILWAY SURVEY. - Erie Railway, Parallel French Creek Bridges, 100 feet South of Millers Station Road, 0.4 mile Northeast of State Route 408, 0.9 mile East of Cambridge Springs, Cambridge Springs, Crawford County, PA

1. July 1971. AERIAL RECONNAISSANCE II, ERIE RAILWAY SURVEY. ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

1. July 1971. AERIAL RECONNAISSANCE II, ERIE RAILWAY SURVEY. - Erie Railway, Parallel French Creek Bridges, 100 feet South of Millers Station Road, 0.4 mile Northeast of State Route 408, 0.9 mile East of Cambridge Springs, Cambridge Springs, Crawford County, PA

Cambridge Desegregation Succeeding.

ERIC Educational Resources Information Center

Alves, Michael

1983-01-01

This paper provides an overview of the controversy concerning "freedom of choice" desegregation plans and presents a case study of the plan adopted by Cambridge, Massachusetts, in 1981. Following the introduction, a short explanation of the plan's distinctive feature, controlled open enrollment, is given. (Under controlled open…

Ecology for conserving our sirenians

USGS Publications Warehouse

Bonde, Robert K.

2012-01-01

Review of: Ecology and conservation of the sirenia: dugongs and manatees. Helene Marsh, Thomas J. O'Shea and John E. Reynolds III. Cambridge University Press, Cambridge, 2012, 521 pp, ISBN 978-0-521-88828-8, US$135 and 978-0-521-71643-7, US$65.

It’s More Than Stamp Collecting: How Genome Sequencing Can Unify Biological Research

PubMed Central

Richards, Stephen

2015-01-01

The availability of reference genome sequences, especially the human reference, has revolutionized the study of biology. However, whilst the genomes of some species have been fully sequenced, a wide range of biological problems still cannot be effectively studied for lack of genome sequence information. Here, I identify neglected areas of biology and describe how both targeted species sequencing and more broad taxonomic surveys of the tree of life can address important biological questions. I enumerate the significant benefits that would accrue from sequencing a broader range of taxa, as well as discuss the technical advances in sequencing and assembly methods that would allow for wide-ranging application of whole-genome analysis. Finally, I suggest that in addition to “Big Science” survey initiatives to sequence the tree of life, a modified infrastructure-funding paradigm would better support reference genome sequence generation for research communities most in need. PMID:26003218

It's more than stamp collecting: how genome sequencing can unify biological research.

PubMed

Richards, Stephen

2015-07-01

The availability of reference genome sequences, especially the human reference, has revolutionized the study of biology. However, while the genomes of some species have been fully sequenced, a wide range of biological problems still cannot be effectively studied for lack of genome sequence information. Here, I identify neglected areas of biology and describe how both targeted species sequencing and more broad taxonomic surveys of the tree of life can address important biological questions. I enumerate the significant benefits that would accrue from sequencing a broader range of taxa, as well as discuss the technical advances in sequencing and assembly methods that would allow for wide-ranging application of whole-genome analysis. Finally, I suggest that in addition to 'big science' survey initiatives to sequence the tree of life, a modified infrastructure-funding paradigm would better support reference genome sequence generation for research communities most in need. Copyright © 2015 Elsevier Ltd. All rights reserved.

Whole Genome Sequencing of Greater Amberjack (Seriola dumerili) for SNP Identification on Aligned Scaffolds and Genome Structural Variation Analysis Using Parallel Resequencing

PubMed Central

Aokic, Jun-ya; Kawase, Junya; Hamada, Kazuhisa; Fujimoto, Hiroshi; Yamamoto, Ikki; Usuki, Hironori

2018-01-01

Greater amberjack (Seriola dumerili) is distributed in tropical and temperate waters worldwide and is an important aquaculture fish. We carried out de novo sequencing of the greater amberjack genome to construct a reference genome sequence to identify single nucleotide polymorphisms (SNPs) for breeding amberjack by marker-assisted or gene-assisted selection as well as to identify functional genes for biological traits. We obtained 200 times coverage and constructed a high-quality genome assembly using next generation sequencing technology. The assembled sequences were aligned onto a yellowtail (Seriola quinqueradiata) radiation hybrid (RH) physical map by sequence homology. A total of 215 of the longest amberjack sequences, with a total length of 622.8 Mbp (92% of the total length of the genome scaffolds), were lined up on the yellowtail RH map. We resequenced the whole genomes of 20 greater amberjacks and mapped the resulting sequences onto the reference genome sequence. About 186,000 nonredundant SNPs were successfully ordered on the reference genome. Further, we found differences in the genome structural variations between two greater amberjack populations using BreakDancer. We also analyzed the greater amberjack transcriptome and mapped the annotated sequences onto the reference genome sequence. PMID:29785397

Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling

PubMed Central

Chang, Chun-Tien; Tsai, Chi-Neu; Tang, Chuan Yi; Chen, Chun-Houh; Lian, Jang-Hau; Hu, Chi-Yu; Tsai, Chia-Lung; Chao, Angel; Lai, Chyong-Huey; Wang, Tzu-Hao; Lee, Yun-Shien

2012-01-01

The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3. PMID:22778697

Reference-guided assembly of four diverse Arabidopsis thaliana genomes

PubMed Central

Schneeberger, Korbinian; Ossowski, Stephan; Ott, Felix; Klein, Juliane D.; Wang, Xi; Lanz, Christa; Smith, Lisa M.; Cao, Jun; Fitz, Joffrey; Warthmann, Norman; Henz, Stefan R.; Huson, Daniel H.; Weigel, Detlef

2011-01-01

We present whole-genome assemblies of four divergent Arabidopsis thaliana strains that complement the 125-Mb reference genome sequence released a decade ago. Using a newly developed reference-guided approach, we assembled large contigs from 9 to 42 Gb of Illumina short-read data from the Landsberg erecta (Ler-1), C24, Bur-0, and Kro-0 strains, which have been sequenced as part of the 1,001 Genomes Project for this species. Using alignments against the reference sequence, we first reduced the complexity of the de novo assembly and later integrated reads without similarity to the reference sequence. As an example, half of the noncentromeric C24 genome was covered by scaffolds that are longer than 260 kb, with a maximum of 2.2 Mb. Moreover, over 96% of the reference genome was covered by the reference-guided assembly, compared with only 87% with a complete de novo assembly. Comparisons with 2 Mb of dideoxy sequence reveal that the per-base error rate of the reference-guided assemblies was below 1 in 10,000. Our assemblies provide a detailed, genomewide picture of large-scale differences between A. thaliana individuals, most of which are difficult to access with alignment-consensus methods only. We demonstrate their practical relevance in studying the expression differences of polymorphic genes and show how the analysis of sRNA sequencing data can lead to erroneous conclusions if aligned against the reference genome alone. Genome assemblies, raw reads, and further information are accessible through http://1001genomes.org/projects/assemblies.html. PMID:21646520

A de novo transcriptome and valid reference genes for quantitative real-time PCR in Colaphellus bowringi.

PubMed

Tan, Qian-Qian; Zhu, Li; Li, Yi; Liu, Wen; Ma, Wei-Hua; Lei, Chao-Liang; Wang, Xiao-Ping

2015-01-01

The cabbage beetle Colaphellus bowringi Baly is a serious insect pest of crucifers and undergoes reproductive diapause in soil. An understanding of the molecular mechanisms of diapause regulation, insecticide resistance, and other physiological processes is helpful for developing new management strategies for this beetle. However, the lack of genomic information and valid reference genes limits knowledge on the molecular bases of these physiological processes in this species. Using Illumina sequencing, we obtained more than 57 million sequence reads derived from C. bowringi, which were assembled into 39,390 unique sequences. A Clusters of Orthologous Groups classification was obtained for 9,048 of these sequences, covering 25 categories, and 16,951 were assigned to 255 Kyoto Encyclopedia of Genes and Genomes pathways. Eleven candidate reference gene sequences from the transcriptome were then identified through reverse transcriptase polymerase chain reaction. Among these candidate genes, EF1α, ACT1, and RPL19 proved to be the most stable reference genes for different reverse transcriptase quantitative polymerase chain reaction experiments in C. bowringi. Conversely, aTUB and GAPDH were the least stable reference genes. The abundant putative C. bowringi transcript sequences reported enrich the genomic resources of this beetle. Importantly, the larger number of gene sequences and valid reference genes provide a valuable platform for future gene expression studies, especially with regard to exploring the molecular mechanisms of different physiological processes in this species.

Point Picking and Distributing on the Disc and Sphere

DTIC Science & Technology

2015-07-01

interesting application of geodesic subdivision is the design of domes, buildings, and structures (e.g., Spaceship Earth14 at Epcot, Walt Disney World; the...Computational Geometry in C. Cambridge (United Kingdom): Cambridge University Press; 1993. 41 14. Spaceship Earth. Walt Disney World; [accessed 2014

A Cognitive Architecture for Solving Ill-Structured Problems

DTIC Science & Technology

1997-08-01

R. C. (1982). Dynamic memory. Cambridge, Mass.: Cambridge University Press. Selfridge, 0. G., & Neisser , U . (1960). Pattern recognition by machine...Page 1 . In tro d u ctio n...1 1.1 Relevance to the ARI M ission ............................................................................... 1 1.2 Components of Analogy U se

A Robust Method of Measuring Other-Race and Other-Ethnicity Effects: The Cambridge Face Memory Test Format

PubMed Central

McKone, Elinor; Stokes, Sacha; Liu, Jia; Cohan, Sarah; Fiorentini, Chiara; Pidcock, Madeleine; Yovel, Galit; Broughton, Mary; Pelleg, Michel

2012-01-01

Other-race and other-ethnicity effects on face memory have remained a topic of consistent research interest over several decades, across fields including face perception, social psychology, and forensic psychology (eyewitness testimony). Here we demonstrate that the Cambridge Face Memory Test format provides a robust method for measuring these effects. Testing the Cambridge Face Memory Test original version (CFMT-original; European-ancestry faces from Boston USA) and a new Cambridge Face Memory Test Chinese (CFMT-Chinese), with European and Asian observers, we report a race-of-face by race-of-observer interaction that was highly significant despite modest sample size and despite observers who had quite high exposure to the other race. We attribute this to high statistical power arising from the very high internal reliability of the tasks. This power also allows us to demonstrate a much smaller within-race other ethnicity effect, based on differences in European physiognomy between Boston faces/observers and Australian faces/observers (using the CFMT-Australian). PMID:23118912

Handbook Of X-ray Astronomy

NASA Astrophysics Data System (ADS)

Arnaud, Keith A.; Smith, R. K.; Siemiginowska, A.; Edgar, R. J.; Grant, C. E.; Kuntz, K. D.; Schwartz, D. A.

2011-09-01

This poster advertises a book to be published in September 2011 by Cambridge University Press. Written for graduate students, professional astronomers and researchers who want to start working in this field, this book is a practical guide to x-ray astronomy. The handbook begins with x-ray optics, basic detector physics and CCDs, before focussing on data analysis. It introduces the reduction and calibration of x-ray data, scientific analysis, archives, statistical issues and the particular problems of highly extended sources. The book describes the main hardware used in x-ray astronomy, emphasizing the implications for data analysis. The concepts behind common x-ray astronomy data analysis software are explained. The appendices present reference material often required during data analysis.

Two new species of the genus Paramitraceras Pickard-Cambridge, 1905 (Opiliones: Laniatores: Stygnopsidae) from Chiapas, Mexico.

PubMed

Cruz-López, Jesús A; Francke, Oscar F

2013-01-01

Parainitraceras pickardcanibridgei sp. nov. and Paramitraceras tzotzil sp. nov. from Chiapas, Mexico are described based on specimens previously determined as Paramitraceras granulatum Pickard-Cambridge, 1905 by Goodnight and Goodnight. The male genitalia of the new species and P. granulatum are illustrated with scanning electronic micrographs (SEMs) or drawings derived from them. The importance of the ocular tubercle, cheliceral dentition and sexual dimorphism, pedipalpal armature and male genitalia as taxonomic characters within the genus is discussed as well as differences and similarities between Paramitraceras Pickard-Cambridge, 1905 and its most similar genus, Sbordonia Šilhavý, 1977.

Spatial profiles of methane at the Swiss Plateau: A confrontation between measurements and emission inventories.

NASA Astrophysics Data System (ADS)

Bamberger, Ines; Eugster, Werner; Buchmann, Nina

2013-04-01

Methane and carbon dioxide are the two most prominent greenhouse gases in the atmosphere and a detailed knowledge about their sources is essential for climate predictions (Solomon et al., 2007). The knowledge about greenhouse gas fluxes is usually merged, albeit including considerable uncertainties, to emission inventories. To increase the quality of the inventories a comparison with measurements is necessary. We evaluate the values given by a Swiss emission inventory with regard to atmospheric measurements of methane in Switzerland. Spatial profiles of carbon dioxide and methane were investigated at the Swiss Plateau during two consecutive warm and sunny summer days in July 2012. For the mobile methane and carbon dioxide measurements a LGR methane analyser and a LI-COR closed-path infrared gas analyser (IRGA) were mounted on a car together with an AIRMAR WeatherStation to track geodetic-coordinates and meteorological parameters. First results of the measurements including aerial profiles of the greenhouse gases and bin-averaged elevation profiles of methane and temperature will be presented and a highly-resolved methane emission inventory will be evaluated in comparison with the spatial profiles of atmospheric methane at the Swiss Plateau. References: Solomon, S., Qin D., et al. (Eds.) (2007) Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change, 996 S. pp., Cambridge University Press, Cambridge.

Assessing public aesthetic preferences towards some urban landscape patterns: the case study of two different geographic groups.

PubMed

Chen, Ziyue; Xu, Bing; Devereux, Bernard

2016-01-01

Landscape aesthetics is closely linked to people's daily life, and a large body of studies has been conducted to understand the public's landscape preferences. These studies commonly focused on comprehensive landscape configuration, yet limited emphasis was placed on the patterns of individual landscape features. This research explored people's preferences towards the composition and patterns of some specific urban features. Questionnaire-based survey was conducted in two cities: Cambridge, UK and Nanjing, China and more than 180 responses were collected, respectively. Respondents from both sites showed similar preferences towards freely growing trees, individual houses, gable roofs and mixed design of green spaces. On the other hand, respondents from Cambridge and Nanjing have different preferences towards the height of trees, the size of green spaces, and the height diversity of buildings. This survey also proved that the factors of age, education, status and length of living have larger influences on landscape preferences than the factors of gender, and major. Furthermore, strong correlations were found between people's aesthetic preferences towards comparative landscape patterns, building types, tree shapes and roof structures. The existence of generally shared landscape preferences makes it feasible to conduct international and standardized projects for acquiring comparable and transferable criteria. The methodology and findings of this research provides landscape planners and decision makers with useful reference to compare, evaluate and improve urban landscape configurations to meet people's needs.

The Ancients' Appliance of Science

ERIC Educational Resources Information Center

Stephenson, Philip; Sword, Frances

2004-01-01

An innovative collaboration between the Fitzwilliam Museum in Cambridge and the University of Cambridge Faculty of Education encourages new questions to be asked of ancient objects. In the museum galleries children work directly from ancient Egyptian objects through activities designed to encourage questioning that unpicks the technologies of the…

An Alternative Approach to the Variable Housing Allowance Program

DTIC Science & Technology

1987-01-01

ACOL values. 1T CBO, p. 31. tm Angus Deaton and John Muellbauer, Economics and Consumer Behavior (New York: Cambridge University Press, 1980), p...London: Chapman and Hall, 1975. Deaton A. S. and J. Muellbauer. Economics and Consumer Behavior . New York« Cambridge University Press, 1980

Neural Networks Applied to Signal Processing

DTIC Science & Technology

1989-09-01

Distributed Processing, The MIT Press, Cambridge, MA, 1988. 3. Marvin Minsky and Seymour Papert, Perceptrons, The MIT Press, Cambridge, MA, 1969. 4...signum function, the linear function, and the sigmoid function. Initial research conducted in the 1950’s and 1960’s by Rosenblat, Minsky and others used

Rhetorical Structure of Biochemistry Research Articles

ERIC Educational Resources Information Center

Kanoksilapatham, Budsaba

2005-01-01

This paper reports on the results of a move analysis [Swales, J. (1990). "Genre analysis." Cambridge: Cambridge University Press] of 60 biochemistry research articles. First, a corpus was systematically compiled to ensure that it represents core journals in the focused discipline. Then, coding reliability analysis was conducted to…

77 FR 46120 - Notice of Inventory Completion: Peabody Museum of Archaeology and Ethnology, Harvard University...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-02

... Inventory Completion: Peabody Museum of Archaeology and Ethnology, Harvard University, Cambridge, MA... Museum of Archaeology and Ethnology, Harvard University, Cambridge, MA. The human remains and associated..., Repatriation Coordinator, Peabody Museum of Archaeology and Ethnology, Harvard University, 11 Divinity Avenue...

76 FR 5829 - Manufacturer of Controlled Substances; Notice of Registration

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-02

... 1, 2010, 75 FR 53719, Cambridge Isotope Lab, 50 Frontage Road, Andover, Massachusetts 01810, made... determined that the registration of Cambridge Isotope Lab to manufacture the listed basic class of controlled substance is consistent with the public interest at this time. DEA has [[Page 5830

Gradations of awareness in a modified sequence learning task.

PubMed

Norman, Elisabeth; Price, Mark C; Duff, Simon C; Mentzoni, Rune A

2007-12-01

We argue performance in the serial reaction time (SRT) task is associated with gradations of awareness that provide examples of fringe consciousness [Mangan, B. (1993b). Taking phenomenology seriously: the "fringe" and its implications for cognitive research. Consciousness and Cognition, 2, 89-108, Mangan, B. (2003). The conscious "fringe": Bringing William James up to date. In B. J. Baars, W. P. Banks & J. B. Newman (Eds.), Essential sources in the scientific study of consciousness (pp. 741-759). Cambridge, MA: The MIT Press.], and address limitations of the traditional SRT procedure, including criticism of exclusion generation tasks. Two experiments are conducted with a modified SRT procedure where irrelevant stimulus attributes obscure the sequence rule. Our modified paradigm, which includes a novel exclusion task, makes it easier to demonstrate a previously controversial influence of response stimulus interval (RSI) on awareness. It also allows identification of participants showing fringe consciousness rather than explicit sequence knowledge, as reflected by dissociations between different awareness measures. The NEO-PI-R variable Openness to Feelings influenced the diversity of subjective feelings reported during two awareness measures, but not the degree of learning and awareness as previously found with traditional SRT tasks [Norman, E., Price, M. C., & Duff, S. C. (2006). Fringe consciousness in sequence learning: the influence of individual differences. Consciousness and Cognition, 15(4), 723-760.]. This suggests possible distinctions between two components of fringe consciousness.

Consequences of splitting whole-genome sequencing effort over multiple breeds on imputation accuracy.

PubMed

Bouwman, Aniek C; Veerkamp, Roel F

2014-10-03

The aim of this study was to determine the consequences of splitting sequencing effort over multiple breeds for imputation accuracy from a high-density SNP chip towards whole-genome sequence. Such information would assist for instance numerical smaller cattle breeds, but also pig and chicken breeders, who have to choose wisely how to spend their sequencing efforts over all the breeds or lines they evaluate. Sequence data from cattle breeds was used, because there are currently relatively many individuals from several breeds sequenced within the 1,000 Bull Genomes project. The advantage of whole-genome sequence data is that it carries the causal mutations, but the question is whether it is possible to impute the causal variants accurately. This study therefore focussed on imputation accuracy of variants with low minor allele frequency and breed specific variants. Imputation accuracy was assessed for chromosome 1 and 29 as the correlation between observed and imputed genotypes. For chromosome 1, the average imputation accuracy was 0.70 with a reference population of 20 Holstein, and increased to 0.83 when the reference population was increased by including 3 other dairy breeds with 20 animals each. When the same amount of animals from the Holstein breed were added the accuracy improved to 0.88, while adding the 3 other breeds to the reference population of 80 Holstein improved the average imputation accuracy marginally to 0.89. For chromosome 29, the average imputation accuracy was lower. Some variants benefitted from the inclusion of other breeds in the reference population, initially determined by the MAF of the variant in each breed, but even Holstein specific variants did gain imputation accuracy from the multi-breed reference population. This study shows that splitting sequencing effort over multiple breeds and combining the reference populations is a good strategy for imputation from high-density SNP panels towards whole-genome sequence when reference populations are small and sequencing effort is limiting. When sequencing effort is limiting and interest lays in multiple breeds or lines this provides imputation of each breed.

Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses

PubMed Central

Pightling, Arthur W.; Petronella, Nicholas; Pagotto, Franco

2014-01-01

The wide availability of whole-genome sequencing (WGS) and an abundance of open-source software have made detection of single-nucleotide polymorphisms (SNPs) in bacterial genomes an increasingly accessible and effective tool for comparative analyses. Thus, ensuring that real nucleotide differences between genomes (i.e., true SNPs) are detected at high rates and that the influences of errors (such as false positive SNPs, ambiguously called sites, and gaps) are mitigated is of utmost importance. The choices researchers make regarding the generation and analysis of WGS data can greatly influence the accuracy of short-read sequence alignments and, therefore, the efficacy of such experiments. We studied the effects of some of these choices, including: i) depth of sequencing coverage, ii) choice of reference-guided short-read sequence assembler, iii) choice of reference genome, and iv) whether to perform read-quality filtering and trimming, on our ability to detect true SNPs and on the frequencies of errors. We performed benchmarking experiments, during which we assembled simulated and real Listeria monocytogenes strain 08-5578 short-read sequence datasets of varying quality with four commonly used assemblers (BWA, MOSAIK, Novoalign, and SMALT), using reference genomes of varying genetic distances, and with or without read pre-processing (i.e., quality filtering and trimming). We found that assemblies of at least 50-fold coverage provided the most accurate results. In addition, MOSAIK yielded the fewest errors when reads were aligned to a nearly identical reference genome, while using SMALT to align reads against a reference sequence that is ∼0.82% distant from 08-5578 at the nucleotide level resulted in the detection of the greatest numbers of true SNPs and the fewest errors. Finally, we show that whether read pre-processing improves SNP detection depends upon the choice of reference sequence and assembler. In total, this study demonstrates that researchers should test a variety of conditions to achieve optimal results. PMID:25144537

75 FR 16178 - Antitrust Division

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-31

... Production Act of 1993--Joint Venture Agreement Between Cambridge Major Laboratories, Inc. and Konarka... Production Act of 1993, 15 U.S.C. 4301 et seq. (``the Act''), Joint Venture Agreement Between Cambridge Major... to the venture and (2) the nature and objectives of the venture. The notifications were filed for the...

Gendered Language in Interactive Discourse

ERIC Educational Resources Information Center

Hussey, Karen A.; Katz, Albert N.; Leith, Scott A.

2015-01-01

Over two studies, we examined the nature of gendered language in interactive discourse. In the first study, we analyzed gendered language from a chat corpus to see whether tokens of gendered language proposed in the gender-as-culture hypothesis (Maltz and Borker in "Language and social identity." Cambridge University Press, Cambridge, pp…

An Evaluation of the Compressive Properties of Helmet Pads Pre- and Post-Shock Wave Overpressure Exposure

DTIC Science & Technology

2015-08-14

by ANSI Std. Z39.18 BLAST DROP TESTS BRAIN DAMAGE VISCOELASTICITY BRAIN CONCUSSION ...Cambridge, UK: Cambridge University Press, 1997. [5] W. C. Moss and M. J. King, "Impact response of US Army and National Football League helmet pad

Oxbridge Redivivus

ERIC Educational Resources Information Center

Ainley, Patrick

2011-01-01

How the dominance of the two medieval universities, namely, (1) The University of Oxford; and (2) The University of Cambridge, was gained and maintained is the subject of the institutional histories by Gillian Evans. She has long been a thorn in the side of successive Cambridge Vice-Chancellors' aspirations to turn that institution--at which she…

The Linguistically Aware Teacher and the Teacher-Aware Linguist

ERIC Educational Resources Information Center

McCartney, Elspeth; Ellis, Sue

2013-01-01

This review evaluates issues of teacher linguistic knowledge relating to their work with children with speech, language and communication difficulties (SLCD). Information is from Ellis and McCartney [(2011a). "Applied linguistics and primary school teaching." Cambridge: Cambridge University Press], a state-of-the-art text deriving from a British…

Embedding Sustainable Development at Cambridge University Engineering Department

ERIC Educational Resources Information Center

Fenner, Richard A.; Ainger, Charles M.; Cruickshank, Heather J.; Guthrie, Peter M.

2005-01-01

Purpose--The paper seeks to examine the latest stage in a process of change aimed at introducing concepts of sustainable development into the activities of the Department of Engineering at Cambridge University, UK. Design/methodology/approach--The rationale behind defining the skills which future engineers require is discussed and vehicles for…

Consensus Knowledge Acquisition

DTIC Science & Technology

1989-12-01

ex- plicit the logical structure of their positions. Structured frameworks for analyzing 3 SOME USEFUL IDEAS 3 arguments ( Toulmin , 1958; Fogelin, 1982...358-87, 1987. Stefik M, et al., Beyond the chalkboard, CACM, 30:1, Jan 1987, pp. 32-47. Toulmin , S. The Uses of Argument. Cambridge, England: Cambridge University Press, 1958. 01

Dynamics of and Characteristics of Numerical Models of Weakly Nonlinear Flows

DTIC Science & Technology

1997-09-30

for Environmental Science 2020 Horns Point Road PO Box 775 Cambridge, MD 21613-0775 phone: (410) 221-8477 fax: (410) 221-8490 email: walstad...AND ADDRESS(ES) University of Maryland Center for Environmental Science ,Horn Point Laboratory,2020 Horns Point Road,Cambridge,MD,21613-0775 8

New Frontiers: Moving the Humanities Model of Curricular Development.

ERIC Educational Resources Information Center

Grady, Elizabeth

1995-01-01

The American Council of Learned Societies (ACLS) humanities model in the Cambridge (Massachusetts) public schools has significantly affected curricular reform and teacher development. The endeavor is in its third year at the Pilot School, a program within the Cambridge Rindge and Latin School. The article describes progressive reform experiences…

77 FR 3118 - Security Zone; Choptank River and Cambridge Channel, Cambridge, MD

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-23

... security regimes designed to safeguard human life, vessels, and waterfront facilities while still... restriction of vessel traffic is necessary to protect life, property and the environment, therefore, a 30-day... maritime safety and security in order to safeguard life, property, and the environment on or near the...

Cambridge Crystallographic Data Centre. II. Structural Data File

ERIC Educational Resources Information Center

Allen, F. H.; And Others

1973-01-01

The Cambridge Crystallographic Data Centre is concerned with the retrieval, evaluation, synthesis, and dissemination of structural data obtained by diffraction methods. This article (Part I is EJ053033) describes the work of the center and deals with the organization and maintenance of a computerized file of numeric crystallographic structural…

Psychiatry in the Harvard Medical School-Cambridge Integrated Clerkship: An Innovative, Year-Long Program

ERIC Educational Resources Information Center

Griswold, Todd; Bullock, Christopher; Gaufberg, Elizabeth; Albanese, Mark; Bonilla, Pedro; Dvorak, Ramona; Epelbaum, Claudia; Givon, Lior; Kueppenbender, Karsten; Joseph, Robert; Boyd, J. Wesley; Shtasel, Derri

2012-01-01

Objective: The authors present what is to their knowledge the first description of a model for longitudinal third-year medical student psychiatry education. Method: A longitudinal, integrated psychiatric curriculum was developed, implemented, and sustained within the Harvard Medical School-Cambridge Integrated Clerkship. Curriculum elements…

75 FR 58431 - Notice of Inventory Completion: Peabody Museum of Archaeology and Ethnology, Harvard University...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-24

... Archaeology and Ethnology, Harvard University, Cambridge, MA; Correction AGENCY: National Park Service... in the possession of the Peabody Museum of Archaeology and Ethnology, Harvard University, Cambridge... was a project of Harvard University faculty in 1972. No known individuals were identified. No...

The Growth of Economic Studies at Cambridge: 1776-1860.

ERIC Educational Resources Information Center

Rashid, Salim

1980-01-01

Traces the resistance toward establishing an economics curriculum at Cambridge University from 1776 to 1860. Complex reasons include inertia, low intellectual standards, fear of being considered partisan, and avoidance of change during good times. The eventual introduction of economics was achieved only when wholesale reforms were enacted within…

Testing the English of Foreign Students in 1930.

ERIC Educational Resources Information Center

Spolsky, Bernard

Tests of English for foreign students conducted by the University of Cambridge Local Examinations Syndicate (England) and the Educational Testing Service were recognized as equivalent, though different in form and approach, in the 1930s. The underlying goal of the Cambridge certificate of proficiency was control of the English curriculum of…

Reference-quality genome sequence of Aegilops tauschii, the source of wheat D genome, shows that recombination shapes genome structure and evolution

USDA-ARS?s Scientific Manuscript database

Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat and an important genetic resource for wheat. A reference-quality sequence for the Ae. tauschii genome was produced with a combination of ordered-clone sequencing, whole-genome shotgun sequencing, and BioNano optical geno...

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae

PubMed Central

Neale, David B.; McGuire, Patrick E.; Wheeler, Nicholas C.; Stevens, Kristian A.; Crepeau, Marc W.; Cardeno, Charis; Zimin, Aleksey V.; Puiu, Daniela; Pertea, Geo M.; Sezen, U. Uzay; Casola, Claudio; Koralewski, Tomasz E.; Paul, Robin; Gonzalez-Ibeas, Daniel; Zaman, Sumaira; Cronn, Richard; Yandell, Mark; Holt, Carson; Langley, Charles H.; Yorke, James A.; Salzberg, Steven L.; Wegrzyn, Jill L.

2017-01-01

A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp). Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir vs. pine and spruce. Comparative genome annotation with angiosperm species reveals gene-family expansion and contraction in Douglas-fir and other conifers which may account for some of the major morphological and physiological differences between the two major plant groups. Notable differences in the size of the NDH-complex gene family and genes underlying the functional basis of shade tolerance/intolerance were observed. This reference genome sequence not only provides an important resource for Douglas-fir breeders and geneticists but also sheds additional light on the evolutionary processes that have led to the divergence of modern angiosperms from the more ancient gymnosperms. PMID:28751502

Draft Genome Sequence of the Serratia rubidaea CIP 103234T Reference Strain, a Human-Opportunistic Pathogen.

PubMed

Bonnin, Rémy A; Girlich, Delphine; Imanci, Dilek; Dortet, Laurent; Naas, Thierry

2015-11-19

We provide here the first genome sequence of a Serratia rubidaea isolate, a human-opportunistic pathogen. This reference sequence will permit a comparison of this species with others of the Serratia genus. Copyright © 2015 Bonnin et al.

Evaluation of nine immunoassay kits (enzyme immunoassay and direct fluorescence) for detection of Giardia lamblia and Cryptosporidium parvum in human fecal specimens.

PubMed Central

Garcia, L S; Shimizu, R Y

1997-01-01

It is well known that Giardia lamblia and Cryptosporidium parvum can cause severe symptoms in humans, particularly those who are immunologically compromised. Immunoassay procedures offer both increased sensitivity and specificity compared to conventional staining methods. These reagents are also helpful when screening large numbers of patients, particularly in an outbreak situation or when screening patients with minimal symptoms. The data obtained by using 9 diagnostic kits were compared: direct fluorescent-antibody assay (DFA) kits (TechLab Giardia/Crypto IF kit, TechLab Crypto IF kit, and Meridian Merifluor Cryptosporidium/Giardia) and enzyme immunoassay (EIA) kits (Alexon ProSpecT Giardia EZ Microplate Assay, Alexon ProSpecT Cryptosporidium Microplate Assay, Cambridge Giardia lamblia Antigen Microwell ELISA, Meridian Premier Giardia lamblia, Meridian Premier Cryptosporidium, TechLab Giardia CELISA, Trend Giardia lamblia EIA). The test with the Meridian Merifluor Cryptosporidium/Giardia kit was used as the reference method. In various combinations, 60 specimens positive for Giardia, 60 specimens positive for Cryptosporidium, 40 specimens positive for a Giardia-Cryptosporidium mix, and 50 negative fecal specimens were tested. Different species (nine protozoa, three coccidia, one microsporidium, five nematodes, three cestodes, and one trematode) were included in the negative specimens. The sensitivity of EIA for Giardia ranged from 94% (Alexon) to 99% (Trend and Cambridge); the specificity was 100% with all EIA kits tested. The sensitivity of EIA for Cryptosporidium ranged from 98% (Alexon) to 99% (Meridian Premier); specificities were 100%. All DFA results were in agreement, with 100% sensitivity and specificity; however, the TechLab reagents resulted in fluorescence intensity that was generally one level below that seen with the reagents used in the reference method. In addition to sensitivity and specificity, factors such as cost, simplicity, ease of interpretation of results (color, intensity of fluorescence), equipment, available personnel, and number of tests ordered are also important considerations prior to kit selection. PMID:9163474

The afterlife of Laurence Sterne (1713-1768): Body snatching, dissection and the role of Cambridge anatomist Charles Collignon.

PubMed

Dittmar, Jenna M; Mitchell, Piers D

2016-11-01

This paper aims to highlight the practice of body snatching from graves in the 1700s for the purpose of providing corpses for anatomical dissection, and for stocking anatomy museums. To do this, we examine the exhumation and dissection of the famous eighteenth-century novelist Laurence Sterne and explore the involvement of Charles Collignon, Professor of Anatomy at the University of Cambridge. We also show that osteological and cut-mark analysis of a skull purported to be that of Sterne, currently housed in the Duckworth Collection at Cambridge, provides the key to solving the mystery surrounding why Sterne was resurrected. © The Author(s) 2015.

The Best That Has Been Thought and Said?

ERIC Educational Resources Information Center

Alexander, Robin

2014-01-01

"FORUM" has marked the progress of the Cambridge Primary Review by three previous articles from Robin Alexander, the Review's director, and by critiques and responses from several others, notably "FORUM"'s Michael Armstrong. In 2013 the Review was superseded by the Cambridge Primary Review Trust, and this article is the text of…

Self-Access and the Adult Language Learner.

ERIC Educational Resources Information Center

Esch, Edith, Ed.

The immediate stimulus for this collection of papers was a conference, Self-Access and the Adult Language Learner, organized by the Centre for Information on Language Teaching and Research (CILT) and the Language Centre of the University of Cambridge in December 1992 at Queen's College, Cambridge. Several 1-day conferences on the same theme were…

77 FR 9682 - Announcement of Funding Awards for the HUD-Veterans Affairs Supportive Housing (HUD-VASH) Program...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-17

... 35804 84,762 25 City of Huntsville. NE. HA Tuscaloosa 2117 Jack Warner Tuscaloosa...... AL 35401 96,333... Street.... Boston MA 02111 520,356 50 Cambridge Housing Authority.. 675 Massachusetts Cambridge....... MA 02139 350,721 25 Avenue. Worcester Housing Authority.. 40 Belmont Street.... Worcester....... MA 01605...

Genetic Influences on Cognitive Function Using the Cambridge Neuropsychological Test Automated Battery

ERIC Educational Resources Information Center

Singer, Jamie J.; MacGregor, Alex J.; Cherkas, Lynn F.; Spector, Tim D.

2006-01-01

The genetic relationship between intelligence and components of cognition remains controversial. Conflicting results may be a function of the limited number of methods used in experimental evaluation. The current study is the first to use CANTAB (The Cambridge Neuropsychological Test Automated Battery). This is a battery of validated computerised…

Final Report of Cambridge Conference on School Mathematics, January 1962 - August 1970.

ERIC Educational Resources Information Center

Cambridge Conference on School Mathematics, Newton, MA.

The Cambridge Conference on School Mathematics (CCSM) was an association of prominent mathematicians who had a concern for mathematics education at school level, from kindergarten through grade twelve. These mathematicians organized three main conferences in three areas of mathematics education, and have carried on activities related to the…

[Probability, Cambridge Conference on School Mathematics Feasibility Study No. 7.

ERIC Educational Resources Information Center

Davis, R.

These materials were written with the aim of reflecting the thinking of the Cambridge Conference on School Mathematics (CCSM) regarding the goals and objectives for school mathematics. They represent a practical response to a proposal by CCSM that some elements of probability be introduced in the elementary grades. These materials provide children…

Trust-Based Cooperative Games and Control Strategies for Autonomous Military Convoys

DTIC Science & Technology

2013-01-01

52] S. Goering, "Postnatal Reproductive Autonomy: Promoting Relational Autonomy and Self-Trust in New Parents," Bioethics , vol. 23, no. 1, pp. 9-19...Systems," Proceedings of the IEEE, vol. 95, no. 1, pp. 215-233, January 2007. [105] O. O’Neill, Autonomy and Trust in Bioethics . Cambridge: Cambridge

The Just Community School: The Theory and the Cambridge Cluster School Experiment.

ERIC Educational Resources Information Center

Kohlberg, Lawrence; And Others

The background, evaluation process, theories, and practical aspects of the Just Community High School in Cambridge, Masachusetts, are presented. The document is organized into four sections. Section 1 briefly discusses the components of a Just School: participatory democracy with teachers and students having equal rights, emphasis on conflict…

Stacking up against Alternative Conceptions: Using Uno Cards to Introduce Discourse and Argumentation

ERIC Educational Resources Information Center

Dunac, Patricia S.; Demi, Kadir

2013-01-01

We engaged secondary science students in a teacher and student constructed Uno card game (UCG) to change their conceptual understanding of the various energy transformations. The paper outlines how we incorporated Toulmin's argumentation pattern (Toulmin 1958 "The Uses of Argument"(Cambridge: Cambridge University Press)) in the UCG,…

The Cambridge Companion to Dewey. Cambridge Companions to Philosophy

ERIC Educational Resources Information Center

Cochran, Molly

2010-01-01

John Dewey (1859-1952) was a major figure of the American cultural and intellectual landscape in the first half of the twentieth century. While not the originator of American pragmatism, he was instrumental to its articulation as a philosophy and the spread of its influence beyond philosophy to other disciplines. His prolific writings encompass…

Argumentation and Participation Patterns in General Chemistry Peer-Led Sessions

ERIC Educational Resources Information Center

Kulatunga, Ushiri; Moog, Richard S.; Lewis, Jennifer E.

2013-01-01

This article focuses on the use of Toulmin's argumentation scheme to investigate the characteristics of student group argumentation in Peer-Led Guided Inquiry sessions for a General Chemistry I course. A coding scheme based on Toulmin's [Toulmin [1958] "The uses of argument." Cambridge: Cambridge University Press] argumentation…

Developing Outcome Measures for a Family Intensive Support Service for Children Presenting with Challenging Behaviours

ERIC Educational Resources Information Center

Mulligan, Bethany; John, Mary; Coombes, Rachel; Singh, Rosemary

2015-01-01

Seven per cent of individuals with learning disabilities also display challenging behaviour ("Challenging behaviour: analysis and intervention in people with severe intellectual disabilities," 2001, Cambridge, Cambridge University Press), which has an effect on the whole family. Services need to be developed to support and reflect this…

The Visual Identity Project

ERIC Educational Resources Information Center

Tennant-Gadd, Laurie; Sansone, Kristina Lamour

2008-01-01

Identity is the focus of the middle-school visual arts program at Cambridge Friends School (CFS) in Cambridge, Massachusetts. Sixth graders enter the middle school and design a personal logo as their first major project in the art studio. The logo becomes a way for students to introduce themselves to their teachers and to represent who they are…

Massive Molecular Outflows and Evidence for AGN Feedback from CO Observations

DTIC Science & Technology

2013-11-13

J. Thomson Avenue, Cambridge CB3 0HE, UK e-mail: c.cicone@mrao.cam.ac.uk 2 Kavli Institute for Cosmology , University of Cambridge, Madingley Road...molecular outflow as a function of AGN luminosity. Theoretical models of AGN feed- back and cosmological simulations predict a coupling efficiency between AGN

Aerodynamics Education: Where We’ve Been and Where We’re Going

DTIC Science & Technology

2013-06-24

2661. June 1992. 3 Kroo. I.. "Aerodynamic Analyses for Design and Education ... AIAA Paper 92-2664 . . lune 1992. 12 American Institute of Aeronautics...Paper 98-2792 . . lune 1998. 13 Anderson. J.D .. A l-/ist01y <~/Aero<~wwmics. Cambridge Univers ity Press. Cambridge. 1998. 14http

Coastal Marine Demonstration of Forecast Information to Mariners for the U.S. East Coast

DTIC Science & Technology

1998-09-30

Maryland Center for Environmental Science PO Box 775 Cambridge, MD 21613-0775 410.221.8477 fax:410.221.8490 walstad@hpl.umces.edu George L. Mellor... Environmental Science ,PO Box 775,Cambridge,MD,21613-0775 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES

Legacies, Policies and Prospects: One Year on from the Cambridge Primary Review

ERIC Educational Resources Information Center

Alexander, Robin

2011-01-01

This article features the "Cambridge Primary Review." The "Review" has been supported from the beginning by Esmee Fairbairn Foundation, and this has given it the independence which is essential to its credibility. Its remit was to investigate, report and make recommendations on the condition and future of primary education in…

How to Run a University

ERIC Educational Resources Information Center

Evans, G. R.

2006-01-01

The Lambert Review of Business-University Collaboration proposed a business model for universities in 2003. Pressure to change university governance to make it match the business model remains strong, and it is being most actively applied to Oxford and Cambridge. The Oxford and Cambridge governance debates (which began in the 1990s) open up the…

The Singapore-Cambridge General Certificate of Education Advanced-Level General Paper Examination

ERIC Educational Resources Information Center

Hassan, Nurul Huda; Shih, Chih-Min

2013-01-01

This article describes and reviews the Singapore-Cambridge General Certificate of Education Advanced Level General Paper (GP) examination. As a written test that is administered to preuniversity students, the GP examination is internationally recognised and accepted by universities and employers as proof of English competence. In this article, the…

Using the Concordancer in Vocabulary Development for the Cambridge Advanced English (CAE) Course.

ERIC Educational Resources Information Center

Somogyi, Emma

1996-01-01

Discusses concordancing activities tailored for use with English-as-a-Second-Language (ESL) students in the Cambridge Advanced English course in Australia. The article focuses on students selecting appropriate vocabulary to complete gapped text. Findings indicate that these activities benefit ESL students by providing authentic examples of…

Democratic Consolidation and Comparative Political Perspective on the 2002 Presidential Election in the ROK

DTIC Science & Technology

2005-01-01

combining presidential system with legislature where no single party has majority status is a kiss of death.”52 According to Giovanni Sartori , the...Cheibub and Limongi, “What Makes Democracies Endure?” p. 46. 53 Giovanni Sartori , Parties and Party Systems (Cambridge: Cambridge University Press

A Computerized Three-Dimensional Program Budget and Its Implementation at Cambridge School Department.

ERIC Educational Resources Information Center

Wong, S. Godwin

This report describes the APL (Accountable unit, Program, and line item) budget system, a computerized three-dimensional program budget system that has been implemented in the Cambridge (Massachusetts) School Department. Various chapters discuss the differences between traditional budgeting and program budgeting, present an overview of te APL…

Accounting Community of Practice Pedagogy: A Course Management Invention for Developing Personal Competencies in Accounting Education

ERIC Educational Resources Information Center

Stephenson, Sandria S.

2017-01-01

This paper reports the findings of an exploratory qualitative study using the implementation of Wenger's [(1998). "Communities of practice: Learning, meaning, and identity." Cambridge, MA: Cambridge University Press; Wenger, E. (2000). Communities of practice and social learning systems. "Organization," 7(2), 225-246] Theory of…

Linguistic Turn and Gendering Language in the Cambridge Advanced Learner's Dictionary

ERIC Educational Resources Information Center

Arimbi, Diah A.; Kwary, Deny A.

2016-01-01

Language constructs how humans perceive things. Since language is a human construction, it tends to be biased as it is mainly men's construction. Using gender perspectives, this paper attempts to discuss the imbalance in gender representations found in the examples given in an English learner's dictionary, that is, the "Cambridge Advanced…

What To Look for in ESL Admission Tests: Cambridge Certificate Exams, IELTS, and TOEFL.

ERIC Educational Resources Information Center

Chalhoub-Deville, Micheline; Turner, Carolyn E.

2000-01-01

Familiarizes test users with issues to consider when employing assessments for screening and admission purposes. Examines the purpose, content, and scoring methods of three English-as-a-Second-Language admissions tests--the Cambridge certificate exams, International English Language Teaching System, and Test of English as a Foreign…

Learner Diary Research with "Cambridge" Examination Candidates.

ERIC Educational Resources Information Center

Parkinson, Brian; Benson, Cathy; Jenkins, Michael

2003-01-01

This paper describes a research project in which volunteers, self-selected from IALS students preparing for one or more of the Cambridge English Examinations, kept journals. Following guidelines, they reflected on their in-class and outside-of-class experiences in the 8 weeks leading up to the exams. They also attended four biweekly meetings with…

Information Systems Technician Rating Stakeholders: Implications for Effective Performance

DTIC Science & Technology

2011-01-01

DeSanctis, and Borge Obel. (2006). Organizational Design: A Step-by-Step Approach. Cambridge, UK: Cambridge University Press. Carroll, G . R., and M...manpower, personnel, and training processes for managing the information systems technician (IT) rating and the effects of these different stakeholders...Strategic Human Resource Management and Management Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Organizational

Physical Fitness of U.S. Navy Special Forces Team Members and Trainees

DTIC Science & Technology

1989-07-07

Resting Heart Rate and Blood Pressure. At the completion of a 12-lead resting EKG (VS4S, Cambridge Instrument Co., Ossining , NY), heart rate (bpm) of...Cambridge Instrument Co., Ossining , NY). Instruments were interfaced with a MINC-23 computer (Digital Equipment Corp., Marlboro, MA) for on-line

The relationship between executive function and fine motor control in young and older adults.

