WorldWideScience

Sample records for previously published sequence

  1. Availability of nuclear decay data in electronic form, including beta spectra not previously published

    International Nuclear Information System (INIS)

    Eckerman, K.F.; Westfall, R.J.; Ryman, J.C.; Cristy, M.

    1994-01-01

    The unabridged data used in preparing ICRP Publication 38 (1983) and a monograph of the Medical Internal Radiation Dose (MIRD) Committee are now available in electronic form. The open-quotes ICRP38 collectionclose quotes contains data on the energies and intensities of radiations emitted by 825 radionuclides (those in ICRP Publication 38 plus 13 from the MIRD monograph), and the open-quotes MIRD collectionclose quotes contains data on 242 radionuclides. Each collection consists of a radiations data file and a beta spectra data file. The radiations data file contains the complete listing of the emitted radiations, their types, mean or unique energies, and absolute intensities for each radionuclide, the probability that a beta particle will be emitted with kinetic energies defined by a standard energy grid. Although summary information from the radiation data files has been published, neither the unabridged data nor the beta spectra have been published. These data files and a data extraction utility, which runs on a personal computer, are available from the Radiation Shielding Information Center at Oak Ridge National Laboratory. 13 refs., 1 fig., 6 tabs

  2. List of new names and new combinations previously effectively, but not validly, published.

    Science.gov (United States)

    2008-09-01

    The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.

  3. An evaluation of Comparative Genome Sequencing (CGS by comparing two previously-sequenced bacterial genomes

    Directory of Open Access Journals (Sweden)

    Herring Christopher D

    2007-08-01

    Full Text Available Abstract Background With the development of new technology, it has recently become practical to resequence the genome of a bacterium after experimental manipulation. It is critical though to know the accuracy of the technique used, and to establish confidence that all of the mutations were detected. Results In order to evaluate the accuracy of genome resequencing using the microarray-based Comparative Genome Sequencing service provided by Nimblegen Systems Inc., we resequenced the E. coli strain W3110 Kohara using MG1655 as a reference, both of which have been completely sequenced using traditional sequencing methods. CGS detected 7 of 8 small sequence differences, one large deletion, and 9 of 12 IS element insertions present in W3110, but did not detect a large chromosomal inversion. In addition, we confirmed that CGS also detected 2 SNPs, one deletion and 7 IS element insertions that are not present in the genome sequence, which we attribute to changes that occurred after the creation of the W3110 lambda clone library. The false positive rate for SNPs was one per 244 Kb of genome sequence. Conclusion CGS is an effective way to detect multiple mutations present in one bacterium relative to another, and while highly cost-effective, is prone to certain errors. Mutations occurring in repeated sequences or in sequences with a high degree of secondary structure may go undetected. It is also critical to follow up on regions of interest in which SNPs were not called because they often indicate deletions or IS element insertions.

  4. Reproducibility discrepancies following reanalysis of raw data for a previously published study on diisononyl phthalate (DINP in rats

    Directory of Open Access Journals (Sweden)

    Min Chen

    2017-08-01

    Full Text Available A 2011 publication by Boberg et al. entitled “Reproductive and behavioral effects of diisononyl phthalate (DINP in perinatally exposed rats” [1] reported statistically significant changes in sperm parameters, testicular histopathology, anogenital distance and retained nipples in developing males. Using the statistical methods as reported by Boberg et al. (2011 [1], we reanalyzed the publically available raw data ([dataset] US EPA (United States Environmental Protection Agency, 2016 [2]. The output of our reanalysis and the discordances with the data as published in Boberg et al. (2011 [1] are highlighted herein. Further discussion of the basis for the replication discordances and the insufficiency of the Boberg et al. (2011 [1] response to address them can be found in a companion letter of correspondence (doi: 10.1016/j.reprotox.2017.03.013.; (Morfeld et al., 2011 [3].

  5. Evaluation of the performance of a p53 sequencing microarray chip using 140 previously sequenced bladder tumor samples

    DEFF Research Database (Denmark)

    Wikman, Friedrik; Lu, Ming-Lan; Andersen, Thomas Thykjær

    2000-01-01

    sensitivity, from 0.92 to 0.84, leading to a much better concordance (92%) with results obtained by traditional sequencing. The chip method detected as little as 1% mutated DNA. Conclusions: Microarray-based sequencing is a novel option to assess TP53 mutations, representing a fast and inexpensive method...

  6. Publisher Correction: Whole genome sequencing in psychiatric disorders: the WGSPD consortium.

    Science.gov (United States)

    Sanders, Stephan J; Neale, Benjamin M; Huang, Hailiang; Werling, Donna M; An, Joon-Yong; Dong, Shan; Abecasis, Goncalo; Arguello, P Alexander; Blangero, John; Boehnke, Michael; Daly, Mark J; Eggan, Kevin; Geschwind, Daniel H; Glahn, David C; Goldstein, David B; Gur, Raquel E; Handsaker, Robert E; McCarroll, Steven A; Ophoff, Roel A; Palotie, Aarno; Pato, Carlos N; Sabatti, Chiara; State, Matthew W; Willsey, A Jeremy; Hyman, Steven E; Addington, Anjene M; Lehner, Thomas; Freimer, Nelson B

    2018-03-16

    In the version of this article initially published, the consortium authorship and corresponding authors were not presented correctly. In the PDF and print versions, the Whole Genome Sequencing for Psychiatric Disorders (WGSPD) consortium was missing from the author list at the beginning of the paper, where it should have appeared as the seventh author; it was present in the author list at the end of the paper, but the footnote directing readers to the Supplementary Note for a list of members was missing. In the HTML version, the consortium was listed as the last author instead of as the seventh, and the line directing readers to the Supplementary Note for a list of members appeared at the end of the paper under Author Information but not in association with the consortium name itself. Also, this line stated that both member names and affiliations could be found in the Supplementary Note; in fact, only names are given. In all versions of the paper, the corresponding author symbols were attached to A. Jeremy Willsey, Steven E. Hyman, Anjene M. Addington and Thomas Lehner; they should have been attached, respectively, to Steven E. Hyman, Anjene M. Addington, Thomas Lehner and Nelson B. Freimer. As a result of this shift, the respective contact links in the HTML version did not lead to the indicated individuals. The errors have been corrected in the HTML and PDF versions of the article.

  7. Is email a reliable means of contacting authors of previously published papers? A study of the Emergency Medicine Journal for 2001.

    Science.gov (United States)

    O'Leary, F

    2003-07-01

    To determine whether it is possible to contact authors of previously published papers via email. A cross sectional study of the Emergency Medicine Journal for 2001. 118 articles were included in the study. The response rate from those with valid email addresses was 73%. There was no statistical difference between the type of email address used and the address being invalid (p=0.392) or between the type of article and the likelihood of a reply (p=0.197). More responses were obtained from work addresses when compared with Hotmail addresses (86% v 57%, p=0.02). Email is a valid means of contacting authors of previously published articles, particularly within the emergency medicine specialty. A work based email address may be a more valid means of contact than a Hotmail address.

  8. Phylogenetic relationships of seven previously unclassified viruses within the family Rhabdoviridae using partial