PubMed

Corti, Emily J; Johnson, Andrew R; Riddle, Hayley; Gasson, Natalie; Kane, Robert; Loftus, Andrea M

2017-01-01

The present study examined the relationship between executive function (EF) and fine motor control in young and older healthy adults. Participants completed 3 measures of executive function; a spatial working memory (SWM) task, the Stockings of Cambridge task (planning), and the Intra-Dimensional Extra-Dimensional Set-Shift task (set-shifting). Fine motor control was assessed using 3 subtests of the Purdue Pegboard (unimanual, bimanual, sequencing). For the younger adults, there were no significant correlations between measures of EF and fine motor control. For the older adults, all EFs significantly correlated with all measures of fine motor control. Three separate regressions examined whether planning, SWM and set-shifting independently predicted unimanual, bimanual, and sequencing scores for the older adults. Planning was the primary predictor of performance on all three Purdue subtests. A multiple-groups mediation model examined whether planning predicted fine motor control scores independent of participants' age, suggesting that preservation of planning ability may support fine motor control in older adults. Planning remained a significant predictor of unimanual performance in the older age group, but not bimanual or sequencing performance. The findings are discussed in terms of compensation theory, whereby planning is a key compensatory resource for fine motor control in older adults. Copyright © 2016 Elsevier B.V. All rights reserved.

Source-Water Protection and Water-Quality Investigations in the Cambridge, Massachusetts, Drinking-Water Supply System

USGS Publications Warehouse

Waldron, Marcus C.; Norton, Chip; MacDonald, Timothy W.D.

1998-01-01

Introduction The Cambridge Water Department (CWD) supplies about 15 million gallons of water each day to more than 95,000 customers in the City of Cambridge, Massachusetts. Most of this water is obtained from a system of reservoirs located in Cambridge and in parts of five other suburban-Boston communities. The drainage basin that contributes water to these reservoirs includes several potential sources of drinking-water contaminants, including major highways, secondary roads, areas of commercial and industrial development, and suburban residential tracts. The CWD is implementing a comprehensive Source-Water Protection Plan to ensure that the highest quality water is delivered to the treatment plant. A key element of this plan is a program that combines systematic monitoring of the drainage basin with detailed investigations of the effects of nonpoint-source contaminants, such as highway-deicing chemicals, nutrients, oxygen-demanding organic compounds, bacteria, and trace metals arising from stormwater runoff. The U.S. Geological Survey (USGS) is working with the CWD and the Massachusetts Highway Department (MassHighway) to develop a better understanding of the sources, transport, and fate of many of these contaminants. This Fact Sheet describes source-water protection and water-quality investigations currently underway in the Cambridge drinking-water supply system. The investigations are designed to complement a national effort by the USGS to provide water suppliers and regulatory agencies with information on the vulnerability of water supplies and the movement and fate of source-water contaminants.

Low-Bandwidth and Non-Compute Intensive Remote Identification of Microbes from Raw Sequencing Reads

PubMed Central

Gautier, Laurent; Lund, Ole

2013-01-01

Cheap DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food products, bioreactors, or environmental samples. We propose a novel general approach to the analysis of sequencing data where a reference genome does not have to be specified. Using a distributed architecture we are able to query a remote server for hints about what the reference might be, transferring a relatively small amount of data. Our system consists of a server with known reference DNA indexed, and a client with raw sequencing reads. The client sends a sample of unidentified reads, and in return receives a list of matching references. Sequences for the references can be retrieved and used for exhaustive computation on the reads, such as alignment. To demonstrate this approach we have implemented a web server, indexing tens of thousands of publicly available genomes and genomic regions from various organisms and returning lists of matching hits from query sequencing reads. We have also implemented two clients: one running in a web browser, and one as a python script. Both are able to handle a large number of sequencing reads and from portable devices (the browser-based running on a tablet), perform its task within seconds, and consume an amount of bandwidth compatible with mobile broadband networks. Such client-server approaches could develop in the future, allowing a fully automated processing of sequencing data and routine instant quality check of sequencing runs from desktop sequencers. A web access is available at http://tapir.cbs.dtu.dk. The source code for a python command-line client, a server, and supplementary data are available at http://bit.ly/1aURxkc. PMID:24391826

Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads.

PubMed

Gautier, Laurent; Lund, Ole

2013-01-01

Cheap DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food products, bioreactors, or environmental samples. We propose a novel general approach to the analysis of sequencing data where a reference genome does not have to be specified. Using a distributed architecture we are able to query a remote server for hints about what the reference might be, transferring a relatively small amount of data. Our system consists of a server with known reference DNA indexed, and a client with raw sequencing reads. The client sends a sample of unidentified reads, and in return receives a list of matching references. Sequences for the references can be retrieved and used for exhaustive computation on the reads, such as alignment. To demonstrate this approach we have implemented a web server, indexing tens of thousands of publicly available genomes and genomic regions from various organisms and returning lists of matching hits from query sequencing reads. We have also implemented two clients: one running in a web browser, and one as a python script. Both are able to handle a large number of sequencing reads and from portable devices (the browser-based running on a tablet), perform its task within seconds, and consume an amount of bandwidth compatible with mobile broadband networks. Such client-server approaches could develop in the future, allowing a fully automated processing of sequencing data and routine instant quality check of sequencing runs from desktop sequencers. A web access is available at http://tapir.cbs.dtu.dk. The source code for a python command-line client, a server, and supplementary data are available at http://bit.ly/1aURxkc.

Implementation of an RBF neural network on embedded systems: real-time face tracking and identity verification.

PubMed

Yang, Fan; Paindavoine, M

2003-01-01

This paper describes a real time vision system that allows us to localize faces in video sequences and verify their identity. These processes are image processing techniques based on the radial basis function (RBF) neural network approach. The robustness of this system has been evaluated quantitatively on eight video sequences. We have adapted our model for an application of face recognition using the Olivetti Research Laboratory (ORL), Cambridge, UK, database so as to compare the performance against other systems. We also describe three hardware implementations of our model on embedded systems based on the field programmable gate array (FPGA), zero instruction set computer (ZISC) chips, and digital signal processor (DSP) TMS320C62, respectively. We analyze the algorithm complexity and present results of hardware implementations in terms of the resources used and processing speed. The success rates of face tracking and identity verification are 92% (FPGA), 85% (ZISC), and 98.2% (DSP), respectively. For the three embedded systems, the processing speeds for images size of 288 /spl times/ 352 are 14 images/s, 25 images/s, and 4.8 images/s, respectively.

Process in manufacturing high efficiency AlGaAs/GaAs solar cells by MO-CVD

NASA Technical Reports Server (NTRS)

Yeh, Y. C. M.; Chang, K. I.; Tandon, J.

1984-01-01

Manufacturing technology for mass producing high efficiency GaAs solar cells is discussed. A progress using a high throughput MO-CVD reactor to produce high efficiency GaAs solar cells is discussed. Thickness and doping concentration uniformity of metal oxide chemical vapor deposition (MO-CVD) GaAs and AlGaAs layer growth are discussed. In addition, new tooling designs are given which increase the throughput of solar cell processing. To date, 2cm x 2cm AlGaAs/GaAs solar cells with efficiency up to 16.5% were produced. In order to meet throughput goals for mass producing GaAs solar cells, a large MO-CVD system (Cambridge Instrument Model MR-200) with a susceptor which was initially capable of processing 20 wafers (up to 75 mm diameter) during a single growth run was installed. In the MR-200, the sequencing of the gases and the heating power are controlled by a microprocessor-based programmable control console. Hence, operator errors can be reduced, leading to a more reproducible production sequence.

Genotyping of Indian antigenic, vaccine, and field Brucella spp. using multilocus sequence typing.

PubMed

Shome, Rajeswari; Krithiga, Natesan; Shankaranarayana, Padmashree B; Jegadesan, Sankarasubramanian; Udayakumar S, Vishnu; Shome, Bibek Ranjan; Saikia, Girin Kumar; Sharma, Narendra Kumar; Chauhan, Harshad; Chandel, Bharat Singh; Jeyaprakash, Rajendhran; Rahman, Habibur

2016-03-31

Brucellosis is one of the most important zoonotic diseases that affects multiple livestock species and causes great economic losses. The highly conserved genomes of Brucella, with > 90% homology among species, makes it important to study the genetic diversity circulating in the country. A total of 26 Brucella spp. (4 reference strains and 22 field isolates) and 1 B. melitensis draft genome sequence from India (B. melitensis Bm IND1) were included for sequence typing. The field isolates were identified by biochemical tests and confirmed by both conventional and quantitative polymerase chain reaction (qPCR) targeting bcsp 31Brucella genus-specific marker. Brucella speciation and biotyping was done by Bruce ladder, probe qPCR, and AMOS PCRs, respectively, and genotyping was done by multilocus sequence typing (MLST). The MLST typing of 27 Brucella spp. revealed five distinct sequence types (STs); the B. abortus S99 reference strain and 21 B. abortus field isolates belonged to ST1. On the other hand, the vaccine strain B. abortus S19 was genotyped as ST5. Similarly, B. melitensis 16M reference strain and one B. melitensis field isolate were grouped into ST7. Another B. melitensis field isolate belonged to ST8 (draft genome sequence from India), and only B. suis 1330 reference strain was found to be ST14. The sequences revealed genetic similarity of the Indian strains to the global reference and field strains. The study highlights the usefulness of MLST for typing of field isolates and validation of reference strains used for diagnosis and vaccination against brucellosis.

Acoustic sequences in non-human animals: a tutorial review and prospectus.

PubMed

Kershenbaum, Arik; Blumstein, Daniel T; Roch, Marie A; Akçay, Çağlar; Backus, Gregory; Bee, Mark A; Bohn, Kirsten; Cao, Yan; Carter, Gerald; Cäsar, Cristiane; Coen, Michael; DeRuiter, Stacy L; Doyle, Laurance; Edelman, Shimon; Ferrer-i-Cancho, Ramon; Freeberg, Todd M; Garland, Ellen C; Gustison, Morgan; Harley, Heidi E; Huetz, Chloé; Hughes, Melissa; Hyland Bruno, Julia; Ilany, Amiyaal; Jin, Dezhe Z; Johnson, Michael; Ju, Chenghui; Karnowski, Jeremy; Lohr, Bernard; Manser, Marta B; McCowan, Brenda; Mercado, Eduardo; Narins, Peter M; Piel, Alex; Rice, Megan; Salmi, Roberta; Sasahara, Kazutoshi; Sayigh, Laela; Shiu, Yu; Taylor, Charles; Vallejo, Edgar E; Waller, Sara; Zamora-Gutierrez, Veronica

2016-02-01

Animal acoustic communication often takes the form of complex sequences, made up of multiple distinct acoustic units. Apart from the well-known example of birdsong, other animals such as insects, amphibians, and mammals (including bats, rodents, primates, and cetaceans) also generate complex acoustic sequences. Occasionally, such as with birdsong, the adaptive role of these sequences seems clear (e.g. mate attraction and territorial defence). More often however, researchers have only begun to characterise - let alone understand - the significance and meaning of acoustic sequences. Hypotheses abound, but there is little agreement as to how sequences should be defined and analysed. Our review aims to outline suitable methods for testing these hypotheses, and to describe the major limitations to our current and near-future knowledge on questions of acoustic sequences. This review and prospectus is the result of a collaborative effort between 43 scientists from the fields of animal behaviour, ecology and evolution, signal processing, machine learning, quantitative linguistics, and information theory, who gathered for a 2013 workshop entitled, 'Analysing vocal sequences in animals'. Our goal is to present not just a review of the state of the art, but to propose a methodological framework that summarises what we suggest are the best practices for research in this field, across taxa and across disciplines. We also provide a tutorial-style introduction to some of the most promising algorithmic approaches for analysing sequences. We divide our review into three sections: identifying the distinct units of an acoustic sequence, describing the different ways that information can be contained within a sequence, and analysing the structure of that sequence. Each of these sections is further subdivided to address the key questions and approaches in that area. We propose a uniform, systematic, and comprehensive approach to studying sequences, with the goal of clarifying research terms used in different fields, and facilitating collaboration and comparative studies. Allowing greater interdisciplinary collaboration will facilitate the investigation of many important questions in the evolution of communication and sociality. © 2014 Cambridge Philosophical Society.

What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual

USDA-ARS?s Scientific Manuscript database

BACKGROUND: Next-generation sequencing projects commonly commence by aligning reads to a reference genome assembly. While improvements in alignment algorithms and computational hardware have greatly enhanced the efficiency and accuracy of alignments, a significant percentage of reads often remain u...

Basic Research on Processing of Ceramics for Space Structures

DTIC Science & Technology

1984-10-01

form. 110 V. References 1. B. Fegley, E. A. Barringer , and H. K. Bowen, J. Am. Ceram. Soc., 1984, 67(6), C113-16. 2. S. Govil and R . C. Mehrotra, Syn...Avenue, Cambridge, MA 02IApt- R h. 8 9 1 708 9. SFONSO1= UNG# WN AGENCY NAME(S) AND 1041SLI. SPONSORING / moNITORING AFOS AO~~IfiI~ jAGENCY REPORT...NUMBER AFOS-83- 192 BLDG O4107OIVIAIUYSAEETlb.OSRUINC I AB DCT 2033g2644 w’wJELE OR8309 U n i t o r mW c p o i t A O Z r 2 1 9 8 9- . 2 ’ a d S C A F w r

Rhesus monkeys employ a procedural strategy to reduce working memory load in a self-ordered spatial search task

PubMed Central

Taffe, Michael A.; Taffe, William J.

2011-01-01

Several nonhuman primate species have been reported to employ a distance-minimizing, traveling salesman-like, strategy during foraging as well as in experimental spatial search tasks involving lesser amounts of locomotion. Spatial sequencing may optimize performance by reducing reference or episodic memory loads, locomotor costs, competition or other demands. A computerized self-ordered spatial search (SOSS) memory task has been adapted from a human neuropsychological testing battery (CANTAB, Cambridge Cognition, Ltd) for use in monkeys. Accurate completion of a trial requires sequential responses to colored boxes in two or more spatial locations without repetition of a previous location. Marmosets have been reported to employ a circling pattern of search, suggesting spontaneous adoption of a strategy to reduce working memory load. In this study the SOSS performance of rhesus monkeys was assessed to determine if the use of a distance-minimizing search path enhances accuracy. A novel strategy score, independent of the trial difficulty and arrangement of boxes, has been devised. Analysis of the performance of 21 monkeys trained on SOSS over two years shows that a distance-minimizing search strategy is associated with improved accuracy. This effect is observed within individuals as they improve over many cumulative sessions of training on the task and across individuals at any given level of training. Erroneous trials were associated with a failure to deploy the strategy. It is concluded that the effect of utilizing the strategy on this locomotion-free, laboratory task is to enhance accuracy by reducing demands on spatial working memory resources. PMID:21840507

Up the Garden Path: A Chemical Trail through the Cambridge University Botanic Garden

ERIC Educational Resources Information Center

Battle, Gary M.; Kyd, Gwenda O.; Groom, Colin R.; Allen, Frank H.; Day, Juliet; Upson, Timothy

2012-01-01

The living world is a rich source of chemicals with many medicines, dyes, flavorings, and foodstuffs having their origins in compounds produced by plants. We describe a chemical trail through the plant holdings of the Cambridge University Botanic Gardens. Visitors to the gardens are provided with a laminated trail guide with 22 stopping points…

Surface-water, water-quality, and meteorological data for the Cambridge, Massachusetts, drinking-water source area, water years 2007-08

USGS Publications Warehouse

Smith, Kirk P.

2011-01-01

Water samples were collected in nearly all of the subbasins in the Cambridge drinking-water source area and from Fresh Pond during the study period. Discrete water samples were collected during base-flow conditions with an antecedent dry period of at least 3 days. Composite sampl

Phillips Lab Project Manager’s Handbook

DTIC Science & Technology

1994-04-15

Phillips Lab continues to be the Air Force Phillips Laboratory (PL) center of excellence for space research and Kirtland AFB, New...POINTS OF CONTACT pages of world history. In 1949, the Cambridge Field Station was renamed the Kirtland AFB: Air Force Cambridge Research Laboratories ...by the Air Force’s facilities are geographically located. Phillips Laboratory at Kirtland Air Force

How Has Dewey's Democratic Theory Influenced the Development of a New Primary School? A Headteacher's Perspective

ERIC Educational Resources Information Center

Higham, Rupert; Biddulph, James

2018-01-01

This article provides the transcript of Dr. Rupert Higham (University College London, Institute of Education) in conversation with Dr. James Biddulph (Headteacher of the University of Cambridge Primary School). Among the topics discussed are: What the University of Cambridge Primary School (UCPS) motto, "Releasing the Imagination: Celebrating…

Old Glory and the Jolly Roger: The Cultural Constraints and Strategic Imperatives of Modern Piracy

DTIC Science & Technology

2009-06-01

41. Watkins , Eric. "Pirates Seize Another Tanker Off Yemen." Oil and Gas Journal (9 January 2009), http://www.ogj.com/display_article/352052/7...Piracy in the Graeco-Roman World. Cambridge: Cambridge University Press, 2002. Dobbins, James, Seth G. Jones, Keith Crane, and Beth Cole DeGrasse. The

[Cambridge Conference on School Mathematics Feasibility Studies 9-13.

ERIC Educational Resources Information Center

Cambridge Conference on School Mathematics, Newton, MA.

These materials are a part of a series of studies sponsored by the Cambridge Conference on School Mathematics which reflects the ideas of CCSM regarding the goals and objectives for school mathematics K-12. Feasibility Studies 9-13 contain a wide range of topics. The following are the titles and brief descriptions of these studies. Number…

Symmetry Motion Classes; Cambridge Conference on School Mathematics Feasibility Study No. 40.

ERIC Educational Resources Information Center

McLane, Lyn

These materials were written with the aim of reflecting the thinking of The Cambridge Conference on School Mathematics (CCSM) regarding the goals and objectives for school mathematics. This document details the planning and response for each of ten lessons involving symmetry motions. The problems focused on (1) combining motions in a given order,…

Informal Geometry for Young Children; Cambridge Conference on School Mathematics; Feasibility Study No. 34b.

ERIC Educational Resources Information Center

Walter, Marion

These materials were written with the aim of reflecting the thinking of The Cambridge Conference on School Mathematics (CCSM) regarding the goals and objectives for school mathematics. These materials are intended to provide children with a variety of informal activities in intuitive geometry in the elementary school. Opportunities are provided…

Inequalities and Real Numbers as a Basis for School Mathematics, Cambridge Conference on School Mathematics Feasibility Study No. 38.

ERIC Educational Resources Information Center

Lomon, Earle

These materials were developed as a practical response to some of the recommendations of the 1963 Cambridge Conference on School Mathematics (CCSM). Experimental sessions are described in detail in this report. In the Estabrook Elementary School, Lexington, Massachusetts, first grade children (1964-65 Academic Year) concentrated on material…

A FIRST STEP TOWARDS THE IMPLEMENTATION OF THE CAMBRIDGE MATHEMATICS CURRICULUM IN A K-12 UNGRADED SCHOOL.

ERIC Educational Resources Information Center

FOSTER, GARRETT R.

A SERIES OF THREE CONFERENCES WAS HELD TO EXPLORE THE FEASIBILITY OF IMPLEMENTING A LONG-RANGE CURRICULUM DEVELOPMENT PROJECT FOR AN UNGRADED, K-12 SCHOOL, BASED ON RECOMMENDATIONS OF THE CAMBRIDGE CONFERENCE ON SCHOOL MATHEMATICS. OVER 50 MATHEMATICIANS, MATHEMATICS EDUCATORS, AND PERSONS INVOLVED IN THEORETICAL AND APPLIED PSYCHOLOGICAL…

Probability Lessons at Hancock School, Lexington; Cambridge Conference on School Mathematics Feasibility Study No. 41.

ERIC Educational Resources Information Center

McLane, Lyn

These materials were written with the aim of reflecting the thinking of Cambridge Conference on School Mathematics (CCSM) regarding the goals and objectives for school mathematics. Presented are plans for teaching 23 probability lessons in the elementary grades at Hancock School, Lexington, Massachusetts. The discovery approach was utilized by the…

Factors Affecting Applications to Oxford and Cambridge--Repeat Survey. Executive Summary with Statistics

ERIC Educational Resources Information Center

Ridley, Kate; White, Kerensa; Styles, Ben; Morrison, Jo

2005-01-01

This research follows up a study conducted in 1998 by the National Foundation for Educational Research (NFER) to investigate teachers' and students' views on the factors affecting students' choices of whether or not to apply to Oxford and Cambridge universities. It identifies what has changed since 1998 and areas in which the universities could…

University Choice: What Influences the Decisions of Academically Successful Post-16 Students?

ERIC Educational Resources Information Center

Whitehead, Joan M.; Raffan, John; Deaney, Rosemary

2006-01-01

The questionnaire survey reported in this paper is part of an ongoing evaluation of the effect of a bursary scheme on recruitment to Cambridge University. It sought to identify factors that encouraged or discouraged highly successful A Level students from applying to Cambridge. Findings reveal three main dimensions associated with the decision to…

Formal-Language-Theoretic Control & Coordination of Mobile Robots

DTIC Science & Technology

2007-10-29

and Applications, Cambridge, UK: Cambridge University Press, 1997. I. Chattopadhyay and A. Ray, ‘‘A complex measure for linear grammars ...under the leadership of Prof. Asok Ray and Dr. Ishanu Chattopadhyay, Pennsylvania State University , University Park, PA. This research project has...Investigator: Professor Asok Ray, Pennsylvania State University Key Contributor: Dr. Ishanu Chattopadhyay, Pennsylvania State University The

77 FR 9169 - Standard Instrument Approach Procedures, and Takeoff Minimums and Obstacle Departure Procedures...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-16

... on 8260-15A. The large number of SIAPs, Takeoff Minimums and ODPs, in addition to their complex... (GPS) Y RWY 20, Amdt 1B Cambridge, MN, Cambridge Muni, Takeoff Minimums and Obstacle DP, Orig Pipestone, MN, Pipestone Muni, NDB RWY 36, Amdt 7, CANCELLED Rushford, MN, Rushford Muni, Takeoff Minimums and...

The Target of the Question: A Taxonomy of Textual Features for Cambridge University "O" Levels English

ERIC Educational Resources Information Center

Benjamin, Shanti Isabelle

2015-01-01

This study investigates the typical textual features that are most frequently targeted in short-answer reading comprehension questions of the Cambridge University "O" Level English Paper 2. Test writers' awareness of how textual features impact on understanding of meanings in text decisions will determine to great extent their decisions…

The Key Political Decisions of the Military Government in Turkey, September 1980-November 1983 and the Impact on Those Decisions.

DTIC Science & Technology

1985-05-01

I-would argue that there is a relevant application of Professor Giovanni Sartoris theory of party systems to the Turkish case, especially in the 1979...1980 time frame. G. Sartori , Parties and Party Systems A Framework for Analysis (Cambridge Eng: Cambridge University Press, 1976). 7

Battle of Narratives

DTIC Science & Technology

2012-06-01

18 De Nooy, Wouter, Andrej Mrvar , and Vladimir Batagelj , Exploratory Social Network Analysis with Pajek (New York: Cambridge University Press, 2005... Mrvar , and Vladimir Batagelj . Exploratory Social Network Analysis with Pajek. New York: Cambridge University Press, 2005. Democratic National...Review 54(1):33-48; Brian Uzzi. 1996 . "The Sources and Consequences of Embeddedness for the Economic Performance of Organizations: The Network Effect

M-DCPS Student Performance in International Baccalaureate and Cambridge Advanced International Certificate of Education Programs. Research Brief. Volume 1102

ERIC Educational Resources Information Center

Blazer, Christie

2011-01-01

This Research Brief summarizes the performance of M-DCPS students participating in the International Baccalaureate (IB) and Cambridge Advanced International Certificate of Education (AICE) programs. Outcome data are provided for the eight M-DCPS schools offering the two programs and corresponding examinations. Participation in international…

76 FR 57713 - Wooden Bedroom Furniture From the People's Republic of China: Amended Final Results of...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-16

... appearance on behalf of Liberty Furniture Industries Inc. (``Liberty'') on August 17, 2011. The law firm also... Department: (1) Left out the word ``Dongguan'' when it listed the entity ``Dongguan Cambridge Furniture Co., Ltd., Glory Oceanic Co., Ltd.'' (``Cambridge'') in the rate table of the Final Results; (2) did not...

Constructivism -- Is the United States Making China an Enemy?

DTIC Science & Technology

2012-03-12

theories to include critical theory , postmodernism, feminist theory , historical institutionalism, sociological institutionalism, symbolic...Alexander Wendt, Social Theory of International Politics (Cambridge: Cambridge University Press, 1999), 103. 2 Vendulka Kubalkova, Nicholas Onuf and Paul...Kowert, eds., International Relations in a Constructed World (Armonk, NY: M.E. Sharpe Inc., 1998), 59. 3 Wendt, Social Theory of International

Innovations and challenges in renal cancer: summary statement from the Third Cambridge Conference.

PubMed

Atkins, Michael B; Bukowski, Ronald M; Escudier, Bernard J; Figlin, Robert A; Hudes, Gary H; Kaelin, William G; Linehan, W Marston; McDermott, David F; Mier, James W; Pedrosa, Ivan; Rini, Brian I; Signoretti, Sabina; Sosman, Jeffrey A; Teh, Bin Tean; Wood, Christopher G; Zurita, Amado J; King, Laura

2009-05-15

The Third Cambridge Conference on Innovations and Challenges in Renal Cancer, a symposium held in Cambridge, Massachusetts, June 27-28, 2008, and chaired by Michael B. Atkins, was convened to discuss the current state of knowledge in the field, critique new data, stimulate communication among those involved in basic and clinical research, and offer recommendations for further study. Four main topics were discussed: genetics and molecular biology of renal cell cancer, staging and prognosis, systemic therapy, and correlative science and biomarkers in stage IV disease. The conference format combined brief presentations with extended periods of discussion. The conclusions and recommendations are summarized in this paper and presented in more detail in the individual papers that follow. (c) 2009 American Cancer Society.

Innovations and Challenges in Renal Cancer: Summary Statement From the Third Cambridge Conference

PubMed Central

Atkins, Michael B.; Bukowski, Ronald M.; Escudier, Bernard J.; Figlin, Robert A.; Hudes, Gary H.; Kaelin, William G.; Linehan, W. Marston; McDermott, David F.; Mier, James W.; Pedrosa, Ivan; Rini, Brian I.; Signoretti, Sabina; Sosman, Jeffrey A.; Teh, Bin Tean; Wood, Christopher G.; Zurita, Amado J.; King, Laura

2009-01-01

The Third Cambridge Conference on Innovations and Challenges in Renal Cancer, a symposium held in Cambridge, Massachusetts, June 27–28, 2008, and chaired by Michael B. Atkins, was convened to discuss the current state of knowledge in the field, critique new data, stimulate communication among those involved in basic and clinical research, and offer recommendations for further study. Four main topics were discussed: genetics and molecular biology of renal cell cancer, staging and prognosis, systemic therapy, and correlative science and biomarkers in stage IV disease. The conference format combined brief presentations with extended periods of discussion. The conclusions and recommendations are summarized in this paper and presented in more detail in the individual papers that follow. PMID:19402064

Cambridge Elementary students enjoy gift of computers

NASA Technical Reports Server (NTRS)

1999-01-01

Children at Cambridge Elementary School, Cocoa, Fla., eagerly unwrap computer equipment donated by Kennedy Space Center. Cambridge is one of 13 Brevard County schools receiving 81 excess contractor computers thanks to an innovative educational outreach project spearheaded by the Nasa k-12 Education Services Office at ksc. Behind the children is Jim Thurston, a school volunteer and retired employee of USBI, who shared in the project. The Astronaut Memorial Foundation, a strategic partner in the effort, and several schools in rural Florida and Georgia also received refurbished computers as part of the year-long project. Ksc employees put in about 3,300 volunteer hours to transform old, excess computers into upgraded, usable units. A total of $90,000 in upgraded computer equipment is being donated.

Lessons for livestock genomics from genome and transcriptome sequencing in cattle and other mammals.

PubMed

Taylor, Jeremy F; Whitacre, Lynsey K; Hoff, Jesse L; Tizioto, Polyana C; Kim, JaeWoo; Decker, Jared E; Schnabel, Robert D

2016-08-17

Decreasing sequencing costs and development of new protocols for characterizing global methylation, gene expression patterns and regulatory regions have stimulated the generation of large livestock datasets. Here, we discuss experiences in the analysis of whole-genome and transcriptome sequence data. We analyzed whole-genome sequence (WGS) data from 132 individuals from five canid species (Canis familiaris, C. latrans, C. dingo, C. aureus and C. lupus) and 61 breeds, three bison (Bison bison), 64 water buffalo (Bubalus bubalis) and 297 bovines from 17 breeds. By individual, data vary in extent of reference genome depth of coverage from 4.9X to 64.0X. We have also analyzed RNA-seq data for 580 samples representing 159 Bos taurus and Rattus norvegicus animals and 98 tissues. By aligning reads to a reference assembly and calling variants, we assessed effects of average depth of coverage on the actual coverage and on the number of called variants. We examined the identity of unmapped reads by assembling them and querying produced contigs against the non-redundant nucleic acids database. By imputing high-density single nucleotide polymorphism data on 4010 US registered Angus animals to WGS using Run4 of the 1000 Bull Genomes Project and assessing the accuracy of imputation, we identified misassembled reference sequence regions. We estimate that a 24X depth of coverage is required to achieve 99.5 % coverage of the reference assembly and identify 95 % of the variants within an individual's genome. Genomes sequenced to low average coverage (e.g., <10X) may fail to cover 10 % of the reference genome and identify <75 % of variants. About 10 % of genomic DNA or transcriptome sequence reads fail to align to the reference assembly. These reads include loci missing from the reference assembly and misassembled genes and interesting symbionts, commensal and pathogenic organisms. Assembly errors and a lack of annotation of functional elements significantly limit the utility of the current draft livestock reference assemblies. The Functional Annotation of Animal Genomes initiative seeks to annotate functional elements, while a 70X Pac-Bio assembly for cow is underway and may result in a significantly improved reference assembly.

Liquid metal fast breeder reactors, 1972--1973

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

1974-01-01

Reference to 1467 publications on liquid sodium fast breeder reactors cited in Nuclear Science Abstracts Volume 26 (1972) through Volume 27 (1973 through June) are contained in this citation to provide information on the contents of the document. References are arranged in order by the original NSA abstract number which approximately places them in chronological order. Sequence numbers appear beside each reference, and the personal author index refers to these sequence numbers. The subject index refers to the original abstract numbers. (auth)

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.

PubMed

Rideout, Jai Ram; He, Yan; Navas-Molina, Jose A; Walters, William A; Ursell, Luke K; Gibbons, Sean M; Chase, John; McDonald, Daniel; Gonzalez, Antonio; Robbins-Pianka, Adam; Clemente, Jose C; Gilbert, Jack A; Huse, Susan M; Zhou, Hong-Wei; Knight, Rob; Caporaso, J Gregory

2014-01-01

We present a performance-optimized algorithm, subsampled open-reference OTU picking, for assigning marker gene (e.g., 16S rRNA) sequences generated on next-generation sequencing platforms to operational taxonomic units (OTUs) for microbial community analysis. This algorithm provides benefits over de novo OTU picking (clustering can be performed largely in parallel, reducing runtime) and closed-reference OTU picking (all reads are clustered, not only those that match a reference database sequence with high similarity). Because more of our algorithm can be run in parallel relative to "classic" open-reference OTU picking, it makes open-reference OTU picking tractable on massive amplicon sequence data sets (though on smaller data sets, "classic" open-reference OTU clustering is often faster). We illustrate that here by applying it to the first 15,000 samples sequenced for the Earth Microbiome Project (1.3 billion V4 16S rRNA amplicons). To the best of our knowledge, this is the largest OTU picking run ever performed, and we estimate that our new algorithm runs in less than 1/5 the time than would be required of "classic" open reference OTU picking. We show that subsampled open-reference OTU picking yields results that are highly correlated with those generated by "classic" open-reference OTU picking through comparisons on three well-studied datasets. An implementation of this algorithm is provided in the popular QIIME software package, which uses uclust for read clustering. All analyses were performed using QIIME's uclust wrappers, though we provide details (aided by the open-source code in our GitHub repository) that will allow implementation of subsampled open-reference OTU picking independently of QIIME (e.g., in a compiled programming language, where runtimes should be further reduced). Our analyses should generalize to other implementations of these OTU picking algorithms. Finally, we present a comparison of parameter settings in QIIME's OTU picking workflows and make recommendations on settings for these free parameters to optimize runtime without reducing the quality of the results. These optimized parameters can vastly decrease the runtime of uclust-based OTU picking in QIIME.

Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing.

PubMed

Kanda, Kojun; Pflug, James M; Sproul, John S; Dasenko, Mark A; Maddison, David R

2015-01-01

In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at least some low-copy nuclear protein-coding genes from all specimens. For example, in one 56-year-old beetle, 4.4 mm in length, our de novo assembly recovered about 63% of approximately 41,900 nucleotides in a target suite of 67 nuclear protein-coding gene fragments, and 70% using a reference-based assembly. Even in the least successfully sequenced carabid specimen, reference-based assembly yielded fragments that were at least 50% of the target length for 34 of 67 nuclear protein-coding gene fragments. Exploration of alternative references for reference-based assembly revealed few signs of bias created by the reference. For all specimens we recovered almost complete copies of ribosomal and mitochondrial genes. We verified the general accuracy of the sequences through comparisons with sequences obtained from PCR and Sanger sequencing, including of conspecific, fresh specimens, and through phylogenetic analysis that tested the placement of sequences in predicted regions. A few possible inaccuracies in the sequences were detected, but these rarely affected the phylogenetic placement of the samples. Although our sample sizes are low, an exploratory regression study suggests that the dominant factor in predicting success at recovering nuclear protein-coding genes is a high number of Illumina reads, with success at PCR of COI and killing by immersion in ethanol being secondary factors; in analyses of only high-read samples, the primary significant explanatory variable was body length, with small beetles being more successfully sequenced.

Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing

PubMed Central

Dasenko, Mark A.

2015-01-01

In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at least some low-copy nuclear protein-coding genes from all specimens. For example, in one 56-year-old beetle, 4.4 mm in length, our de novo assembly recovered about 63% of approximately 41,900 nucleotides in a target suite of 67 nuclear protein-coding gene fragments, and 70% using a reference-based assembly. Even in the least successfully sequenced carabid specimen, reference-based assembly yielded fragments that were at least 50% of the target length for 34 of 67 nuclear protein-coding gene fragments. Exploration of alternative references for reference-based assembly revealed few signs of bias created by the reference. For all specimens we recovered almost complete copies of ribosomal and mitochondrial genes. We verified the general accuracy of the sequences through comparisons with sequences obtained from PCR and Sanger sequencing, including of conspecific, fresh specimens, and through phylogenetic analysis that tested the placement of sequences in predicted regions. A few possible inaccuracies in the sequences were detected, but these rarely affected the phylogenetic placement of the samples. Although our sample sizes are low, an exploratory regression study suggests that the dominant factor in predicting success at recovering nuclear protein-coding genes is a high number of Illumina reads, with success at PCR of COI and killing by immersion in ethanol being secondary factors; in analyses of only high-read samples, the primary significant explanatory variable was body length, with small beetles being more successfully sequenced. PMID:26716693

Arrays of nucleic acid probes on biological chips

DOEpatents

Chee, Mark; Cronin, Maureen T.; Fodor, Stephen P. A.; Huang, Xiaohua X.; Hubbell, Earl A.; Lipshutz, Robert J.; Lobban, Peter E.; Morris, MacDonald S.; Sheldon, Edward L.

1998-11-17

DNA chips containing arrays of oligonucleotide probes can be used to determine whether a target nucleic acid has a nucleotide sequence identical to or different from a specific reference sequence. The array of probes comprises probes exactly complementary to the reference sequence, as well as probes that differ by one or more bases from the exactly complementary probes.

PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy.

PubMed

Decelle, Johan; Romac, Sarah; Stern, Rowena F; Bendif, El Mahdi; Zingone, Adriana; Audic, Stéphane; Guiry, Michael D; Guillou, Laure; Tessier, Désiré; Le Gall, Florence; Gourvil, Priscillia; Dos Santos, Adriana L; Probert, Ian; Vaulot, Daniel; de Vargas, Colomban; Christen, Richard

2015-11-01

Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing. © 2015 John Wiley & Sons Ltd.

Tsunami Catalogues for the Eastern Mediterranean - Revisited.

NASA Astrophysics Data System (ADS)

Ambraseys, N.; Synolakis, C. E.

2008-12-01

We critically examine examine tsunami catalogues of tsunamis in the Eastern Mediterranean published in the last decade, by reference to the original sources, see Ambraseys (2008). Such catalogues have been widely used in the aftermath of the 2004 Boxing Day tsunami for probabilistic hazard analysis, even to make projections for a ten year time frame. On occasion, such predictions have caused panic and have reduced the credibility of the scientific community in making hazard assessments. We correct classification and other spurious errors in earlier catalogues and posit a new list. We conclude that for some historic events, any assignment of magnitude, even on a six point intensity scale is inappropriate due to lack of information. Further we assert that any tsunami catalogue, including ours, can only be used in conjunction with sedimentologic evidence to quantitatively infer the return period of larger events. Statistical analyses correlating numbers of tsunami events derived solely from catalogues with their inferred or imagined intensities are meaningless, at least when focusing on specific locales where only a handful of tsunamis are known to have been historically reported. Quantitative hazard assessments based on scenario events of historic tsunamis for which -at best- only the size and approximate location of the parent earthquake is known should be undertaken with extreme caution and only with benefit of geologic studies to enhance the understanding of the local tectonics. Ambraseys N. (2008) Earthquakes in the Eastern Mediterranean and the Middle East: multidisciplinary study of 2000 years of seimicity, Cambridge Univ. Press, Cambridge (ISBN 9780521872928).

Cambridge community Optometry Glaucoma Scheme.

PubMed

Keenan, Jonathan; Shahid, Humma; Bourne, Rupert R; White, Andrew J; Martin, Keith R

2015-04-01

With a higher life expectancy, there is an increased demand for hospital glaucoma services in the United Kingdom. The Cambridge community Optometry Glaucoma Scheme (COGS) was initiated in 2010, where new referrals for suspected glaucoma are evaluated by community optometrists with a special interest in glaucoma, with virtual electronic review and validation by a consultant ophthalmologist with special interest in glaucoma. 1733 patients were evaluated by this scheme between 2010 and 2013. Clinical assessment is performed by the optometrist at a remote site. Goldmann applanation tonometry, pachymetry, monoscopic colour optic disc photographs and automated Humphrey visual field testing are performed. A clinical decision is made as to whether a patient has glaucoma or is a suspect, and referred on or discharged as a false positive referral. The clinical findings, optic disc photographs and visual field test results are transmitted electronically for virtual review by a consultant ophthalmologist. The number of false positive referrals from initial referral into the scheme. Of the patients, 46.6% were discharged at assessment and a further 5.7% were discharged following virtual review. Of the patients initially discharged, 2.8% were recalled following virtual review. Following assessment at the hospital, a further 10.5% were discharged after a single visit. The COGS community-based glaucoma screening programme is a safe and effective way of evaluating glaucoma referrals in the community and reducing false-positive referrals for glaucoma into the hospital system. © 2014 Royal Australian and New Zealand College of Ophthalmologists.

Mitochondrial DNA sequence analysis of four Alzheimer`s and Parkinson`s disease patients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, M.D.; Shoffner, J.M.; Wallace, D.C.

1996-01-22

The mitochondrial DNA (mtDNA) sequence was determined on 3 patients with Alzheimer`s disease (AD) exhibiting AD plus Parkinson`s disease (PD) neuropathologic changes and one patient with PD. Patient mtDNA sequences were compared to the standard Cambridge sequence to identify base changes. In the first AD + PD patient, 2 of the 15 nucleotide substitutions may contribute to the neuropathology, a nucleotide pair (np) 4336 transition in the tRNA{sup Gln} gene found 7.4 times more frequently in patients than in controls, and a unique np 721 transition in the 12S rRNA gene which was not found in 70 other patients ormore » 905 controls. In the second AD + PD patient, 27 nucleotide substitutions were detected, including an np 3397 transition in the ND1 gene which converts a conserved methionine to a valine. In the third AD + PD patient, 2 polymorphic base substitutions frequently found at increased frequency in Leber`s hereditary optic neuropathy patients were observed, an np 4216 transition in ND1 and an np 13708 transition in the ND5 gene. For the PD patient, 2 novel variants were observed among 25 base substitutions, an np 1709 substitution in the 16S rRNA gene and an np 15851 missense mutation in the cytb gene. Further studies will be required to demonstrate a casual role for these base substitutions in neurodegenerative disease. 68 refs., 2 tabs.« less

Determination of hematology and plasma chemistry reference intervals for 3 populations of captive Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus).

PubMed

Matsche, Mark A; Arnold, Jill; Jenkins, Erin; Townsend, Howard; Rosemary, Kevin

2014-09-01

The imperiled status of Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus), a large, long-lived, anadromous fish found along the Atlantic coast of North America, has prompted efforts at captive propagation for research and stock enhancement. The purpose of this study was to establish hematology and plasma chemistry reference intervals of captive Atlantic sturgeon maintained under different culture conditions. Blood specimens were collected from a total of 119 fish at 3 hatcheries: Lamar, PA (n = 36, ages 10-14 years); Chalk Point, MD (n = 40, siblings of Lamar); and Horn Point, Cambridge, MD (n = 43, mixed population from Chesapeake Bay). Reference intervals (using robust techniques), median, mean, and standard deviations were determined for WBC, RBC, thrombocytes, PCV, HGB, MCV, MCH, MCHC, and absolute counts for lymphocytes (L), neutrophils (N), monocytes, and eosinophils. Chemistry analytes included concentrations of total proteins, albumin, glucose, urea, calcium, phosphate, sodium, potassium, chloride, and globulins, AST, CK, and LDH activities, and osmolality. Mean concentrations of total proteins, albumin, and glucose were at or below the analytic range. Statistical comparisons showed significant differences among hatcheries for each remaining plasma chemistry analyte and for PCV, RBC, MCHC, MCH, eosinophil and monocyte counts, and N:L ratio throughout all 3 groups. Therefore, reference intervals were calculated separately for each population. Reference intervals for fish maintained under differing conditions should be established per population. © 2014 American Society for Veterinary Clinical Pathology and European Society for Veterinary Clinical Pathology.

Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study.

PubMed

Cerdeira, Louise Teixeira; Carneiro, Adriana Ribeiro; Ramos, Rommel Thiago Jucá; de Almeida, Sintia Silva; D'Afonseca, Vivian; Schneider, Maria Paula Cruz; Baumbach, Jan; Tauch, Andreas; McCulloch, John Anthony; Azevedo, Vasco Ariston Carvalho; Silva, Artur

2011-08-01

Due to the advent of the so-called Next-Generation Sequencing (NGS) technologies the amount of monetary and temporal resources for whole-genome sequencing has been reduced by several orders of magnitude. Sequence reads can be assembled either by anchoring them directly onto an available reference genome (classical reference assembly), or can be concatenated by overlap (de novo assembly). The latter strategy is preferable because it tends to maintain the architecture of the genome sequence the however, depending on the NGS platform used, the shortness of read lengths cause tremendous problems the in the subsequent genome assembly phase, impeding closing of the entire genome sequence. To address the problem, we developed a multi-pronged hybrid de novo strategy combining De Bruijn graph and Overlap-Layout-Consensus methods, which was used to assemble from short reads the entire genome of Corynebacterium pseudotuberculosis strain I19, a bacterium with immense importance in veterinary medicine that causes Caseous Lymphadenitis in ruminants, principally ovines and caprines. Briefly, contigs were assembled de novo from the short reads and were only oriented using a reference genome by anchoring. Remaining gaps were closed using iterative anchoring of short reads by craning to gap flanks. Finally, we compare the genome sequence assembled using our hybrid strategy to a classical reference assembly using the same data as input and show that with the availability of a reference genome, it pays off to use the hybrid de novo strategy, rather than a classical reference assembly, because more genome sequences are preserved using the former. Copyright © 2011 Elsevier B.V. All rights reserved.

DNA Sequences over the Internet Provide Greater Speed and Accuracy for Health Sciences Reference Librarians.

ERIC Educational Resources Information Center

Harzbecker, Joseph, Jr.

1993-01-01

Describes the National Institute of Health's GenBank DNA sequence database and how it can be accessed through the Internet. A real reference question, which was answered successfully using the database, is reproduced to illustrate and elaborate on the potential of the Internet for information retrieval. (10 references) (KRN)

In Living Memory: The Dying Art of Learning Poetry and a Case for Revival

ERIC Educational Resources Information Center

Pullinger, Debbie

2012-01-01

This article considers the practice of learning poems and the value of poetry in the memory, and emerges from the Cambridge Poetry Teaching Project, a small-scale research study co-ordinated through the Faculty of Education at the University of Cambridge. Drawing on the subset of findings in relation to learning and memory, the essay locates the…

Goals for Mathematical Education of Elementary School Teachers: A Report of the Cambridge Conference on Teacher Training.

ERIC Educational Resources Information Center

Education Development Center, Inc., Newton, MA.

This report is intended to provide attention to issues that the Cambridge Conference feels are related to the mathematical training of elementary school teachers. The document is divided into three parts. Part I, titled "The Problems and Proposals Towards the Solution," contains the following chapters: (1) Introduction to the Report; (2)…

An Experimental Text in Transformational Geometry, Student Text; Cambridge Conference on School Mathematics Feasibility Study No. 43a.

ERIC Educational Resources Information Center

Cambridge Conference on School Mathematics, Newton, MA.

This is part of a student text which was written with the aim of reflecting the thinking of The Cambridge Conference on School Mathematics (CCSM) regarding the goals and objectives for mathematics. The instructional materials were developed for teaching geometry in the secondary schools. This document is chapter six and titled Motions and…

[Geometry Through Symmetry, Cambridge Conference on School Mathematics Feasibility Study No. 32.

ERIC Educational Resources Information Center

Friedman, Bernard

These materials were written for the use of a class of eighth grade high ability students in a four week course sponsored by Educational Services Incorporated on the Stanford campus. They represent a practical response to the proposal by the Cambridge Conference of 1963 that geometry be taught by vector space methods. Instead of using vector…

Inequality Lessons at Adams School, Lexington; Cambridge Conference on School Mathematics Feasibility Study No. 42.

ERIC Educational Resources Information Center

Fitzgerald, B.

These materials were written with the aim of reflecting the thinking of The Cambridge Conference on School Mathematics (CCSM) regarding the goals and objectives for school mathematics. Presented are plans for teaching 15 inequality lessons for above average first grade students. The discovery approach is utilized by the teacher in order to involve…

A Flexible Approach to Quantifying Various Dimensions of Environmental Complexity

DTIC Science & Technology

2004-08-01

dissertation, Cambridge University, Cambridge, England, 1989. [15] C. J. C. H. Watkins and P. Dayan, “Q-learning,” Machine Learning , vol. 8, pp. 279–292, 1992...16] I. Szita, B. Takács, and A. Lörincz, “²-MDPs: Learning in varying environments,” Journal of Machine Learning Research, vol. 3, pp. 145–174, 2002

Problem Articulation and the Processes of Assistance: An Activity Theoretic View of Mediation in Game Play

ERIC Educational Resources Information Center

Stone, Lynda D.; Gutierrez, Kris D.

2007-01-01

In this article, we study a local adaptation of the Fifth Dimension [Cole, M. (1996). "Cultural psychology: A once and future discipline." Cambridge: Cambridge University Press] known as Las Redes (i.e., Networks of Collaboration in the Fifth Dimension) to examine how the multiple activity systems of Las Redes, e.g. the undergraduate course and…

"Please Do Not Leave Any Notes for the Cleaning Lady, as Many Do Not Speak English Fluently": Policy, Power, and Language Brokering in a Multilingual Workplace

ERIC Educational Resources Information Center

Gonçalves, Kellie; Schluter, Anne

2017-01-01

This article investigates the covert language policy and micro-language planning practices of one female Brazilian-American entrepreneur, Magda, within her multilingual cleaning company. Because Magda is plurilingual (Spolsky in "Language policy." Cambridge University Press, Cambridge, 2004), she is able to draw on her metalinguistic…

Satisficing Decision-Making in Supervisory Control. Part 2.

DTIC Science & Technology

1986-07-31

purpose of the United States Government. C-P Department of Mechanical Engineering Massachusetts Institute of Technology Cambridge, Massachusetts 02139...of Mechanical Engineering Massachusetts Institute of Technology Cambridge MA 02139 Satisficing Decision-Making in Supervisory Control Leonid Charny...example, that there are two attributes, speed and accuracy, and one is selecting a robot manipulator based -4n these two parameters. A set of alternatives

The Cambridge Primary Review: A Reply to R. J. Campbell

ERIC Educational Resources Information Center

Armstrong, Michael

2010-01-01

The author was disappointed by R. J. Campbell's sour critique of the Cambridge Primary Review in "FORUM" Volume 52 Number 1 2010. His description of the Review's proposals on curriculum and pedagogy as "backward-looking, cumbersome and partial" is such a bizarre misjudgement that it calls for some response. The author comments in turn on R. J.…

Robot Programming.

DTIC Science & Technology

1982-12-01

Paris, France, June, 1982, 519-530. Latoinbe, J. C. "Equipe Intelligence Artificielle et Robotique: Etat d’avancement des recherches," Laboratoire...8217AD-A127 233 ROBOT PROGRRMMING(U) MASSACHUSETTS INST OFGTECHi/ CAMBRIDGE ARTIFICIAL INTELLIGENCE LAB T LOZANO-PEREZ UNCLASSIFIED DC8 AI-9 N884...NAME AND ADDRESS 10. PROGRAM ELEMENT. PROJECT. TASK Artificial Intelligence Laboratory AREA I WORK UNIT NUMBERS ,. 545 Technology Square Cambridge

Quantum simulation of transverse Ising models with Rydberg atoms

NASA Astrophysics Data System (ADS)

Schauss, Peter

2018-04-01

Quantum Ising models are canonical models for the study of quantum phase transitions (Sachdev 1999 Quantum Phase Transitions (Cambridge: Cambridge University Press)) and are the underlying concept for many analogue quantum computing and quantum annealing ideas (Tanaka et al Quantum Spin Glasses, Annealing and Computation (Cambridge: Cambridge University Press)). Here we focus on the implementation of finite-range interacting Ising spin models, which are barely tractable numerically. Recent experiments with cold atoms have reached the interaction-dominated regime in quantum Ising magnets via optical coupling of trapped neutral atoms to Rydberg states. This approach allows for the tunability of all relevant terms in an Ising spin Hamiltonian with 1/{r}6 interactions in transverse and longitudinal fields. This review summarizes the recent progress of these implementations in Rydberg lattices with site-resolved detection. Strong correlations in quantum Ising models have been observed in several experiments, starting from a single excitation in the superatom regime up to the point of crystallization. The rapid progress in this field makes spin systems based on Rydberg atoms a promising platform for quantum simulation because of the unmatched flexibility and strength of interactions combined with high control and good isolation from the environment.

HPV-QUEST: A highly customized system for automated HPV sequence analysis capable of processing Next Generation sequencing data set.

PubMed

Yin, Li; Yao, Jiqiang; Gardner, Brent P; Chang, Kaifen; Yu, Fahong; Goodenow, Maureen M

2012-01-01

Next Generation sequencing (NGS) applied to human papilloma viruses (HPV) can provide sensitive methods to investigate the molecular epidemiology of multiple type HPV infection. Currently a genotyping system with a comprehensive collection of updated HPV reference sequences and a capacity to handle NGS data sets is lacking. HPV-QUEST was developed as an automated and rapid HPV genotyping system. The web-based HPV-QUEST subtyping algorithm was developed using HTML, PHP, Perl scripting language, and MYSQL as the database backend. HPV-QUEST includes a database of annotated HPV reference sequences with updated nomenclature covering 5 genuses, 14 species and 150 mucosal and cutaneous types to genotype blasted query sequences. HPV-QUEST processes up to 10 megabases of sequences within 1 to 2 minutes. Results are reported in html, text and excel formats and display e-value, blast score, and local and coverage identities; provide genus, species, type, infection site and risk for the best matched reference HPV sequence; and produce results ready for additional analyses.

Sequencing of individual chromosomes of plant pathogenic Fusarium oxysporum.

PubMed

Kashiwa, Takeshi; Kozaki, Toshinori; Ishii, Kazuo; Turgeon, B Gillian; Teraoka, Tohru; Komatsu, Ken; Arie, Tsutomu

2017-01-01

A small chromosome in reference isolate 4287 of F. oxysporum f. sp. lycopersici (Fol) has been designated as a 'pathogenicity chromosome' because it carries several pathogenicity related genes such as the Secreted In Xylem (SIX) genes. Sequence assembly of small chromosomes in other isolates, based on a reference genome template, is difficult because of karyotype variation among isolates and a high number of sequences associated with transposable elements. These factors often result in misassembly of sequences, making it unclear whether other isolates possess the same pathogenicity chromosome harboring SIX genes as in the reference isolate. To overcome this difficulty, single chromosome sequencing after Contour-clamped Homogeneous Electric Field (CHEF) separation of chromosomes was performed, followed by de novo assembly of sequences. The assembled sequences of individual chromosomes were consistent with results of probing gels of CHEF separated chromosomes with SIX genes. Individual chromosome sequencing revealed that several SIX genes are located on a single small chromosome in two pathogenic forms of F. oxysporum, beyond the reference isolate 4287, and in the cabbage yellows fungus F. oxysporum f. sp. conglutinans. The particular combination of SIX genes on each small chromosome varied. Moreover, not all SIX genes were found on small chromosomes; depending on the isolate, some were on big chromosomes. This suggests that recombination of chromosomes and/or translocation of SIX genes may occur frequently. Our method improves sequence comparison of small chromosomes among isolates. Copyright © 2016 Elsevier Inc. All rights reserved.

Development of the Fray-Farthing-Chen Cambridge Process: Towards the Sustainable Production of Titanium and Its Alloys

NASA Astrophysics Data System (ADS)

Hu, Di; Dolganov, Aleksei; Ma, Mingchan; Bhattacharya, Biyash; Bishop, Matthew T.; Chen, George Z.

2018-02-01

The Kroll process has been employed for titanium extraction since the 1950s. It is a labour and energy intensive multi-step semi-batch process. The post-extraction processes for making the raw titanium into alloys and products are also excessive, including multiple remelting steps. Invented in the late 1990s, the Fray-Farthing-Chen (FFC) Cambridge process extracts titanium from solid oxides at lower energy consumption via electrochemical reduction in molten salts. Its ability to produce alloys and powders, while retaining the cathode shape also promises energy and material efficient manufacturing. Focusing on titanium and its alloys, this article reviews the recent development of the FFC-Cambridge process in two aspects, (1) resource and process sustainability and (2) advanced post-extraction processing.

Completed Genome Sequences of Strains from 36 Serotypes of Salmonella

PubMed Central

Robertson, James; Yoshida, Catherine; Gurnik, Simone; Rankin, Marisa

2018-01-01

ABSTRACT We report here the completed closed genome sequences of strains representing 36 serotypes of Salmonella. These genome sequences will provide useful references for understanding the genetic variation between serotypes, particularly as references for mapping of raw reads or to create assemblies of higher quality, as well as to aid in studies of comparative genomics of Salmonella. PMID:29348347

Nuclear medicine. Bibliography from Nuclear Science Abstracts, Volumes 31--33

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1976-12-01

References to 4362 publications related to nuclear medicine announced in Nuclear Science Abstracts (NSA) volumes 31(Jan.--June 1975), 32(July--Dec. 1975), and 33(Jan.--June 1976) are contained in this bibliography. References are arranged in order by the original NSA abstract number which approximately places them in chronological order. Sequence numbers appear beside each reference, and the indexes refer to these sequence numbers. Indexes included are: Corporate, Personal Author, Subject, and Report Number.

HIA: a genome mapper using hybrid index-based sequence alignment.

PubMed

Choi, Jongpill; Park, Kiejung; Cho, Seong Beom; Chung, Myungguen

2015-01-01

A number of alignment tools have been developed to align sequencing reads to the human reference genome. The scale of information from next-generation sequencing (NGS) experiments, however, is increasing rapidly. Recent studies based on NGS technology have routinely produced exome or whole-genome sequences from several hundreds or thousands of samples. To accommodate the increasing need of analyzing very large NGS data sets, it is necessary to develop faster, more sensitive and accurate mapping tools. HIA uses two indices, a hash table index and a suffix array index. The hash table performs direct lookup of a q-gram, and the suffix array performs very fast lookup of variable-length strings by exploiting binary search. We observed that combining hash table and suffix array (hybrid index) is much faster than the suffix array method for finding a substring in the reference sequence. Here, we defined the matching region (MR) is a longest common substring between a reference and a read. And, we also defined the candidate alignment regions (CARs) as a list of MRs that is close to each other. The hybrid index is used to find candidate alignment regions (CARs) between a reference and a read. We found that aligning only the unmatched regions in the CAR is much faster than aligning the whole CAR. In benchmark analysis, HIA outperformed in mapping speed compared with the other aligners, without significant loss of mapping accuracy. Our experiments show that the hybrid of hash table and suffix array is useful in terms of speed for mapping NGS sequencing reads to the human reference genome sequence. In conclusion, our tool is appropriate for aligning massive data sets generated by NGS sequencing.

A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping

PubMed Central

2012-01-01

Background Most modern citrus cultivars have an interspecific origin. As a foundational step towards deciphering the interspecific genome structures, a reference whole genome sequence was produced by the International Citrus Genome Consortium from a haploid derived from Clementine mandarin. The availability of a saturated genetic map of Clementine was identified as an essential prerequisite to assist the whole genome sequence assembly. Clementine is believed to be a ‘Mediterranean’ mandarin × sweet orange hybrid, and sweet orange likely arose from interspecific hybridizations between mandarin and pummelo gene pools. The primary goals of the present study were to establish a Clementine reference map using codominant markers, and to perform comparative mapping of pummelo, sweet orange, and Clementine. Results Five parental genetic maps were established from three segregating populations, which were genotyped with Single Nucleotide Polymorphism (SNP), Simple Sequence Repeats (SSR) and Insertion-Deletion (Indel) markers. An initial medium density reference map (961 markers for 1084.1 cM) of the Clementine was established by combining male and female Clementine segregation data. This Clementine map was compared with two pummelo maps and a sweet orange map. The linear order of markers was highly conserved in the different species. However, significant differences in map size were observed, which suggests a variation in the recombination rates. Skewed segregations were much higher in the male than female Clementine mapping data. The mapping data confirmed that Clementine arose from hybridization between ‘Mediterranean’ mandarin and sweet orange. The results identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome. Conclusions A reference genetic map of citrus, used to facilitate the chromosome assembly of the first citrus reference genome sequence, was established. The high conservation of marker order observed at the interspecific level should allow reasonable inferences of most citrus genome sequences by mapping next-generation sequencing (NGS) data in the reference genome sequence. The genome of the haploid Clementine used to establish the citrus reference genome sequence appears to have been inherited primarily from the ‘Mediterranean’ mandarin. The high frequency of skewed allelic segregations in the male Clementine data underline the probable extent of deviation from Mendelian segregation for characters controlled by heterozygous loci in male parents. PMID:23126659

Software for pre-processing Illumina next-generation sequencing short read sequences

PubMed Central

2014-01-01

Background When compared to Sanger sequencing technology, next-generation sequencing (NGS) technologies are hindered by shorter sequence read length, higher base-call error rate, non-uniform coverage, and platform-specific sequencing artifacts. These characteristics lower the quality of their downstream analyses, e.g. de novo and reference-based assembly, by introducing sequencing artifacts and errors that may contribute to incorrect interpretation of data. Although many tools have been developed for quality control and pre-processing of NGS data, none of them provide flexible and comprehensive trimming options in conjunction with parallel processing to expedite pre-processing of large NGS datasets. Methods We developed ngsShoRT (next-generation sequencing Short Reads Trimmer), a flexible and comprehensive open-source software package written in Perl that provides a set of algorithms commonly used for pre-processing NGS short read sequences. We compared the features and performance of ngsShoRT with existing tools: CutAdapt, NGS QC Toolkit and Trimmomatic. We also compared the effects of using pre-processed short read sequences generated by different algorithms on de novo and reference-based assembly for three different genomes: Caenorhabditis elegans, Saccharomyces cerevisiae S288c, and Escherichia coli O157 H7. Results Several combinations of ngsShoRT algorithms were tested on publicly available Illumina GA II, HiSeq 2000, and MiSeq eukaryotic and bacteria genomic short read sequences with the focus on removing sequencing artifacts and low-quality reads and/or bases. Our results show that across three organisms and three sequencing platforms, trimming improved the mean quality scores of trimmed sequences. Using trimmed sequences for de novo and reference-based assembly improved assembly quality as well as assembler performance. In general, ngsShoRT outperformed comparable trimming tools in terms of trimming speed and improvement of de novo and reference-based assembly as measured by assembly contiguity and correctness. Conclusions Trimming of short read sequences can improve the quality of de novo and reference-based assembly and assembler performance. The parallel processing capability of ngsShoRT reduces trimming time and improves the memory efficiency when dealing with large datasets. We recommend combining sequencing artifacts removal, and quality score based read filtering and base trimming as the most consistent method for improving sequence quality and downstream assemblies. ngsShoRT source code, user guide and tutorial are available at http://research.bioinformatics.udel.edu/genomics/ngsShoRT/. ngsShoRT can be incorporated as a pre-processing step in genome and transcriptome assembly projects. PMID:24955109

Discovery of common sequences absent in the human reference genome using pooled samples from next generation sequencing.

PubMed

Liu, Yu; Koyutürk, Mehmet; Maxwell, Sean; Xiang, Min; Veigl, Martina; Cooper, Richard S; Tayo, Bamidele O; Li, Li; LaFramboise, Thomas; Wang, Zhenghe; Zhu, Xiaofeng; Chance, Mark R

2014-08-16

Sequences up to several megabases in length have been found to be present in individual genomes but absent in the human reference genome. These sequences may be common in populations, and their absence in the reference genome may indicate rare variants in the genomes of individuals who served as donors for the human genome project. As the reference genome is used in probe design for microarray technology and mapping short reads in next generation sequencing (NGS), this missing sequence could be a source of bias in functional genomic studies and variant analysis. One End Anchor (OEA) and/or orphan reads from paired-end sequencing have been used to identify novel sequences that are absent in reference genome. However, there is no study to investigate the distribution, evolution and functionality of those sequences in human populations. To systematically identify and study the missing common sequences (micSeqs), we extended the previous method by pooling OEA reads from large number of individuals and applying strict filtering methods to remove false sequences. The pipeline was applied to data from phase 1 of the 1000 Genomes Project. We identified 309 micSeqs that are present in at least 1% of the human population, but absent in the reference genome. We confirmed 76% of these 309 micSeqs by comparison to other primate genomes, individual human genomes, and gene expression data. Furthermore, we randomly selected fifteen micSeqs and confirmed their presence using PCR validation in 38 additional individuals. Functional analysis using published RNA-seq and ChIP-seq data showed that eleven micSeqs are highly expressed in human brain and three micSeqs contain transcription factor (TF) binding regions, suggesting they are functional elements. In addition, the identified micSeqs are absent in non-primates and show dynamic acquisition during primate evolution culminating with most micSeqs being present in Africans, suggesting some micSeqs may be important sources of human diversity. 76% of micSeqs were confirmed by a comparative genomics approach. Fourteen micSeqs are expressed in human brain or contain TF binding regions. Some micSeqs are primate-specific, conserved and may play a role in the evolution of primates.

Windows of Opportunity: East Timor and Australian Strategic Decision Making (1975-1999)

DTIC Science & Technology

2014-06-01

could not be further from the truth. Australia has always been consistent, adjusting its foreign policy to take advantage of shifting international ... International Security. Cambridge; New York: Cambridge University Press, 2003. Carey, P. B. R, and G. Carter Bentley. East Timor at the Crossroads: The...DISTRIBUTION A. Approved for public release: distribution unlimited. WINDOWS OF OPPORTUNITY: EAST TIMOR AND AUSTRALIAN STRATEGIC DECISION

Undergraduate-postgraduate astronomy in Cambridge - a student's perspective

NASA Astrophysics Data System (ADS)

Williams, Robin

1991-01-01

This article describes the astronomical scene at Cambridge University from the point of view of a one-time graduate there: I'm now a first-year postgraduate. I progressed from an interest in Maths and Physics at sixth-form level to a degree in Physics and Theoretical Physics, a postgraduate Applied Maths and Theoretical Physics course (Part III) and now to the Institute of Astronomy.

Use of a Photosimulation Laboratory for Estimating Vehicle Detection Probability and Comparing Detection Metrics

DTIC Science & Technology

2003-04-15

the monitors, the authors are confident that the color fidelity is accurate. The primary physical difference of field versus lab tests is the level... Creelman , C. Douglas, Detection theory: A user’s guide, Cambridge University Press, Cambridge, U.K., 1991, pp. 189-190. *For more information, contact Dr. Thomas Meitzler at (586) 574-5405, email: meitzlet@tacom.army.mil

Provisional Approaches to Goals for School Mathematics; Cambridge Conference on School Mathematics Feasibility Study No. 37.

ERIC Educational Resources Information Center

Cambridge Conference on School Mathematics, Newton, MA.

These materials were written with the aim of reflecting the thinking of Cambridge Conference on School Mathematics (CCSM) regarding the goals and objectives for school mathematics K-6. In view of the experiences of other curriculum groups and of the general discussions since 1963, the present report initiates the next step in evolving the "Goals".…

Trajectories of Offending and Their Relation to Life Failure in Late Middle Age: Findings from the Cambridge Study in Delinquent Development

ERIC Educational Resources Information Center

Piquero, Alex R.; Farrington, David P.; Nagin, Daniel S.; Moffitt, Terrie E.

2010-01-01

Researchers have hypothesized that over the life course, criminal offending varies with problems in other domains, including life failure and physical and mental health. To examine this issue, the authors use data from the Cambridge Study in Delinquent Development, a prospective longitudinal survey of 411 South London males first studied at age 8…

Preparing for College Success: Exploring the Impact of the High School Cambridge Acceleration Program on U.S. University Students

ERIC Educational Resources Information Center

Shaw, Stuart D.; Werno, Magda A.

2016-01-01

This case study sought to gain a better understanding of the impact of the Cambridge Acceleration Program on students' transition from high school to college at one American university. The findings from an online questionnaire indicate that many participants develop a range of skills that are perceived as important in the context of university…

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 4. Examples of Discovery-Based Learning Using the Complete Cambridge Structural Database

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

2011-01-01

Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 3. The Cambridge Structural Database System: Information Content and Access Software in Educational Applications

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

2011-01-01

Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

Classification of Complex Sounds.

DTIC Science & Technology

1992-10-31

spectral weights may be useful in developing signal enhancement techniques based on psychological aspects of the listener (providing a complement to...Journals) Green, D.M., and Berg, B.G. (1991). Spectral weights and the profile bowl. Quarterly Journal of Experimental Psychology , 43A, 449-458. Dai, H...Macmillan and C.D. Creelman . Cambridge/NY: Cambridge Universi- ty Press, 1991.) J. Math. Psych., in press. Training Currently, there are two graduate

Performance on Cambridge Neuropsychological Test Automated Battery Subtests Sensitive to Frontal Lobe Function in People with Autistic Disorder: Evidence from the Collaborative Programs of Excellence in Autism Network

ERIC Educational Resources Information Center

Ozonoff, Sally; Cook, Ian; Coon, Hilary; Dawson, Geraldine; Joseph, Robert M.; Klin, Ami; McMahon, William M.; Minshew, Nancy; Munson, Jeffrey A.

2004-01-01

Recent structural and functional imaging work, as well as neuropathology and neuropsychology studies, provide strong empirical support for the involvement of frontal cortex in autism. The Cambridge Neuropsychological Test Automated Battery (CANTAB) is a computer-administered set of neuropsychological tests developed to examine specific components…

Beaches of the Future: Analyzing Territorial Disputes in South America

DTIC Science & Technology

2016-09-01

Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204, Arlington, VA 22202-4302, and to the Office of Management and Budget, Paperwork...in the Twentieth Century (Cambridge: Cambridge University Press, 2002), 16. 28 Ibid. 11 realist approach that finds leaders concurrently managing ...United Kingdom107 Alternatively, these arbitration treaties managed to cool tensions between the Argentina and Chile, two stockpiling players involved

COmmunications and Networking with QUantum Operationally-Secure Technology for Maritime Deployment (CONQUEST)

DTIC Science & Technology

2017-03-06

Raytheon BBN Technologies ; Dr. Saikat Guha Contractor Address: 10 Moulton Street, Cambridge, MA 02138 Title of the Project : COmmunications and...BBN Technologies 10 Moulton Street Cambridge, MA 02138 6 March 2017 US Navy Office of Naval Research One Liberty Center 875 North Randolph...Networking with QUantum operationally-Secure Technology for Maritime Deployment (CONQUEST) Contract Period of Performance: 2 September 2016 – 1

Generic Software for Emulating Multiprocessor Architectures.

DTIC Science & Technology

1985-05-01

RD-A157 662 GENERIC SOFTWARE FOR EMULATING MULTIPROCESSOR 1/2 AlRCHITECTURES(J) MASSACHUSETTS INST OF TECH CAMBRIDGE U LRS LAB FOR COMPUTER SCIENCE R...AREA & WORK UNIT NUMBERS MIT Laboratory for Computer Science 545 Technology Square Cambridge, MA 02139 ____________ I I. CONTROLLING OFFICE NAME AND...aide If neceeasy end Identify by block number) Computer architecture, emulation, simulation, dataf low 20. ABSTRACT (Continue an reverse slde It

Intelligence Collection Targeting and Interdiction of Dark Networks

DTIC Science & Technology

2014-06-01

2006): 346. 26 Wouter de Nooy, Andrej Mrvar , and Vladimir Batagelj . Exploratory Social Network Analysis with Pajek, 2nd ed. (Cambridge: Cambridge...Pittsburgh, PA: Carnegie Mellon University, 2013. de Nooy, Wouter, Andrej Mrvar , and Vladimir Batagelj . Exploratory Social Network Analysis with...al-Qaeda’s leaders had closely followed the April 1996 assassination of Dzhokhar Dudayev, the Chechen prime minister, who was killed by a Russian

Investigation of Elliptical Cooling Channels for a Naval Electromagnetic Railgun

DTIC Science & Technology

2005-05-09

Numerical Recipes in C : The Art of Scientific Computing, Second Edition. Cambridge: Cambridge University Press, 1992. Ramanujan , S. Ramanujan’s...by Midshipman 1/ c Elizabeth R. Kealey, Class of 2005 United States Naval Academy Annapolis, MD ___________________________________ (signature...system 55 10 Equation 46: Fourier number 55 Equation 47: General heat equation with coefficients a, b, c , and d 55 Equation 48: Tridiagonal matrix

Assisting Design Given Multiple Performance Criteria

DTIC Science & Technology

1988-08-01

with uninstantiated operators is created then each operator’s implementation is selected. g - Keywords: computer-aided design, artificial...IEEE Trans- actions on Software Engineering, SE-7(1), 1981. [BG86] Forrest D. Brewer and Daniel D. Gajski . An expert-system paradigm for de- sign. In...Teukolsky, api William T. Vet- terling. Numerical Recipes. Cambridge University Press, Cambridge, England, 1987. [RFS83] G . G . Rassweiler, M. D

Investigation of Prolific Sheep from UK and Ireland for Evidence on Origin of the Mutations in BMP15 (FecXG, FecXB) and GDF9 (FecGH) in Belclare and Cambridge Sheep

PubMed Central

Mullen, Michael P.; Hanrahan, James P.; Howard, Dawn J.

2013-01-01

This paper concerns the likely origin of three mutations with large effects on ovulation rate identified in the Belclare and Cambridge sheep breeds; two in the BMP15 gene (FecXG and FecXB) and the third (FecGH) in GDF9. All three mutations segregate in Belclare sheep while one, FecXB, has not been found in the Cambridge. Both Belclare and Cambridge breeds are relatively recently developed composites that have common ancestry through the use of genetic material from the Finnish Landrace and Lleyn breeds. The development of both composites also involved major contributions from exceptionally prolific ewes screened from flocks in Ireland (Belclare) and Britain (Cambridge) during the 1960s. The objective of the current study was to establish the likely origin of the mutations (FecXG, FecXB and FecGH) through analysis of DNA from Finnish Landrace and Lleyn sheep, and Galway and Texel breeds which contributed to the development of the Belclare breed. Ewes with exceptionally high prolificacy (hyper-prolific ewes) in current flocks on Irish farms were identified to simulate the screening of ewes from Irish flocks in the 1960s. DNA was obtained from: prolific ewes in extant flocks of Lleyn sheep (n = 44) on the Lleyn peninsula in Wales; hyper-prolific ewes (n = 41); prolific Galway (n = 41) ewes; Finnish Landrace (n = 124) and Texel (n = 19) ewes. The FecXG mutation was identified in Lleyn but not in Finnish Landrace, Galway or Texel sheep; FecXB was only found among the hyper-prolific ewes. The FecGH mutation was identified in the sample of Lleyn sheep. It was concluded from these findings that the Lleyn breed was the most likely source of the FecXG and FecGH mutations in Belclare and Cambridge sheep and that the FecXB mutation came from the High Fertility line that was developed using prolific ewes selected from commercial flocks in Ireland in the 1960′s and subsequently used in the genesis of the Belclare. PMID:23301039

SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses.

PubMed

Barker, Michael S; Dlugosch, Katrina M; Reddy, A Chaitanya C; Amyotte, Sarah N; Rieseberg, Loren H

2009-02-15

Scaffolded and Corrected Assembly of Roche 454 (SCARF) is a next-generation sequence assembly tool for evolutionary genomics that is designed especially for assembling 454 EST sequences against high-quality reference sequences from related species. The program was created to knit together 454 contigs that do not assemble during traditional de novo assembly, using a reference sequence library to orient the 454 sequences. SCARF is freely available at http://msbarker.com/software.htm, and is released under the open source GPLv3 license (http://www.opensource.org/licenses/gpl-3.0.html.

Two new computational methods for universal DNA barcoding: a benchmark using barcode sequences of bacteria, archaea, animals, fungi, and land plants.

PubMed

Tanabe, Akifumi S; Toju, Hirokazu

2013-01-01

Taxonomic identification of biological specimens based on DNA sequence information (a.k.a. DNA barcoding) is becoming increasingly common in biodiversity science. Although several methods have been proposed, many of them are not universally applicable due to the need for prerequisite phylogenetic/machine-learning analyses, the need for huge computational resources, or the lack of a firm theoretical background. Here, we propose two new computational methods of DNA barcoding and show a benchmark for bacterial/archeal 16S, animal COX1, fungal internal transcribed spacer, and three plant chloroplast (rbcL, matK, and trnH-psbA) barcode loci that can be used to compare the performance of existing and new methods. The benchmark was performed under two alternative situations: query sequences were available in the corresponding reference sequence databases in one, but were not available in the other. In the former situation, the commonly used "1-nearest-neighbor" (1-NN) method, which assigns the taxonomic information of the most similar sequences in a reference database (i.e., BLAST-top-hit reference sequence) to a query, displays the highest rate and highest precision of successful taxonomic identification. However, in the latter situation, the 1-NN method produced extremely high rates of misidentification for all the barcode loci examined. In contrast, one of our new methods, the query-centric auto-k-nearest-neighbor (QCauto) method, consistently produced low rates of misidentification for all the loci examined in both situations. These results indicate that the 1-NN method is most suitable if the reference sequences of all potentially observable species are available in databases; otherwise, the QCauto method returns the most reliable identification results. The benchmark results also indicated that the taxon coverage of reference sequences is far from complete for genus or species level identification in all the barcode loci examined. Therefore, we need to accelerate the registration of reference barcode sequences to apply high-throughput DNA barcoding to genus or species level identification in biodiversity research.

Two New Computational Methods for Universal DNA Barcoding: A Benchmark Using Barcode Sequences of Bacteria, Archaea, Animals, Fungi, and Land Plants

PubMed Central

Tanabe, Akifumi S.; Toju, Hirokazu

2013-01-01

Taxonomic identification of biological specimens based on DNA sequence information (a.k.a. DNA barcoding) is becoming increasingly common in biodiversity science. Although several methods have been proposed, many of them are not universally applicable due to the need for prerequisite phylogenetic/machine-learning analyses, the need for huge computational resources, or the lack of a firm theoretical background. Here, we propose two new computational methods of DNA barcoding and show a benchmark for bacterial/archeal 16S, animal COX1, fungal internal transcribed spacer, and three plant chloroplast (rbcL, matK, and trnH-psbA) barcode loci that can be used to compare the performance of existing and new methods. The benchmark was performed under two alternative situations: query sequences were available in the corresponding reference sequence databases in one, but were not available in the other. In the former situation, the commonly used “1-nearest-neighbor” (1-NN) method, which assigns the taxonomic information of the most similar sequences in a reference database (i.e., BLAST-top-hit reference sequence) to a query, displays the highest rate and highest precision of successful taxonomic identification. However, in the latter situation, the 1-NN method produced extremely high rates of misidentification for all the barcode loci examined. In contrast, one of our new methods, the query-centric auto-k-nearest-neighbor (QCauto) method, consistently produced low rates of misidentification for all the loci examined in both situations. These results indicate that the 1-NN method is most suitable if the reference sequences of all potentially observable species are available in databases; otherwise, the QCauto method returns the most reliable identification results. The benchmark results also indicated that the taxon coverage of reference sequences is far from complete for genus or species level identification in all the barcode loci examined. Therefore, we need to accelerate the registration of reference barcode sequences to apply high-throughput DNA barcoding to genus or species level identification in biodiversity research. PMID:24204702

DUK - A Fast and Efficient Kmer Based Sequence Matching Tool

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Mingkun; Copeland, Alex; Han, James

2011-03-21

A new tool, DUK, is developed to perform matching task. Matching is to find whether a query sequence partially or totally matches given reference sequences or not. Matching is similar to alignment. Indeed many traditional analysis tasks like contaminant removal use alignment tools. But for matching, there is no need to know which bases of a query sequence matches which position of a reference sequence, it only need know whether there exists a match or not. This subtle difference can make matching task much faster than alignment. DUK is accurate, versatile, fast, and has efficient memory usage. It uses Kmermore » hashing method to index reference sequences and Poisson model to calculate p-value. DUK is carefully implemented in C++ in object oriented design. The resulted classes can also be used to develop other tools quickly. DUK have been widely used in JGI for a wide range of applications such as contaminant removal, organelle genome separation, and assembly refinement. Many real applications and simulated dataset demonstrate its power.« less

Children's reasoning about physics within and across ontological kinds.

PubMed

Heyman, Gail D; Phillips, Ann T; Gelman, Susan A

2003-08-01

Reasoning about seven physics principles within and across ontological kinds was examined among 188 5- and 7-year-olds and 59 adults. Individuals in all age groups tended to appropriately generalize what they learned across ontological kinds. However, children also showed sensitivity to ontological kind in their projections: when learning principles with reference to people they were more likely to assume that the principles apply to another person than to an inanimate object, and when learning with reference to an inanimate object they were more likely to assume that the principles apply to another inanimate object than to a person. Five-year-olds, but not 7-year-olds, projected concepts learned about people to a greater extent than principles learned about inanimate objects, closely paralleling the findings of Carey for the biological domain (Carey, S. (1985). Conceptual change in childhood. Cambridge, MA: MIT Press). Results from a separate sample of 22 5-year-olds suggest that the primary findings cannot be explained by response perseveration. The present findings indicate that children understand physics principles that apply to both animate and inanimate objects, but distinguish between these ontological kinds.

Reconfiguring the optics of the critical gaze in science education (after the critique of critique): (re)thinking "what counts" through Foucaultian prismatics

NASA Astrophysics Data System (ADS)

Higgins, Marc

2018-03-01

The purpose of this article is to explore what Michel Foucault refers to as "the" critical attitude and its relationship to science education, drawing from Foucault's (The politics of truth. Semiotext(e), New York, 1997) insight that the critical attitude is but a critical attitude. This article is a rejoinder to Anna Danielsonn, Maria Berge, and Malena Lidar's paper, "Knowledge and power in the technology classroom: a framework for studying teachers and students in action". Where Danielsonn and colleagues think with Foucaultian power/knowledge to examine and (re)consider teacher-student didactic relations in science and technology education, this article critically examines the power/knowledge relationship between science educators and science education to critically explore the modes of criticality produced and produceable. Particularly, I explore possibilities for and of critique that stem from and respond to what Bruno Latour (Politics of nature: How to bring the sciences into democracy. Harvard University Press, Cambridge, 1993) refers to as the crisis and critique of critique.

Response and Commentary.

PubMed

Pocock, J G A

2016-01-01

Barbarism and Religion, the first half of J. G. A. Pocock's study of Gibbon's Decline and Fall, was designed to set Gibbon's work in context, using a method developed in Cambridge, by juxtaposing his narrative to many others-to some but not all of which he explicitly referred. Helena Rosenblatt has misunderstood Pocock's intent, which was to show that Gibbon's work took much of its inspiration for its treatment of Christianity from a world of ecclesiastical scholarship. Though Pierre Force shows that Voltaire's erudition was richer than has been thought, he and Gibbon pursued very different forms of learning. And though Pocock agrees with Jonathan Israel that many thinkers challenged traditional Christian theology, their efforts were far more varied than Israel holds. Brief studies of Jean LeClerc and Ralph call Israel's vision of radical Enlightenment into question.

Genome Sequencing of Steroid Producing Bacteria Using Ion Torrent Technology and a Reference Genome.

PubMed

Sola-Landa, Alberto; Rodríguez-García, Antonio; Barreiro, Carlos; Pérez-Redondo, Rosario

2017-01-01

The Next-Generation Sequencing technology has enormously eased the bacterial genome sequencing and several tens of thousands of genomes have been sequenced during the last 10 years. Most of the genome projects are published as draft version, however, for certain applications the complete genome sequence is required.In this chapter, we describe the strategy that allowed the complete genome sequencing of Mycobacterium neoaurum NRRL B-3805, an industrial strain exploited for steroid production, using Ion Torrent sequencing reads and the genome of a close strain as the reference. This protocol can be applied to analyze the genetic variations between closely related strains; for example, to elucidate the point mutations between a parental strain and a random mutagenesis-derived mutant.

Physical Causation. Phil Dowe, Physical causation (Cambridge Studies in Probability, Induction, and Decision Theory), Cambridge University Press, Cambridge, 2000, pp. ix+224, price US60.00, ISBN: 0-521-78049-7 hbk

NASA Astrophysics Data System (ADS)

Hausman, Daniel M.

Causation is a frustrating subject. Suppose one begins with some promising idea such as that causation is counterfactual dependence or statistical relevance. One then develops this idea with care and intelligence, revises and improves it to cope with criticisms, and by the time one is finished, sane people will be looking elsewhere. If one wants conclusive reasons to reject the counterfactual theory of causation, one can do no better than to read Lewis' (1986) many postscripts. If one wants the best refutation of a probabilistic theory of causation, then one should read my colleague, Ellery Eells' (1991) magisterial defense. In Physical Causation, Phil Dowe performs the same service for physical process/interaction theories of causation.

A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts.

PubMed

Nilsson, R Henrik; Tedersoo, Leho; Ryberg, Martin; Kristiansson, Erik; Hartmann, Martin; Unterseher, Martin; Porter, Teresita M; Bengtsson-Palme, Johan; Walker, Donald M; de Sousa, Filipe; Gamper, Hannes Andres; Larsson, Ellen; Larsson, Karl-Henrik; Kõljalg, Urmas; Edgar, Robert C; Abarenkov, Kessy

2015-01-01

The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric-artificially joined-DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation.

A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts

PubMed Central

Nilsson, R. Henrik; Tedersoo, Leho; Ryberg, Martin; Kristiansson, Erik; Hartmann, Martin; Unterseher, Martin; Porter, Teresita M.; Bengtsson-Palme, Johan; Walker, Donald M.; de Sousa, Filipe; Gamper, Hannes Andres; Larsson, Ellen; Larsson, Karl-Henrik; Kõljalg, Urmas; Edgar, Robert C.; Abarenkov, Kessy

2015-01-01

The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric—artificially joined—DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation. PMID:25786896

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.

PubMed

Wymant, Chris; Blanquart, François; Golubchik, Tanya; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Croucher, Nicholas J; Hall, Matthew; Hillebregt, Mariska; Ong, Swee Hoe; Ratmann, Oliver; Albert, Jan; Bannert, Norbert; Fellay, Jacques; Fransen, Katrien; Gourlay, Annabelle; Grabowski, M Kate; Gunsenheimer-Bartmeyer, Barbara; Günthard, Huldrych F; Kivelä, Pia; Kouyos, Roger; Laeyendecker, Oliver; Liitsola, Kirsi; Meyer, Laurence; Porter, Kholoud; Ristola, Matti; van Sighem, Ard; Berkhout, Ben; Cornelissen, Marion; Kellam, Paul; Reiss, Peter; Fraser, Christophe

2018-01-01

Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user's choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver's constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also successfully applied shiver to whole-genome samples of Hepatitis C Virus and Respiratory Syncytial Virus. shiver is publicly available from https://github.com/ChrisHIV/shiver.

Unraveling systematic inventory of Echinops (Asteraceae) with special reference to nrDNA ITS sequence-based molecular typing of Echinops abuzinadianus.

PubMed

Ali, M A; Al-Hemaid, F M; Lee, J; Hatamleh, A A; Gyulai, G; Rahman, M O

2015-10-02

The present study explored the systematic inventory of Echinops L. (Asteraceae) of Saudi Arabia, with special reference to the molecular typing of Echinops abuzinadianus Chaudhary, an endemic species to Saudi Arabia, based on the internal transcribed spacer (ITS) sequences (ITS1-5.8S-ITS2) of nuclear ribosomal DNA. A sequence similarity search using BLAST and a phylogenetic analysis of the ITS sequence of E. abuzinadianus revealed a high level of sequence similarity with E. glaberrimus DC. (section Ritropsis). The novel primary sequence and the secondary structure of ITS2 of E. abuzinadianus could potentially be used for molecular genotyping.

Native South American genetic structure and prehistory inferred from hierarchical modeling of mtDNA.

PubMed

Lewis, Cecil M; Long, Jeffrey C

2008-03-01

Genetic diversity in Native South Americans forms a complex pattern at both the continental and local levels. In comparing the West to the East, there is more variation within groups and smaller genetic distances between groups. From this pattern, researchers have proposed that there is more variation in the West and that a larger, more genetically diverse, founding population entered the West than the East. Here, we question this characterization of South American genetic variation and its interpretation. Our concern arises because others have inferred regional variation from the mean variation within local populations without taking into account the variation among local populations within the same region. This failure produces a biased view of the actual variation in the East. In this study, we analyze the mitochondrial DNA sequence between positions 16040 and 16322 of the Cambridge reference sequence. Our sample represents a total of 886 people from 27 indigenous populations from South (22), Central (3), and North America (2). The basic unit of our analyses is nucleotide identity by descent, which is easily modeled and proportional to nucleotide diversity. We use a forward modeling strategy to fit a series of nested models to identity by descent within and between all pairs of local populations. This method provides estimates of identity by descent at different levels of population hierarchy without assuming homogeneity within populations, regions, or continents. Our main discovery is that Eastern South America harbors more genetic variation than has been recognized. We find no evidence that there is increased identity by descent in the East relative to the total for South America. By contrast, we discovered that populations in the Western region, as a group, harbor more identity by descent than has been previously recognized, despite the fact that average identity by descent within groups is lower. In this light, there is no need to postulate separate founding populations for the East and the West because the variability in the East could serve as a source for the Western gene pools.

In America’s Wake: A Comparison of Rising Power Foreign Policies

DTIC Science & Technology

2016-06-01

judgments or pronouncements as to the propriety or impropriety of any particular course of action. The author is unconvinced that ex post facto ...Expansion, 3rd ed, Cambridge Imperial and Post -Colonial Studies Series (Houndmills, Basingstoke, Hampshire ; New York: Palgrave/Macmillan, 2002), 14...Century, 1815-1914: A Study of Empire and Expansion, 3rd ed, Cambridge Imperial and Post -Colonial Studies Series (Houndmills, Basingstoke, Hampshire

Motion Simulation in the Environment for Auditory Research

DTIC Science & Technology

2011-08-01

Toolbox, Centre for Digital Music , Queen Mary University of London, 2009. http://www.isophonics.net/content/spatial-audio- matlab-toolbox (accessed July 27...this work. 46 Student Bio I studied Music Technology at Northwestern University, graduating as valedictorian of the School of... Music in 2008. In 2009, I was awarded the Gates Cambridge Scholarship to fund a postgraduate degree at the University of Cambridge. I read for a

Goals for the Correlation of Elementary Science and Mathematics; The Report of the Cambridge Conference on the Correlation of Science and Mathematics in Schools.

ERIC Educational Resources Information Center

Cambridge Conference on School Mathematics, Newton, MA.

This is The Report of the 1967 Cambridge Conference on the Correlation of Science and Mathematics in the Schools. It is addressed to professionals in education, and is designed to stimulate dialogue among them concerning the mathematics-science curriculum. The report is organized in five chapters, each dealing respectively with (1) educational…

Computing Environments for Data Analysis. Part 3. Programming Environments.

DTIC Science & Technology

1986-05-21

to understand how the existing system works and how to modify them to get the desired effect. This depends on the programming ...editor that performs automatic syntax checking for all the programming languages. 3.3 How S fits in To make efficient use of the machine (maximize the... programming , manuscript from Symbolics, Inc., 5 Cambridge Center, Cambridge, Mass. 02142. [101 DEITEL H.M., (1983) An Introduction to Operating

Sensing Strategies for Disambiguating among Multiple Objects in Known Poses.

DTIC Science & Technology

1985-08-01

ELEMENT. PROIECT. TASK Artificial Inteligence Laboratory AE OKUI UBR 545 Technology Square Cambridge, MA 021.39 11. CONTROLLING OFFICE NAME AND ADDRESS 12...AD-Ali65 912 SENSING STRATEGIES FOR DISAMBIGURTING MONG MULTIPLE 1/1 OBJECTS IN KNOWN POSES(U) MASSACHUSETTS INST OF TECH CAMBRIDGE ARTIFICIAL ...or Dist Special 1 ’ MASSACHUSETTS INSTITUTE OF TECHNOLOGY ARTIFICIAL INTELLIGENCE LABORATORY A. I. Memo 855 August, 1985 Sensing Strategies for

Herbert: A Second Generation Mobile Robot.

DTIC Science & Technology

1988-01-01

PROJECT. TASK S Artificial Inteligence Laboratory AREA A WORK UNIT NUMBERS ’ ~ 545 Technology Square Cambridge, MA 02139 11. CONTROLLING OFFICE NAME...AD-AI93 632 WMRT: A SECOND GENERTION MOBILE ROWT(U) / MASSACHUSETTS IMST OF TECH CAMBRIDGE ARTIFICIAL INTELLIGENCE LAB R BROOKS ET AL .JAN l8 Al-M...MASSACHUSETTS INSTITUTE OF TECHNOLOGY ARTIFICIAL INTELLIGENCE LABORATORY A. I. Memo 1016 January, 1988 HERBERT: A SECOND GENERATION MOBILE ROBOT Rodney A

Content Questions In American Sign Language: An RRG Analysis

DTIC Science & Technology

2004-12-08

a temporal framework, someone might sign (29) DURING FIVE YEAR YONDER GALLAUDET … During my five years at Gallaudet …. Until a new topic is...Language: A Teacher’s Resource on Grammar and Culture. Washington, D.C.: Gallaudet University Press. BATTISON, ROBBIN. 1978. Loan Signs from...Typology and Syntactic Description, ed. by Timothy Shopen. Cambridge, MA: Cambridge University Press. —. In press b. Clause Types. Language Typology

Self-Stabilizing and Efficient Robust Uncertainty Management

DTIC Science & Technology

2011-10-01

Group decision making in honey bee swarms. American Scientist. 94:220-229. 71 Frisch, Karl von. (1967) The Dance Language and Orientation of... Bees . Cambridge, Mass.: The Belknap Press of Harvard University Press. 18 Thom et al. (21 August 2007) The Scent of the Waggle Dance . PLoS Biology...Orientation of Bees . Cambridge, Mass.: The Belknap Press of Harvard University Press. 02 Frisch, Karl von. (1967) The Dance Language and

Civil Wars in Britain, 1640-1646 Military Revolution on Campaign

DTIC Science & Technology

2001-01-01

revolution thesis. In the 1980s David Parrott argued that the tactical reforms described by Roberts were in practice nearly irrelevant to the battles...Social Order: Reading and Writing in Tudor and Stuart England (Cambridge: Cambridge University Press, 1980 ), passim. 8A royal license was obtained by...Finlayson, Clement Little and His Library: The Origins of Edinburgh University Library (Edinburgh: Edinburgh University, 1980 ). 10Jean R. Guild and

Full Spectrum Operations: An Analysis of Course Content at the Command and General Staff College

DTIC Science & Technology

2008-05-01

Dynamics of Military Revolutions 1300-2050. Cambridge: Cambridge University Press, 2001. Kolb , David A. Experiential Learning : Experience as the... experiential learning provides latitude for the student or instructor to deviate from the structured lesson plan and pursue alternate avenues to...their contribution. The cognitive learning environment of CGSC is best understood by reviewing the adult learning model and the experiential learning

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 2. Teaching Units that Utilize an Interactive Web-Accessible Subset of the Cambridge Structural Database

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

2010-01-01

A series of online interactive teaching units have been developed that illustrate the use of experimentally measured three-dimensional (3D) structures to teach fundamental chemistry concepts. The units integrate a 500-structure subset of the Cambridge Structural Database specially chosen for their pedagogical value. The units span a number of key…

Hydronic Heating Retrofits for Low-Rise Multifamily Buildings: Boiler Control Replacement and Monitoring

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dentz, J.; Henderson, H.; Varshney, K.

2013-10-01

The ARIES Collaborative, a U.S. Department of Energy Building America research team, partnered with NeighborWorks America affiliate Homeowners' Rehab Inc. of Cambridge, Massachusetts, to implement and study improvements to the central hydronic heating system in one of the nonprofit's housing developments. The heating control systems in the three-building, 42-unit Columbia Cambridge Alliance for Spanish Tenants housing development were upgraded.

The British Experience in Iraq, 2007: A Perspective on the Utility of Force

DTIC Science & Technology

2012-05-17

exploit JAM’s temporary disarray to muscle in on the electricity franchise . This provoked a violent backlash from JAM whose fighters besieged Wahili’s...approximation to absolute war, although its instrumental value is difficult to divine given its self-defeating absurdity.) 13 Beatrice Heuser, The Evolution ...Heuser, The Evolution of Strategy, (Cambridge: Cambridge University Press, 2010), Page 489. “The Clausewitzian model according to which governments

Parallel Algorithms for Computer Vision.

DTIC Science & Technology

1989-01-01

34 IEEE Tran. Pattern Ankyaij and Ma- Artifcial Intelligence , Tokyo, 1979. chine Intelligence , 6, 1984. Kirkpatrick, S., C.D. Gelatt, Jr. and M.P. Vecchi...MASSACHUSETTS INST OF TECH CAMBRIDGE ARTIFICIAL INTELLIGENCE LAB T P06010 JAN 89 ETL-0529 UNCLASSIFIED DACA76-85-C-0010 F.’G 12/1I N mommiimmmiiso...PoggioI Massachusetts Institute of Technology i Artificial Intelligence Laboratory 545 Technology Square Cambridge, Massachusetts 02139 DTIC January

Understanding Tumor Dormancy as a Means of Secondary Prevention

DTIC Science & Technology

2017-10-01

Hannon CONTRACTING ORGANIZATION: University of Cambridge, UK Cambridge, CB 0RE REPORT DATE: October 2017 TYPE OF REPORT : Annual PREPARED FOR...Distribution Unlimited The views, opinions and/or findings contained in this report are those of the author(s) and should not be construed as an official...Department of the Army position, policy or decision unless so designated by other documentation. REPORT DOCUMENTATION PAGE Form Approved OMB No

Natural Object Categorization.

DTIC Science & Technology

1987-11-01

6-A194 103 NATURAL OBJECT CATEGORIZATION(U) MASSACHUSETTS INST OF 1/3 TECH CAMBRIDGE ARTIFICIAL INTELLIGENCE LAB R F DBICK NOY 87 AI-TR-1091 NBSSI4...ORGANI1ZATION NAME AN40 ACORES$ 10. PROGRAM ELEMENT. PROJECT. TASK Artificial Inteligence Laboratory AREA A WORK UNIT MUMBERS 545 Technology Square Cambridge...describes research done at the Department of Brain and Cognitive Sciences and the Artificial Intelligence Laboratory at the Massachusetts Institute of

Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.

PubMed

Card, Daren C; Schield, Drew R; Reyes-Velasco, Jacobo; Fujita, Matthew K; Andrew, Audra L; Oyler-McCance, Sara J; Fike, Jennifer A; Tomback, Diana F; Ruggiero, Robert P; Castoe, Todd A

2014-01-01

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5-5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.

Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies

USGS Publications Warehouse

Card, Daren C.; Schield, Drew R.; Reyes-Velasco, Jacobo; Fujita, Matthre K.; Andrew, Audra L.; Oyler-McCance, Sara J.; Fike, Jennifer A.; Tomback, Diana F.; Ruggiero, Robert P.; Castoe, Todd A.

2014-01-01

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (~3.5–5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.

Analysis of pharmacist-patient communication using the Calgary-Cambridge guide.

PubMed

Greenhill, Nicola; Anderson, Claire; Avery, Anthony; Pilnick, Alison

2011-06-01

This study explored communication between pharmacists and patients through application of the Calgary-Cambridge guide [1] to appointment-based pharmacist-patient consultations and considers use of the guide in pharmacy education. Eighteen patients attending appointment-based consultations with five pharmacists were recruited to this qualitative study. Consultations were audio-recorded and observed. Transcripts were coded according to the use of skills within the guide and analysed thematically. The results showed good use of many skills by pharmacists, particularly signposting and closing the session. Some skills were poorly represented such as listening effectively, eliciting the patient's perspective, effective use of computers and creating patient-centred consultations. A key theme of social conversation was present in the data but this skill was not defined in the guide. The Calgary-Cambridge guide was developed for use in medical consultations but its application to pharmacist-patient consultations showed that the guide could be successfully used in pharmacy with some minor alterations. Pharmacists may need more training to improve the use of specific communication skills including how to conduct a patient-centred consultation. The Calgary-Cambridge guide is well aligned with many aspects of pharmacist-patient consultations and could help pharmacists to improve their consultation skills. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Nutrition in medical education: reflections from an initiative at the University of Cambridge

PubMed Central

Ball, Lauren; Crowley, Jennifer; Laur, Celia; Rajput-Ray, Minha; Gillam, Stephen; Ray, Sumantra

2014-01-01

Landmark reports have confirmed that it is within the core responsibilities of doctors to address nutrition in patient care. There are ongoing concerns that doctors receive insufficient nutrition education during medical training. This paper provides an overview of a medical nutrition education initiative at the University of Cambridge, School of Clinical Medicine, including 1) the approach to medical nutrition education, 2) evaluation of the medical nutrition education initiative, and 3) areas identified for future improvement. The initiative utilizes a vertical, spiral approach during the clinically focused years of the Cambridge undergraduate and graduate medical degrees. It is facilitated by the Nutrition Education Review Group, a group associated with the UK Need for Nutrition Education/Innovation Programme, and informed by the experiences of their previous nutrition education interventions. Three factors were identified as contributing to the success of the nutrition education initiative including the leadership and advocacy skills of the nutrition academic team, the variety of teaching modes, and the multidisciplinary approach to teaching. Opportunities for continuing improvement to the medical nutrition education initiative included a review of evaluation tools, inclusion of nutrition in assessment items, and further alignment of the Cambridge curriculum with the recommended UK medical nutrition education curriculum. This paper is intended to inform other institutions in ongoing efforts in medical nutrition education. PMID:24899813

Instability, investment, disasters, and demography: natural disasters and fertility in Italy (1820-1962) and Japan (1671-1965).

PubMed

Lin, C-Y Cynthia

2010-03-01

This article examines whether natural disasters affect fertility-a topic little explored but of policy importance given relevance to policies regarding disaster insurance, foreign aid, and the environment. The identification strategy uses historic regional data to exploit natural variation within each of two countries: one European country-Italy (1820-1962), and one Asian country-Japan (1671-1965). The choice of study settings allows consideration of Jones' (The European miracle, Cambridge University Press, Cambridge, 1981) theory that preindustrial differences in income and population between Asia and Europe resulted from the fertility response to different environmental risk profiles. According to the results, short-run instability, particularly that arising from the natural environment, appears to be associated with a decrease in fertility-thereby suggesting that environmental shocks and economic volatility are associated with a decrease in investment in the population size of future generations. The results also show that, contrary to Jones' (The European miracle, Cambridge University Press, Cambridge, 1981) theory, differences in fertility between Italy and Japan cannot be explained away by disaster proneness alone. Research on the effects of natural disasters may enable social scientists and environmentalists alike to better predict the potential effects of the increase in natural disasters that may result from global climate change.

Comparison of the Equine Reference Sequence with Its Sanger Source Data and New Illumina Reads

PubMed Central

Rebolledo-Mendez, Jovan; Hestand, Matthew S.; Coleman, Stephen J.; Zeng, Zheng; Orlando, Ludovic; MacLeod, James N.; Kalbfleisch, Ted

2015-01-01

The reference assembly for the domestic horse, EquCab2, published in 2009, was built using approximately 30 million Sanger reads from a Thoroughbred mare named Twilight. Contiguity in the assembly was facilitated using nearly 315 thousand BAC end sequences from Twilight’s half brother Bravo. Since then, it has served as the foundation for many genome-wide analyses that include not only the modern horse, but ancient horses and other equid species as well. As data mapped to this reference has accumulated, consistent variation between mapped datasets and the reference, in terms of regions with no read coverage, single nucleotide variants, and small insertions/deletions have become apparent. In many cases, it is not clear whether these differences are the result of true sequence variation between the research subjects’ and Twilight’s genome or due to errors in the reference. EquCab2 is regarded as “The Twilight Assembly.” The objective of this study was to identify inconsistencies between the EquCab2 assembly and the source Twilight Sanger data used to build it. To that end, the original Sanger and BAC end reads have been mapped back to this equine reference and assessed with the addition of approximately 40X coverage of new Illumina Paired-End sequence data. The resulting mapped datasets identify those regions with low Sanger read coverage, as well as variation in genomic content that is not consistent with either the original Twilight Sanger data or the new genomic sequence data generated from Twilight on the Illumina platform. As the haploid EquCab2 reference assembly was created using Sanger reads derived largely from a single individual, the vast majority of variation detected in a mapped dataset comprised of those same Sanger reads should be heterozygous. In contrast, homozygous variations would represent either errors in the reference or contributions from Bravo's BAC end sequences. Our analysis identifies 720,843 homozygous discrepancies between new, high throughput genomic sequence data generated for Twilight and the EquCab2 reference assembly. Most of these represent errors in the assembly, while approximately 10,000 are demonstrated to be contributions from another horse. Other results are presented that include the binary alignment map file of the mapped Sanger reads, a list of variants identified as discrepancies between the source data and resulting reference, and a BED annotation file that lists the regions of the genome whose consensus was likely derived from low coverage alignments. PMID:26107638

GeneImp: Fast Imputation to Large Reference Panels Using Genotype Likelihoods from Ultralow Coverage Sequencing

PubMed Central

Spiliopoulou, Athina; Colombo, Marco; Orchard, Peter; Agakov, Felix; McKeigue, Paul

2017-01-01

We address the task of genotype imputation to a dense reference panel given genotype likelihoods computed from ultralow coverage sequencing as inputs. In this setting, the data have a high-level of missingness or uncertainty, and are thus more amenable to a probabilistic representation. Most existing imputation algorithms are not well suited for this situation, as they rely on prephasing for computational efficiency, and, without definite genotype calls, the prephasing task becomes computationally expensive. We describe GeneImp, a program for genotype imputation that does not require prephasing and is computationally tractable for whole-genome imputation. GeneImp does not explicitly model recombination, instead it capitalizes on the existence of large reference panels—comprising thousands of reference haplotypes—and assumes that the reference haplotypes can adequately represent the target haplotypes over short regions unaltered. We validate GeneImp based on data from ultralow coverage sequencing (0.5×), and compare its performance to the most recent version of BEAGLE that can perform this task. We show that GeneImp achieves imputation quality very close to that of BEAGLE, using one to two orders of magnitude less time, without an increase in memory complexity. Therefore, GeneImp is the first practical choice for whole-genome imputation to a dense reference panel when prephasing cannot be applied, for instance, in datasets produced via ultralow coverage sequencing. A related future application for GeneImp is whole-genome imputation based on the off-target reads from deep whole-exome sequencing. PMID:28348060

Reference-guided de novo assembly approach improves genome reconstruction for related species.

PubMed

Lischer, Heidi E L; Shimizu, Kentaro K

2017-11-10

The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due to short read length, missing data, repetitive regions, polymorphisms and sequencing errors. As more and more genomes are sequenced, reference-guided assembly approaches can be used to assist the assembly process. However, previous methods mostly focused on the assembly of other genotypes within the same species. We adapted and extended a reference-guided de novo assembly approach, which enables the usage of a related reference sequence to guide the genome assembly. In order to compare and evaluate de novo and our reference-guided de novo assembly approaches, we used a simulated data set of a repetitive and heterozygotic plant genome. The extended reference-guided de novo assembly approach almost always outperforms the corresponding de novo assembly program even when a reference of a different species is used. Similar improvements can be observed in high and low coverage situations. In addition, we show that a single evaluation metric, like the widely used N50 length, is not enough to properly rate assemblies as it not always points to the best assembly evaluated with other criteria. Therefore, we used the summed z-scores of 36 different statistics to evaluate the assemblies. The combination of reference mapping and de novo assembly provides a powerful tool to improve genome reconstruction by integrating information of a related genome. Our extension of the reference-guided de novo assembly approach enables the application of this strategy not only within but also between related species. Finally, the evaluation of genome assemblies is often not straight forward, as the truth is not known. Thus one should always use a combination of evaluation metrics, which not only try to assess the continuity but also the accuracy of an assembly.

One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies

PubMed Central

Yuan, Shuai; Johnston, H. Richard; Zhang, Guosheng; Li, Yun; Hu, Yi-Juan; Qin, Zhaohui S.

2015-01-01

With rapid decline of the sequencing cost, researchers today rush to embrace whole genome sequencing (WGS), or whole exome sequencing (WES) approach as the next powerful tool for relating genetic variants to human diseases and phenotypes. A fundamental step in analyzing WGS and WES data is mapping short sequencing reads back to the reference genome. This is an important issue because incorrectly mapped reads affect the downstream variant discovery, genotype calling and association analysis. Although many read mapping algorithms have been developed, the majority of them uses the universal reference genome and do not take sequence variants into consideration. Given that genetic variants are ubiquitous, it is highly desirable if they can be factored into the read mapping procedure. In this work, we developed a novel strategy that utilizes genotypes obtained a priori to customize the universal haploid reference genome into a personalized diploid reference genome. The new strategy is implemented in a program named RefEditor. When applying RefEditor to real data, we achieved encouraging improvements in read mapping, variant discovery and genotype calling. Compared to standard approaches, RefEditor can significantly increase genotype calling consistency (from 43% to 61% at 4X coverage; from 82% to 92% at 20X coverage) and reduce Mendelian inconsistency across various sequencing depths. Because many WGS and WES studies are conducted on cohorts that have been genotyped using array-based genotyping platforms previously or concurrently, we believe the proposed strategy will be of high value in practice, which can also be applied to the scenario where multiple NGS experiments are conducted on the same cohort. The RefEditor sources are available at https://github.com/superyuan/refeditor. PMID:26267278

Next-Generation Sequencing Platforms

NASA Astrophysics Data System (ADS)

Mardis, Elaine R.

2013-06-01

Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

Using genic sequence capture in combination with a syntenic pseudo genome to map a deletion mutant in a wheat species.

PubMed

Gardiner, Laura-Jayne; Gawroński, Piotr; Olohan, Lisa; Schnurbusch, Thorsten; Hall, Neil; Hall, Anthony

2014-12-01

Mapping-by-sequencing analyses have largely required a complete reference sequence and employed whole genome re-sequencing. In species such as wheat, no finished genome reference sequence is available. Additionally, because of its large genome size (17 Gb), re-sequencing at sufficient depth of coverage is not practical. Here, we extend the utility of mapping by sequencing, developing a bespoke pipeline and algorithm to map an early-flowering locus in einkorn wheat (Triticum monococcum L.) that is closely related to the bread wheat genome A progenitor. We have developed a genomic enrichment approach using the gene-rich regions of hexaploid bread wheat to design a 110-Mbp NimbleGen SeqCap EZ in solution capture probe set, representing the majority of genes in wheat. Here, we use the capture probe set to enrich and sequence an F2 mapping population of the mutant. The mutant locus was identified in T. monococcum, which lacks a complete genome reference sequence, by mapping the enriched data set onto pseudo-chromosomes derived from the capture probe target sequence, with a long-range order of genes based on synteny of wheat with Brachypodium distachyon. Using this approach we are able to map the region and identify a set of deleted genes within the interval. © 2014 The Authors.The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

Metabarcoding of marine nematodes – evaluation of reference datasets used in tree-based taxonomy assignment approach

PubMed Central

2016-01-01

Abstract Background Metabarcoding is becoming a common tool used to assess and compare diversity of organisms in environmental samples. Identification of OTUs is one of the critical steps in the process and several taxonomy assignment methods were proposed to accomplish this task. This publication evaluates the quality of reference datasets, alongside with several alignment and phylogeny inference methods used in one of the taxonomy assignment methods, called tree-based approach. This approach assigns anonymous OTUs to taxonomic categories based on relative placements of OTUs and reference sequences on the cladogram and support that these placements receive. New information In tree-based taxonomy assignment approach, reliable identification of anonymous OTUs is based on their placement in monophyletic and highly supported clades together with identified reference taxa. Therefore, it requires high quality reference dataset to be used. Resolution of phylogenetic trees is strongly affected by the presence of erroneous sequences as well as alignment and phylogeny inference methods used in the process. Two preparation steps are essential for the successful application of tree-based taxonomy assignment approach. Curated collections of genetic information do include erroneous sequences. These sequences have detrimental effect on the resolution of cladograms used in tree-based approach. They must be identified and excluded from the reference dataset beforehand. Various combinations of multiple sequence alignment and phylogeny inference methods provide cladograms with different topology and bootstrap support. These combinations of methods need to be tested in order to determine the one that gives highest resolution for the particular reference dataset. Completing the above mentioned preparation steps is expected to decrease the number of unassigned OTUs and thus improve the results of the tree-based taxonomy assignment approach. PMID:27932919

Metabarcoding of marine nematodes - evaluation of reference datasets used in tree-based taxonomy assignment approach.

PubMed

Holovachov, Oleksandr

2016-01-01

Metabarcoding is becoming a common tool used to assess and compare diversity of organisms in environmental samples. Identification of OTUs is one of the critical steps in the process and several taxonomy assignment methods were proposed to accomplish this task. This publication evaluates the quality of reference datasets, alongside with several alignment and phylogeny inference methods used in one of the taxonomy assignment methods, called tree-based approach. This approach assigns anonymous OTUs to taxonomic categories based on relative placements of OTUs and reference sequences on the cladogram and support that these placements receive. In tree-based taxonomy assignment approach, reliable identification of anonymous OTUs is based on their placement in monophyletic and highly supported clades together with identified reference taxa. Therefore, it requires high quality reference dataset to be used. Resolution of phylogenetic trees is strongly affected by the presence of erroneous sequences as well as alignment and phylogeny inference methods used in the process. Two preparation steps are essential for the successful application of tree-based taxonomy assignment approach. Curated collections of genetic information do include erroneous sequences. These sequences have detrimental effect on the resolution of cladograms used in tree-based approach. They must be identified and excluded from the reference dataset beforehand.Various combinations of multiple sequence alignment and phylogeny inference methods provide cladograms with different topology and bootstrap support. These combinations of methods need to be tested in order to determine the one that gives highest resolution for the particular reference dataset.Completing the above mentioned preparation steps is expected to decrease the number of unassigned OTUs and thus improve the results of the tree-based taxonomy assignment approach.

The importance of being fractional in mixing: optimal choice of the index s in H-s norm

NASA Astrophysics Data System (ADS)

Vermach, Lukas; Caulfield, C. P.

2015-11-01

A natural measure of homogeneity of a mixture is the variance of the concentration field, which in the case of a zero-mean field is the L2-norm. Mathew et al. (Physica D, 2005) introduced a new multi-scale measure to quantify mixing referred to as the mix-norm, which is equivalent to the H - 1 / 2 norm, the Sobolev norm of negative fractional index. Unlike the L2-norm, the mix-norm is not conserved by the advection equation and thus captures mixing even in the non-diffusive systems. Furthermore, the mix-norm is consistent with the ergodic definition of mixing and Lin et al. (JFM, 2011) showed that this property extends to any norm from the class H-s , s > 0 . We consider a zero-mean passive scalar field organised into two layers of different concentrations advected by a flow field in a torus. We solve two non-linear optimisation problems. We identify the optimal initial perturbation of the velocity field with given initial energy as well as the optimal forcing with given total action (the time integral of the kinetic energy of the flow) which both yield maximal mixing by a target time horizon. We analyse sensitivity of the results with respect to s-variation and thus address the importance of the choice of the fractional index This work was supported by the UK Engineering and Physical Sciences Research Council (EPSRC) grant EP/H023348/1 for the University of Cambridge Centre for Doctoral Training, the Cambridge Centre for Analysis.

Initial validation of a transdiagnostic compulsivity questionnaire: the Cambridge-Chicago Compulsivity Trait Scale.

PubMed

Chamberlain, Samuel R; Grant, Jon E

2018-05-07

Compulsivity refers to a tendency toward repetitive habitual behaviors. Multiple disorders have compulsive symptoms at their core, including substance use disorders, gambling disorder, and obsessive-compulsive disorder. The aim of this study was to validate a scale for the objective, transdiagnostic measurement of compulsivity. The 15-item Cambridge-Chicago Compulsivity Trait Scale (CHI-T) was developed for the rapid but comprehensive measurement of compulsivity. Adults aged 18-29y were recruited using media advertisements, and completed the CHI-T in addition to demographic, clinical, and cognitive assessment. The validity and psychometric properties of the scale were quantified. A total of 112 participants completed the study. The scale yielded a normal distribution with very few outliers. It had excellent psychometric properties, with high internal consistency (Cronbach's alpha=0.8), and excellent convergent validity against gold-standard assessments of compulsive symptoms (each p<0.001 for gambling disorder, obsessive-compulsive, and substance use disorder symptoms). Total scores on the scale correlated significantly with less risk-adjustment on the decision-making task (rigid response style), and divergent validity was confirmed against other cognitive domains (response inhibition and executive planning). The above significant findings withstood Bonferroni correction. Factor analysis suggested the existence of two latent factors: one related mainly to reward-seeking and the need for perfection, and the other relating to anxiolytic/soothing features of compulsivity. The CHI-T, a scale designed to measure transdiagnostic compulsivity, appears to show excellent psychometric properties in a normative population and merits further investigation in the context of clinical patient populations, including in treatment trials.

A Semantics of Synchronization.

DTIC Science & Technology

1980-09-01

suggestion of having very hungry philosophers. One can easily imagine the complexity of the equivalent implementation using semaphores . Synchronization types...Edinburgh, July 1978. [STAR79] Stark, E.W., " Semaphore Primitives and Fair Mutual Exclusion," TM-158, Laboratory for Computer Science, M.I.T., Cambridge...AD-AQ91 015 MASSACHUSETTS INST OF TECH CAMBRIDGE LAB FOR COMPUTE--ETC F/S 9/2 A SEMANTICS OF SYNCHRONIZATION .(U) .C SEP 80 C A SEAQUIST N00015-75

New Insights on Visual Cortex. Abstracts. Center for Visual Science Symposium (16th) Held in Rochester, New York on June 16-18, 1988

DTIC Science & Technology

1988-06-01

Cortex of the Cat John G. Robson Craik Physiological Laboratory Cambridge University Cambridge, England When tested with spatially-localized stimuli...University, New York, NY Stanley Klein - School of Optometry, University Berkeley, Berkeley, CA Jennifer Knight - Neurobiology & Behavior, Cornell University...Village, Poughkeepsie, NY Jeffrcy Lubin - Psychology Department, University of PA, Philadelphia, PA Jennifer S. Lund - University of Pittsburgh

Autobiography of Sir George Biddell Airy

NASA Astrophysics Data System (ADS)

Airy, George Biddell; Airy, Wilfred

2010-06-01

Preface; 1. Personal sketch of George Biddell Airy; 2. From his birth to his taking his B.A. degree; 3. At Trinity College, Cambridge; 4. At Cambridge Observatory; 5. At Greenwich Observatory, 1836-1846; 6. At Greenwich Observatory, 1846-1856; 7. At Greenwich Observatory, 1856-1866; 8. At Greenwich Observatory, 1866-1876; 9. At Greenwich Observatory to his resignation in 1881; 10. At the White House, Greewich, to his death; Appendix: List of printed papers; Index.

A Set of Orthogonal Polynomials That Generalize the Racah Coefficients or 6 - j Symbols.

DTIC Science & Technology

1978-03-01

Generalized Hypergeometric Functions, Cambridge Univ. Press, Cambridge, 1966. [11] D. Stanton, Some basic hypergeometric polynomials arising from... Some bas ic hypergeometr ic an a logues of the classical orthogonal polynomials and applications , to appear. [3] C. de Boor and G. H. Golub , The...Report #1833 A SET OF ORTHOGONAL POLYNOMIALS THAT GENERALIZE THE RACAR COEFFICIENTS OR 6 — j SYMBOLS Richard Askey and James Wilson •

DDN (Defence Data Network) Protocol Implementations and Vendors Guide

DTIC Science & Technology

1988-08-01

Artificial Intelligence Laboratory Room NE43-723 545 Technology Square Cambridge, MA 02139 (617) 253-8843 S John Wroclawski, (JTW@AI.AJ.MIT.EDU...Massachusetts Institute of Technology Artificial Intelligence Laboratory Room NE43-743 545 Technology Square 0 Cambridge, MA 02139 (617) 253-7885 ORDERING...TCP/IP Network Software for PC-DOS Systems CPU: IBM-PC/XT/AT/compatible in conjunction with EXOS 205 Inteligent Ethernet Controller for PCbus 0/s

Exploiting Lexical Regularities in Designing Natural Language Systems.

DTIC Science & Technology

1988-04-01

ELEMENT. PROJECT. TASKN Artificial Inteligence Laboratory A1A4WR NTumet 0) 545 Technology Square Cambridge, MA 02139 Ln *t- CONTROLLING OFFICE NAME AND...RO-RI95 922 EXPLOITING LEXICAL REGULARITIES IN DESIGNING NATURAL 1/1 LANGUAGE SYSTENS(U) MASSACHUSETTS INST OF TECH CAMBRIDGE ARTIFICIAL INTELLIGENCE...oes.ary and ftdou.Ip hr Nl wow" L,2This paper presents the lexical component of the START Question Answering system developed at the MIT Artificial

Human Factors in Aircraft Maintenance

DTIC Science & Technology

2001-03-01

795 - 3-798. Reason, J . (1990). Human Error. Cambridge: Cambridge University Press. Schmidt, J ., Schmorrow, D . and Figlock, R. (2000). Human factors...and so on. When each step is described in sufficient detail, the task description is complete and task analysis can begin (e.g. Drury, Paramore , Van... Paramore , B., Van Cott, H.P., Grey, S.M. and Corlett, E.M.(1987). Task analysis. In G. Salvendy (Ed) Handbook of Human Factors, Chapter 3.4. New

The Characterization and Circumvention of Carbon Nanotube Junctions - The Route to Practical Carbon Conductors Through Extreme Frequency, Fields, and Light

DTIC Science & Technology

2015-05-22

Conductors Through Extreme Frequency, Fields, and Light Krzysztof Koziol THE CHANCELLOR, MASTER AND SCHOLARS OF THE UNIVERISTY OF CAMBRIDGE...2011 to 31 August 2014 Air Force Research Laboratory Air Force Office of Scientific Research European Office of Aerospace Research and...Carbon Conductors Through Extreme Frequency, Fields, and Light Krzysztof Koziol THE CHANCELLOR, MASTER AND SCHOLARS OF THE UNIVERISTY OF CAMBRIDGE THE

Selection and Effects of Channels in Distributed Communication and Decision Making Tasks: A Theoretical Review and a Proposed Research Paradigm

DTIC Science & Technology

1988-02-01

1982). Integration and involvement in speaking, writing, and oral literture. In Deborah Tannen (Ed.) Spoken and written lanquage: Exploring orality and...University. Gump rz, John J. (1982). Discourse strategies. Cambridge: Cambridge University Press. Gumperz, John J., & Tannen , Deborah . (1978...and the transition to literacy. In Deborah Tannen (Ed.) Coherence in spoken and written discourse. Gutek, Barbara A., Bikson, Tora K., & Mankin, Don

Conflict for Resources: Water in the Lake Chad Basin

DTIC Science & Technology

2009-01-01

Security 19 (1994), http://www.library.utoronto.ca/pcs/evidence (accessed 10 February 2009). 11 Miriam Lowi, Water and Power (Cambridge, UK : Cambridge...states wage wars and how scarce natural resources influence the states. Carl von Clausewitz’s treatise, On War serves as a starting point for any...has lots of water, very little of it is freshwater. Miriam Lowi, author of Water and Power describes political dynamics of high and low politics. High

The production of oxygen and metal from lunar regolith

NASA Astrophysics Data System (ADS)

Schwandt, Carsten; Hamilton, James A.; Fray, Derek J.; Crawford, Ian A.

2012-12-01

The present article summarises the various methods that have been, and still are, explored for the production of oxygen from lunar materials. These include the classical concepts based on chemical reduction with hydrogen or methane, vapour phase pyrolysis, sulphuric acid treatment, and molten oxide electrolysis. Our main focus in this paper is on a novel approach developed at the University of Cambridge that employs molten salt electrochemistry to achieve the combined winning of oxygen and metal from solid lunar materials of varying composition. This makes the Cambridge process attractive because it will work equally well in mare as in highland regions. We also discuss the implications of the recent apparent discovery of water ice at the poles of the Moon and conclude that, even if this discovery is confirmed, it will nevertheless be desirable to provide oxygen at non-polar localities, and the Cambridge process is a strong candidate for achieving this.

Economic dynamics with financial fragility and mean-field interaction: A model

NASA Astrophysics Data System (ADS)

Di Guilmi, C.; Gallegati, M.; Landini, S.

2008-06-01

Following Aoki’s statistical mechanics methodology [Masanao Aoki, New Approaches to Macroeconomic Modeling, Cambridge University Press, 1996; Masanao Aoki, Modeling Aggregate Behaviour and Fluctuations in Economics, Cambridge University Press, 2002; Masanao Aoki, and Hiroshi Yoshikawa, Reconstructing Macroeconomics, Cambridge University Press, 2006], we provide some insights into the well-known works of [Bruce Greenwald, Joseph Stiglitz, Macroeconomic models with equity and credit rationing, in: R. Hubbard (Ed.), Information, Capital Markets and Investment, Chicago University Press, Chicago, 1990; Bruce Greenwald, Joseph Stiglitz, Financial markets imperfections and business cycles, Quarterly journal of Economics (1993)]. Specifically, we reach analytically a closed form solution of their models overcoming the aggregation problem. The key idea is to represent the economy as an evolving complex system, composed by heterogeneous interacting agents, that can be partitioned into a space of macroscopic states. This meso level of aggregation permits to adopt mean-field interaction modeling and master equation techniques.

Immunoglobulin heavy variable (IGHV) genes and alleles: new entities, new names and implications for research and prognostication in chronic lymphocytic leukaemia.

PubMed

Xochelli, Aliki; Agathangelidis, Andreas; Kavakiotis, Ioannis; Minga, Evangelia; Sutton, Lesley Ann; Baliakas, Panagiotis; Chouvarda, Ioanna; Giudicelli, Véronique; Vlahavas, Ioannis; Maglaveras, Nikos; Bonello, Lisa; Trentin, Livio; Tedeschi, Alessandra; Panagiotidis, Panagiotis; Geisler, Christian; Langerak, Anton W; Pospisilova, Sarka; Jelinek, Diane F; Oscier, David; Chiorazzi, Nicholas; Darzentas, Nikos; Davi, Fred; Ghia, Paolo; Rosenquist, Richard; Hadzidimitriou, Anastasia; Belessi, Chrysoula; Lefranc, Marie-Paule; Stamatopoulos, Kostas

2015-01-01

Νext generation sequencing studies in Homo sapiens have identified novel immunoglobulin heavy variable (IGHV) genes and alleles necessitating changes in the international ImMunoGeneTics information system (IMGT) GENE-DB and reference directories of IMGT/V-QUEST. In chronic lymphocytic leukaemia (CLL), the somatic hypermutation (SHM) status of the clonotypic rearranged IGHV gene is strongly associated with patient outcome. Correct determination of this parameter strictly depends on the comparison of the nucleotide sequence of the clonotypic rearranged IGHV gene with that of the closest germline counterpart. Consequently, changes in the reference directories could, in principle, affect the correct interpretation of the IGHV mutational status in CLL. To this end, we analyzed 8066 productive IG heavy chain (IGH) rearrangement sequences from our consortium both before and after the latest update of the IMGT/V-QUEST reference directory. Differences were identified in 405 cases (5 % of the cohort). In 291/405 sequences (71.9 %), changes concerned only the IGHV gene or allele name, whereas a change in the percent germline identity (%GI) was noted in 114/405 (28.1 %) sequences; in 50/114 (43.8 %) sequences, changes in the %GI led to a change in the mutational set. In conclusion, recent changes in the IMGT reference directories affected the interpretation of SHM in a sizeable number of IGH rearrangement sequences from CLL patients. This indicates that both physicians and researchers should consider a re-evaluation of IG sequence data, especially for those IGH rearrangement sequences that, up to date, have a GI close to 98 %, where caution is warranted.

Single haplotype assembly of the human genome from a hydatidiform mole.

PubMed

Steinberg, Karyn Meltz; Schneider, Valerie A; Graves-Lindsay, Tina A; Fulton, Robert S; Agarwala, Richa; Huddleston, John; Shiryev, Sergey A; Morgulis, Aleksandr; Surti, Urvashi; Warren, Wesley C; Church, Deanna M; Eichler, Evan E; Wilson, Richard K

2014-12-01

A complete reference assembly is essential for accurately interpreting individual genomes and associating variation with phenotypes. While the current human reference genome sequence is of very high quality, gaps and misassemblies remain due to biological and technical complexities. Large repetitive sequences and complex allelic diversity are the two main drivers of assembly error. Although increasing the length of sequence reads and library fragments can improve assembly, even the longest available reads do not resolve all regions. In order to overcome the issue of allelic diversity, we used genomic DNA from an essentially haploid hydatidiform mole, CHM1. We utilized several resources from this DNA including a set of end-sequenced and indexed BAC clones and 100× Illumina whole-genome shotgun (WGS) sequence coverage. We used the WGS sequence and the GRCh37 reference assembly to create an assembly of the CHM1 genome. We subsequently incorporated 382 finished BAC clone sequences to generate a draft assembly, CHM1_1.1 (NCBI AssemblyDB GCA_000306695.2). Analysis of gene, repetitive element, and segmental duplication content show this assembly to be of excellent quality and contiguity. However, comparison to assembly-independent resources, such as BAC clone end sequences and PacBio long reads, indicate misassembled regions. Most of these regions are enriched for structural variation and segmental duplication, and can be resolved in the future. This publicly available assembly will be integrated into the Genome Reference Consortium curation framework for further improvement, with the ultimate goal being a completely finished gap-free assembly. © 2014 Steinberg et al.; Published by Cold Spring Harbor Laboratory Press.

Single haplotype assembly of the human genome from a hydatidiform mole

PubMed Central

Steinberg, Karyn Meltz; Schneider, Valerie A.; Graves-Lindsay, Tina A.; Fulton, Robert S.; Agarwala, Richa; Huddleston, John; Shiryev, Sergey A.; Morgulis, Aleksandr; Surti, Urvashi; Warren, Wesley C.; Church, Deanna M.; Eichler, Evan E.; Wilson, Richard K.

2014-01-01

A complete reference assembly is essential for accurately interpreting individual genomes and associating variation with phenotypes. While the current human reference genome sequence is of very high quality, gaps and misassemblies remain due to biological and technical complexities. Large repetitive sequences and complex allelic diversity are the two main drivers of assembly error. Although increasing the length of sequence reads and library fragments can improve assembly, even the longest available reads do not resolve all regions. In order to overcome the issue of allelic diversity, we used genomic DNA from an essentially haploid hydatidiform mole, CHM1. We utilized several resources from this DNA including a set of end-sequenced and indexed BAC clones and 100× Illumina whole-genome shotgun (WGS) sequence coverage. We used the WGS sequence and the GRCh37 reference assembly to create an assembly of the CHM1 genome. We subsequently incorporated 382 finished BAC clone sequences to generate a draft assembly, CHM1_1.1 (NCBI AssemblyDB GCA_000306695.2). Analysis of gene, repetitive element, and segmental duplication content show this assembly to be of excellent quality and contiguity. However, comparison to assembly-independent resources, such as BAC clone end sequences and PacBio long reads, indicate misassembled regions. Most of these regions are enriched for structural variation and segmental duplication, and can be resolved in the future. This publicly available assembly will be integrated into the Genome Reference Consortium curation framework for further improvement, with the ultimate goal being a completely finished gap-free assembly. PMID:25373144

What are Whole Exome Sequencing and Whole Genome Sequencing?

MedlinePlus

... the future. For more information about DNA sequencing technologies and their use: Genetics Home Reference discusses whether ... University in St. Louis describes the different sequencing technologies and what the new technologies have meant for ...

PARRoT- a homology-based strategy to quantify and compare RNA-sequencing from non-model organisms.

PubMed

Gan, Ruei-Chi; Chen, Ting-Wen; Wu, Timothy H; Huang, Po-Jung; Lee, Chi-Ching; Yeh, Yuan-Ming; Chiu, Cheng-Hsun; Huang, Hsien-Da; Tang, Petrus

2016-12-22

Next-generation sequencing promises the de novo genomic and transcriptomic analysis of samples of interests. However, there are only a few organisms having reference genomic sequences and even fewer having well-defined or curated annotations. For transcriptome studies focusing on organisms lacking proper reference genomes, the common strategy is de novo assembly followed by functional annotation. However, things become even more complicated when multiple transcriptomes are compared. Here, we propose a new analysis strategy and quantification methods for quantifying expression level which not only generate a virtual reference from sequencing data, but also provide comparisons between transcriptomes. First, all reads from the transcriptome datasets are pooled together for de novo assembly. The assembled contigs are searched against NCBI NR databases to find potential homolog sequences. Based on the searched result, a set of virtual transcripts are generated and served as a reference transcriptome. By using the same reference, normalized quantification values including RC (read counts), eRPKM (estimated RPKM) and eTPM (estimated TPM) can be obtained that are comparable across transcriptome datasets. In order to demonstrate the feasibility of our strategy, we implement it in the web service PARRoT. PARRoT stands for Pipeline for Analyzing RNA Reads of Transcriptomes. It analyzes gene expression profiles for two transcriptome sequencing datasets. For better understanding of the biological meaning from the comparison among transcriptomes, PARRoT further provides linkage between these virtual transcripts and their potential function through showing best hits in SwissProt, NR database, assigning GO terms. Our demo datasets showed that PARRoT can analyze two paired-end transcriptomic datasets of approximately 100 million reads within just three hours. In this study, we proposed and implemented a strategy to analyze transcriptomes from non-reference organisms which offers the opportunity to quantify and compare transcriptome profiles through a homolog based virtual transcriptome reference. By using the homolog based reference, our strategy effectively avoids the problems that may cause from inconsistencies among transcriptomes. This strategy will shed lights on the field of comparative genomics for non-model organism. We have implemented PARRoT as a web service which is freely available at http://parrot.cgu.edu.tw .

A 2016 Ganymede stellar occultation event

NASA Astrophysics Data System (ADS)

D'Aversa, Emiliano; Oliva, Fabrizio; Sindoni, Giuseppe; Hinse, Tobias Cornelius; Plainaki, Christina; Aoki, Shohei; Person, Michael J.; Carlson, Robert W.; Orton, Glenn S.

2017-04-01

On 2016 April,13th the Jovian satellite Ganymede occulted a 7th magnitude star. The predicted occultation track crossed the Northern Pacific Ocean, Japan, and South Korea. Hence, it was a very favorable event due to the star brightness and to the visibility from the large aperture telescopes at Hawaii. While no other similar event is expected for the next 10 years, only two occultation events are reported in literature in the past, from Earth in 1972 [1] and from Voyager [2], in large disagreement in respect to the atmosphere detection. However, evidence of an exosphere around Ganymede was inferred by [3], through H Lyman alpha emission detected by Galileo UVS, and by [4], through HST/GHRS detection of far-UV atomic O airglow emissions, signature of dissociated molecular oxygen ([5],[6]). Later, the HST/STIS observations by [7] provided further evidence for exospheric neutral hydrogen. Since Ganymede is known to have an intrinsic magnetic field ([8]) reconnecting with the Jovian magnetic field and (partially) shielding the surface equatorial latitudes from the electron impact, the UV emissions have been so far attributed to auroral processes ([6]). Nevertheless, the physical mechanisms governing these processes are not known with certainty (e.g. whether the emissions morphology is determined by the spatial distribution of magnetospheric electrons or by an uneven O2 exosphere or both, see e.g.[9]). We took advantage of this event in order to search for a signature of Ganymede's exosphere in the occultation light curve, by using facilities on Mauna Kea at Hawaii (NASA-IRTF observatory) and at Sobaeksan Optical Astronomy Observatory (SOAO) in South Korea. At IRTF, both MORIS [10] and SpeX [11] instruments have been used, fed by the same optical entrance through a dichroic beam splitter at 0.95 micron. MORIS acquired a high-rate sequence of images about 0.25 sec apart in the visible range, while SpeX acquired a sequence of spectra at a bit lower rate, covering the 0.9-2.5 micron range. Unfortunately, a planned MORIS movie-mode sequence at higher rate failed in starting acquisition. The field of view of the instruments was not large enough to include a reference unocculted body, hence sky fluctuations are the major noise source. At SOAO, a CCD camera in clear filter was used to obtain a shorter sequence of images at a lower rate (about 1 Hz). However, since the larger field of view allowed to observe simultaneously Ganymede and Callisto, we can use the latter as a reference unocculted body in order to cancel out telluric fluctuations. Results from the occultation light curve analysis on the three datasets will be discussed. Acknowledgments - The Infrared Telescope Facility is operated by the University of Hawaii under contract NNH14CK55B with the National Aeronautics and Space Administration. We express special thanks to Bobby Bus as support astronomer for both MORIS and SpeX observations. SOAO is managed by the Korean Astronomy and Space Science Istitute (KASI). References - [1] Carlson et al.,1973,Science,182,4107. [2] Broadfoot et al.,1981,Journ.of Geophys.Res.,86,8259. [3] Barth et al.,1996,EOS Suppl.77,F430. [4] Hall et al.,1998,ApJ,499,475. [5] McGrath et al.,2004,Cambridge Univ.Press,ISBN 0-521-81808-7,2004,p.457-483. [6] McGrath et al.,2013,Journ.of Geophys.Res.,118,2043. [7] Feldman et al.,2000,ApJ,535,1085. [8] Kivelson et al.,1996,Nature,384,537. [9] Plainaki et al.,2015,Icarus,245,306. [10] Gulbis et al.,2011,PASP,123,461. [11] Rayner et al.2003,PASP,115,362.

Comprehensive red blood cell and platelet antigen prediction from whole genome sequencing: proof of principle

PubMed Central

Westhoff, Connie M.; Uy, Jon Michael; Aguad, Maria; Smeland‐Wagman, Robin; Kaufman, Richard M.; Rehm, Heidi L.; Green, Robert C.; Silberstein, Leslie E.

2015-01-01

BACKGROUND There are 346 serologically defined red blood cell (RBC) antigens and 33 serologically defined platelet (PLT) antigens, most of which have known genetic changes in 45 RBC or six PLT genes that correlate with antigen expression. Polymorphic sites associated with antigen expression in the primary literature and reference databases are annotated according to nucleotide positions in cDNA. This makes antigen prediction from next‐generation sequencing data challenging, since it uses genomic coordinates. STUDY DESIGN AND METHODS The conventional cDNA reference sequences for all known RBC and PLT genes that correlate with antigen expression were aligned to the human reference genome. The alignments allowed conversion of conventional cDNA nucleotide positions to the corresponding genomic coordinates. RBC and PLT antigen prediction was then performed using the human reference genome and whole genome sequencing (WGS) data with serologic confirmation. RESULTS Some major differences and alignment issues were found when attempting to convert the conventional cDNA to human reference genome sequences for the following genes: ABO, A4GALT, RHD, RHCE, FUT3, ACKR1 (previously DARC), ACHE, FUT2, CR1, GCNT2, and RHAG. However, it was possible to create usable alignments, which facilitated the prediction of all RBC and PLT antigens with a known molecular basis from WGS data. Traditional serologic typing for 18 RBC antigens were in agreement with the WGS‐based antigen predictions, providing proof of principle for this approach. CONCLUSION Detailed mapping of conventional cDNA annotated RBC and PLT alleles can enable accurate prediction of RBC and PLT antigens from whole genomic sequencing data. PMID:26634332

Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms.

PubMed

Zapata, Luis; Ding, Jia; Willing, Eva-Maria; Hartwig, Benjamin; Bezdan, Daniela; Jiao, Wen-Biao; Patel, Vipul; Velikkakam James, Geo; Koornneef, Maarten; Ossowski, Stephan; Schneeberger, Korbinian

2016-07-12

Resequencing or reference-based assemblies reveal large parts of the small-scale sequence variation. However, they typically fail to separate such local variation into colinear and rearranged variation, because they usually do not recover the complement of large-scale rearrangements, including transpositions and inversions. Besides the availability of hundreds of genomes of diverse Arabidopsis thaliana accessions, there is so far only one full-length assembled genome: the reference sequence. We have assembled 117 Mb of the A. thaliana Landsberg erecta (Ler) genome into five chromosome-equivalent sequences using a combination of short Illumina reads, long PacBio reads, and linkage information. Whole-genome comparison against the reference sequence revealed 564 transpositions and 47 inversions comprising ∼3.6 Mb, in addition to 4.1 Mb of nonreference sequence, mostly originating from duplications. Although rearranged regions are not different in local divergence from colinear regions, they are drastically depleted for meiotic recombination in heterozygotes. Using a 1.2-Mb inversion as an example, we show that such rearrangement-mediated reduction of meiotic recombination can lead to genetically isolated haplotypes in the worldwide population of A. thaliana Moreover, we found 105 single-copy genes, which were only present in the reference sequence or the Ler assembly, and 334 single-copy orthologs, which showed an additional copy in only one of the genomes. To our knowledge, this work gives first insights into the degree and type of variation, which will be revealed once complete assemblies will replace resequencing or other reference-dependent methods.

Book Catalogs; Selected References.

ERIC Educational Resources Information Center

Brandhorst, Wesley T.

The 116 citations on book catalogs are divided into the following two main sections: (1) Selected References, in alphabetic sequence by personal or institutional author and (2) Anonymous Entries, in alphabetic sequence by title. One hundred and seven of the citations cover the years 1960 through March 1969. There are five scattered citations in…

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics.

PubMed

Straub, Shannon C K; Parks, Matthew; Weitemier, Kevin; Fishbein, Mark; Cronn, Richard C; Liston, Aaron

2012-02-01

Just as Sanger sequencing did more than 20 years ago, next-generation sequencing (NGS) is poised to revolutionize plant systematics. By combining multiplexing approaches with NGS throughput, systematists may no longer need to choose between more taxa or more characters. Here we describe a genome skimming (shallow sequencing) approach for plant systematics. Through simulations, we evaluated optimal sequencing depth and performance of single-end and paired-end short read sequences for assembly of nuclear ribosomal DNA (rDNA) and plastomes and addressed the effect of divergence on reference-guided plastome assembly. We also used simulations to identify potential phylogenetic markers from low-copy nuclear loci at different sequencing depths. We demonstrated the utility of genome skimming through phylogenetic analysis of the Sonoran Desert clade (SDC) of Asclepias (Apocynaceae). Paired-end reads performed better than single-end reads. Minimum sequencing depths for high quality rDNA and plastome assemblies were 40× and 30×, respectively. Divergence from the reference significantly affected plastome assembly, but relatively similar references are available for most seed plants. Deeper rDNA sequencing is necessary to characterize intragenomic polymorphism. The low-copy fraction of the nuclear genome was readily surveyed, even at low sequencing depths. Nearly 160000 bp of sequence from three organelles provided evidence of phylogenetic incongruence in the SDC. Adoption of NGS will facilitate progress in plant systematics, as whole plastome and rDNA cistrons, partial mitochondrial genomes, and low-copy nuclear markers can now be efficiently obtained for molecular phylogenetics studies.

Automatic phylogenetic classification of bacterial beta-lactamase sequences including structural and antibiotic substrate preference information.

PubMed

Ma, Jianmin; Eisenhaber, Frank; Maurer-Stroh, Sebastian

2013-12-01

Beta lactams comprise the largest and still most effective group of antibiotics, but bacteria can gain resistance through different beta lactamases that can degrade these antibiotics. We developed a user friendly tree building web server that allows users to assign beta lactamase sequences to their respective molecular classes and subclasses. Further clinically relevant information includes if the gene is typically chromosomal or transferable through plasmids as well as listing the antibiotics which the most closely related reference sequences are known to target and cause resistance against. This web server can automatically build three phylogenetic trees: the first tree with closely related sequences from a Tachyon search against the NCBI nr database, the second tree with curated reference beta lactamase sequences, and the third tree built specifically from substrate binding pocket residues of the curated reference beta lactamase sequences. We show that the latter is better suited to recover antibiotic substrate assignments through nearest neighbor annotation transfer. The users can also choose to build a structural model for the query sequence and view the binding pocket residues of their query relative to other beta lactamases in the sequence alignment as well as in the 3D structure relative to bound antibiotics. This web server is freely available at http://blac.bii.a-star.edu.sg/.

First AXAF Fellowships Awarded

NASA Astrophysics Data System (ADS)

1998-03-01

The AXAF (Advanced X-ray Astrophysics Facility) Science Center has announced the selection of five scientists to inaugurate the AXAF Postdoctoral Fellowship Program. Competition for the fellowships was open to all recent astronomy and astrophysics graduates worldwide. The AXAF Fellows will work for three years at a host astronomical institution in the United States where they will investigate topics broadly related to the scientific mission of AXAF. Additional AXAF Fellows will be selected each year over the course of the program. The AXAF Fellowship Program is a joint venture between NASA and the AXAF Science Center in cooperation with the host institutions. The AXAF Science Center is operated by the Smithsonian Astrophysical Observatory in Cambridge, Massachusetts and funded by NASA through the Marshall Space Flight Center. "We are elated at the outstanding group of Fellows," said Harvey Tananbaum, the Director of the AXAF Science Center. "They will be working during the exciting period when the first X-ray images will be received from AXAF." Nancy Remage Evans, AXAF Fellowship Program Coordinator added, "The program will also encourage AXAF related work at institutions throughout the United States." An independent panel of scientists selected the honorees. The first AXAF Fellows and the host institutions at which they will hold their fellowships are: David Buote (University of California, Santa Cruz), Tiziana Di Matteo (Harvard-Smithsonian Center for Astrophysics), Ann Esin (California Institute of Technology), Joseph Mohr (University of Chicago), and Edward Moran (Massachusetts Institute of Technology). AXAF, the third of NASA's Great Observatories after the Hubble Space Telescope and the Compton Gamma Ray Observatory, is the largest and most sophisticated X-ray telescope ever built. When it is launched in December of this year, AXAF's high resolution will provide new information about exploding stars, black holes, colliding galaxies, and other extremely hot regions of the universe. Further information about the AXAF satellite is available at the World Wide Web at http://xrtpub.harvard.edu/. Further information about the Fellowship program is available at http://asc.harvard.edu/fellows/. Supplemental Information on 1998 AXAF Fellows: * David Buote graduated from MIT, Cambridge MA 02139 * Tiziana DiMatteo graduated from Cambridge University, Cambridge CB30HA UK * Ann Esin graduated from Harvard University, Cambridge, MA 02138 * Joseph Mohr graduated from Harvard University, Cambridge, MA 02138 * Edward Moran graduated from Columbia University, New York City, NY 10027

Oxford and Cambridge Boat Race: Performance, Pacing and Tactics Between 1890 and 2014.

PubMed

Edwards, Andrew M; Guy, Joshua H; Hettinga, Florentina J

2016-10-01

Currently no studies have examined the historical performances of Oxford and Cambridge Boat Race crews in the context of performance, pacing and tactics which is surprising as the event has routinely taken place annually for over 150 years on the same course. The purpose of this study was twofold, to firstly examine the historical development of performances and physical characteristics of crews over 124 years of the Oxford and Cambridge Boat Race between 1890 and 2014 and secondly to investigate the pacing and tactics employed by crews over that period. Linear regression modelling was applied to investigate the development of performance and body size for crews of eight male individuals over time from Boat Race archive data. Performance change over time was further assessed in 10-year clusters while four intra-race checkpoints were used to examine pacing and tactics. Significant correlations were observed between performance and time (1890-2014) for both Oxford (r = -0.67; p < 0.01) and Cambridge (r = -0.64; p < 0.01). There was no difference in mean performance times for Oxford (1170 ± 88 s) and Cambridge (1168 ± 89.8 s) during 1890-2014. Crew performance times improved over time with significant gains from baseline achieved in the 1950s (Cambridge) and the 1960s (Oxford), which coincided with significant change in the physicality of the competing crews (p < 0.01). There was no tactical advantage from commencing on either the Surrey or Middlesex station beyond chance alone; however, all crews (n = 228) adopted a fast-start strategy, with 81 % of victories achieved by the crew leading the race at the first intra-race checkpoint (24 % of total distance). Crews leading the race at the final checkpoint (83 % of total distance; 1143 m) achieved victory on 94 % of occasions. Performances and physical characteristics of the crews have changed markedly since 1890, with faster heavier crews now common. Tactically, gaining the early lead position with a fast-start strategy seems particularly meaningful to success in the Boat Race throughout the years, and has been of greater importance to race outcome than factors such as the starting station.

Investigation of prolific sheep from UK and Ireland for evidence on origin of the mutations in BMP15 (FecX(G), FecX(B)) and GDF9 (FecG(H)) in Belclare and Cambridge sheep.

PubMed

Mullen, Michael P; Hanrahan, James P; Howard, Dawn J; Powell, Richard

2013-01-01

This paper concerns the likely origin of three mutations with large effects on ovulation rate identified in the Belclare and Cambridge sheep breeds; two in the BMP15 gene (FecX(G) and FecX(B)) and the third (FecG(H)) in GDF9. All three mutations segregate in Belclare sheep while one, FecX(B), has not been found in the Cambridge. Both Belclare and Cambridge breeds are relatively recently developed composites that have common ancestry through the use of genetic material from the Finnish Landrace and Lleyn breeds. The development of both composites also involved major contributions from exceptionally prolific ewes screened from flocks in Ireland (Belclare) and Britain (Cambridge) during the 1960s. The objective of the current study was to establish the likely origin of the mutations (FecX(G), FecX(B) and FecG(H)) through analysis of DNA from Finnish Landrace and Lleyn sheep, and Galway and Texel breeds which contributed to the development of the Belclare breed. Ewes with exceptionally high prolificacy (hyper-prolific ewes) in current flocks on Irish farms were identified to simulate the screening of ewes from Irish flocks in the 1960s. DNA was obtained from: prolific ewes in extant flocks of Lleyn sheep (n = 44) on the Lleyn peninsula in Wales; hyper-prolific ewes (n = 41); prolific Galway (n = 41) ewes; Finnish Landrace (n = 124) and Texel (n = 19) ewes. The FecX(G) mutation was identified in Lleyn but not in Finnish Landrace, Galway or Texel sheep; FecX(B) was only found among the hyper-prolific ewes. The FecG(H) mutation was identified in the sample of Lleyn sheep. It was concluded from these findings that the Lleyn breed was the most likely source of the FecX(G) and FecG(H) mutations in Belclare and Cambridge sheep and that the FecX(B) mutation came from the High Fertility line that was developed using prolific ewes selected from commercial flocks in Ireland in the 1960's and subsequently used in the genesis of the Belclare.

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

PubMed Central

Beier, Sebastian; Himmelbach, Axel; Colmsee, Christian; Zhang, Xiao-Qi; Barrero, Roberto A.; Zhang, Qisen; Li, Lin; Bayer, Micha; Bolser, Daniel; Taudien, Stefan; Groth, Marco; Felder, Marius; Hastie, Alex; Šimková, Hana; Staňková, Helena; Vrána, Jan; Chan, Saki; Muñoz-Amatriaín, María; Ounit, Rachid; Wanamaker, Steve; Schmutzer, Thomas; Aliyeva-Schnorr, Lala; Grasso, Stefano; Tanskanen, Jaakko; Sampath, Dharanya; Heavens, Darren; Cao, Sujie; Chapman, Brett; Dai, Fei; Han, Yong; Li, Hua; Li, Xuan; Lin, Chongyun; McCooke, John K.; Tan, Cong; Wang, Songbo; Yin, Shuya; Zhou, Gaofeng; Poland, Jesse A.; Bellgard, Matthew I.; Houben, Andreas; Doležel, Jaroslav; Ayling, Sarah; Lonardi, Stefano; Langridge, Peter; Muehlbauer, Gary J.; Kersey, Paul; Clark, Matthew D.; Caccamo, Mario; Schulman, Alan H.; Platzer, Matthias; Close, Timothy J.; Hansson, Mats; Zhang, Guoping; Braumann, Ilka; Li, Chengdao; Waugh, Robbie; Scholz, Uwe; Stein, Nils; Mascher, Martin

2017-01-01

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. ‘Morex’ was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX). PMID:28448065

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

PubMed Central

Schneider, Valerie A.; Graves-Lindsay, Tina; Howe, Kerstin; Bouk, Nathan; Chen, Hsiu-Chuan; Kitts, Paul A.; Murphy, Terence D.; Pruitt, Kim D.; Thibaud-Nissen, Françoise; Albracht, Derek; Fulton, Robert S.; Kremitzki, Milinn; Magrini, Vincent; Markovic, Chris; McGrath, Sean; Steinberg, Karyn Meltz; Auger, Kate; Chow, William; Collins, Joanna; Harden, Glenn; Hubbard, Timothy; Pelan, Sarah; Simpson, Jared T.; Threadgold, Glen; Torrance, James; Wood, Jonathan M.; Clarke, Laura; Koren, Sergey; Boitano, Matthew; Peluso, Paul; Li, Heng; Chin, Chen-Shan; Phillippy, Adam M.; Durbin, Richard; Wilson, Richard K.; Flicek, Paul; Eichler, Evan E.; Church, Deanna M.

2017-01-01

The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. For the first time, the reference assembly contains sequence-based representations for the centromeres. We also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. We demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions, and impact variant interpretation at clinically relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that although the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. We assert that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health. PMID:28396521

Assessing the Impact of Strategic Culture on Chinese Regional Security Policies in South Asia

DTIC Science & Technology

2011-05-19

36John Milton Cooper, Breaking the Heart of the World: Woodrow Wilson and the Fight for the League of Nations (Cambridge: Cambridge University Press...investment vehicles. 44Thomas L. Friedman , The Lexus and the Olive Tree (New York: Farrar, Straus, Giroux, 1999), 155. 16 regarding the control...Washington Post, June 13, 1999, A27. Cooper, John Milton . Breaking the Heart of the World: Woodrow Wilson and the Fight for the League of Nations

Inspection Methods in Programming: Cliches and Plans.

DTIC Science & Technology

1987-12-01

PROGRAM ELEMENT. PROJECT. TASK Artificial Inteligence Laboratory AREA & WORK UN IT NUMBERS J 545 Technology Square Cambridge, MA 02139 $L. CONTROLLING...U) MASSACHUSETTS INST OF TECH CAMBRIDGE ARTIFICIAL INTELLIGENCE LAB C RICH DEC 87 AI-M-±05 UNCLASSIFIED NW014-B5-K-0124 F/G 12/5 NL ’lllll l l l...S %P W. J % % %s MASSACHUSETTS INSTITUTE OF TECHNOLOGY N ARTIFICIAL INTELLIGENCE LABORATORY 00 A.I. Memo No. 1005 December 1987 N Inspection Methods

Aircraft Wake Vortices: An Assessment of the Current Situation

DTIC Science & Technology

1991-01-01

1979 , DOT/TSC, Cambridge, MA. 36. Burnham, D.C., "Chicago Monostatic Acoustic Vortex Sensing System, Vol. I : Data Collection and Reduction," FAA-RD-79...April 1979 , DOT/TSC, Cambridge, MA. 45. Hallock, J.N., "Vortex Advisory System Safety Analysis; Vol. I : Analytical Model," FAA-RD-78-68. I , September...Industry Representatives," March 1979 , Economics & Science Planning Inc., Washington, DC. 106. Hallock, J.N., "Vortex Advisory System, Vol. I : Effectiveness

Governing Geoengineering Research: A Political and Technical Vulnerability Analysis of Potential Near-Term Options

DTIC Science & Technology

2011-01-01

weather events, or the spread of tropical diseases into North America. The net A Vulnerability-and-Response-Option Analysis Framework for a Risk...Avoidable Surprises, Cambridge: Cambridge University Press, 2002. Doney, Scott C., Victoria J. Fabry , Richard A. Feely, and Joan A. Kleypas, “Ocean...Falkenmark, Louise Karlberg, Robert W. Corell, Victoria J. Fabry , James Hansen, Brian Walker, Diana Liverman, Katherine Richardson, Paul Crutzen, and

Special Relationship What are the Strategic Choices available to the UK after the US Pivot to Asia

DTIC Science & Technology

2013-02-14

Emergency’ see Jones, Matthew, Conflict and Confrontation in South East Asia , 1961 – 1965, (Cambridge: CUP, 2002). 7 A spokesman at the Bureau of Asian...Stanford: Stanford University Press, 2010. Jones, Matthew. Conflict and Confrontation in South East Asia , 1961 – 1965. Cambridge: CUP, 2002...greater role in influencing events in the Asia -Pacific region. This strategic decision is complicated by the fact that the United States is trying to

The Alliance Decides the Mission? Multilateral Decision Making at the UN and NATO on Libya, 2010-2011

DTIC Science & Technology

2012-06-01

Bruce D. Jones, Shepard Forman, and Richard Gowan, 20-44, (Cambridge: Cambridge University Press, 2010). 65 Steve Weber, “Shaping the Postwar Balance...because the United States provided strong counterbalancing leadership, it also enabled increased French- German cooperation, wherein French concerns of... German military power were somewhat mitigated by the U.S. promise of continued involvement.93 An investigation of a few key articles in the North

Selection and Effects of Channels in Distributed Communication and Decision-Making Tasks: A Theoretical Review and a Proposed Research Paradigm

DTIC Science & Technology

1988-04-01

in speaking, writing, and oral literture. In Deborah Tannen (Ed.) Spoken and written lanquage: Exploring orality and literacy. Norwood, NJ: Ablex...strategies. Cambridge: Cambridge .’. University Press. Gumperz, John J., Tannen , Deborah . (1978). Individual and social differences in lanquaqe use. In W. Wang...Hannah, & O’Connor, Mary Catherine. (1984). Cohesion in spoken and written discourse: Ethnic style and the transition to literacy. In Deborah Tannen (Ed

Instantly Basing Locust Swarms: New Options for Future Air Operations

DTIC Science & Technology

2012-06-01

force’s fighting potential.”51 Moreover, JP 3-0 specifically emphasizes “Securing and protecting forces, bases, JSAs [Joint Storage Areas], and LOCs ...Smith and Leo Marx (Cambridge, MA: The MIT Press, 1994), 101-113. 64 Hughes, “Technological Momentum,”108. 65 John Law, "Technology and Heterogeneous...Technology Drive History?, edited by Merritt Roe Smith and Leo Marx, 101-113. Cambridge, MA: The MIT Press, 1994. Jean, Grace V. "Remotely Piloted

Fighting Dark Networks: Using Social Network Analysis to Implement the Special Operations Targeting Process for Direct and Indirect Approaches

DTIC Science & Technology

2013-03-01

Wouter De Nooy, Andrej Mrvar and Vladimir Batagelj , Exploratory Social Network Analysis with Pajek, (New York: Cambridge University Press, 2005), 5...Granovetter, “The Strength of Weak Ties,” 1350–1368. 151 de Nooy, Mrvar , and Batagelj , Exploratory Social Network Analysis with Pajek, 151. 152...Spacetime Wrinkles Exhibit (1995). de Nooy, Wouter, Andrej Mrvar , and Vladimir Batagelj . Exploratory Social Network Analysis with Pajek. Cambridge

A Grey Area: Congressional Oversight of the Middle Ground Between Title 10 and Title 50

DTIC Science & Technology

2012-06-01

for 1981, Title V. 43 Eric Rosenbach and Aki J. Peritz, Trials by Fire , Counterterrorism and the Law (Cambridge: Belfer Center for Science and...Potomac Books, 2005), 59. The authors use different terms to describe the same phenomena, Johnson uses police patrolling and fire fighting instead. 56...Trials by Fire , Counterterrorism and the Law (Cambridge: Belfer Center for Science and International Affairs, 2010), 8. 44 Kibbe, “The Rise of the

Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. A response to the letter by the Cambridge Crystallographic Data Centre.

PubMed

Baldi, Pierre

2011-12-27

A response is presented to sentiments expressed in "Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress. A Response from The Cambridge Crystallographic Data Centre", recently published in the Journal of Chemical Information and Modeling, (1) which may give readers a misleading impression regarding significant impediments to scientific research posed by the CCDC.

Stability of libration points in the restricted four-body problem with variable mass

NASA Astrophysics Data System (ADS)

Mittal, Amit; Aggarwal, Rajiv; Suraj, Md. Sanam; Bisht, Virender Singh

2016-10-01

We have investigated the stability of the Lagrangian solutions for the restricted four-body problem with variable mass. It has been assumed that the three primaries with masses m1, m2 and m3 form an equilateral triangle, wherein m2=m3. According to Jeans' law (Astronomy and Cosmogony, Cambridge University Press, Cambridge, 1928), the infinitesimal body varies its mass m with time. The space-time transformations of Meshcherskii (Studies on the Mechanics of Bodies of Variable Mass, GITTL, Moscow, 1949) are used by taking the values of the parameters q=1/2, k=0, n=1. The equations of motion of the infinitesimal body with variable mass have been determined. The equations of motion of the current problem differ from the ones of the restricted four-body problem with constant mass. There exist eight libration points, out of which two are collinear with the primary m1 and the rest are non-collinear for a fixed value of parameters γ (m {at time} t/m {at initial time}, 0<γ≤1 ), α (the proportionality constant in Jeans' law (Astronomy and Cosmogony, Cambridge University Press, Cambridge, 1928), 0≤α≤2.2) and μ=0.019 (the mass parameter). All the libration points are found to be unstable. The zero velocity surfaces (ZVS) are also drawn and regions of motion are discussed.

Two Low Coverage Bird Genomes and a Comparison of Reference-Guided versus De Novo Genome Assemblies

PubMed Central

Card, Daren C.; Schield, Drew R.; Reyes-Velasco, Jacobo; Fujita, Matthew K.; Andrew, Audra L.; Oyler-McCance, Sara J.; Fike, Jennifer A.; Tomback, Diana F.; Ruggiero, Robert P.; Castoe, Todd A.

2014-01-01

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5–5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies. PMID:25192061

IECON '87: Industrial applications of control and simulation; Proceedings of the 1987 International Conference on Industrial Electronics, Control, and Instrumentation, Cambridge, MA, Nov. 3, 4, 1987

NASA Technical Reports Server (NTRS)

Hartley, Tom T. (Editor)

1987-01-01

Recent advances in control-system design and simulation are discussed in reviews and reports. Among the topics considered are fast algorithms for generating near-optimal binary decision programs, trajectory control of robot manipulators with compensation of load effects via a six-axis force sensor, matrix integrators for real-time simulation, a high-level control language for an autonomous land vehicle, and a practical engineering design method for stable model-reference adaptive systems. Also addressed are the identification and control of flexible-limb robots with unknown loads, adaptive control and robust adaptive control for manipulators with feedforward compensation, adaptive pole-placement controllers with predictive action, variable-structure strategies for motion control, and digital signal-processor-based variable-structure controls.

Iron Age and Anglo-Saxon genomes from East England reveal British migration history.

PubMed

Schiffels, Stephan; Haak, Wolfgang; Paajanen, Pirita; Llamas, Bastien; Popescu, Elizabeth; Loe, Louise; Clarke, Rachel; Lyons, Alice; Mortimer, Richard; Sayer, Duncan; Tyler-Smith, Chris; Cooper, Alan; Durbin, Richard

2016-01-19

British population history has been shaped by a series of immigrations, including the early Anglo-Saxon migrations after 400 CE. It remains an open question how these events affected the genetic composition of the current British population. Here, we present whole-genome sequences from 10 individuals excavated close to Cambridge in the East of England, ranging from the late Iron Age to the middle Anglo-Saxon period. By analysing shared rare variants with hundreds of modern samples from Britain and Europe, we estimate that on average the contemporary East English population derives 38% of its ancestry from Anglo-Saxon migrations. We gain further insight with a new method, rarecoal, which infers population history and identifies fine-scale genetic ancestry from rare variants. Using rarecoal we find that the Anglo-Saxon samples are closely related to modern Dutch and Danish populations, while the Iron Age samples share ancestors with multiple Northern European populations including Britain.

Origins and challenges of viral dark matter.

PubMed

Krishnamurthy, Siddharth R; Wang, David

2017-07-15

The accurate classification of viral dark matter - metagenomic sequences that originate from viruses but do not align to any reference virus sequences - is one of the major obstacles in comprehensively defining the virome. Depending on the sample, viral dark matter can make up from anywhere between 40 and 90% of sequences. This review focuses on the specific nature of dark matter as it relates to viral sequences. We identify three factors that contribute to the existence of viral dark matter: the divergence and length of virus sequences, the limitations of alignment based classification, and limited representation of viruses in reference sequence databases. We then discuss current methods that have been developed to at least partially circumvent these limitations and thereby reduce the extent of viral dark matter. Copyright © 2017 Elsevier B.V. All rights reserved.

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver

PubMed Central

Blanquart, François; Golubchik, Tanya; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Croucher, Nicholas J; Hall, Matthew; Hillebregt, Mariska; Ratmann, Oliver; Albert, Jan; Bannert, Norbert; Fellay, Jacques; Fransen, Katrien; Gourlay, Annabelle; Grabowski, M Kate; Gunsenheimer-Bartmeyer, Barbara; Günthard, Huldrych F; Kivelä, Pia; Kouyos, Roger; Laeyendecker, Oliver; Liitsola, Kirsi; Meyer, Laurence; Porter, Kholoud; Ristola, Matti; van Sighem, Ard; Cornelissen, Marion; Kellam, Paul; Reiss, Peter

2018-01-01

Abstract Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user’s choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver’s constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also successfully applied shiver to whole-genome samples of Hepatitis C Virus and Respiratory Syncytial Virus. shiver is publicly available from https://github.com/ChrisHIV/shiver. PMID:29876136

New Approaches and Technologies to Sequence de novo Plant reference Genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

ScienceCinema

Schmutz, Jeremy

2018-02-01

Jeremy Schmutz of the HudsonAlpha Institute for Biotechnology on New approaches and technologies to sequence de novo plant reference genomes at the 8th Annual Genomics of Energy Environment Meeting on March 27, 2013 in Walnut Creek, CA.

Swine transcriptome characterization by combined Iso-Seq and RNA-seq for annotating the emerging long read-based reference genome

USDA-ARS?s Scientific Manuscript database

PacBio long-read sequencing technology is increasingly popular in genome sequence assembly and transcriptome cataloguing. Recently, a new-generation pig reference genome was assembled based on long reads from this technology. To finely annotate this genome assembly, transcriptomes of nine tissues fr...

New Approaches and Technologies to Sequence de novo Plant reference Genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schmutz, Jeremy

2013-03-01

Jeremy Schmutz of the HudsonAlpha Institute for Biotechnology on New approaches and technologies to sequence de novo plant reference genomes at the 8th Annual Genomics of Energy Environment Meeting on March 27, 2013 in Walnut Creek, CA.

The diploid genome sequence of an Asian individual

PubMed Central

Wang, Jun; Wang, Wei; Li, Ruiqiang; Li, Yingrui; Tian, Geng; Goodman, Laurie; Fan, Wei; Zhang, Junqing; Li, Jun; Zhang, Juanbin; Guo, Yiran; Feng, Binxiao; Li, Heng; Lu, Yao; Fang, Xiaodong; Liang, Huiqing; Du, Zhenglin; Li, Dong; Zhao, Yiqing; Hu, Yujie; Yang, Zhenzhen; Zheng, Hancheng; Hellmann, Ines; Inouye, Michael; Pool, John; Yi, Xin; Zhao, Jing; Duan, Jinjie; Zhou, Yan; Qin, Junjie; Ma, Lijia; Li, Guoqing; Yang, Zhentao; Zhang, Guojie; Yang, Bin; Yu, Chang; Liang, Fang; Li, Wenjie; Li, Shaochuan; Li, Dawei; Ni, Peixiang; Ruan, Jue; Li, Qibin; Zhu, Hongmei; Liu, Dongyuan; Lu, Zhike; Li, Ning; Guo, Guangwu; Zhang, Jianguo; Ye, Jia; Fang, Lin; Hao, Qin; Chen, Quan; Liang, Yu; Su, Yeyang; san, A.; Ping, Cuo; Yang, Shuang; Chen, Fang; Li, Li; Zhou, Ke; Zheng, Hongkun; Ren, Yuanyuan; Yang, Ling; Gao, Yang; Yang, Guohua; Li, Zhuo; Feng, Xiaoli; Kristiansen, Karsten; Wong, Gane Ka-Shu; Nielsen, Rasmus; Durbin, Richard; Bolund, Lars; Zhang, Xiuqing; Li, Songgang; Yang, Huanming; Wang, Jian

2009-01-01

Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics. PMID:18987735

Identification of Mycobacterium spp. of veterinary importance using rpoB gene sequencing

PubMed Central

2011-01-01

Background Studies conducted on Mycobacterium spp. isolated from human patients indicate that sequencing of a 711 bp portion of the rpoB gene can be useful in assigning a species identity, particularly for members of the Mycobacterium avium complex (MAC). Given that MAC are important pathogens in livestock, companion animals, and zoo/exotic animals, we were interested in evaluating the use of rpoB sequencing for identification of Mycobacterium isolates of veterinary origin. Results A total of 386 isolates, collected over 2008 - June 2011 from 378 animals (amphibians, reptiles, birds, and mammals) underwent PCR and sequencing of a ~ 711 bp portion of the rpoB gene; 310 isolates (80%) were identified to the species level based on similarity at ≥ 98% with a reference sequence. The remaining 76 isolates (20%) displayed < 98% similarity with reference sequences and were assigned to a clade based on their location in a neighbor-joining tree containing reference sequences. For a subset of 236 isolates that received both 16S rRNA and rpoB sequencing, 167 (70%) displayed a similar species/clade assignation for both sequencing methods. For the remaining 69 isolates, species/clade identities were different with each sequencing method. Mycobacterium avium subsp. hominissuis was the species most frequently isolated from specimens from pigs, cervids, companion animals, cattle, and exotic/zoo animals. Conclusions rpoB sequencing proved useful in identifying Mycobacterium isolates of veterinary origin to clade, species, or subspecies levels, particularly for assemblages (such as the MAC) where 16S rRNA sequencing alone is not adequate to demarcate these taxa. rpoB sequencing can represent a cost-effective identification tool suitable for routine use in the veterinary diagnostic laboratory. PMID:22118247

FRESCO: Referential compression of highly similar sequences.

PubMed

Wandelt, Sebastian; Leser, Ulf

2013-01-01

In many applications, sets of similar texts or sequences are of high importance. Prominent examples are revision histories of documents or genomic sequences. Modern high-throughput sequencing technologies are able to generate DNA sequences at an ever-increasing rate. In parallel to the decreasing experimental time and cost necessary to produce DNA sequences, computational requirements for analysis and storage of the sequences are steeply increasing. Compression is a key technology to deal with this challenge. Recently, referential compression schemes, storing only the differences between a to-be-compressed input and a known reference sequence, gained a lot of interest in this field. In this paper, we propose a general open-source framework to compress large amounts of biological sequence data called Framework for REferential Sequence COmpression (FRESCO). Our basic compression algorithm is shown to be one to two orders of magnitudes faster than comparable related work, while achieving similar compression ratios. We also propose several techniques to further increase compression ratios, while still retaining the advantage in speed: 1) selecting a good reference sequence; and 2) rewriting a reference sequence to allow for better compression. In addition,we propose a new way of further boosting the compression ratios by applying referential compression to already referentially compressed files (second-order compression). This technique allows for compression ratios way beyond state of the art, for instance,4,000:1 and higher for human genomes. We evaluate our algorithms on a large data set from three different species (more than 1,000 genomes, more than 3 TB) and on a collection of versions of Wikipedia pages. Our results show that real-time compression of highly similar sequences at high compression ratios is possible on modern hardware.

Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.)

PubMed Central

Kim, Seungill; Kim, Myung-Shin; Kim, Yong-Min; Yeom, Seon-In; Cheong, Kyeongchae; Kim, Ki-Tae; Jeon, Jongbum; Kim, Sunggil; Kim, Do-Sun; Sohn, Seong-Han; Lee, Yong-Hwan; Choi, Doil

2015-01-01

The onion (Allium cepa L.) is one of the most widely cultivated and consumed vegetable crops in the world. Although a considerable amount of onion transcriptome data has been deposited into public databases, the sequences of the protein-coding genes are not accurate enough to be used, owing to non-coding sequences intermixed with the coding sequences. We generated a high-quality, annotated onion transcriptome from de novo sequence assembly and intensive structural annotation using the integrated structural gene annotation pipeline (ISGAP), which identified 54,165 protein-coding genes among 165,179 assembled transcripts totalling 203.0 Mb by eliminating the intron sequences. ISGAP performed reliable annotation, recognizing accurate gene structures based on reference proteins, and ab initio gene models of the assembled transcripts. Integrative functional annotation and gene-based SNP analysis revealed a whole biological repertoire of genes and transcriptomic variation in the onion. The method developed in this study provides a powerful tool for the construction of reference gene sets for organisms based solely on de novo transcriptome data. Furthermore, the reference genes and their variation described here for the onion represent essential tools for molecular breeding and gene cloning in Allium spp. PMID:25362073

Sequence verification of synthetic DNA by assembly of sequencing reads

PubMed Central

Wilson, Mandy L.; Cai, Yizhi; Hanlon, Regina; Taylor, Samantha; Chevreux, Bastien; Setubal, João C.; Tyler, Brett M.; Peccoud, Jean

2013-01-01

Gene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the sequences of construction intermediates and the final product of a gene synthesis project is a critical part of the workflow, yet one that has received the least attention. Sequence validation is equally important for other kinds of curated clone collections. Ensuring that the physical sequence of a clone matches its published sequence is a common quality control step performed at least once over the course of a research project. GenoREAD is a web-based application that breaks the sequence verification process into two steps: the assembly of sequencing reads and the alignment of the resulting contig with a reference sequence. GenoREAD can determine if a clone matches its reference sequence. Its sophisticated reporting features help identify and troubleshoot problems that arise during the sequence verification process. GenoREAD has been experimentally validated on thousands of gene-sized constructs from an ORFeome project, and on longer sequences including whole plasmids and synthetic chromosomes. Comparing GenoREAD results with those from manual analysis of the sequencing data demonstrates that GenoREAD tends to be conservative in its diagnostic. GenoREAD is available at www.genoread.org. PMID:23042248

The Relationship between India’s Geographic Element of Power and its Military Element of Power

DTIC Science & Technology

1991-06-07

provided the background knowledge necessary to begin this project. The Cambridge Encyclopedia of India, Pakistan, BanAladesh and Srilanka , by Francis...and Burma and in the west, by Pakistan. Just south of India’s southern tip lies Srilanka . Location. The bulk of India’s land mass lies between 70...Affairs, (Rand McNally & Co., 1963), 319. 2. Francis Robinson, The Cambridge Encyclopedia of India, Pakistan, Bangladesh, Srilanka , Nepal, Bhutan and

Edge Detection,

DTIC Science & Technology

1985-09-01

PROJECT. T ASK0 Artificial Inteligence Laboratory AREA It WORK UNIT NUMBERS V 545 Technology Square ( Cambridge, HA 02139 I I* CONTOOL1LIN@4OFFICE NAME...ARD-A1t62 62 EDGE DETECTION(U) NASSACNUSETTS INST OF TECH CAMBRIDGE 1/1 ARTIFICIAL INTELLIGENCE LAB E C HILDRETH SEP 85 AI-M-8 N99SI4-8S-C-6595...used to carry out this analysis. cce~iO a N) ’.~" D LI’BL. P p ------------ Sj. t i MASSACHUSETTS INSTITUTE OF TECHNOLOGY i ARTIFICIAL INTELLIGENCE

Using a neural network to proximity correct patterns written with a Cambridge electron beam microfabricator 10.5 lithography system

NASA Astrophysics Data System (ADS)

Cummings, K. D.; Frye, R. C.; Rietman, E. A.

1990-10-01

This letter describes the initial results of using a theoretical determination of the proximity function and an adaptively trained neural network to proximity-correct patterns written on a Cambridge electron beam lithography system. The methods described are complete and may be applied to any electron beam exposure system that can modify the dose during exposure. The patterns produced in resist show the effects of proximity correction versus noncorrected patterns.

Proceedings of the International Symposium on Methodologies for Intelligent Systems (Poster Session) (7th) held at Trondheim, Norway, on 15-18 June, 1993

DTIC Science & Technology

1993-06-18

David Hislop (US Army Research Office), Eero Hyvonen (VTT, Finland), Marek Karpinski (Bonn, Germany), Yves Kodratoff (Paris VI, France), Jan...21] M. P. Marcus, A theory of Syntactic Recognition for Natural Language, The MIT Press, Cambridge, Mass., 1980 [221 K.R. McKeown, The TEXT System...H. Simon, The Sciences of the Artificial, The MIT Press, Cambridge, MA, ( 1980 ). 3. M.D. Mesarovich, D. Macko, Y. Takahara Y., Theory of Hierarchical

An Optimal Dissipative Encoder for the Toric Code

DTIC Science & Technology

2014-01-16

Topological quantummemory J. Math. Phys. 43 4452–505 [6] Diehl S, Micheli A, Kantian A, Kraus B, Büchler H P and Zoller P 2008 Quantum states and phases in...Diehl S, Kantian A, Micheli A and Zoller P 2008 Preparation of entangled states by quantum Markov processes Phys. Rev. A 78 042307 [12] Marvian I 2013...Information Theory (Cambridge: Cambridge University Press) [20] Wolf M and Cirac J I 2008 Dividing quantum channels Commun. Math. Phys. 279 147 11

The Polish Collection at the Alliance College Library in Cambridge Springs, PA: The Origins of the Collection in 1950, Its Rapid Development in the 1970's and the Introduction of the Online Computer Library Center (OCLC) in 1982.

ERIC Educational Resources Information Center

Kozaczka, Stanley J.

This essay outlines the development, present condition, and future direction of the 20,000-volume Polish research collection at Alliance College, located in Cambridge Springs, Pennsylvania. Alliance College was founded in 1912 by the Polish National Alliance (PNA), a life insurance fraternal organization. In 1931 its entire library collection was…

Application of Ada (Trade Name) Higher Order Language to Guidance and Control

DTIC Science & Technology

1986-05-01

name "DoD-0"). The name Ada honors the mathematician of the 19th century who, as colleague to Charles Babbage , developed an instruction set for the as...Avenue St Charles , MO 63301 USA SPEAKERS Mr R.E.Bolz 6751 South Dahlia Court Modem Prograimning Languages Littleton, CO 80122 USA Dr O.Roubine...WHITTREDGE, R. S. PAA : C/( Charles Stark Draper Laboratory, Inc., Cambridge, MA) CORP: Draper ( Charles Stark) Lab., Inc., Cambridge, Mass. IN

Massive Molecular Outflows and Evidence for AGN Feedback from CO Observations

DTIC Science & Technology

2014-01-01

19 J. J. Thomson Avenue, Cambridge CB3 0HE, UK e-mail: c.cicone@mrao.cam.ac.uk 2 Kavli Institute for Cosmology , University of Cambridge, Madingley...about 25 arcsec from the galactic centre (corresponding to 1.6 kpc with the cosmology adopted in this paper). The CO(1–0) integrated flux in this com...power of the molecular outflow as a function of AGN luminosity. Theoretical models of AGN feedback and cosmological simulations predict a coupling effi

Analysis of a Novel Paralogue of SWI/SNF Member p270, Which is Frequently Down-Regulated in Breast Cancer

DTIC Science & Technology

2005-07-01

Viruses and Cell Cycle Control, July 2004, University of Wisconsin, Madison (NCI Travel Award to attend ($750)). "* Norman G. Nagl, Jr., Xiaomei Wang...DNA Tumor Viruses and Cell Cycle Control, July 2002, University of Wisconsin, Madison "* Norman G. Nagl, Jr., Xiaomei Wang, Deborah Wilsker, Michael...Presented at the 2001 Meeting on Small DNA Tumor Viruses and Cell Cycle Control, Cambridge University, Cambridge, UK (NCI Travel Award to attend the 2001

A Tale of Two Countries: Why Some British Muslims Turned to Terrorism and French Muslims Did Not

DTIC Science & Technology

2010-03-01

this protection. Joel S. Fetzer and J. Christopher Soper , Muslims and the State in Britain, France, and Germany. (New York: Cambridge University...Press, 2005), 16. 3 Joel S. Fetzer and J. Christopher Soper , Muslims and the State in Britain, France, and Germany. (New York: Cambridge University...Oxford University Press, 2006), 5. 5 Fetzer and Soper , Muslims and the State, 3. 6 Ibid. 3 This concern developed as they settled permanently in

ABACAS: algorithm-based automatic contiguation of assembled sequences

PubMed Central

Assefa, Samuel; Keane, Thomas M.; Otto, Thomas D.; Newbold, Chris; Berriman, Matthew

2009-01-01

Summary: Due to the availability of new sequencing technologies, we are now increasingly interested in sequencing closely related strains of existing finished genomes. Recently a number of de novo and mapping-based assemblers have been developed to produce high quality draft genomes from new sequencing technology reads. New tools are necessary to take contigs from a draft assembly through to a fully contiguated genome sequence. ABACAS is intended as a tool to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. The input to ABACAS is a set of contigs which will be aligned to the reference genome, ordered and orientated, visualized in the ACT comparative browser, and optimal primer sequences are automatically generated. Availability and Implementation: ABACAS is implemented in Perl and is freely available for download from http://abacas.sourceforge.net Contact: sa4@sanger.ac.uk PMID:19497936

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

PubMed Central

2010-01-01

Background Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short reads from next-generation sequencing due to computational complexity issues and lack of phylogenetic signal. "Phylogenetic placement," where a reference tree is fixed and the unknown query sequences are placed onto the tree via a reference alignment, is a way to bring the inferential power offered by likelihood-based approaches to large data sets. Results This paper introduces pplacer, a software package for phylogenetic placement and subsequent visualization. The algorithm can place twenty thousand short reads on a reference tree of one thousand taxa per hour per processor, has essentially linear time and memory complexity in the number of reference taxa, and is easy to run in parallel. Pplacer features calculation of the posterior probability of a placement on an edge, which is a statistically rigorous way of quantifying uncertainty on an edge-by-edge basis. It also can inform the user of the positional uncertainty for query sequences by calculating expected distance between placement locations, which is crucial in the estimation of uncertainty with a well-sampled reference tree. The software provides visualizations using branch thickness and color to represent number of placements and their uncertainty. A simulation study using reads generated from 631 COG alignments shows a high level of accuracy for phylogenetic placement over a wide range of alignment diversity, and the power of edge uncertainty estimates to measure placement confidence. Conclusions Pplacer enables efficient phylogenetic placement and subsequent visualization, making likelihood-based phylogenetics methodology practical for large collections of reads; it is freely available as source code, binaries, and a web service. PMID:21034504

Are special read alignment strategies necessary and cost-effective when handling sequencing reads from patient-derived tumor xenografts?

PubMed

Tso, Kai-Yuen; Lee, Sau Dan; Lo, Kwok-Wai; Yip, Kevin Y

2014-12-23

Patient-derived tumor xenografts in mice are widely used in cancer research and have become important in developing personalized therapies. When these xenografts are subject to DNA sequencing, the samples could contain various amounts of mouse DNA. It has been unclear how the mouse reads would affect data analyses. We conducted comprehensive simulations to compare three alignment strategies at different mutation rates, read lengths, sequencing error rates, human-mouse mixing ratios and sequenced regions. We also sequenced a nasopharyngeal carcinoma xenograft and a cell line to test how the strategies work on real data. We found the "filtering" and "combined reference" strategies performed better than aligning reads directly to human reference in terms of alignment and variant calling accuracies. The combined reference strategy was particularly good at reducing false negative variants calls without significantly increasing the false positive rate. In some scenarios the performance gain of these two special handling strategies was too small for special handling to be cost-effective, but it was found crucial when false non-synonymous SNVs should be minimized, especially in exome sequencing. Our study systematically analyzes the effects of mouse contamination in the sequencing data of human-in-mouse xenografts. Our findings provide information for designing data analysis pipelines for these data.

Effect of endogenous reference genes on digital PCR assessment of genetically engineered canola events.

PubMed

Demeke, Tigst; Eng, Monika

2018-05-01

Droplet digital PCR (ddPCR) has been used for absolute quantification of genetically engineered (GE) events. Absolute quantification of GE events by duplex ddPCR requires the use of appropriate primers and probes for target and reference gene sequences in order to accurately determine the amount of GE materials. Single copy reference genes are generally preferred for absolute quantification of GE events by ddPCR. Study has not been conducted on a comparison of reference genes for absolute quantification of GE canola events by ddPCR. The suitability of four endogenous reference sequences ( HMG-I/Y , FatA(A), CruA and Ccf) for absolute quantification of GE canola events by ddPCR was investigated. The effect of DNA extraction methods and DNA quality on the assessment of reference gene copy numbers was also investigated. ddPCR results were affected by the use of single vs. two copy reference genes. The single copy, FatA(A), reference gene was found to be stable and suitable for absolute quantification of GE canola events by ddPCR. For the copy numbers measured, the HMG-I/Y reference gene was less consistent than FatA(A) reference gene. The expected ddPCR values were underestimated when CruA and Ccf (two copy endogenous Cruciferin sequences) were used because of high number of copies. It is important to make an adjustment if two copy reference genes are used for ddPCR in order to obtain accurate results. On the other hand, real-time quantitative PCR results were not affected by the use of single vs. two copy reference genes.

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.

PubMed

Schoch, Conrad L; Robbertse, Barbara; Robert, Vincent; Vu, Duong; Cardinali, Gianluigi; Irinyi, Laszlo; Meyer, Wieland; Nilsson, R Henrik; Hughes, Karen; Miller, Andrew N; Kirk, Paul M; Abarenkov, Kessy; Aime, M Catherine; Ariyawansa, Hiran A; Bidartondo, Martin; Boekhout, Teun; Buyck, Bart; Cai, Qing; Chen, Jie; Crespo, Ana; Crous, Pedro W; Damm, Ulrike; De Beer, Z Wilhelm; Dentinger, Bryn T M; Divakar, Pradeep K; Dueñas, Margarita; Feau, Nicolas; Fliegerova, Katerina; García, Miguel A; Ge, Zai-Wei; Griffith, Gareth W; Groenewald, Johannes Z; Groenewald, Marizeth; Grube, Martin; Gryzenhout, Marieka; Gueidan, Cécile; Guo, Liangdong; Hambleton, Sarah; Hamelin, Richard; Hansen, Karen; Hofstetter, Valérie; Hong, Seung-Beom; Houbraken, Jos; Hyde, Kevin D; Inderbitzin, Patrik; Johnston, Peter R; Karunarathna, Samantha C; Kõljalg, Urmas; Kovács, Gábor M; Kraichak, Ekaphan; Krizsan, Krisztina; Kurtzman, Cletus P; Larsson, Karl-Henrik; Leavitt, Steven; Letcher, Peter M; Liimatainen, Kare; Liu, Jian-Kui; Lodge, D Jean; Luangsa-ard, Janet Jennifer; Lumbsch, H Thorsten; Maharachchikumbura, Sajeewa S N; Manamgoda, Dimuthu; Martín, María P; Minnis, Andrew M; Moncalvo, Jean-Marc; Mulè, Giuseppina; Nakasone, Karen K; Niskanen, Tuula; Olariaga, Ibai; Papp, Tamás; Petkovits, Tamás; Pino-Bodas, Raquel; Powell, Martha J; Raja, Huzefa A; Redecker, Dirk; Sarmiento-Ramirez, J M; Seifert, Keith A; Shrestha, Bhushan; Stenroos, Soili; Stielow, Benjamin; Suh, Sung-Oui; Tanaka, Kazuaki; Tedersoo, Leho; Telleria, M Teresa; Udayanga, Dhanushka; Untereiner, Wendy A; Diéguez Uribeondo, Javier; Subbarao, Krishna V; Vágvölgyi, Csaba; Visagie, Cobus; Voigt, Kerstin; Walker, Donald M; Weir, Bevan S; Weiß, Michael; Wijayawardene, Nalin N; Wingfield, Michael J; Xu, J P; Yang, Zhu L; Zhang, Ning; Zhuang, Wen-Ying; Federhen, Scott

2014-01-01

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353. Published by Oxford University Press 2013. This work is written by US Government employees and is in the public domain in the US.

Aligner optimization increases accuracy and decreases compute times in multi-species sequence data.

PubMed

Robinson, Kelly M; Hawkins, Aziah S; Santana-Cruz, Ivette; Adkins, Ricky S; Shetty, Amol C; Nagaraj, Sushma; Sadzewicz, Lisa; Tallon, Luke J; Rasko, David A; Fraser, Claire M; Mahurkar, Anup; Silva, Joana C; Dunning Hotopp, Julie C

2017-09-01

As sequencing technologies have evolved, the tools to analyze these sequences have made similar advances. However, for multi-species samples, we observed important and adverse differences in alignment specificity and computation time for bwa- mem (Burrows-Wheeler aligner-maximum exact matches) relative to bwa-aln. Therefore, we sought to optimize bwa-mem for alignment of data from multi-species samples in order to reduce alignment time and increase the specificity of alignments. In the multi-species cases examined, there was one majority member (i.e. Plasmodium falciparum or Brugia malayi ) and one minority member (i.e. human or the Wolbachia endosymbiont w Bm) of the sequence data. Increasing bwa-mem seed length from the default value reduced the number of read pairs from the majority sequence member that incorrectly aligned to the reference genome of the minority sequence member. Combining both source genomes into a single reference genome increased the specificity of mapping, while also reducing the central processing unit (CPU) time. In Plasmodium , at a seed length of 18 nt, 24.1 % of reads mapped to the human genome using 1.7±0.1 CPU hours, while 83.6 % of reads mapped to the Plasmodium genome using 0.2±0.0 CPU hours (total: 107.7 % reads mapping; in 1.9±0.1 CPU hours). In contrast, 97.1 % of the reads mapped to a combined Plasmodium- human reference in only 0.7±0.0 CPU hours. Overall, the results suggest that combining all references into a single reference database and using a 23 nt seed length reduces the computational time, while maximizing specificity. Similar results were found for simulated sequence reads from a mock metagenomic data set. We found similar improvements to computation time in a publicly available human-only data set.

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.

PubMed

Schneider, Valerie A; Graves-Lindsay, Tina; Howe, Kerstin; Bouk, Nathan; Chen, Hsiu-Chuan; Kitts, Paul A; Murphy, Terence D; Pruitt, Kim D; Thibaud-Nissen, Françoise; Albracht, Derek; Fulton, Robert S; Kremitzki, Milinn; Magrini, Vincent; Markovic, Chris; McGrath, Sean; Steinberg, Karyn Meltz; Auger, Kate; Chow, William; Collins, Joanna; Harden, Glenn; Hubbard, Timothy; Pelan, Sarah; Simpson, Jared T; Threadgold, Glen; Torrance, James; Wood, Jonathan M; Clarke, Laura; Koren, Sergey; Boitano, Matthew; Peluso, Paul; Li, Heng; Chin, Chen-Shan; Phillippy, Adam M; Durbin, Richard; Wilson, Richard K; Flicek, Paul; Eichler, Evan E; Church, Deanna M

2017-05-01

The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. For the first time, the reference assembly contains sequence-based representations for the centromeres. We also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. We demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions, and impact variant interpretation at clinically relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that although the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. We assert that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health. © 2017 Schneider et al.; Published by Cold Spring Harbor Laboratory Press.

The use of PacBio and Hi-C data in denovo assembly of the goat genome

USDA-ARS?s Scientific Manuscript database

Generating de novo reference genome assemblies for non-model organisms is a laborious task that often requires a large amount of data from several sequencing platforms and cytogenetic surveys. By using PacBio sequence data and new library creation techniques, we present a de novo, high quality refer...

Validity of the Cambridge Cognitive Examination-Revised new Executive Function Scores in the diagnosis of dementia: some early findings.

PubMed

Heinik, Jeremia; Solomesh, Isaac

2007-03-01

The Cambridge Cognitive Examination-Revised introduces 2 new executive items (Ideational Fluency and Visual Reasoning), which separately or combined with 2 executive items in the former version (word list generation and similarities) might constitute an Executive Function Score (EFS). The authors studied the validity of these new EFSs in 51 demented (dementia of the Alzheimer's type, vascular dementia) and nondemented individuals (depressives and normals). The new EFSs were found valid to accurately differentiate between demented and nondemented subjects; however, they were considerably less so when specific diagnoses were considered. Correlations between the variously combined executive scores and the cognitive scales and subscales studied were prevalently low to moderate, and ranged from high and significant to low and nonsignificant when the 4 executive items were correlated to each other. The ability of the executive scores to discriminate demented from nondemented individuals was lower compared with the Cambridge Cognitive Examination-Revised scores. EFS was found internally consistent.

How the Weak Variance of Momentum Can Turn Out to be Negative

NASA Astrophysics Data System (ADS)

Feyereisen, M. R.

2015-05-01

Weak values are average quantities, therefore investigating their associated variance is crucial in understanding their place in quantum mechanics. We develop the concept of a position-postselected weak variance of momentum as cohesively as possible, building primarily on material from Moyal (Mathematical Proceedings of the Cambridge Philosophical Society, Cambridge University Press, Cambridge, 1949) and Sonego (Found Phys 21(10):1135, 1991) . The weak variance is defined in terms of the Wigner function, using a standard construction from probability theory. We show this corresponds to a measurable quantity, which is not itself a weak value. It also leads naturally to a connection between the imaginary part of the weak value of momentum and the quantum potential. We study how the negativity of the Wigner function causes negative weak variances, and the implications this has on a class of `subquantum' theories. We also discuss the role of weak variances in studying determinism, deriving the classical limit from a variational principle.

The linguistically aware teacher and the teacher-aware linguist.

PubMed

McCartney, Elspeth; Ellis, Sue

2013-07-01

This review evaluates issues of teacher linguistic knowledge relating to their work with children with speech, language and communication difficulties (SLCD). Information is from Ellis and McCartney [(2011a). Applied linguistics and primary school teaching. Cambridge: Cambridge University Press], a state-of-the-art text deriving from a British Association of Applied Linguistics/Cambridge University Press expert seminar series that details: linguistic research underpinning primary school curricula and pedagogy; the form of linguistic knowledge useful for teachers supporting children with SLCD in partnership with speech and language therapists; and how and when teachers acquire and learn to apply such knowledge. Critical analysis of the options presented for teacher learning indicate that policy enjoinders now include linguistic application as an expected part of teachers' professional knowledge, for all children including those with SLCD, but there is a large unmet learning need. It is concluded that there is a role for clinical linguists to disseminate useable knowledge to teachers in an accessible format. Ways of achieving this are considered.

Taxonomic notes on the crab spider genera Stephanopoides and Isaloides (Araneae: Thomisidae: Stephanopinae).

PubMed

Teixeira, Renato Augusto; Barros, Bruno Augusto Reis

2015-05-08

According to current catalogues, two species are allocated to the genus Parastephanops F. O. Pickard-Cambridge, 1900. The examination of the type of Parastephanops cognatus (O. Pickard-Cambridge, 1892) (type-species of Parastephanops) has revealed the presence of a high cephalic region, legs with dark metatarsus and apex of tibia, and triangular epigynum with median ridge, all diagnostic features of Stephanopoides Keyserling, 1880. However, the female of P. echinatus (Banks, 1914) has a low cephalic region, a median ocular quadrangle longer than wide and a large atrium of the epigynum, which are diagnostic features of Isaloides F. O. Pickard-Cambridge, 1900. Thus, Parastephanops is synonymized with Stephanopoides and its two species, P. cognatus and P. echinatus, are redescribed, illustrated and assigned to Stephanopoides and Isaloides, respectively. We also propose that Pyresthesis berlandi Caporiacco, 1947 is a junior synonym of Stephanopoides simoni Keyserling, 1880 based on shape and arrangement of the epigynal plate, copulatory ducts and spermathecae.

Applications of the Cambridge Structural Database in chemical education1

PubMed Central

Battle, Gary M.; Ferrence, Gregory M.; Allen, Frank H.

2010-01-01

The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal–organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout. PMID:20877495

The Cambridge Structural Database in retrospect and prospect.

PubMed

Groom, Colin R; Allen, Frank H

2014-01-13

The Cambridge Crystallographic Data Centre (CCDC) was established in 1965 to record numerical, chemical and bibliographic data relating to published organic and metal-organic crystal structures. The Cambridge Structural Database (CSD) now stores data for nearly 700,000 structures and is a comprehensive and fully retrospective historical archive of small-molecule crystallography. Nearly 40,000 new structures are added each year. As X-ray crystallography celebrates its centenary as a subject, and the CCDC approaches its own 50th year, this article traces the origins of the CCDC as a publicly funded organization and its onward development into a self-financing charitable institution. Principally, however, we describe the growth of the CSD and its extensive associated software system, and summarize its impact and value as a basis for research in structural chemistry, materials science and the life sciences, including drug discovery and drug development. Finally, the article considers the CCDC's funding model in relation to open access and open data paradigms. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Diagnosis of mild chronic pancreatitis (Cambridge classification): comparative study using secretin injection-magnetic resonance cholangiopancreatography and endoscopic retrograde pancreatography.

PubMed

Sai, Jin-Kan; Suyama, Masafumi; Kubokawa, Yoshihiro; Watanabe, Sumio

2008-02-28

To investigate the usefulness of secretin injection-MRCP for the diagnosis of mild chronic pancreatitis. Sixteen patients having mild chronic pancreatitis according to the Cambridge classification and 12 control subjects with no abnormal findings on the pancreatogram were examined for the diagnostic accuracy of secretin injection-MRCP regarding abnormal branch pancreatic ducts associated with mild chronic pancreatitis (Cambridge Classification), using endoscopic retrograde cholangiopancreatography (ERCP) for comparison. The sensitivity and specificity for abnormal branch pancreatic ducts determined by two reviewers were respectively 55%-63% and 75%-83% in the head, 57%-64% and 82%-83% in the body, and 44%-44% and 72%-76% in the tail of the pancreas. The sensitivity and specificity for mild chronic pancreatitis were 56%-63% and 92%-92%, respectively. Interobserver agreement (kappa statistics) concerning the diagnosis of an abnormal branch pancreatic duct and of mild chronic pancreatitis was good to excellent. Secretin injection-MRCP might be useful for the diagnosis of mild chronic pancreatitis.

A natural history of mathematics: George Peacock and the making of English algebra.

PubMed

Lambert, Kevin

2013-06-01

In a series of papers read to the Cambridge Philosophical Society through the 1820s, the Cambridge mathematician George Peacock laid the foundation for a natural history of arithmetic that would tell a story of human progress from counting to modern arithmetic. The trajectory of that history, Peacock argued, established algebraic analysis as a form of universal reasoning that used empirically warranted operations of mind to think with symbols on paper. The science of counting would suggest arithmetic, arithmetic would suggest arithmetical algebra, and, finally, arithmetical algebra would suggest symbolic algebra. This philosophy of suggestion provided the foundation for Peacock's "principle of equivalent forms," which justified the practice of nineteenth-century English symbolic algebra. Peacock's philosophy of suggestion owed a considerable debt to the early Cambridge Philosophical Society culture of natural history. The aim of this essay is to show how that culture of natural history was constitutively significant to the practice of nineteenth-century English algebra.

Applications of the Cambridge Structural Database in chemical education.

PubMed

Battle, Gary M; Ferrence, Gregory M; Allen, Frank H

2010-10-01

The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal-organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout.

From Charles Darwin's botanical country-house studies to modern plant biology.

PubMed

Kutschera, U; Briggs, W R

2009-11-01

As a student of theology at Cambridge University, Charles Darwin (1809-1882) attended the lectures of the botanist John S. Henslow (1796-1861). This instruction provided the basis for his life-long interest in plants as well as the species question. This was a major reason why in his book On the Origin of Species, which was published 150 years ago, Darwin explained his metaphorical phrase 'struggle for life' with respect to animals and plants. In this article, we review Darwin's botanical work with reference to the following topics: the struggle for existence in the vegetable kingdom with respect to the phytochrome-mediated shade avoidance response; the biology of flowers and Darwin's plant-insect co-evolution hypothesis; climbing plants and the discovery of action potentials; the power of movement in plants and Darwin's conflict with the German plant physiologist Julius Sachs; and light perception by growing grass coleoptiles with reference to the phototropins. Finally, we describe the establishment of the scientific discipline of Plant Biology that took place in the USA 80 years ago, and define this area of research with respect to Darwin's work on botany and the physiology of higher plants.

Fast single-pass alignment and variant calling using sequencing data

USDA-ARS?s Scientific Manuscript database

Sequencing research requires efficient computation. Few programs use already known information about DNA variants when aligning sequence data to the reference map. New program findmap.f90 reads the previous variant list before aligning sequence, calling variant alleles, and summing the allele counts...

RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations

PubMed Central

Munger, Steven C.; Raghupathy, Narayanan; Choi, Kwangbom; Simons, Allen K.; Gatti, Daniel M.; Hinerfeld, Douglas A.; Svenson, Karen L.; Keller, Mark P.; Attie, Alan D.; Hibbs, Matthew A.; Graber, Joel H.; Chesler, Elissa J.; Churchill, Gary A.

2014-01-01

Massively parallel RNA sequencing (RNA-seq) has yielded a wealth of new insights into transcriptional regulation. A first step in the analysis of RNA-seq data is the alignment of short sequence reads to a common reference genome or transcriptome. Genetic variants that distinguish individual genomes from the reference sequence can cause reads to be misaligned, resulting in biased estimates of transcript abundance. Fine-tuning of read alignment algorithms does not correct this problem. We have developed Seqnature software to construct individualized diploid genomes and transcriptomes for multiparent populations and have implemented a complete analysis pipeline that incorporates other existing software tools. We demonstrate in simulated and real data sets that alignment to individualized transcriptomes increases read mapping accuracy, improves estimation of transcript abundance, and enables the direct estimation of allele-specific expression. Moreover, when applied to expression QTL mapping we find that our individualized alignment strategy corrects false-positive linkage signals and unmasks hidden associations. We recommend the use of individualized diploid genomes over reference sequence alignment for all applications of high-throughput sequencing technology in genetically diverse populations. PMID:25236449

Classification of Plant Associated Bacteria Using RIF, a Computationally Derived DNA Marker

PubMed Central

Schneider, Kevin L.; Marrero, Glorimar; Alvarez, Anne M.; Presting, Gernot G.

2011-01-01

A DNA marker that distinguishes plant associated bacteria at the species level and below was derived by comparing six sequenced genomes of Xanthomonas, a genus that contains many important phytopathogens. This DNA marker comprises a portion of the dnaA replication initiation factor (RIF). Unlike the rRNA genes, dnaA is a single copy gene in the vast majority of sequenced bacterial genomes, and amplification of RIF requires genus-specific primers. In silico analysis revealed that RIF has equal or greater ability to differentiate closely related species of Xanthomonas than the widely used ribosomal intergenic spacer region (ITS). Furthermore, in a set of 263 Xanthomonas, Ralstonia and Clavibacter strains, the RIF marker was directly sequenced in both directions with a success rate approximately 16% higher than that for ITS. RIF frameworks for Xanthomonas, Ralstonia and Clavibacter were constructed using 682 reference strains representing different species, subspecies, pathovars, races, hosts and geographic regions, and contain a total of 109 different RIF sequences. RIF sequences showed subspecific groupings but did not place strains of X. campestris or X. axonopodis into currently named pathovars nor R. solanacearum strains into their respective races, confirming previous conclusions that pathovar and race designations do not necessarily reflect genetic relationships. The RIF marker also was sequenced for 24 reference strains from three genera in the Enterobacteriaceae: Pectobacterium, Pantoea and Dickeya. RIF sequences of 70 previously uncharacterized strains of Ralstonia, Clavibacter, Pectobacterium and Dickeya matched, or were similar to, those of known reference strains, illustrating the utility of the frameworks to classify bacteria below the species level and rapidly match unknown isolates to reference strains. The RIF sequence frameworks are available at the online RIF database, RIFdb, and can be queried for diagnostic purposes with RIF sequences obtained from unknown strains in both chromatogram and FASTA format. PMID:21533033

Complex Routes of Nosocomial Vancomycin-Resistant Enterococcus faecium Transmission Revealed by Genome Sequencing.

PubMed

Raven, Kathy E; Gouliouris, Theodore; Brodrick, Hayley; Coll, Francesc; Brown, Nicholas M; Reynolds, Rosy; Reuter, Sandra; Török, M Estée; Parkhill, Julian; Peacock, Sharon J

2017-04-01

Vancomycin-resistant Enterococcus faecium (VREfm) is a leading cause of nosocomial infection. Here, we describe the utility of whole-genome sequencing in defining nosocomial VREfm transmission. A retrospective study at a single hospital in the United Kingdom identified 342 patients with E. faecium bloodstream infection over 7 years. Of these, 293 patients had a stored isolate and formed the basis for the study. The first stored isolate from each case was sequenced (200 VREfm [197 vanA, 2 vanB, and 1 isolate containing both vanA and vanB], 93 vancomycin-susceptible E. faecium) and epidemiological data were collected. Genomes were also available for E. faecium associated with bloodstream infections in 15 patients in neighboring hospitals, and 456 patients across the United Kingdom and Ireland. The majority of infections in the 293 patients were hospital-acquired (n = 249) or healthcare-associated (n = 42). Phylogenetic analysis showed that 291 of 293 isolates resided in a hospital-associated clade that contained numerous discrete clusters of closely related isolates, indicative of multiple introductions into the hospital followed by clonal expansion associated with transmission. Fine-scale analysis of 6 exemplar phylogenetic clusters containing isolates from 93 patients (32%) identified complex transmission routes that spanned numerous wards and years, extending beyond the detection of conventional infection control. These contained both vancomycin-resistant and -susceptible isolates. We also identified closely related isolates from patients at Cambridge University Hospitals NHS Foundation Trust and regional and national hospitals, suggesting interhospital transmission. These findings provide important insights for infection control practice and signpost areas for interventions. We conclude that sequencing represents a powerful tool for the enhanced surveillance and control of nosocomial E. faecium transmission and infection. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America.

Conflict in the Cosmos: the Hoyle-Ryle clashes

NASA Astrophysics Data System (ADS)

Mitton, S.

2005-08-01

Fred Hoyle (1915-2001) made great contributions to both astrophysics and cosmology. His work in accretion theory (1939-45) and nuclear astrophysics (1946-57) continues to be admired and widely quoted. In cosmology, the field for which he is best known among the general public, his achievement is more questionable and marked by controversy. He was the first to use the expression Big Bang to describe the evolving universes of Eddington, Lemaitre, and Gamow. He named his own theory Continuous Creation, although the expression Steady State, coined by Bondi and Gold, became associated with Hoyle's model of a universe of infinite age, infinite extent, and matter creation. By 1952 the Cambridge radio astronomer Martin Ryle (1918-84) realised that his group could join the observational cosmology game. They would use counts of radio sources to discriminate between evolution and steady state. Ryle's first two surveys were inadequate and unreliable, although he did not see it that way, believing from the outset that he had proved Hoyle wrong. The third and fourth surveys did point to an evolutionary universe, but Hoyle refused to accept this, given Ryle's earlier track record in observational cosmology. The two argued passionately for a period of 20 years in a way that came to do serious harm to the standing of astronomy in the University of Cambridge. The paper examines the reasons for the failure of the two Cambridge astronomers to be more co-operative. This research was supported by St Edmund's College, Cambridge.

The Cambridge-Cambridge x-ray serendipity survey. 2: Classification of x-ray luminous galaxies

NASA Technical Reports Server (NTRS)

Boyle, B. J.; Mcmahon, R. G.; Wilkes, B. J.; Elvis, Martin

1994-01-01

We present the results of an intermediate-resolution (1.5 A) spectroscopic study of 17 x-ray luminous narrow emission-line galaxies previously identified in the Cambridge-Cambridge ROSAT Serendipity Survey and the Einstein Extended Medium Sensitivity Survey. Emission-line ratios reveal that the sample is composed of ten Seyfert and seven starburst galaxies. Measured linewidths for the narrow H alpha emission lines lie in the range 170 - 460 km s(exp -1). Five of the objects show clear evidence for asymmetry in the (OIII) lambda 5007 emission-line profile. Broad H alpha emission is detected in six of the Seyfert galaxies, which range in type from Seyfert 1.5 to 2. Broad H beta emission is only detected in one Seyfert galaxy. The mean full width at half maximum for the broad lines in the Seyfert galaxies is FWHM = 3900 +/- 1750 km s(exp -1). Broad (FWHM = 2200 +/- 600 km s(exp -1) H alpha emission is also detected in three of the starburst galaxies, which could originate from stellar winds or supernovae remnants. The mean Balmer decrement for the sample is H alpha / H beta = 3, consistent with little or no reddening for the bulk of the sample. There is no evidence for any trend with x-ray luminosity in the ratio of starburst galaxies to Seyfert galaxies. Based on our previous observations, it is therefore likely that both classes of object comprise approximately 10 percent of the 2 keV x-ray background.

Calibration standards for major greenhouse gases and carbon monoxide: status and challenges.

NASA Astrophysics Data System (ADS)

Zellweger, Christoph; Mohn, Joachim; Wyss, Simon A.; Brewer, Paul; Mace, Tatiana; Nieuwenkamp, Gerard; Pearce-Hill, Ruth; Tarhan, Tanil; Walden, Jari; Emmenegger, Lukas

2017-04-01

Human influence on increasing greenhouse gas mole fractions in the atmosphere and effects on positive radiative forcing as well as observed global warming and sea level rise are well accepted [1]. For interpretation of global or continental scale greenhouse gas data, obtained from different laboratories, measurement results have to coincide within compatibility goals set by the World Meteorological Organization (WMO) [2]. Despite significant advances in measurement techniques [3], WMO compatibility goals are regularly missed, shown by round-robin experiments of standard gases and comparisons of field samples or parallel measurements. Therefore, precise and accurate calibration using standards with good long-term stability is needed to reduce uncertainties of atmospheric measurements. This is addressed by the WMO Global Atmosphere Watch Programme (GAW), where Central Calibration Laboratories (CCLs) maintain calibration scales to ensure consistency of measurements within the network to primary reference materials. Furthermore, participating GAW laboratories are supported by World Calibration Centres (WCCs) performing audits and organizing round-robin comparisons. The CCL participates regularly in comparisons with independent primary scales to assure traceability of established primary reference materials to fundamental quantities (SI) [e.g. 4]. Within the European Metrology Research Programme (EMRP) ENV52 project "Metrology for high-impact greenhouse gases" (HIGHGAS), static and dynamic primary reference gas mixtures for ambient levels of CO2, CH4, N2O and CO in air were prepared by different National Metrology Institutes (NMIs). In order to progress beyond the state of the art, research focused on improving passivation chemistry, quantification of target impurities in the air matrix, and determining the isotopic composition. These primary reference gas mixtures were compared in a round robin experiment against standards calibrated against reference gases currently used by the GAW community. We will show results of the comparison of the HIGHGAS and the WMO reference standards, and put this into the context of the WMO/GAW quality management framework. [1] IPCC, 2013: Climate Change 2013: The Physical Science Basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change [Stocker, T.F., D. Qin, G.-K. Plattner, M. Tignor, S.K. Allen, J. Boschung, A. Nauels, Y. Xia, V. Bex and P.M. Midgley (eds.)]. Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA, 1535 pp. [2] WMO: 18th WMO/IAEA Meeting on Carbon Dioxide, Other Greenhouse Gases and Related Tracers Measurement Techniques (GGMT-2015), La Jolla, CA, USA, 13-17 September 2015, GAW Report No. 229, World Meteorological Organization, Geneva, Switzerland, 2016. [3] Zellweger, C., Emmenegger, L., Firdaus, M., Hatakka, J., Heimann, M., Kozlova, E., Spain, T. G., Steinbacher, M., van der Schoot, M. V., and Buchmann, B.: Assessment of recent advances in measurement techniques for atmospheric carbon dioxide and methane observations, Atmos. Meas. Tech., 9, 4737-4757, 2016. [4] Flores, E., Viallon, J., Choteau, T., Moussay, P., Wielgosz, R., Kang, N., Kim, B. M., Zalewska, E., van der Veen, A., Konopelko, L., Wu, H., Han, Q., Rhoderick, G., Guenther, F. R., Watanabe, T., Shimosaka, T., Kato, K., Hall, B., and Brewer, P.: International comparison CCQM-K82: methane in air at ambient level (1800 to 2200) nmol/mol, Metrologia, 52, 08001, 2015.

Can the CAMCOG be a good cognitive test for patients with Alzheimer's disease with low levels of education?

PubMed

Aprahamian, Ivan; Martinelli, José Eduardo; Cecato, Juliana; Izbicki, Rafael; Yassuda, Mônica Sanches

2011-02-01

The Cambridge Cognitive Examination (CAMCOG) is a useful test in screening for Alzheimer's disease (AD). However, the interpretation of CAMCOG cut-off scores is problematic and reference values are needed for different educational strata. Given the importance of earlier diagnoses of mild dementia, new cut-off values are required which take into account patients with low levels of education. This study aims to evaluate whether the CAMCOG can be used as an accurate screening test among AD patients and normal controls with different educational levels. Cross-sectional assessment was undertaken of 113 AD and 208 elderly controls with heterogeneous educational levels (group 1: 1-4 years; group 2: 5-8 years; and group 3: ≥ 9 years) from a geriatric clinic. submitted to a thorough diagnostic evaluation for AD including the Cambridge Examination for Mental Disorders of the Elderly (CAMDEX). Controls had no cognitive or mood complaints. Sensitivity (SE) and specificity (SP) for the CAMCOG in each educational group was assessed with receiver-operator-characteristic (ROC) curves. CAMCOG mean values were lower when education was reduced in both diagnostic groups (controls - group 1: 87; group 2: 91; group 3: 96; AD - group 1: 63; group 2: 62; group 3: 77). Cut-off scores for the three education groups were 79, 80 and 90, respectively. SE and SP varied among the groups (group 1: 88.1% and 83.5%; group 2: 84.6% and 96%; group 3: 70.8% and 90%). The CAMCOG can be used as a cognitive test for patients with low educational level with good accuracy. Patients with higher education showed lower scores than previously reported.

Stochastic Geometry and Quantum Gravity: Some Rigorous Results

NASA Astrophysics Data System (ADS)

Zessin, H.

The aim of these lectures is a short introduction into some recent developments in stochastic geometry which have one of its origins in simplicial gravity theory (see Regge Nuovo Cimento 19: 558-571, 1961). The aim is to define and construct rigorously point processes on spaces of Euclidean simplices in such a way that the configurations of these simplices are simplicial complexes. The main interest then is concentrated on their curvature properties. We illustrate certain basic ideas from a mathematical point of view. An excellent representation of this area can be found in Schneider and Weil (Stochastic and Integral Geometry, Springer, Berlin, 2008. German edition: Stochastische Geometrie, Teubner, 2000). In Ambjørn et al. (Quantum Geometry Cambridge University Press, Cambridge, 1997) you find a beautiful account from the physical point of view. More recent developments in this direction can be found in Ambjørn et al. ("Quantum gravity as sum over spacetimes", Lect. Notes Phys. 807. Springer, Heidelberg, 2010). After an informal axiomatic introduction into the conceptual foundations of Regge's approach the first lecture recalls the concepts and notations used. It presents the fundamental zero-infinity law of stochastic geometry and the construction of cluster processes based on it. The second lecture presents the main mathematical object, i.e. Poisson-Delaunay surfaces possessing an intrinsic random metric structure. The third and fourth lectures discuss their ergodic behaviour and present the two-dimensional Regge model of pure simplicial quantum gravity. We terminate with the formulation of basic open problems. Proofs are given in detail only in a few cases. In general the main ideas are developed. Sufficiently complete references are given.

Evaluation of a brief anti-stigma campaign in Cambridge: do short-term campaigns work?

PubMed

Evans-Lacko, Sara; London, Jillian; Little, Kirsty; Henderson, Claire; Thornicroft, Graham

2010-06-14

In view of the high costs of mass-media campaigns, it is important to understand whether it is possible for a media campaign to have significant population effects over a short period of time. This paper explores this question specifically in reference to stigma and discrimination against people with mental health problems using the Time to Change Cambridge anti-stigma campaign as an example. 410 face-to-face interviews were performed pre, during and post campaign activity to assess campaign awareness and mental health-related knowledge, attitudes and behaviours. Although campaign awareness was not sustained following campaign activity, significant and sustained shifts occurred for mental health-related knowledge items. Specifically, there was a 24% (p < 0.001) increase in persons agreeing with the statement: If a friend had a mental health problem, I know what advice to give them to get professional help, following the campaign. Additionally, for the statement: Medication can be an effective treatment for people with mental health problems, there was a 10% rise (p = 0.05) in the proportion of interviewees responding 'agree' or 'strongly agree' following the campaign. These changes, however, were not evident for attitudinal or behaviour related questions. Although these results only reflect the impact of one small scale campaign, these preliminary findings suggest several considerations for mass-media campaign development and evaluation strategies such as: (1) Aiming to influence outcomes pertaining to knowledge in the short term; (2) Planning realistic and targeted outcomes over the short, medium and long term during sustained campaigns; and (3) Monitoring indirect campaign effects such as social discourse or other social networking/contact in the evaluation.

The weather and climate: emergent laws and multifractal cascades

NASA Astrophysics Data System (ADS)

Lovejoy, Shaun; Schertzer, Daniel

2013-04-01

Science in general and physics and geophysics in particular are hierarchies of interlocking theories and models with low level, fundamental laws such as quantum mechanics and statistical mechanics providing the underpinnings for the emergence of the qualitatively new, higher level laws of thermodynamics and continuum mechanics that provide the current bases for modelling the weather and climate. Yest it was the belief of generations of turbulence pioneers (notably Richardson, Kolmogorov, Obhukhov, Corrsin, Bolgiano) that at sufficiently high levels of nonlinearity (quantified by the Reynold's number, of the order 10**12 in the atmosphere) that new even higher level laws would emerge describing "fully developed turbulence". However for atmospheric applications, the pioneers' eponymous laws suffered from two basic restrictions - isotropy and homogeneity - that prevented them from being valid over wide ranges of scale. Over the last thirty years both of these restrictions have been overcome - the former with the generalization from isotropic to strongly anisotropic notions of scale (to account notably for stratification), and from homogeneity to strong heterogeneity (intermittency) via multifractal cascades. In this presentation we give an overview of recent developments and analyses covering huge ranges of space-time scales (including weather, macroweather and climate time scales). We show how the combination of strong anisotropy and strong intermittency commonly leads to the "phenomenological fallacy" in which morphology is confounded with mechanism. With the help of stochastic models, we show how processes with vastly different large and small scale morphologies can arise from a unique multifractal dynamical mechanisms [Lovejoy and Schertzer, 2013]. References: Lovejoy, S., and D. Schertzer (2013), The Weather and Climate: Emergent Laws and Multifractal Cascades, 480 pp., Cambridge University Press, Cambridge.

Cosmic Noise: The Pioneers of Early Radio Astronomy and Their Discoveries

NASA Astrophysics Data System (ADS)

Sullivan, Woodruff T., III

2012-01-01

Extraterrestrial radio waves (the galactic background), often referred to as "cosmic noise", were first detected accidentally by Karl Jansky at a frequency of 20 MHz in 1932, with significant followup by Grote Reber. Yet after World War II it was England and Australia that dominated the field. An entirely different sky from that of visual astronomy was revealed by the discoveries of solar noise, "radio stars” (discrete sources such as Cas A, Tau A, Cyg A, Cen A and Vir A), galactic noise, lunar and meteor radar experiments, the detection of the 21 cm hydrogen line, and eventually optical identifications such as the Crab Nebula and M87. Key players included wartime radar experts such as Stanley Hey (the British Army's Operational Research Group), Martin Ryle (Cambridge University), Bernard Lovell (Jodrell Bank) and Joe Pawsey (Radiophysics Lab, Sydney). Younger leaders also emerged such as Graham Smith, Tony Hewish, John Davies, "Chris" Christiansen, Bernie Mills, Paul Wild, and John Bolton. Some optical astronomers (Jan Oort, Henk van de Hulst, Jesse Greenstein, Rudolph Minkowski, and Walter Baade) were also extremely supportive. By the end of the postwar decade, radio astronomy was firmly established within the gamut of astronomy, although very few of its practitioners had been trained as astronomers. I will also trace the technical and social aspects of this wholly new type of astronomy, with special attention on military and national influences. I argue that radio astronomy represents one of the key developments in twentieth century astronomy not only because of its own discoveries, but also its pathfinding for the further opening the electromagnetic spectrum. This study is based on exhaustive archival research and over one hundred interviews with pioneering radio astronomers. Full details are available in the book "Cosmic Noise: A History of Early Radio Astronomy" (Cambridge Univ. Pr.).

Contrasting patterns of deficits in visuospatial memory and executive function in patients with major depression with and without ECT referral.

PubMed

Tsaltas, E; Kalogerakou, S; Papakosta, V-M; Kontis, D; Theochari, E; Koutroumpi, M; Anyfandi, E; Michopoulos, I; Poulopoulou, C; Papadimitriou, G; Oulis, P

2011-05-01

The pretreatment neuropsychological profile of drug-resistant patients with major depressive disorder (MDD) referred for electroconvulsive therapy (ECT) may differ from that of their drug-respondent MDD counterparts. Such differences could help in identifying distinct MDD subtypes, thus offering insights into the neuropathology underlying differential treatment responses. Depressed patients with ECT referral (ECTs), depressed patients with no ECT referral (NECTs) and non-psychiatric Controls (matched groups, n=15) were assessed with memory and executive function tests from the Cambridge Neuropsychological Test Automated Battery (CANTAB). ECTs scored significantly lower than NECTs in the Mini-Mental State Examination (MMSE; p=0.01). NECTs performed worse than Controls in the Paired Associates Learning (PAL) task (p<0.03; Control/NECT p<0.01) and the Spatial Recognition Memory (SRM) task (p<0.05; Controls/NECTs p<0.05); ECTs performed between Controls and NECTs, not differing from either. In the Intra/Extradimensional (IED) set-shifting task, ECTs performed worse that Controls and NECTS (IED: p<0.01; Controls/ECTs p<0.01), particularly in the shift phases, which suggests reduced attentional flexibility. In Stockings of Cambridge (SOC), ECTs abandoned the test early more often than Controls and NECTs (H=11, p<0.01) but ECTs who completed SOC performed comparably to the other two groups. A double dissociation emerged from the comparison of cognitive profiles of ECT and NECT patients. ECTs showed executive deficits, particularly in attentional flexibility, but mild deficits in tests of visuospatial memory. NECTs presented the opposite pattern. This suggests predominantly frontostriatal involvement in ECT versus temporal involvement in NECT depressives.

Minimizing the average distance to a closest leaf in a phylogenetic tree.

PubMed

Matsen, Frederick A; Gallagher, Aaron; McCoy, Connor O

2013-11-01

When performing an analysis on a collection of molecular sequences, it can be convenient to reduce the number of sequences under consideration while maintaining some characteristic of a larger collection of sequences. For example, one may wish to select a subset of high-quality sequences that represent the diversity of a larger collection of sequences. One may also wish to specialize a large database of characterized "reference sequences" to a smaller subset that is as close as possible on average to a collection of "query sequences" of interest. Such a representative subset can be useful whenever one wishes to find a set of reference sequences that is appropriate to use for comparative analysis of environmentally derived sequences, such as for selecting "reference tree" sequences for phylogenetic placement of metagenomic reads. In this article, we formalize these problems in terms of the minimization of the Average Distance to the Closest Leaf (ADCL) and investigate algorithms to perform the relevant minimization. We show that the greedy algorithm is not effective, show that a variant of the Partitioning Around Medoids (PAM) heuristic gets stuck in local minima, and develop an exact dynamic programming approach. Using this exact program we note that the performance of PAM appears to be good for simulated trees, and is faster than the exact algorithm for small trees. On the other hand, the exact program gives solutions for all numbers of leaves less than or equal to the given desired number of leaves, whereas PAM only gives a solution for the prespecified number of leaves. Via application to real data, we show that the ADCL criterion chooses chimeric sequences less often than random subsets, whereas the maximization of phylogenetic diversity chooses them more often than random. These algorithms have been implemented in publicly available software.

TotalReCaller: improved accuracy and performance via integrated alignment and base-calling.

PubMed

Menges, Fabian; Narzisi, Giuseppe; Mishra, Bud

2011-09-01

Currently, re-sequencing approaches use multiple modules serially to interpret raw sequencing data from next-generation sequencing platforms, while remaining oblivious to the genomic information until the final alignment step. Such approaches fail to exploit the full information from both raw sequencing data and the reference genome that can yield better quality sequence reads, SNP-calls, variant detection, as well as an alignment at the best possible location in the reference genome. Thus, there is a need for novel reference-guided bioinformatics algorithms for interpreting analog signals representing sequences of the bases ({A, C, G, T}), while simultaneously aligning possible sequence reads to a source reference genome whenever available. Here, we propose a new base-calling algorithm, TotalReCaller, to achieve improved performance. A linear error model for the raw intensity data and Burrows-Wheeler transform (BWT) based alignment are combined utilizing a Bayesian score function, which is then globally optimized over all possible genomic locations using an efficient branch-and-bound approach. The algorithm has been implemented in soft- and hardware [field-programmable gate array (FPGA)] to achieve real-time performance. Empirical results on real high-throughput Illumina data were used to evaluate TotalReCaller's performance relative to its peers-Bustard, BayesCall, Ibis and Rolexa-based on several criteria, particularly those important in clinical and scientific applications. Namely, it was evaluated for (i) its base-calling speed and throughput, (ii) its read accuracy and (iii) its specificity and sensitivity in variant calling. A software implementation of TotalReCaller as well as additional information, is available at: http://bioinformatics.nyu.edu/wordpress/projects/totalrecaller/ fabian.menges@nyu.edu.

Genotype imputation in a coalescent model with infinitely-many-sites mutation

PubMed Central

Huang, Lucy; Buzbas, Erkan O.; Rosenberg, Noah A.

2012-01-01

Empirical studies have identified population-genetic factors as important determinants of the properties of genotype-imputation accuracy in imputation-based disease association studies. Here, we develop a simple coalescent model of three sequences that we use to explore the theoretical basis for the influence of these factors on genotype-imputation accuracy, under the assumption of infinitely-many-sites mutation. Employing a demographic model in which two populations diverged at a given time in the past, we derive the approximate expectation and variance of imputation accuracy in a study sequence sampled from one of the two populations, choosing between two reference sequences, one sampled from the same population as the study sequence and the other sampled from the other population. We show that under this model, imputation accuracy—as measured by the proportion of polymorphic sites that are imputed correctly in the study sequence—increases in expectation with the mutation rate, the proportion of the markers in a chromosomal region that are genotyped, and the time to divergence between the study and reference populations. Each of these effects derives largely from an increase in information available for determining the reference sequence that is genetically most similar to the sequence targeted for imputation. We analyze as a function of divergence time the expected gain in imputation accuracy in the target using a reference sequence from the same population as the target rather than from the other population. Together with a growing body of empirical investigations of genotype imputation in diverse human populations, our modeling framework lays a foundation for extending imputation techniques to novel populations that have not yet been extensively examined. PMID:23079542

Recovery and characterization of a Citrus clementina Hort. ex Tan. 'Clemenules' haploid plant selected to establish the reference whole Citrus genome sequence.

PubMed

Aleza, Pablo; Juárez, José; Hernández, María; Pina, José A; Ollitrault, Patrick; Navarro, Luis

2009-08-22

In recent years, the development of structural genomics has generated a growing interest in obtaining haploid plants. The use of homozygous lines presents a significant advantage for the accomplishment of sequencing projects. Commercial citrus species are characterized by high heterozygosity, making it difficult to assemble large genome sequences. Thus, the International Citrus Genomic Consortium (ICGC) decided to establish a reference whole citrus genome sequence from a homozygous plant. Due to the existence of important molecular resources and previous success in obtaining haploid clementine plants, haploid clementine was selected as the target for the implementation of the reference whole genome citrus sequence. To obtain haploid clementine lines we used the technique of in situ gynogenesis induced by irradiated pollen. Flow cytometry, chromosome counts and SSR marker (Simple Sequence Repeats) analysis facilitated the identification of six different haploid lines (2n = x = 9), one aneuploid line (2n = 2x+4 = 22) and one doubled haploid plant (2n = 2x = 18) of 'Clemenules' clementine. One of the haploids, obtained directly from an original haploid embryo, grew vigorously and produced flowers after four years. This is the first haploid plant of clementine that has bloomed and we have, for the first time, characterized the histology of haploid and diploid flowers of clementine. Additionally a double haploid plant was obtained spontaneously from this haploid line. The first haploid plant of 'Clemenules' clementine produced directly by germination of a haploid embryo, which grew vigorously and produced flowers, has been obtained in this work. This haploid line has been selected and it is being used by the ICGC to establish the reference sequence of the nuclear genome of citrus.

The Pfam protein families database: towards a more sustainable future.

PubMed

Finn, Robert D; Coggill, Penelope; Eberhardt, Ruth Y; Eddy, Sean R; Mistry, Jaina; Mitchell, Alex L; Potter, Simon C; Punta, Marco; Qureshi, Matloob; Sangrador-Vegas, Amaia; Salazar, Gustavo A; Tate, John; Bateman, Alex

2016-01-04

In the last two years the Pfam database (http://pfam.xfam.org) has undergone a substantial reorganisation to reduce the effort involved in making a release, thereby permitting more frequent releases. Arguably the most significant of these changes is that Pfam is now primarily based on the UniProtKB reference proteomes, with the counts of matched sequences and species reported on the website restricted to this smaller set. Building families on reference proteomes sequences brings greater stability, which decreases the amount of manual curation required to maintain them. It also reduces the number of sequences displayed on the website, whilst still providing access to many important model organisms. Matches to the full UniProtKB database are, however, still available and Pfam annotations for individual UniProtKB sequences can still be retrieved. Some Pfam entries (1.6%) which have no matches to reference proteomes remain; we are working with UniProt to see if sequences from them can be incorporated into reference proteomes. Pfam-B, the automatically-generated supplement to Pfam, has been removed. The current release (Pfam 29.0) includes 16 295 entries and 559 clans. The facility to view the relationship between families within a clan has been improved by the introduction of a new tool. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.).

PubMed

Kim, Seungill; Kim, Myung-Shin; Kim, Yong-Min; Yeom, Seon-In; Cheong, Kyeongchae; Kim, Ki-Tae; Jeon, Jongbum; Kim, Sunggil; Kim, Do-Sun; Sohn, Seong-Han; Lee, Yong-Hwan; Choi, Doil

2015-02-01

The onion (Allium cepa L.) is one of the most widely cultivated and consumed vegetable crops in the world. Although a considerable amount of onion transcriptome data has been deposited into public databases, the sequences of the protein-coding genes are not accurate enough to be used, owing to non-coding sequences intermixed with the coding sequences. We generated a high-quality, annotated onion transcriptome from de novo sequence assembly and intensive structural annotation using the integrated structural gene annotation pipeline (ISGAP), which identified 54,165 protein-coding genes among 165,179 assembled transcripts totalling 203.0 Mb by eliminating the intron sequences. ISGAP performed reliable annotation, recognizing accurate gene structures based on reference proteins, and ab initio gene models of the assembled transcripts. Integrative functional annotation and gene-based SNP analysis revealed a whole biological repertoire of genes and transcriptomic variation in the onion. The method developed in this study provides a powerful tool for the construction of reference gene sets for organisms based solely on de novo transcriptome data. Furthermore, the reference genes and their variation described here for the onion represent essential tools for molecular breeding and gene cloning in Allium spp. © The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Directional Emissivity Effects on Martian Surface Brightness Temperatures

NASA Astrophysics Data System (ADS)

Pitman, K. M.; Wolff, M. J.; Bandfield, J. L.; Clancy, R. T.; Clayton, G. C.

2001-11-01

The angular dependence of thermal emission from the surface of Mars has not been well characterized. Although nadir sequences constitute most of the MGS/TES Martian surface observations [1,2], a significant number scans of Martian surfaces at multiple emission angles (emission phase function (EPF) sequences) also exist. Such data can provide insight into surface structures, thermal inertias, and non-isotropic corrections to thermal emission measurements [3]. The availability of abundant EPF data as well as the added utility of such observations for atmospheric characterization provide the impetus for examining the phenomenon of directional emissivity. We present examples of directional emissivity effects on brightness temperature spectra for a variety of typical Martian surfaces. We examine the theoretical development by Hapke (1993, 1996) [4,5] and compare his algorithm to that of Mishchenko et al. (1999) [6]. These results are then compared to relevant TES EPF data. This work is supported through NASA grant NAGS-9820 (MJW) and JPL contract no. 961471 (RTC). [1] Smith et al. (1998), AAS-DPS meeting # 30, # 11.P07. [2] Kieffer, Mullins, & Titus (1998), EOS, 79, 533. [3] Jakosky, Finiol, & Henderson (1990), JGR, 17, 985--988. [4] Hapke, B. (1993), Theory of Reflectance & Emittance Spectroscopy, Cambridge Univ. Press, NY. [5] Hapke, B. (1996), JGR, 101, E7, 16817--16831. [6] Mishchenko et al. (1999), JQSRT, 63, 409--432.

PREFACE: International Conference on Strongly Correlated Electron Systems (SCES 2011)

NASA Astrophysics Data System (ADS)

Littlewood, P. B.; Lonzarich, G. G.; Saxena, S. S.; Sutherland, M. L.; Sebastian, S. E.; Artacho, E.; Grosche, F. M.; Hadzibabic, Z.

2012-11-01

The Strongly Correlated Electron Systems Conference (SCES) 2011, was held from 29 August-3 September 2011, in Cambridge, UK. SCES'2011 was dedicated to 100 years of superconductivity and covered a range of topics in the area of strongly correlated systems. The correlated electronic and magnetic materials featured include f-electron based heavy fermion intermetallics and d-electron based transition metal compounds. The meeting welcomed to Cambridge 657 participants from 23 countries, who presented 127 talks (including 16 plenary, 57 invited, and 54 contributed) and 736 posters in 40 sessions over five full days of meetings. This proceedings volume contains papers reporting on the science presented at the meeting. This work deepens our understanding of the rich physical phenomena that arise from correlation effects. Strongly correlated systems are known for their remarkable array of emergent phenomena: the traditional subjects of superconductivity, magnetism and metal-insulator transitions have been joined by non-Fermi liquid phenomena, topologically protected quantum states, atomic and photonic gases, and quantum phase transitions. These are some of the most challenging and interesting phenomena in science. As well as the science driver, there is underlying interest in energy-dense materials, which make use of 'small' electrons packed to the highest possible density. These are by definition 'strongly correlated'. For example: good photovoltaics must be efficient optical absorbers, which means that photons will generate tightly bound electron-hole pairs (excitons) that must then be ionised at a heterointerface and transported to contacts; efficient solid state refrigeration depends on substantial entropy changes in a unit cell, with large local electrical or magnetic moments; efficient lighting is in a real sense the inverse of photovoltaics; the limit of an efficient battery is a supercapacitor employing mixed valent ions; fuel cells and solar to fuel conversion require us to understand electrochemistry on the scale of a single atom; and we already know that the only prospect for effective high temperature superconductivity involves strongly correlated materials. Even novel IT technologies are now seen to have value not just for novel function but also for efficiency. While strongly correlated electron systems continue to excite researchers and the public alike due to the fundamental science issues involved, it seems increasingly likely that support for the science will be leveraged by its impact on energy and sustainability. The conference owes its success to the large number of devoted workers for the cause, which includes the organising and programme committees and a considerable number of workers on the ground who contributed to the smooth running of the meeting. The conference received major sponsorship from CamCool Research Limited, the International Institute for Complex Adaptive Matter, from the European Science Foundation through the program INTELBIOMAT, and the Cambridge Central Asia Forum. On behalf of Conference Chairs: P B Littlewood and G G Lonzarich Secretary: S Saxena Treasurer: M Sutherland Local Organising Committee Chair: S E Sebastian Programme Committee Chairs: E Artacho, F M Grosche, Z Hadzibabic (The PDF file also contains photographs from the conference.) Programme Committee E. Artacho, Cambridge (chair)D. Cox, DavisM. Norman, Argonne M. Grosche, Cambridge (chair)H. Ding, IOP, ChinaY. Onuki, Osaka Z. Hadzibabic, Cambridge (chair)M. Ellerby, LondonC. Panagopoulos, Singapore H. Alloul, Paris Z. Fisk, IrvineS. Ramakrishnan, Mumbai E. Baggio-Saitovich, Rio Di JaneiroJ. Flouquet, GrenobleA. Ramirez, Santa Cruz E. Bauer, ViennaA. Galatanu, RomaniaF. Rivadulla, Compostela N. Berloff, CambridgeP. Gegenwart, GottingenS. E. Sebastian, Cambridge D. Bonn, VancouverL. Greene, UrbanaV. Sechovsky, Prague J. van den Brink, DresdenH. Hwang, TokyoS. Simon, Oxford R. Budhani, DelhiA. P. Mackenzie, St.AndrewsD. Snoke, Pittsburgh P. Chandra, PiscatawayN. Mathur, CambridgeJ.C. Gomez-Sal, Santander S-W. Cheong, RutgersK. Miyake, OsakaV. Tripathi, Mumbai P. Coleman, PiscatawayA Navrotsky, DavisA. Vasiliev, Moscow M. Vojta, Cologne Local Committee S. E. Sebastian (chair)R. NeedsJ. Keeling N. MathurE. PughD. Khmelnitskii M. ParishM. CarpenterM. Koehl M. AtatureR. CowburnW. Milne C. BarnesJ. McManus DriscollS. Redfern N. BerloffA. FerrariD. Ritchie M. BlamireC. GreyJ. Robertson J. BaumbergZ. HadzibabicB. Simons A. Cheetham National Advisory Committee G. Aeppli, LondonV. Falko, LancasterM. Pepper, Cambridge A. Ardavan, OxfordR. Friend, CambridgeT. Perring, Didcot P. Attfield, EdinburghC. Frost, RutherfordJ. Saunders, London A. Boothroyd, OxfordG. Gehring, ShefieldA. Schofield, Birmingham A. Coldea, OxfordS. Hayden, BristolN. Shannon, Bristol L. Eaves, NottinghamN. Hussey, BristolM. Skolnick, Sheffield D. Edwards, LondonA. Huxley, EdinburghS. Thompson, York M. Ellerby, LondonH. Wilhelm, Didcot International Advisory Committee E. Abrahams, UCLAG. Kotliar, Piscataway E. V. Sampathkumaran, Mumbai G. Aeppli, LondonD. Khmelnitskii, CambridgeUK J. Sarrao, Los Alamos J. W. Allen, Ann ArborK. Kugel, MoscowJ. Schilling, St. Louise P. W. Anderson, Princeton C. Lacroix, Grenoble A. Schofield, Birmingham M. Aronson, Stony Brook P. A. LeeCambridge, USA V. Sechovsky, Prague Y. K. Bang, Kwangju and Pohang C.T. Liang, Taipei T. Senthil, Cambridge, USA M. Barma, Mumbai P. Majumdar, Allahabad J. G. Sereni, Bariloche G. Baskaran, Chennai Y. Maeno, Kyoto K. Shimizu, Osaka E. Bauer, Vienna J. Mannhart, Augsburg Q. Si, Houston G. Boebinger, Tallahassee M. B. Maple, San Diego M. Sigrist, Zurich R. Budhani, Delhi Y. Matsuda, Kyoto A. Simoni, Trento P. Canfield, Ames R. Moessner, Dresden D. Singh, Oak Ridge M. Continentino, Rio di Janiero A. Millis, New York A. Sood, Bangalore S. Coppersmith, Madison J. Mydosh, Leiden J. Spalek, Krakow B. Coqblin, Paris S. Nakatsuji, Tokyo F. Steglich, Dresden A. Chubukov, Madison G. Oomi, Kyushu G. R. Stewart, Gainesville C. Di Castro, Rome R. Osborn, Chicago H. Takagi, Tokyo M. Eremets, Mainz S. Ovchnikov, Krasnoyarsk L. Taillefer, Sherbrooke M. Fiebig, Bonn C. Panagopoulos, Singapore & Heraklion J. D. Thompson, Los Alamos Z. FiskIrvine S. Paschen, Vienna Y. Tokura, Tokyo J. Flouquet, Grenoble C. Pfleiderer, Munich K. Ueda, Tokyo P. Fulde, Dresden P. Phillips, Urbana C. M. Varma, Riverside A. Geim, Manchester D. Pines, Davis T. Vojta, Rolla J.C. Gomez-Sal, Santander T. V. Ramakrishnan, Bangalore N.L. Wang, Beijing A. Kavokin, Southampton A.K. Raychaudhuri, Calcutta T. Xiang, Beijing J. Goodenough, Austin M. Reifers, Kosice L. Yu, Beijing H. Hosono, Tokyo P. Riseborough, Philadelphia F. C. Zhang, Hong Kong S. Julian, Toronto M. L Saboungi, Orleans G. Zwicknagl, Braunschweig Operational Team Anson Cheung (co-ordinator)Hyeong Jin KimPaul Nahai-Williamson Beng Tan (co-ordinator)Jack GillettPeter Logg Cheng Liu (co-ordinator)Jo WensleyPrajakti Kalra Swee K. Goh (co-ordinator)Jonathan SilverRichard Brierley Adam HalskiLara SibleyRobert Hay Edd CavannaLeona HopeSeb Haines Felix NissenLina KlintbergSitikantha Das Gareth ConduitMarianne BauerStephen Rowley Gerie LonzarichMatt BurgessSven Friedemann Greg LeverMuhammad Ahsan ZebYang Zou Hannah PriceNick BristoweYiqian Xu Haruka TaniguchiOleksandr PoplavskyyZhuo Feng

Experience of targeted Usher exome sequencing as a clinical test

PubMed Central

Besnard, Thomas; García-García, Gema; Baux, David; Vaché, Christel; Faugère, Valérie; Larrieu, Lise; Léonard, Susana; Millan, Jose M; Malcolm, Sue; Claustres, Mireille; Roux, Anne-Françoise

2014-01-01

We show that massively parallel targeted sequencing of 19 genes provides a new and reliable strategy for molecular diagnosis of Usher syndrome (USH) and nonsyndromic deafness, particularly appropriate for these disorders characterized by a high clinical and genetic heterogeneity and a complex structure of several of the genes involved. A series of 71 patients including Usher patients previously screened by Sanger sequencing plus newly referred patients was studied. Ninety-eight percent of the variants previously identified by Sanger sequencing were found by next-generation sequencing (NGS). NGS proved to be efficient as it offers analysis of all relevant genes which is laborious to reach with Sanger sequencing. Among the 13 newly referred Usher patients, both mutations in the same gene were identified in 77% of cases (10 patients) and one candidate pathogenic variant in two additional patients. This work can be considered as pilot for implementing NGS for genetically heterogeneous diseases in clinical service. PMID:24498627

Sequencing in SLA: Phonological Memory, Chunking, and Points of Order.

ERIC Educational Resources Information Center

Ellis, Nick C.

1996-01-01

Argues that much of language acquisition is sequence learning and that the resultant long-term knowledge base of language sequences serves as the database for grammar acquisition. The article also proposes mechanisms to analyze sequence information that result in knowledge of underlying grammar. (184 references) (Author/CK)

Active Contours for Multispectral Images With Non-Homogeneous Sub-Regions

DTIC Science & Technology

2005-09-16

Marching Methods. Cambridge Monographs on Applied and Computational Mathematics, Cambridge University Press, 2nd ed., 1999. [76] R . Malladi and J. Sethian...F. Dibos, “A geometric model for active contours,” Numerische Mathematik, p. 19, 1993. [80] R . Malladi , J. Sethian, and C. Vemuri, “Shape modeling... Malladi et al. [80, 76] proposed a similar model given by ∂φ(x, y) ∂t = g(I(x, y))(κ(φ(x, y)) + ν)|∇φ(x, y)|, (3.14) where g(·) : Ω → < denotes the

Merging Multiple-Partial-Depth Data Time Series Using Objective Empirical Orthogonal Function Fitting

DTIC Science & Technology

2010-05-01

F. J. Lermusiaux, “Adaptive modeling, adaptive data assimilation and adaptive sampling,” Physica D, vol. 230, pp. 172–196, 2007 . [9] T. P. Sapsis and...DOI: 10.1016/j.physd.2009.09.017. [10] P. F. J. Lermusiaux, P. Malanotte-Rizzoli, D. Stammer , J. Carton, J. Cummings, and A. M. Moore, “Progress and...Oceanography, vol. 20, pp. 156–167, 2007 . [12] C. Wunsch, The Ocean Circulation Inverse Problem. Cambridge, U.K.: Cambridge Univ. Press, 1996, ch. 3. [13] H

The Cambridge MRI database for animal models of Huntington disease.

PubMed

Sawiak, Stephen J; Morton, A Jennifer

2016-01-01

We describe the Cambridge animal brain magnetic resonance imaging repository comprising 400 datasets to date from mouse models of Huntington disease. The data include raw images as well as segmented grey and white matter images with maps of cortical thickness. All images and phenotypic data for each subject are freely-available without restriction from (http://www.dspace.cam.ac.uk/handle/1810/243361/). Software and anatomical population templates optimised for animal brain analysis with MRI are also available from this site. Copyright © 2015. Published by Elsevier Inc.

Internal quality assurance in a clinical virology laboratory. II. Internal quality control.

PubMed Central

Gray, J J; Wreghitt, T G; McKee, T A; McIntyre, P; Roth, C E; Smith, D J; Sutehall, G; Higgins, G; Geraghty, R; Whetstone, R

1995-01-01

AIMS--In April 1991 additional quality control procedures were introduced into the virology section of the Clinical Microbiology and Public Health Laboratory, Cambridge. Internal quality control (IQC) samples were gradually included in the serological assays performed in the laboratory and supplemented kit controls and standard sera. METHODS--From April 1991 to December 1993, 2421 IQC procedures were carried out with reference sera. RESULTS--The IQC samples were evaluated according to the Westgard rules. Violations were recorded in 60 of 1808 (3.3%) controls and were highest in the IQC samples of complement fixation tests (25/312 (8%) of controls submitted for complement fixation tests). CONCLUSIONS--The inclusion of IQC samples in the serological assays performed in the laboratory has highlighted batch to batch variation in commercial assays. The setting of acceptable limits for the IQC samples has increased confidence in the validity of assay results. PMID:7730475

Physics of the Earth

NASA Astrophysics Data System (ADS)

Stacey, Frank D.; Davis, Paul M.

he fourth edition of Physics of the Earth maintains the original philosophy of this classic graduate textbook on fundamental solid earth geophysics, while being completely revised, updated, and restructured into a more modular format to make individual topics even more accessible. Building on the success of previous editions, which have served generations of students and researchers for nearly forty years, this new edition will be an invaluable resource for graduate students looking for the necessary physical and mathematical foundations to embark on their own research careers in geophysics. Several completely new chapters have been added and a series of appendices, presenting fundamental data and advanced mathematical concepts, and an extensive reference list, are provided as tools to aid readers wishing to pursue topics beyond the level of the book. Over 140 student exercises of varying levels of difficulty are also included, and full solutions are available online at www.cambridge.org/9780521873628.

Chemical Oceanography and the Marine Carbon Cycle

NASA Astrophysics Data System (ADS)

Emerson, Steven; Hedges, John

The principles of chemical oceanography provide insight into the processes regulating the marine carbon cycle. The text offers a background in chemical oceanography and a description of how chemical elements in seawater and ocean sediments are used as tracers of physical, biological, chemical and geological processes in the ocean. The first seven chapters present basic topics of thermodynamics, isotope systematics and carbonate chemistry, and explain the influence of life on ocean chemistry and how it has evolved in the recent (glacial-interglacial) past. This is followed by topics essential to understanding the carbon cycle, including organic geochemistry, air-sea gas exchange, diffusion and reaction kinetics, the marine and atmosphere carbon cycle and diagenesis in marine sediments. Figures are available to download from www.cambridge.org/9780521833134. Ideal as a textbook for upper-level undergraduates and graduates in oceanography, environmental chemistry, geochemistry and earth science and a valuable reference for researchers in oceanography.

Artifact formation during smoke trapping: An improved method for determination of N-nitrosamines in cigarette smoke

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caldwell, W.S.; Conner, J.M.

Studies in our laboratory revealed artifactual formation of N-nitrosamines during trapping of mainstream and sidestream tobacco smoke by the method of Hoffmann and coworkers. Both volatile and tobacco-specific N-nitrosamines were produced. This artifact formation took place on the Cambridge filter, which is part of the collection train used in the previously published procedure. When the filter was treated with ascorbic acid before smoke collection, artifact formation was inhibited. The improved method resulting from these studies was applied to a comparative analysis of N-nitrosamines in smoke from cigarettes that heat, but do not burn, tobacco (the test cigarette) and several referencemore » cigarettes. Concentrations of volatile and tobacco-specific N-nitrosamines in both mainstream and sidestream smoke from the test cigarette were substantially lower than in the reference cigarettes.« less

Hubert Airy, contemporary men of science and the migraine aura.

PubMed

Eadie, M J

2009-09-01

Although there had been occasional references to the visual aura of migraine even in ancient medicine, little attention was given to the phenomenon until the first half of the nineteenth century when French authors began to describe it. In the medicine of English-speaking countries, apart from a few descriptions, it went largely unnoticed until the British Astronomer Royal, Sir George Airy, described his own experience of the visual aura in 1865. Five years later his son, Hubert Airy, also described his experience of it and that of a number of eminent contemporary men of science. The topic of the migraine aura was almost immediately taken up by two of the younger Airy's contemporaries and fellow Cambridge medical graduates, Peter Wallrock Latham and Edward Liveing, in their monographs. Subsequently, migraine with aura quickly became a well-recognised clinical entity in British medicine.

Harriet Brooks: Canada's First Woman Physicist

NASA Astrophysics Data System (ADS)

Rayner-Canham, Geoffrey

2004-03-01

During those early halcyon days of the study of radioactivity, one young Canadian woman, Harriet Brooks, joined Ernest Rutherford's group as his first research student. Later, she joined J.J. Thomson's group in Cambridge and, finally, Marie Curie's group in Paris. During her short research career, she made several important contributions to science. She investigated the nature of 'emanation' from radium; discovered that radioactive substances could undergo successive decay; and first reported the recoil of the radioactive atom. Much of this research was published under her name alone though Rutherford made extensive reference to her discoveries in his Bakerian lecture of 1904. Brooks life is of interest not only in what she accomplished, but also in the challenges she faced as a pioneering woman scientist in the early part of the twentieth century. In the presentation we will blend the account of her life and work with the societal context. This work was accomplished jointly with Marelene F. Rayner-Canham.

Quantitative Modeling of Earth Surface Processes

NASA Astrophysics Data System (ADS)

Pelletier, Jon D.

This textbook describes some of the most effective and straightforward quantitative techniques for modeling Earth surface processes. By emphasizing a core set of equations and solution techniques, the book presents state-of-the-art models currently employed in Earth surface process research, as well as a set of simple but practical research tools. Detailed case studies demonstrate application of the methods to a wide variety of processes including hillslope, fluvial, aeolian, glacial, tectonic, and climatic systems. Exercises at the end of each chapter begin with simple calculations and then progress to more sophisticated problems that require computer programming. All the necessary computer codes are available online at www.cambridge.org/9780521855976. Assuming some knowledge of calculus and basic programming experience, this quantitative textbook is designed for advanced geomorphology courses and as a reference book for professional researchers in Earth and planetary science looking for a quantitative approach to Earth surface processes.

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.

PubMed

He, Yan; Caporaso, J Gregory; Jiang, Xiao-Tao; Sheng, Hua-Fang; Huse, Susan M; Rideout, Jai Ram; Edgar, Robert C; Kopylova, Evguenia; Walters, William A; Knight, Rob; Zhou, Hong-Wei

2015-01-01

The operational taxonomic unit (OTU) is widely used in microbial ecology. Reproducibility in microbial ecology research depends on the reliability of OTU-based 16S ribosomal subunit RNA (rRNA) analyses. Here, we report that many hierarchical and greedy clustering methods produce unstable OTUs, with membership that depends on the number of sequences clustered. If OTUs are regenerated with additional sequences or samples, sequences originally assigned to a given OTU can be split into different OTUs. Alternatively, sequences assigned to different OTUs can be merged into a single OTU. This OTU instability affects alpha-diversity analyses such as rarefaction curves, beta-diversity analyses such as distance-based ordination (for example, Principal Coordinate Analysis (PCoA)), and the identification of differentially represented OTUs. Our results show that the proportion of unstable OTUs varies for different clustering methods. We found that the closed-reference method is the only one that produces completely stable OTUs, with the caveat that sequences that do not match a pre-existing reference sequence collection are discarded. As a compromise to the factors listed above, we propose using an open-reference method to enhance OTU stability. This type of method clusters sequences against a database and includes unmatched sequences by clustering them via a relatively stable de novo clustering method. OTU stability is an important consideration when analyzing microbial diversity and is a feature that should be taken into account during the development of novel OTU clustering methods.

Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences

PubMed Central

2018-01-01

Prediction of taxonomy for marker gene sequences such as 16S ribosomal RNA (rRNA) is a fundamental task in microbiology. Most experimentally observed sequences are diverged from reference sequences of authoritatively named organisms, creating a challenge for prediction methods. I assessed the accuracy of several algorithms using cross-validation by identity, a new benchmark strategy which explicitly models the variation in distances between query sequences and the closest entry in a reference database. When the accuracy of genus predictions was averaged over a representative range of identities with the reference database (100%, 99%, 97%, 95% and 90%), all tested methods had ≤50% accuracy on the currently-popular V4 region of 16S rRNA. Accuracy was found to fall rapidly with identity; for example, better methods were found to have V4 genus prediction accuracy of ∼100% at 100% identity but ∼50% at 97% identity. The relationship between identity and taxonomy was quantified as the probability that a rank is the lowest shared by a pair of sequences with a given pair-wise identity. With the V4 region, 95% identity was found to be a twilight zone where taxonomy is highly ambiguous because the probabilities that the lowest shared rank between pairs of sequences is genus, family, order or class are approximately equal. PMID:29682424

HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads

PubMed Central

Li, Pinghao; Jiang, Xiaoqian; Wang, Shuang; Kim, Jihoon; Xiong, Hongkai; Ohno-Machado, Lucila

2014-01-01

Background and objective Short-read sequencing is becoming the standard of practice for the study of structural variants associated with disease. However, with the growth of sequence data largely surpassing reasonable storage capability, the biomedical community is challenged with the management, transfer, archiving, and storage of sequence data. Methods We developed Hierarchical mUlti-reference Genome cOmpression (HUGO), a novel compression algorithm for aligned reads in the sorted Sequence Alignment/Map (SAM) format. We first aligned short reads against a reference genome and stored exactly mapped reads for compression. For the inexact mapped or unmapped reads, we realigned them against different reference genomes using an adaptive scheme by gradually shortening the read length. Regarding the base quality value, we offer lossy and lossless compression mechanisms. The lossy compression mechanism for the base quality values uses k-means clustering, where a user can adjust the balance between decompression quality and compression rate. The lossless compression can be produced by setting k (the number of clusters) to the number of different quality values. Results The proposed method produced a compression ratio in the range 0.5–0.65, which corresponds to 35–50% storage savings based on experimental datasets. The proposed approach achieved 15% more storage savings over CRAM and comparable compression ratio with Samcomp (CRAM and Samcomp are two of the state-of-the-art genome compression algorithms). The software is freely available at https://sourceforge.net/projects/hierachicaldnac/with a General Public License (GPL) license. Limitation Our method requires having different reference genomes and prolongs the execution time for additional alignments. Conclusions The proposed multi-reference-based compression algorithm for aligned reads outperforms existing single-reference based algorithms. PMID:24368726

Recruiting Human Microbiome Shotgun Data to Site-Specific Reference Genomes

PubMed Central

Xie, Gary; Lo, Chien-Chi; Scholz, Matthew; Chain, Patrick S. G.

2014-01-01

The human body consists of innumerable multifaceted environments that predispose colonization by a number of distinct microbial communities, which play fundamental roles in human health and disease. In addition to community surveys and shotgun metagenomes that seek to explore the composition and diversity of these microbiomes, there are significant efforts to sequence reference microbial genomes from many body sites of healthy adults. To illustrate the utility of reference genomes when studying more complex metagenomes, we present a reference-based analysis of sequence reads generated from 55 shotgun metagenomes, selected from 5 major body sites, including 16 sub-sites. Interestingly, between 13% and 92% (62.3% average) of these shotgun reads were aligned to a then-complete list of 2780 reference genomes, including 1583 references for the human microbiome. However, no reference genome was universally found in all body sites. For any given metagenome, the body site-specific reference genomes, derived from the same body site as the sample, accounted for an average of 58.8% of the mapped reads. While different body sites did differ in abundant genera, proximal or symmetrical body sites were found to be most similar to one another. The extent of variation observed, both between individuals sampled within the same microenvironment, or at the same site within the same individual over time, calls into question comparative studies across individuals even if sampled at the same body site. This study illustrates the high utility of reference genomes and the need for further site-specific reference microbial genome sequencing, even within the already well-sampled human microbiome. PMID:24454771

Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research.

PubMed

Xu, Jiajia; Li, Yuanyuan; Ma, Xiuling; Ding, Jianfeng; Wang, Kai; Wang, Sisi; Tian, Ye; Zhang, Hui; Zhu, Xin-Guang

2013-09-01

Setaria viridis is an emerging model species for genetic studies of C4 photosynthesis. Many basic molecular resources need to be developed to support for this species. In this paper, we performed a comprehensive transcriptome analysis from multiple developmental stages and tissues of S. viridis using next-generation sequencing technologies. Sequencing of the transcriptome from multiple tissues across three developmental stages (seed germination, vegetative growth, and reproduction) yielded a total of 71 million single end 100 bp long reads. Reference-based assembly using Setaria italica genome as a reference generated 42,754 transcripts. De novo assembly generated 60,751 transcripts. In addition, 9,576 and 7,056 potential simple sequence repeats (SSRs) covering S. viridis genome were identified when using the reference based assembled transcripts and the de novo assembled transcripts, respectively. This identified transcripts and SSR provided by this study can be used for both reverse and forward genetic studies based on S. viridis.

A reference human genome dataset of the BGISEQ-500 sequencer.

PubMed

Huang, Jie; Liang, Xinming; Xuan, Yuankai; Geng, Chunyu; Li, Yuxiang; Lu, Haorong; Qu, Shoufang; Mei, Xianglin; Chen, Hongbo; Yu, Ting; Sun, Nan; Rao, Junhua; Wang, Jiahao; Zhang, Wenwei; Chen, Ying; Liao, Sha; Jiang, Hui; Liu, Xin; Yang, Zhaopeng; Mu, Feng; Gao, Shangxian

2017-05-01

BGISEQ-500 is a new desktop sequencer developed by BGI. Using DNA nanoball and combinational probe anchor synthesis developed from Complete Genomics™ sequencing technologies, it generates short reads at a large scale. Here, we present the first human whole-genome sequencing dataset of BGISEQ-500. The dataset was generated by sequencing the widely used cell line HG001 (NA12878) in two sequencing runs of paired-end 50 bp (PE50) and two sequencing runs of paired-end 100 bp (PE100). We also include examples of the raw images from the sequencer for reference. Finally, we identified variations using this dataset, estimated the accuracy of the variations, and compared to that of the variations identified from similar amounts of publicly available HiSeq2500 data. We found similar single nucleotide polymorphism (SNP) detection accuracy for the BGISEQ-500 PE100 data (false positive rate [FPR] = 0.00020%, sensitivity = 96.20%) compared to the PE150 HiSeq2500 data (FPR = 0.00017%, sensitivity = 96.60%) better SNP detection accuracy than the PE50 data (FPR = 0.0006%, sensitivity = 94.15%). But for insertions and deletions (indels), we found lower accuracy for BGISEQ-500 data (FPR = 0.00069% and 0.00067% for PE100 and PE50 respectively, sensitivity = 88.52% and 70.93%) than the HiSeq2500 data (FPR = 0.00032%, sensitivity = 96.28%). Our dataset can serve as the reference dataset, providing basic information not just for future development, but also for all research and applications based on the new sequencing platform. © The Authors 2017. Published by Oxford University Press.

Classification of HCV and HIV-1 Sequences with the Branching Index

PubMed Central

Hraber, Peter; Kuiken, Carla; Waugh, Mark; Geer, Shaun; Bruno, William J.; Leitner, Thomas

2009-01-01

SUMMARY Classification of viral sequences should be fast, objective, accurate, and reproducible. Most methods that classify sequences use either pairwise distances or phylogenetic relations, but cannot discern when a sequence is unclassifiable. The branching index (BI) combines distance and phylogeny methods to compute a ratio that quantifies how closely a query sequence clusters with a subtype clade. In the hypothesis-testing framework of statistical inference, the BI is compared with a threshold to test whether sufficient evidence exists for the query sequence to be classified among known sequences. If above the threshold, the null hypothesis of no support for the subtype relation is rejected and the sequence is taken as belonging to the subtype clade with which it clusters on the tree. This study evaluates statistical properties of the branching index for subtype classification in HCV and HIV-1. Pairs of BI values with known positive and negative test results were computed from 10,000 random fragments of reference alignments. Sampled fragments were of sufficient length to contain phylogenetic signal that groups reference sequences together properly into subtype clades. For HCV, a threshold BI of 0.71 yields 95.1% agreement with reference subtypes, with equal false positive and false negative rates. For HIV-1, a threshold of 0.66 yields 93.5% agreement. Higher thresholds can be used where lower false positive rates are required. In synthetic recombinants, regions without breakpoints are recognized accurately; regions with breakpoints do not uniquely represent any known subtype. Web-based services for viral subtype classification with the branching index are available online. PMID:18753218

A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project.

PubMed

Yebra, Gonzalo; Frampton, Dan; Gallo Cassarino, Tiziano; Raffle, Jade; Hubb, Jonathan; Ferns, R Bridget; Waters, Laura; Tong, C Y William; Kozlakidis, Zisis; Hayward, Andrew; Kellam, Paul; Pillay, Deenan; Clark, Duncan; Nastouli, Eleni; Leigh Brown, Andrew J

2018-01-01

The ICONIC project has developed an automated high-throughput pipeline to generate HIV nearly full-length genomes (NFLG, i.e. from gag to nef) from next-generation sequencing (NGS) data. The pipeline was applied to 420 HIV samples collected at University College London Hospitals NHS Trust and Barts Health NHS Trust (London) and sequenced using an Illumina MiSeq at the Wellcome Trust Sanger Institute (Cambridge). Consensus genomes were generated and subtyped using COMET, and unique recombinants were studied with jpHMM and SimPlot. Maximum-likelihood phylogenetic trees were constructed using RAxML to identify transmission networks using the Cluster Picker. The pipeline generated sequences of at least 1Kb of length (median = 7.46Kb, IQR = 4.01Kb) for 375 out of the 420 samples (89%), with 174 (46.4%) being NFLG. A total of 365 sequences (169 of them NFLG) corresponded to unique subjects and were included in the down-stream analyses. The most frequent HIV subtypes were B (n = 149, 40.8%) and C (n = 77, 21.1%) and the circulating recombinant form CRF02_AG (n = 32, 8.8%). We found 14 different CRFs (n = 66, 18.1%) and multiple URFs (n = 32, 8.8%) that involved recombination between 12 different subtypes/CRFs. The most frequent URFs were B/CRF01_AE (4 cases) and A1/D, B/C, and B/CRF02_AG (3 cases each). Most URFs (19/26, 73%) lacked breakpoints in the PR+RT pol region, rendering them undetectable if only that was sequenced. Twelve (37.5%) of the URFs could have emerged within the UK, whereas the rest were probably imported from sub-Saharan Africa, South East Asia and South America. For 2 URFs we found highly similar pol sequences circulating in the UK. We detected 31 phylogenetic clusters using the full dataset: 25 pairs (mostly subtypes B and C), 4 triplets and 2 quadruplets. Some of these were not consistent across different genes due to inter- and intra-subtype recombination. Clusters involved 70 sequences, 19.2% of the dataset. The initial analysis of genome sequences detected substantial hidden variability in the London HIV epidemic. Analysing full genome sequences, as opposed to only PR+RT, identified previously undetected recombinants. It provided a more reliable description of CRFs (that would be otherwise misclassified) and transmission clusters.

Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II

PubMed Central

Norman, Paul J.; Norberg, Steven J.; Guethlein, Lisbeth A.; Nemat-Gorgani, Neda; Royce, Thomas; Wroblewski, Emily E.; Dunn, Tamsen; Mann, Tobias; Alicata, Claudia; Hollenbach, Jill A.; Chang, Weihua; Shults Won, Melissa; Gunderson, Kevin L.; Abi-Rached, Laurent; Ronaghi, Mostafa; Parham, Peter

2017-01-01

The most polymorphic part of the human genome, the MHC, encodes over 160 proteins of diverse function. Half of them, including the HLA class I and II genes, are directly involved in immune responses. Consequently, the MHC region strongly associates with numerous diseases and clinical therapies. Notoriously, the MHC region has been intractable to high-throughput analysis at complete sequence resolution, and current reference haplotypes are inadequate for large-scale studies. To address these challenges, we developed a method that specifically captures and sequences the 4.8-Mbp MHC region from genomic DNA. For 95 MHC homozygous cell lines we assembled, de novo, a set of high-fidelity contigs and a sequence scaffold, representing a mean 98% of the target region. Included are six alternative MHC reference sequences of the human genome that we completed and refined. Characterization of the sequence and structural diversity of the MHC region shows the approach accurately determines the sequences of the highly polymorphic HLA class I and HLA class II genes and the complex structural diversity of complement factor C4A/C4B. It has also uncovered extensive and unexpected diversity in other MHC genes; an example is MUC22, which encodes a lung mucin and exhibits more coding sequence alleles than any HLA class I or II gene studied here. More than 60% of the coding sequence alleles analyzed were previously uncharacterized. We have created a substantial database of robust reference MHC haplotype sequences that will enable future population scale studies of this complicated and clinically important region of the human genome. PMID:28360230

Complete genome sequence analysis of novel human bocavirus reveals genetic recombination between human bocavirus 2 and human bocavirus 4.

PubMed

Khamrin, Pattara; Okitsu, Shoko; Ushijima, Hiroshi; Maneekarn, Niwat

2013-07-01

Epidemiological surveillance of human bocavirus (HBoV) was conducted on fecal specimens collected from hospitalized children with diarrhea in Chiang Mai, Thailand in 2011. By partial sequence analysis of VP1 gene, an unusual strain of HBoV (CMH-S011-11), was initially identified as HBoV4. The complete genome sequence of CMH-S011-11 was performed and analyzed further to clarify whether it was a recombinant strain or a new HBoV variant. Analysis of complete genome sequence revealed that the coding sequence starting from NS1, NP1 to VP1/VP2 was 4795 nucleotides long. Interestingly, the nucleotide sequence of NS1 gene of CMH-S011-11 was most closely related to the HBoV2 reference strains detected in Pakistan, which contradicted to the initial genotyping result of the partial VP1 region in the previous study. In addition, comparison of NP1 nucleotide sequence of CMH-S011-11 with those of other HBoV1-4 reference strains also revealed a high level of sequence identity with HBoV2. On the other hand, nucleotide sequence of VP1/VP2 gene of CMH-S011-11 was most closely related to those of HBoV4 reference strains detected in Nigeria. The overall full-length sequence analysis revealed that this CMH-S011-11 was grouped within HBoV4 species, but located in a separate branch from other HBoV4 prototype strains. Recombination analysis revealed that CMH-S011-11 was the result of recombination between HBoV2 and HBoV4 strains with the break point located near the start codon of VP2. Copyright © 2013 Elsevier B.V. All rights reserved.

Exome copy number variation detection: Use of a pool of unrelated healthy tissue as reference sample.

PubMed

Wenric, Stephane; Sticca, Tiberio; Caberg, Jean-Hubert; Josse, Claire; Fasquelle, Corinne; Herens, Christian; Jamar, Mauricette; Max, Stéphanie; Gothot, André; Caers, Jo; Bours, Vincent

2017-01-01

An increasing number of bioinformatic tools designed to detect CNVs (copy number variants) in tumor samples based on paired exome data where a matched healthy tissue constitutes the reference have been published in the recent years. The idea of using a pool of unrelated healthy DNA as reference has previously been formulated but not thoroughly validated. As of today, the gold standard for CNV calling is still aCGH but there is an increasing interest in detecting CNVs by exome sequencing. We propose to design a metric allowing the comparison of two CNV profiles, independently of the technique used and assessed the validity of using a pool of unrelated healthy DNA instead of a matched healthy tissue as reference in exome-based CNV detection. We compared the CNV profiles obtained with three different approaches (aCGH, exome sequencing with a matched healthy tissue as reference, exome sequencing with a pool of eight unrelated healthy tissue as reference) on three multiple myeloma samples. We show that the usual analyses performed to compare CNV profiles (deletion/amplification ratios and CNV size distribution) lack in precision when confronted with low LRR values, as they only consider the binary status of each CNV. We show that the metric-based distance constitutes a more accurate comparison of two CNV profiles. Based on these analyses, we conclude that a reliable picture of CNV alterations in multiple myeloma samples can be obtained from whole-exome sequencing in the absence of a matched healthy sample. © 2016 WILEY PERIODICALS, INC.

BAC-end sequence-based SNP mining in Allotetraploid Cotton (Gossypium) utilizing re-sequencing data, phylogenetic inferences and perspectives for genetic mapping

USDA-ARS?s Scientific Manuscript database

A bacterial artificial chromosome (BAC) library and BAC-end sequences for Gossypium hirsutum L. have recently been developed. Here we report on genomic-based genome-wide SNP mining utilizing re-sequencing data with a BAC-end sequence reference for twelve G. hirsutum L. lines, one G. barbadense L. li...

The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now

PubMed Central

Engel, Stacia R.; Dietrich, Fred S.; Fisk, Dianna G.; Binkley, Gail; Balakrishnan, Rama; Costanzo, Maria C.; Dwight, Selina S.; Hitz, Benjamin C.; Karra, Kalpana; Nash, Robert S.; Weng, Shuai; Wong, Edith D.; Lloyd, Paul; Skrzypek, Marek S.; Miyasato, Stuart R.; Simison, Matt; Cherry, J. Michael

2014-01-01

The genome of the budding yeast Saccharomyces cerevisiae was the first completely sequenced from a eukaryote. It was released in 1996 as the work of a worldwide effort of hundreds of researchers. In the time since, the yeast genome has been intensively studied by geneticists, molecular biologists, and computational scientists all over the world. Maintenance and annotation of the genome sequence have long been provided by the Saccharomyces Genome Database, one of the original model organism databases. To deepen our understanding of the eukaryotic genome, the S. cerevisiae strain S288C reference genome sequence was updated recently in its first major update since 1996. The new version, called “S288C 2010,” was determined from a single yeast colony using modern sequencing technologies and serves as the anchor for further innovations in yeast genomic science. PMID:24374639

The Cambridge Car Memory Test: a task matched in format to the Cambridge Face Memory Test, with norms, reliability, sex differences, dissociations from face memory, and expertise effects.

PubMed

Dennett, Hugh W; McKone, Elinor; Tavashmi, Raka; Hall, Ashleigh; Pidcock, Madeleine; Edwards, Mark; Duchaine, Bradley

2012-06-01

Many research questions require a within-class object recognition task matched for general cognitive requirements with a face recognition task. If the object task also has high internal reliability, it can improve accuracy and power in group analyses (e.g., mean inversion effects for faces vs. objects), individual-difference studies (e.g., correlations between certain perceptual abilities and face/object recognition), and case studies in neuropsychology (e.g., whether a prosopagnosic shows a face-specific or object-general deficit). Here, we present such a task. Our Cambridge Car Memory Test (CCMT) was matched in format to the established Cambridge Face Memory Test, requiring recognition of exemplars across view and lighting change. We tested 153 young adults (93 female). Results showed high reliability (Cronbach's alpha = .84) and a range of scores suitable both for normal-range individual-difference studies and, potentially, for diagnosis of impairment. The mean for males was much higher than the mean for females. We demonstrate independence between face memory and car memory (dissociation based on sex, plus a modest correlation between the two), including where participants have high relative expertise with cars. We also show that expertise with real car makes and models of the era used in the test significantly predicts CCMT performance. Surprisingly, however, regression analyses imply that there is an effect of sex per se on the CCMT that is not attributable to a stereotypical male advantage in car expertise.

NewsMars: Express journey to Mars ASE 2003: Knocked out by meteorites Events: Sun-Earth Day ASE 2003: Fun Physics - popular as ever Appointments: Sykes to bring science to the people UK Science Education: The future's bright, the future's science ASE 2003: A grand finale for Catherine Teaching Resources: UK goes to the planets Cambridge Physics Update: Basement physics Conferences: Earth Science Teachers' Association Conference 2003 New Website: JESEI sets sail GIREP: Teacher education seminar Malaysia: Rewards for curriculum change Cambridge Physics Update: My boomerang will come back! Teaching Resources: Widening particiption through ideas and evidence with the University of Surrey Wales: First Ffiseg Events: Nuna: Solar car on tour Physics on Stage: Physics on Stage 3 embraces life Symposium: In what sense a nuclear 'debate'? Gifted and Talented: Able pupils experiencing challenging science Australia: ISS flies high Down Under

NASA Astrophysics Data System (ADS)

2003-03-01

Mars: Express journey to Mars ASE 2003: Knocked out by meteorites Events: Sun-Earth Day ASE 2003: Fun Physics - popular as ever Appointments: Sykes to bring science to the people UK Science Education: The future's bright, the future's science ASE 2003: A grand finale for Catherine Teaching Resources: UK goes to the planets Cambridge Physics Update: Basement physics Conferences: Earth Science Teachers' Association Conference 2003 New Website: JESEI sets sail GIREP: Teacher education seminar Malaysia: Rewards for curriculum change Cambridge Physics Update: My boomerang will come back! Teaching Resources: Widening particiption through ideas and evidence with the University of Surrey Wales: First Ffiseg Events: Nuna: Solar car on tour Physics on Stage: Physics on Stage 3 embraces life Symposium: In what sense a nuclear 'debate'? Gifted and Talented: Able pupils experiencing challenging science Australia: ISS flies high Down Under

GWAS and fine-mapping of 35 production, reproduction and conformation traits with imputed sequences of 27K Holstein bulls

USDA-ARS?s Scientific Manuscript database

Fine-mapping of causal variants is becoming feasible for complex traits in livestock GWAS, as an increasing number of animals are sequenced. Imputation has been routinely applied to ascertain sequence variants in large genotyped populations based on small reference populations of sequenced animals. ...

High-Quality Genome Sequence of the Highly Resistant Bacterium Staphylococcus haemolyticus, Isolated from a Neonatal Bloodstream Infection.

PubMed

Hosseinkhani, Farideh; Emaneini, Mohammad; van Leeuwen, Willem

2017-07-20

Using Illumina HiSeq and PacBio technologies, we sequenced the genome of the multidrug-resistant bacterium Staphylococcus haemolyticus , originating from a bloodstream infection in a neonate. The sequence data can be used as an accurate reference sequence. Copyright © 2017 Hosseinkhani et al.

GWAS and fine-mapping of 35 production, reproduction, and conformation traits with imputed sequences of 27K Holstein bulls

USDA-ARS?s Scientific Manuscript database

Imputation has been routinely applied to ascertain sequence variants in large genotyped populations based on reference populations of sequenced animals. With the implementation of the 1000 Bull Genomes Project and increasing numbers of animals sequenced, fine-mapping of causal variants is becoming f...

Protein domain analysis of genomic sequence data reveals regulation of LRR related domains in plant transpiration in Ficus.

PubMed

Lang, Tiange; Yin, Kangquan; Liu, Jinyu; Cao, Kunfang; Cannon, Charles H; Du, Fang K

2014-01-01

Predicting protein domains is essential for understanding a protein's function at the molecular level. However, up till now, there has been no direct and straightforward method for predicting protein domains in species without a reference genome sequence. In this study, we developed a functionality with a set of programs that can predict protein domains directly from genomic sequence data without a reference genome. Using whole genome sequence data, the programming functionality mainly comprised DNA assembly in combination with next-generation sequencing (NGS) assembly methods and traditional methods, peptide prediction and protein domain prediction. The proposed new functionality avoids problems associated with de novo assembly due to micro reads and small single repeats. Furthermore, we applied our functionality for the prediction of leucine rich repeat (LRR) domains in four species of Ficus with no reference genome, based on NGS genomic data. We found that the LRRNT_2 and LRR_8 domains are related to plant transpiration efficiency, as indicated by the stomata index, in the four species of Ficus. The programming functionality established in this study provides new insights for protein domain prediction, which is particularly timely in the current age of NGS data expansion.

acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data

DOE PAGES

Lux, Markus; Kruger, Jan; Rinke, Christian; ...

2016-12-20

A major obstacle in single-cell sequencing is sample contamination with foreign DNA. To guarantee clean genome assemblies and to prevent the introduction of contamination into public databases, considerable quality control efforts are put into post-sequencing analysis. Contamination screening generally relies on reference-based methods such as database alignment or marker gene search, which limits the set of detectable contaminants to organisms with closely related reference species. As genomic coverage in the tree of life is highly fragmented, there is an urgent need for a reference-free methodology for contaminant identification in sequence data. We present acdc, a tool specifically developed to aidmore » the quality control process of genomic sequence data. By combining supervised and unsupervised methods, it reliably detects both known and de novo contaminants. First, 16S rRNA gene prediction and the inclusion of ultrafast exact alignment techniques allow sequence classification using existing knowledge from databases. Second, reference-free inspection is enabled by the use of state-of-the-art machine learning techniques that include fast, non-linear dimensionality reduction of oligonucleotide signatures and subsequent clustering algorithms that automatically estimate the number of clusters. The latter also enables the removal of any contaminant, yielding a clean sample. Furthermore, given the data complexity and the ill-posedness of clustering, acdc employs bootstrapping techniques to provide statistically profound confidence values. Tested on a large number of samples from diverse sequencing projects, our software is able to quickly and accurately identify contamination. Results are displayed in an interactive user interface. Acdc can be run from the web as well as a dedicated command line application, which allows easy integration into large sequencing project analysis workflows. Acdc can reliably detect contamination in single-cell genome data. In addition to database-driven detection, it complements existing tools by its unsupervised techniques, which allow for the detection of de novo contaminants. Our contribution has the potential to drastically reduce the amount of resources put into these processes, particularly in the context of limited availability of reference species. As single-cell genome data continues to grow rapidly, acdc adds to the toolkit of crucial quality assurance tools.« less

acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lux, Markus; Kruger, Jan; Rinke, Christian

A major obstacle in single-cell sequencing is sample contamination with foreign DNA. To guarantee clean genome assemblies and to prevent the introduction of contamination into public databases, considerable quality control efforts are put into post-sequencing analysis. Contamination screening generally relies on reference-based methods such as database alignment or marker gene search, which limits the set of detectable contaminants to organisms with closely related reference species. As genomic coverage in the tree of life is highly fragmented, there is an urgent need for a reference-free methodology for contaminant identification in sequence data. We present acdc, a tool specifically developed to aidmore » the quality control process of genomic sequence data. By combining supervised and unsupervised methods, it reliably detects both known and de novo contaminants. First, 16S rRNA gene prediction and the inclusion of ultrafast exact alignment techniques allow sequence classification using existing knowledge from databases. Second, reference-free inspection is enabled by the use of state-of-the-art machine learning techniques that include fast, non-linear dimensionality reduction of oligonucleotide signatures and subsequent clustering algorithms that automatically estimate the number of clusters. The latter also enables the removal of any contaminant, yielding a clean sample. Furthermore, given the data complexity and the ill-posedness of clustering, acdc employs bootstrapping techniques to provide statistically profound confidence values. Tested on a large number of samples from diverse sequencing projects, our software is able to quickly and accurately identify contamination. Results are displayed in an interactive user interface. Acdc can be run from the web as well as a dedicated command line application, which allows easy integration into large sequencing project analysis workflows. Acdc can reliably detect contamination in single-cell genome data. In addition to database-driven detection, it complements existing tools by its unsupervised techniques, which allow for the detection of de novo contaminants. Our contribution has the potential to drastically reduce the amount of resources put into these processes, particularly in the context of limited availability of reference species. As single-cell genome data continues to grow rapidly, acdc adds to the toolkit of crucial quality assurance tools.« less

A Head Start to a Healthy Heart

NASA Technical Reports Server (NTRS)

2002-01-01

Cambridge Heart, Inc., has licensed the only U.S. Food and Drug Administration-cleared tool to identify those at risk for sudden cardiac death (SCD). The Microvolt T-Wave Alternans Test(TM) was invented by Dr. Richard J. Cohen, a professor at the Harvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, with developmental support and funding from NASA's Johnson Space Center and the National Space Biomedical Research Institute (NSBRI) in Houston, Texas. In 1993, MIT licensed the technology to Cambridge Heart, Inc., a start-up company that Dr. Cohen helped to establish. Cambridge Heart's non-invasive technology measures T-wave alternans, a change from one heartbeat to the next that is too minute to be detected by a standard electrocardiogram. Cardiac patients with such a change in heartbeat regulation are faced with a much greater risk of ventricular arrhythmia and SCD than those without it. The company's ability to measure electrical alternans on a microvolt level has been clinically proven to be just as accurate as - and in some studies, more accurate than - more costly and somewhat risky, invasive procedures, such as electrophysiological testing.

The Monthly Sky Guide: Sixth Edition

NASA Astrophysics Data System (ADS)

Ridpath, Ian; Tirion, Wil

2003-06-01

The latest edition of Ian Ridpath and Wil Tirion's popular guide to the night sky is updated for planet positions and forthcoming eclipses up to the end of the year 2007. With one chapter for each month of the year, this is an easy-to-use handbook for anyone wanting to identify constellations, star clusters, nebulae, to plot the movement of planets, or witness solar and lunar eclipses. Most of the features discussed are visible to the naked eye and all can be seen with a small telescope or binoculars. Ian Ridpath has been a full-time writer, broadcaster and lecturer on astronomy and space for more than twenty-five years. He has written and edited more than 40 books, including A Comet Called Haley (Cambridge, 1985). Wil Tirion made his first star map in 1977. It showed stars to the magnitude of 6.5 and was issued as a set of maps by the British Astronomical Association in 1981. He has illustrated numerous books and magazines, including The Cambridge Star Atlas (Cambridge, 2001). Previous Edition Pb (1999): 0-521-66771-2

Trials and tribulations of playing the devil's advocate

NASA Astrophysics Data System (ADS)

Narlikar, Jayant V.

2015-01-01

Beginning with his student days at school and college, the author describes his training at Cambridge with special emphasis on his mentor Fred Hoyle. His early experience of participating in a controversy at Cambridge played a major role in giving him the confidence to defend his scientific ideas. All through his later life he chose areas that were not part of mainstream research. These included the steady state theory and later the quasi steady state cosmology, action at a distance, noncosmological redshifts, quantum conformal cosmology, etc. After being a founding member of the Institute of Theoretical Astronomy (IOTA) at Cambridge, the author joined the Tata Institute of Fundamental Research (TIFR) in Mumbai and later moved to Pune to set up the Inter-University Centre for Astronomy and Astrophysics (IUCAA). He briefly reviews his own work and ends by pointing out the difficulties a non-conformist scientist faces in his professional life. In the conclusion, he mentions his interests in science popularization and science fiction for which he has won awards and appreciation, including UNESCO's Kalinga Prize.

Isolates of viral hemorrhagic septicemia virus from North America and Europe can be detected and distinguished by DNA probes

USGS Publications Warehouse

Batts, W.N.; Arakawa, C.K.; Bernard, J.; Winton, J.R.

1993-01-01

Biotinylated DNA probes were constructed to hybndize with speclfic sequences within the messenger RNA (mRNA) of the nucleoprotein (N) gene of vlral hemorrhagic septicemia virus (VHSV) reference strains from Europe (07-71) and North Arnenca (Makah) Probes were synthesized that were complementary to (1) a 29-nucleotide sequence near the center of the N gene conlmon to both the 07-71 and Makah reference strains of the virus (2) a unique 28- nucleotide sequence that followed the open readng frame of the Makah N gene mRNA most of which was absent In the 07-71 strain, and (3) a 22-nucleobde sequence wthin the 07-71 N gene that had 6 nllsmatches \

The complete CDS of the prion protein (PRNP) gene of African lion (Panthera leo).

PubMed

Maj, Andrzej; Spellman, Garth M; Sarver, Shane K

2008-04-01

We provide the complete PRNP CDS sequence for the African lion, which is different from the previously published sequence and more similar to other carnivore sequences. The newly obtained prion protein sequence differs from the domestic cat sequence at three amino acid positions and contains only four octapeptide repeats. We recommend that this sequence be used as the reference sequence for future studies of the PRNP gene for this species.

A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection

PubMed Central

Goodacre, Norman; Aljanahi, Aisha; Nandakumar, Subhiksha; Mikailov, Mike

2018-01-01

ABSTRACT Detection of distantly related viruses by high-throughput sequencing (HTS) is bioinformatically challenging because of the lack of a public database containing all viral sequences, without abundant nonviral sequences, which can extend runtime and obscure viral hits. Our reference viral database (RVDB) includes all viral, virus-related, and virus-like nucleotide sequences (excluding bacterial viruses), regardless of length, and with overall reduced cellular sequences. Semantic selection criteria (SEM-I) were used to select viral sequences from GenBank, resulting in a first-generation viral database (VDB). This database was manually and computationally reviewed, resulting in refined, semantic selection criteria (SEM-R), which were applied to a new download of updated GenBank sequences to create a second-generation VDB. Viral entries in the latter were clustered at 98% by CD-HIT-EST to reduce redundancy while retaining high viral sequence diversity. The viral identity of the clustered representative sequences (creps) was confirmed by BLAST searches in NCBI databases and HMMER searches in PFAM and DFAM databases. The resulting RVDB contained a broad representation of viral families, sequence diversity, and a reduced cellular content; it includes full-length and partial sequences and endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Testing of RVDBv10.2, with an in-house HTS transcriptomic data set indicated a significantly faster run for virus detection than interrogating the entirety of the NCBI nonredundant nucleotide database, which contains all viral sequences but also nonviral sequences. RVDB is publically available for facilitating HTS analysis, particularly for novel virus detection. It is meant to be updated on a regular basis to include new viral sequences added to GenBank. IMPORTANCE To facilitate bioinformatics analysis of high-throughput sequencing (HTS) data for the detection of both known and novel viruses, we have developed a new reference viral database (RVDB) that provides a broad representation of different virus species from eukaryotes by including all viral, virus-like, and virus-related sequences (excluding bacteriophages), regardless of their size. In particular, RVDB contains endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Sequences were clustered to reduce redundancy while retaining high viral sequence diversity. A particularly useful feature of RVDB is the reduction of cellular sequences, which can enhance the run efficiency of large transcriptomic and genomic data analysis and increase the specificity of virus detection. PMID:29564396

A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection.

PubMed

Goodacre, Norman; Aljanahi, Aisha; Nandakumar, Subhiksha; Mikailov, Mike; Khan, Arifa S

2018-01-01

Detection of distantly related viruses by high-throughput sequencing (HTS) is bioinformatically challenging because of the lack of a public database containing all viral sequences, without abundant nonviral sequences, which can extend runtime and obscure viral hits. Our reference viral database (RVDB) includes all viral, virus-related, and virus-like nucleotide sequences (excluding bacterial viruses), regardless of length, and with overall reduced cellular sequences. Semantic selection criteria (SEM-I) were used to select viral sequences from GenBank, resulting in a first-generation viral database (VDB). This database was manually and computationally reviewed, resulting in refined, semantic selection criteria (SEM-R), which were applied to a new download of updated GenBank sequences to create a second-generation VDB. Viral entries in the latter were clustered at 98% by CD-HIT-EST to reduce redundancy while retaining high viral sequence diversity. The viral identity of the clustered representative sequences (creps) was confirmed by BLAST searches in NCBI databases and HMMER searches in PFAM and DFAM databases. The resulting RVDB contained a broad representation of viral families, sequence diversity, and a reduced cellular content; it includes full-length and partial sequences and endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Testing of RVDBv10.2, with an in-house HTS transcriptomic data set indicated a significantly faster run for virus detection than interrogating the entirety of the NCBI nonredundant nucleotide database, which contains all viral sequences but also nonviral sequences. RVDB is publically available for facilitating HTS analysis, particularly for novel virus detection. It is meant to be updated on a regular basis to include new viral sequences added to GenBank. IMPORTANCE To facilitate bioinformatics analysis of high-throughput sequencing (HTS) data for the detection of both known and novel viruses, we have developed a new reference viral database (RVDB) that provides a broad representation of different virus species from eukaryotes by including all viral, virus-like, and virus-related sequences (excluding bacteriophages), regardless of their size. In particular, RVDB contains endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Sequences were clustered to reduce redundancy while retaining high viral sequence diversity. A particularly useful feature of RVDB is the reduction of cellular sequences, which can enhance the run efficiency of large transcriptomic and genomic data analysis and increase the specificity of virus detection.

Chirped pulse digital holography for measuring the sequence of ultrafast optical wavefronts

NASA Astrophysics Data System (ADS)

Karasawa, Naoki

2018-04-01

Optical setups for measuring the sequence of ultrafast optical wavefronts using a chirped pulse as a reference wave in digital holography are proposed and analyzed. In this method, multiple ultrafast object pulses are used to probe the temporal evolution of ultrafast phenomena and they are interfered with a chirped reference wave to record a digital hologram. Wavefronts at different times can be reconstructed separately from the recorded hologram when the reference pulse can be treated as a quasi-monochromatic wave during the pulse width of each object pulse. The feasibility of this method is demonstrated by numerical simulation.

Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

PubMed Central

2011-01-01

Background Many plants have large and complex genomes with an abundance of repeated sequences. Many plants are also polyploid. Both of these attributes typify the genome architecture in the tribe Triticeae, whose members include economically important wheat, rye and barley. Large genome sizes, an abundance of repeated sequences, and polyploidy present challenges to genome-wide SNP discovery using next-generation sequencing (NGS) of total genomic DNA by making alignment and clustering of short reads generated by the NGS platforms difficult, particularly in the absence of a reference genome sequence. Results An annotation-based, genome-wide SNP discovery pipeline is reported using NGS data for large and complex genomes without a reference genome sequence. Roche 454 shotgun reads with low genome coverage of one genotype are annotated in order to distinguish single-copy sequences and repeat junctions from repetitive sequences and sequences shared by paralogous genes. Multiple genome equivalents of shotgun reads of another genotype generated with SOLiD or Solexa are then mapped to the annotated Roche 454 reads to identify putative SNPs. A pipeline program package, AGSNP, was developed and used for genome-wide SNP discovery in Aegilops tauschii-the diploid source of the wheat D genome, and with a genome size of 4.02 Gb, of which 90% is repetitive sequences. Genomic DNA of Ae. tauschii accession AL8/78 was sequenced with the Roche 454 NGS platform. Genomic DNA and cDNA of Ae. tauschii accession AS75 was sequenced primarily with SOLiD, although some Solexa and Roche 454 genomic sequences were also generated. A total of 195,631 putative SNPs were discovered in gene sequences, 155,580 putative SNPs were discovered in uncharacterized single-copy regions, and another 145,907 putative SNPs were discovered in repeat junctions. These SNPs were dispersed across the entire Ae. tauschii genome. To assess the false positive SNP discovery rate, DNA containing putative SNPs was amplified by PCR from AL8/78 and AS75 and resequenced with the ABI 3730 xl. In a sample of 302 randomly selected putative SNPs, 84.0% in gene regions, 88.0% in repeat junctions, and 81.3% in uncharacterized regions were validated. Conclusion An annotation-based genome-wide SNP discovery pipeline for NGS platforms was developed. The pipeline is suitable for SNP discovery in genomic libraries of complex genomes and does not require a reference genome sequence. The pipeline is applicable to all current NGS platforms, provided that at least one such platform generates relatively long reads. The pipeline package, AGSNP, and the discovered 497,118 Ae. tauschii SNPs can be accessed at (http://avena.pw.usda.gov/wheatD/agsnp.shtml). PMID:21266061

mtDNA variation in caste populations of Andhra Pradesh, India.

PubMed

Bamshad, M; Fraley, A E; Crawford, M H; Cann, R L; Busi, B R; Naidu, J M; Jorde, L B

1996-02-01

Various anthropological analyses have documented extensive regional variation among populations on the subcontinent of India using morphological, protein, blood group, and nuclear DNA polymorphisms. These patterns are the product of complex population structure (genetic drift, gene flow) and a population history noted for numerous branching events. As a result, the interpretation of relationships among caste populations of South India and between Indians and continental populations remains controversial. The Hindu caste system is a general model of genetic differentiation among endogamous populations stratified by social forces (e.g., religion and occupation). The mitochondrial DNA (mtDNA) molecule has unique properties that facilitate the exploration of population structure. We analyzed 36 Hindu men born in Andhra Pradesh who were unrelated matrilineally through at least 3 generations and who represent 4 caste populations: Brahmin (9), Yadava (10), Kapu (7), and Relli (10). Individuals from Africa (36), Asia (36), and Europe (36) were sampled for comparison. A 200-base-pair segment of hypervariable segment 2 (HVS2) of the mtDNA control region was sequenced in all individuals. In the Indian castes 25 distinct haplotypes are identified. Aside from the Cambridge reference sequence, only two haplotypes are shared between caste populations. Middle castes form a highly supported cluster in a neighbor-joining network. Mean nucleotide diversity within each caste is 0.015, 0.012, 0.011, and 0.012 for the Brahmin, Yadava, Kapu, and Relli, respectively. mtDNA variation is highly structured between castes (GST = 0.17; p < 0.002). The effects of social structure on mtDNA variation are much greater than those on variation measured by traditional markers. Explanations for this discordance include (1) the higher resolving power of mtDNA, (2) sex-dependent gene flow, (3) differences in male and female effective population sizes, and (4) elements of the kinship structure. Thirty distinct haplotypes are found in Africans, 17 in Asians, and 13 in Europeans. Mean nucleotide diversity is 0.019, 0.014, 0.009, and 0.007 for Africans, Indians, Asians, and Europeans, respectively. These populations are highly structured geographically (GST = 0.15; p < 0.001). The caste populations of Andhra Pradesh cluster more often with Africans than with Asians or Europeans. This is suggestive of admixture with African populations.

Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study

PubMed Central

García-Álvarez, Laura; Holden, Matthew TG; Lindsay, Heather; Webb, Cerian R; Brown, Derek FJ; Curran, Martin D; Walpole, Enid; Brooks, Karen; Pickard, Derek J; Teale, Christopher; Parkhill, Julian; Bentley, Stephen D; Edwards, Giles F; Girvan, E Kirsty; Kearns, Angela M; Pichon, Bruno; Hill, Robert LR; Larsen, Anders Rhod; Skov, Robert L; Peacock, Sharon J; Maskell, Duncan J; Holmes, Mark A

2011-01-01

Summary Background Animals can act as a reservoir and source for the emergence of novel meticillin-resistant Staphylococcus aureus (MRSA) clones in human beings. Here, we report the discovery of a strain of S aureus (LGA251) isolated from bulk milk that was phenotypically resistant to meticillin but tested negative for the mecA gene and a preliminary investigation of the extent to which such strains are present in bovine and human populations. Methods Isolates of bovine MRSA were obtained from the Veterinary Laboratories Agency in the UK, and isolates of human MRSA were obtained from diagnostic or reference laboratories (two in the UK and one in Denmark). From these collections, we searched for mecA PCR-negative bovine and human S aureus isolates showing phenotypic meticillin resistance. We used whole-genome sequencing to establish the genetic basis for the observed antibiotic resistance. Findings A divergent mecA homologue (mecALGA251) was discovered in the LGA251 genome located in a novel staphylococcal cassette chromosome mec element, designated type-XI SCCmec. The mecALGA251 was 70% identical to S aureus mecA homologues and was initially detected in 15 S aureus isolates from dairy cattle in England. These isolates were from three different multilocus sequence type lineages (CC130, CC705, and ST425); spa type t843 (associated with CC130) was identified in 60% of bovine isolates. When human mecA-negative MRSA isolates were tested, the mecALGA251 homologue was identified in 12 of 16 isolates from Scotland, 15 of 26 from England, and 24 of 32 from Denmark. As in cows, t843 was the most common spa type detected in human beings. Interpretation Although routine culture and antimicrobial susceptibility testing will identify S aureus isolates with this novel mecA homologue as meticillin resistant, present confirmatory methods will not identify them as MRSA. New diagnostic guidelines for the detection of MRSA should consider the inclusion of tests for mecALGA251. Funding Department for Environment, Food and Rural Affairs, Higher Education Funding Council for England, Isaac Newton Trust (University of Cambridge), and the Wellcome Trust. PMID:21641281

37 CFR 1.823 - Requirements for nucleotide and/or amino acid sequences as part of the application.

Code of Federal Regulations, 2011 CFR

2011-07-01

... and/or amino acid sequences as part of the application. 1.823 Section 1.823 Patents, Trademarks, and... Amino Acid Sequences § 1.823 Requirements for nucleotide and/or amino acid sequences as part of the... incorporation-by-reference of the Sequence Listing as required by § 1.52(e)(5). The presentation of the...

37 CFR 1.823 - Requirements for nucleotide and/or amino acid sequences as part of the application.

Code of Federal Regulations, 2013 CFR

2013-07-01

... and/or amino acid sequences as part of the application. 1.823 Section 1.823 Patents, Trademarks, and... Amino Acid Sequences § 1.823 Requirements for nucleotide and/or amino acid sequences as part of the... incorporation-by-reference of the Sequence Listing as required by § 1.52(e)(5). The presentation of the...

37 CFR 1.823 - Requirements for nucleotide and/or amino acid sequences as part of the application.

Code of Federal Regulations, 2012 CFR

2012-07-01

... and/or amino acid sequences as part of the application. 1.823 Section 1.823 Patents, Trademarks, and... Amino Acid Sequences § 1.823 Requirements for nucleotide and/or amino acid sequences as part of the... incorporation-by-reference of the Sequence Listing as required by § 1.52(e)(5). The presentation of the...

37 CFR 1.823 - Requirements for nucleotide and/or amino acid sequences as part of the application.

Code of Federal Regulations, 2010 CFR

2010-07-01

... and/or amino acid sequences as part of the application. 1.823 Section 1.823 Patents, Trademarks, and... Amino Acid Sequences § 1.823 Requirements for nucleotide and/or amino acid sequences as part of the... incorporation-by-reference of the Sequence Listing as required by § 1.52(e)(5). The presentation of the...

37 CFR 1.823 - Requirements for nucleotide and/or amino acid sequences as part of the application.

Code of Federal Regulations, 2014 CFR

2014-07-01

... and/or amino acid sequences as part of the application. 1.823 Section 1.823 Patents, Trademarks, and... Amino Acid Sequences § 1.823 Requirements for nucleotide and/or amino acid sequences as part of the... incorporation-by-reference of the Sequence Listing as required by § 1.52(e)(5). The presentation of the...

Performance evaluation of Sanger sequencing for the diagnosis of primary hyperoxaluria and comparison with targeted next generation sequencing

PubMed Central

Williams, Emma L; Bagg, Eleanor A L; Mueller, Michael; Vandrovcova, Jana; Aitman, Timothy J; Rumsby, Gill

2015-01-01

Definitive diagnosis of primary hyperoxaluria (PH) currently utilizes sequential Sanger sequencing of the AGXT, GRPHR, and HOGA1 genes but efficacy is unproven. This analysis is time-consuming, relatively expensive, and delays in diagnosis and inappropriate treatment can occur if not pursued early in the diagnostic work-up. We reviewed testing outcomes of Sanger sequencing in 200 consecutive patient samples referred for analysis. In addition, the Illumina Truseq custom amplicon system was evaluated for paralleled next-generation sequencing (NGS) of AGXT,GRHPR, and HOGA1 in 90 known PH patients. AGXT sequencing was requested in all patients, permitting a diagnosis of PH1 in 50%. All remaining patients underwent targeted exon sequencing of GRHPR and HOGA1 with 8% diagnosed with PH2 and 8% with PH3. Complete sequencing of both GRHPR and HOGA1 was not requested in 25% of patients referred leaving their diagnosis in doubt. NGS analysis showed 98% agreement with Sanger sequencing and both approaches had 100% diagnostic specificity. Diagnostic sensitivity of Sanger sequencing was 98% and for NGS it was 97%. NGS has comparable diagnostic performance to Sanger sequencing for the diagnosis of PH and, if implemented, would screen for all forms of PH simultaneously ensuring prompt diagnosis at decreased cost. PMID:25629080

Characterization of NIST human mitochondrial DNA SRM-2392 and SRM-2392-I standard reference materials by next generation sequencing.

PubMed

Riman, Sarah; Kiesler, Kevin M; Borsuk, Lisa A; Vallone, Peter M

2017-07-01

Standard Reference Materials SRM 2392 and 2392-I are intended to provide quality control when amplifying and sequencing human mitochondrial genome sequences. The National Institute of Standards and Technology (NIST) offers these SRMs to laboratories performing DNA-based forensic human identification, molecular diagnosis of mitochondrial diseases, mutation detection, evolutionary anthropology, and genetic genealogy. The entire mtGenome (∼16569bp) of SRM 2392 and 2392-I have previously been characterized at NIST by Sanger sequencing. Herein, we used the sensitivity, specificity, and accuracy offered by next generation sequencing (NGS) to: (1) re-sequence the certified values of the SRM 2392 and 2392-I; (2) confirm Sanger data with a high coverage new sequencing technology; (3) detect lower level heteroplasmies (<20%); and thus (4) support mitochondrial sequencing communities in the adoption of NGS methods. To obtain a consensus sequence for the SRMs as well as identify and control any bias, sequencing was performed using two NGS platforms and data was analyzed using different bioinformatics pipelines. Our results confirm five low level heteroplasmy sites that were not previously observed with Sanger sequencing: three sites in the GM09947A template in SRM 2392 and two sites in the HL-60 template in SRM 2392-I. Copyright © 2017 Elsevier B.V. All rights reserved.

Perfusion CT to assess angiogenesis in colon cancer: technical limitations and practical challenges.

PubMed

Dighe, S; Castellano, E; Blake, H; Jeyadevan, N; Koh, M U; Orten, M; Swift, I; Brown, G

2012-10-01

Perfusion CT may have the potential to quantify the degree of angiogenesis of solid tumours in vivo. This study aims to identify the practical and technical challenges inherent to the technique, and evaluate its feasibility in colorectal tumours. 51 patients from 2 institutions prospectively underwent a single perfusion CT on 2 different multidetector scanners. The patients were advised to breath-hold as long as possible, followed by shallow breathing, and were given intravenous buscopan to reduce movement. Numerous steps were explored to identify the challenges. 43 patients successfully completed the perfusion CT as per protocol. Inability to detect the tumour (n=3), misplacement of dynamic sequence co-ordinates (n=2), failure of contrast injection (n=2) and displacement of tumour (n=1) were the reasons for failure. In 14 cases excessive respiratory motion displaced the tumour out of the scanning field along the temporal sequence, leading to erroneous data capture. In nine patients, minor displacements of the tumour were corrected by repositioning the region of interest (ROI) to its original position after reviewing each dynamic sequence slice. In 20 patients the tumour was stable, and data captured from the ROI were representative, and could have been analysed by commercially available Body Tumor Perfusion 3.0® software (GE Healthcare, Waukesha, WI). Hence all data were manually analysed by MATLAB® processing software (MathWorks, Cambridge, UK). Perfusion CT in tumours susceptible to motion during acquisition makes accurate data capture challenging and requires meticulous attention to detail. Motion correction software is essential if perfusion CT is to be used routinely in colorectal cancer.

British Pharmacological Society Cambridge Symposia. 5-7 January 2000, Cambridge, UK.

PubMed

Lawson, K

2000-04-01

This meeting covered a broad range of pharmacological topics, although the main themes were covered in four mini-symposia. This report concentrates on the cannabinoid, pain and cardiac ischemia symposia. The cannabinoid system was identified as a major area of potential therapeutic interest, offering a number of clinical targets that may be modified through the actions of selective ligands. Novel approaches to the treatment of neurogenic pain, where conventional analgesics have limited value, are being explored with significant success. The role of delayed preconditioning in cardiac ischemia was also addressed as a mechanism of cardioprotection.

Brief history of the Cambridge STEM aberration correction project and its progeny.

PubMed

Brown, L Michael; Batson, Philip E; Dellby, Niklas; Krivanek, Ondrej L

2015-10-01

We provide a brief history of the project to correct the spherical aberration of the scanning transmission electron microscope (STEM) that started in Cambridge (UK) and continued in Kirkland (WA, USA), Yorktown Heights (NY, USA), and other places. We describe the project in the full context of other aberration correction research and related work, partly in response to the incomplete context presented in the paper "In quest of perfection in electron optics: A biographical sketch of Harald Rose on the occasion of his 80th birthday", recently published in Ultramicroscopy. Copyright © 2015 Elsevier B.V. All rights reserved.

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

PubMed Central

Degner, Jacob F.; Marioni, John C.; Pai, Athma A.; Pickrell, Joseph K.; Nkadori, Everlyne; Gilad, Yoav; Pritchard, Jonathan K.

2009-01-01

Motivation: Next-generation sequencing has become an important tool for genome-wide quantification of DNA and RNA. However, a major technical hurdle lies in the need to map short sequence reads back to their correct locations in a reference genome. Here, we investigate the impact of SNP variation on the reliability of read-mapping in the context of detecting allele-specific expression (ASE). Results: We generated 16 million 35 bp reads from mRNA of each of two HapMap Yoruba individuals. When we mapped these reads to the human genome we found that, at heterozygous SNPs, there was a significant bias toward higher mapping rates of the allele in the reference sequence, compared with the alternative allele. Masking known SNP positions in the genome sequence eliminated the reference bias but, surprisingly, did not lead to more reliable results overall. We find that even after masking, ∼5–10% of SNPs still have an inherent bias toward more effective mapping of one allele. Filtering out inherently biased SNPs removes 40% of the top signals of ASE. The remaining SNPs showing ASE are enriched in genes previously known to harbor cis-regulatory variation or known to show uniparental imprinting. Our results have implications for a variety of applications involving detection of alternate alleles from short-read sequence data. Availability: Scripts, written in Perl and R, for simulating short reads, masking SNP variation in a reference genome and analyzing the simulation output are available upon request from JFD. Raw short read data were deposited in GEO (http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE18156. Contact: jdegner@uchicago.edu; marioni@uchicago.edu; gilad@uchicago.edu; pritch@uchicago.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19808877

Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis

PubMed Central

Mason, Annaliese S.; Rousseau-Gueutin, Mathieu; Morice, Jérôme; Bayer, Philipp E.; Besharat, Naghmeh; Cousin, Anouska; Pradhan, Aneeta; Parkin, Isobel A. P.; Chèvre, Anne-Marie; Batley, Jacqueline; Nelson, Matthew N.

2016-01-01

Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from Brassica interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina Brassica 60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the Brassica A and C genomes to the reference Brassica napus genome. Gene and transposable element density across the B. napus genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate. PMID:26614742

Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis.

PubMed

Mason, Annaliese S; Rousseau-Gueutin, Mathieu; Morice, Jérôme; Bayer, Philipp E; Besharat, Naghmeh; Cousin, Anouska; Pradhan, Aneeta; Parkin, Isobel A P; Chèvre, Anne-Marie; Batley, Jacqueline; Nelson, Matthew N

2016-02-01

Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from Brassica interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina Brassica 60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the Brassica A and C genomes to the reference Brassica napus genome. Gene and transposable element density across the B. napus genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate. Copyright © 2016 by the Genetics Society of America.

Automated Sanger Analysis Pipeline (ASAP): A Tool for Rapidly Analyzing Sanger Sequencing Data with Minimum User Interference.

PubMed

Singh, Aditya; Bhatia, Prateek

2016-12-01

Sanger sequencing platforms, such as applied biosystems instruments, generate chromatogram files. Generally, for 1 region of a sequence, we use both forward and reverse primers to sequence that area, in that way, we have 2 sequences that need to be aligned and a consensus generated before mutation detection studies. This work is cumbersome and takes time, especially if the gene is large with many exons. Hence, we devised a rapid automated command system to filter, build, and align consensus sequences and also optionally extract exonic regions, translate them in all frames, and perform an amino acid alignment starting from raw sequence data within a very short time. In full capabilities of Automated Mutation Analysis Pipeline (ASAP), it is able to read "*.ab1" chromatogram files through command line interface, convert it to the FASTQ format, trim the low-quality regions, reverse-complement the reverse sequence, create a consensus sequence, extract the exonic regions using a reference exonic sequence, translate the sequence in all frames, and align the nucleic acid and amino acid sequences to reference nucleic acid and amino acid sequences, respectively. All files are created and can be used for further analysis. ASAP is available as Python 3.x executable at https://github.com/aditya-88/ASAP. The version described in this paper is 0.28.

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.

PubMed

Delaneau, Olivier; Marchini, Jonathan

2014-06-13

A major use of the 1000 Genomes Project (1000 GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000 GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants.

Reference genome sequence of the model plant Setaria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bennetzen, Jeffrey L; Schmutz, Jeremy; Wang, Hao

We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ~400-Mb assembly covers ~80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species thatmore » demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).« less

Reference genome sequence of the model plant Setaria.

PubMed

Bennetzen, Jeffrey L; Schmutz, Jeremy; Wang, Hao; Percifield, Ryan; Hawkins, Jennifer; Pontaroli, Ana C; Estep, Matt; Feng, Liang; Vaughn, Justin N; Grimwood, Jane; Jenkins, Jerry; Barry, Kerrie; Lindquist, Erika; Hellsten, Uffe; Deshpande, Shweta; Wang, Xuewen; Wu, Xiaomei; Mitros, Therese; Triplett, Jimmy; Yang, Xiaohan; Ye, Chu-Yu; Mauro-Herrera, Margarita; Wang, Lin; Li, Pinghua; Sharma, Manoj; Sharma, Rita; Ronald, Pamela C; Panaud, Olivier; Kellogg, Elizabeth A; Brutnell, Thomas P; Doust, Andrew N; Tuskan, Gerald A; Rokhsar, Daniel; Devos, Katrien M

2012-05-13

We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ∼400-Mb assembly covers ∼80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

Entomopathogen ID: a curated sequence resource for entomopathogenic fungi

USDA-ARS?s Scientific Manuscript database

We report the development of a publicly accessible, curated database of Hypocrealean entomopathogenic fungi sequence data. The goal is to provide a platform for users to easily access sequence data from reference strains. The database can be used to accurately identify unknown entomopathogenic fungi...

A new hybrid approach for MHC genotyping: high-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra).

PubMed

Fuselli, S; Baptista, R P; Panziera, A; Magi, A; Guglielmi, S; Tonin, R; Benazzo, A; Bauzer, L G; Mazzoni, C J; Bertorelle, G

2018-03-24

The major histocompatibility complex (MHC) acts as an interface between the immune system and infectious diseases. Accurate characterization and genotyping of the extremely variable MHC loci are challenging especially without a reference sequence. We designed a combination of long-range PCR, Illumina short-reads, and Oxford Nanopore MinION long-reads approaches to capture the genetic variation of the MHC II DRB locus in an Italian population of the Alpine chamois (Rupicapra rupicapra). We utilized long-range PCR to generate a 9 Kb fragment of the DRB locus. Amplicons from six different individuals were fragmented, tagged, and simultaneously sequenced with Illumina MiSeq. One of these amplicons was sequenced with the MinION device, which produced long reads covering the entire amplified fragment. A pipeline that combines short and long reads resolved several short tandem repeats and homopolymers and produced a de novo reference, which was then used to map and genotype the short reads from all individuals. The assembled DRB locus showed a high level of polymorphism and the presence of a recombination breakpoint. Our results suggest that an amplicon-based NGS approach coupled with single-molecule MinION nanopore sequencing can efficiently achieve both the assembly and the genotyping of complex genomic regions in multiple individuals in the absence of a reference sequence.

The value of new genome references.

PubMed

Worley, Kim C; Richards, Stephen; Rogers, Jeffrey

2017-09-15

Genomic information has become a ubiquitous and almost essential aspect of biological research. Over the last 10-15 years, the cost of generating sequence data from DNA or RNA samples has dramatically declined and our ability to interpret those data increased just as remarkably. Although it is still possible for biologists to conduct interesting and valuable research on species for which genomic data are not available, the impact of having access to a high quality whole genome reference assembly for a given species is nothing short of transformational. Research on a species for which we have no DNA or RNA sequence data is restricted in fundamental ways. In contrast, even access to an initial draft quality genome (see below for definitions) opens a wide range of opportunities that are simply not available without that reference genome assembly. Although a complete discussion of the impact of genome sequencing and assembly is beyond the scope of this short paper, the goal of this review is to summarize the most common and highest impact contributions that whole genome sequencing and assembly has had on comparative and evolutionary biology. Copyright © 2016. Published by Elsevier Inc.

Extensive sequencing of seven human genomes to characterize benchmark reference materials

PubMed Central

Zook, Justin M.; Catoe, David; McDaniel, Jennifer; Vang, Lindsay; Spies, Noah; Sidow, Arend; Weng, Ziming; Liu, Yuling; Mason, Christopher E.; Alexander, Noah; Henaff, Elizabeth; McIntyre, Alexa B.R.; Chandramohan, Dhruva; Chen, Feng; Jaeger, Erich; Moshrefi, Ali; Pham, Khoa; Stedman, William; Liang, Tiffany; Saghbini, Michael; Dzakula, Zeljko; Hastie, Alex; Cao, Han; Deikus, Gintaras; Schadt, Eric; Sebra, Robert; Bashir, Ali; Truty, Rebecca M.; Chang, Christopher C.; Gulbahce, Natali; Zhao, Keyan; Ghosh, Srinka; Hyland, Fiona; Fu, Yutao; Chaisson, Mark; Xiao, Chunlin; Trow, Jonathan; Sherry, Stephen T.; Zaranek, Alexander W.; Ball, Madeleine; Bobe, Jason; Estep, Preston; Church, George M.; Marks, Patrick; Kyriazopoulou-Panagiotopoulou, Sofia; Zheng, Grace X.Y.; Schnall-Levin, Michael; Ordonez, Heather S.; Mudivarti, Patrice A.; Giorda, Kristina; Sheng, Ying; Rypdal, Karoline Bjarnesdatter; Salit, Marc

2016-01-01

The Genome in a Bottle Consortium, hosted by the National Institute of Standards and Technology (NIST) is creating reference materials and data for human genome sequencing, as well as methods for genome comparison and benchmarking. Here, we describe a large, diverse set of sequencing data for seven human genomes; five are current or candidate NIST Reference Materials. The pilot genome, NA12878, has been released as NIST RM 8398. We also describe data from two Personal Genome Project trios, one of Ashkenazim Jewish ancestry and one of Chinese ancestry. The data come from 12 technologies: BioNano Genomics, Complete Genomics paired-end and LFR, Ion Proton exome, Oxford Nanopore, Pacific Biosciences, SOLiD, 10X Genomics GemCode WGS, and Illumina exome and WGS paired-end, mate-pair, and synthetic long reads. Cell lines, DNA, and data from these individuals are publicly available. Therefore, we expect these data to be useful for revealing novel information about the human genome and improving sequencing technologies, SNP, indel, and structural variant calling, and de novo assembly. PMID:27271295

Reference genotype and exome data from an Australian Aboriginal population for health-based research

PubMed Central

Tang, Dave; Anderson, Denise; Francis, Richard W.; Syn, Genevieve; Jamieson, Sarra E.; Lassmann, Timo; Blackwell, Jenefer M.

2016-01-01

Genetic analyses, including genome-wide association studies and whole exome sequencing (WES), provide powerful tools for the analysis of complex and rare genetic diseases. To date there are no reference data for Aboriginal Australians to underpin the translation of health-based genomic research. Here we provide a catalogue of variants called after sequencing the exomes of 72 Aboriginal individuals to a depth of 20X coverage in ∼80% of the sequenced nucleotides. We determined 320,976 single nucleotide variants (SNVs) and 47,313 insertions/deletions using the Genome Analysis Toolkit. We had previously genotyped a subset of the Aboriginal individuals (70/72) using the Illumina Omni2.5 BeadChip platform and found ~99% concordance at overlapping sites, which suggests high quality genotyping. Finally, we compared our SNVs to six publicly available variant databases, such as dbSNP and the Exome Sequencing Project, and 70,115 of our SNVs did not overlap any of the single nucleotide polymorphic sites in all the databases. Our data set provides a useful reference point for genomic studies on Aboriginal Australians. PMID:27070114

Reference genotype and exome data from an Australian Aboriginal population for health-based research.

PubMed

Tang, Dave; Anderson, Denise; Francis, Richard W; Syn, Genevieve; Jamieson, Sarra E; Lassmann, Timo; Blackwell, Jenefer M

2016-04-12

Genetic analyses, including genome-wide association studies and whole exome sequencing (WES), provide powerful tools for the analysis of complex and rare genetic diseases. To date there are no reference data for Aboriginal Australians to underpin the translation of health-based genomic research. Here we provide a catalogue of variants called after sequencing the exomes of 72 Aboriginal individuals to a depth of 20X coverage in ∼80% of the sequenced nucleotides. We determined 320,976 single nucleotide variants (SNVs) and 47,313 insertions/deletions using the Genome Analysis Toolkit. We had previously genotyped a subset of the Aboriginal individuals (70/72) using the Illumina Omni2.5 BeadChip platform and found ~99% concordance at overlapping sites, which suggests high quality genotyping. Finally, we compared our SNVs to six publicly available variant databases, such as dbSNP and the Exome Sequencing Project, and 70,115 of our SNVs did not overlap any of the single nucleotide polymorphic sites in all the databases. Our data set provides a useful reference point for genomic studies on Aboriginal Australians.

Devonian paleomagnetism of the North Tien Shan: Implications for the middle-Late Paleozoic paleogeography of Eurasia

NASA Astrophysics Data System (ADS)

Levashova, Natalia M.; Mikolaichuk, Alexander V.; McCausland, Philip J. A.; Bazhenov, Mikhail L.; Van der Voo, Rob

2007-05-01

The Ural-Mongol belt (UMB), between Siberia, Baltica and Tarim, is widely recognized as the locus of Asia's main growth during the Paleozoic, but its evolution remains highly controversial, as illustrated by the disparate paleogeographic models published in the last decade. One of the largest tectonic units of the UMB is the Kokchetav-North Tien Shan Domain (KNTD) that stretches from Tarim in the south nearly to the West Siberian Basin. The KNTD comprises several Precambrian microcontinents and numerous remnants of Early Paleozoic island arcs, marginal basins and accretionary complexes. In Late Ordovician time, all these structures had amalgamated into a single contiguous domain. Its paleogeographic position is of crucial importance for elucidating the Paleozoic evolution of the UMB in general and of the Urals in particular. The Aral Formation, located in Kyrgyzstan in the southern part of the KNTD, consists of a thick Upper Devonian (Frasnian) basalt-andesite sequence. Paleomagnetic data show a dual-polarity characteristic component (Dec/Inc = 286° / + 56°, α95 = 9°, k = 21, N = 15 sites). The primary origin of this magnetization is confirmed by a positive test on intraformational conglomerates. We combine this result with other Paleozoic data from the KNTD and show its latitudinal motion from the Late Ordovician to the end of the Paleozoic. The observed paleolatitudes are found to agree well with the values extrapolated from Baltica to a common reference point (42.5°N, 73°E) in our sampling area for the entire interval; hence coherent motion of the KNTD and Baltica is strongly indicated for most of the Paleozoic. This finding contradicts most published models of the UMB evolution, where the KNTD is separated from Baltica by a rather wide Ural Ocean containing one or more major plate boundaries. An exception is the model of Şengör and Natal'in [A.M.C. Şengör, B.A. Natal'in, Paleotectonics of Asia: fragments of a synthesis, in: A. Yin and M. Harrison (eds.), The tectonic evolution of Asia, Cambridge University Press, Cambridge (1996) 486-640], in which coherent paleolatitudinal motion of Baltica and the KNTD is hypothesized — the latter as part of the Kipchak Arc. We suggest a parallel hypothesis, which explains coherent motion of the KNTD and Baltica. In particular, we argue that if a basin with oceanic crust ever existed between the KNTD and Baltica, it was a narrow one without (significant) active spreading in Middle to Late Paleozoic time. Notably, the paleogeographic position of Siberia during the Middle Paleozoic and hence, the width of the Khanty-Mansi Ocean between Siberia, on the one hand, and Baltica-KNTD, on the other hand, remains largely unconstrained, because of the paucity of high-quality Silurian, Devonian and Carboniferous paleomagnetic results from Siberia.

Transcriptome Assembly, Gene Annotation and Tissue Gene Expression Atlas of the Rainbow Trout

PubMed Central

Salem, Mohamed; Paneru, Bam; Al-Tobasei, Rafet; Abdouni, Fatima; Thorgaard, Gary H.; Rexroad, Caird E.; Yao, Jianbo

2015-01-01

Efforts to obtain a comprehensive genome sequence for rainbow trout are ongoing and will be complemented by transcriptome information that will enhance genome assembly and annotation. Previously, transcriptome reference sequences were reported using data from different sources. Although the previous work added a great wealth of sequences, a complete and well-annotated transcriptome is still needed. In addition, gene expression in different tissues was not completely addressed in the previous studies. In this study, non-normalized cDNA libraries were sequenced from 13 different tissues of a single doubled haploid rainbow trout from the same source used for the rainbow trout genome sequence. A total of ~1.167 billion paired-end reads were de novo assembled using the Trinity RNA-Seq assembler yielding 474,524 contigs > 500 base-pairs. Of them, 287,593 had homologies to the NCBI non-redundant protein database. The longest contig of each cluster was selected as a reference, yielding 44,990 representative contigs. A total of 4,146 contigs (9.2%), including 710 full-length sequences, did not match any mRNA sequences in the current rainbow trout genome reference. Mapping reads to the reference genome identified an additional 11,843 transcripts not annotated in the genome. A digital gene expression atlas revealed 7,678 housekeeping and 4,021 tissue-specific genes. Expression of about 16,000–32,000 genes (35–71% of the identified genes) accounted for basic and specialized functions of each tissue. White muscle and stomach had the least complex transcriptomes, with high percentages of their total mRNA contributed by a small number of genes. Brain, testis and intestine, in contrast, had complex transcriptomes, with a large numbers of genes involved in their expression patterns. This study provides comprehensive de novo transcriptome information that is suitable for functional and comparative genomics studies in rainbow trout, including annotation of the genome. PMID:25793877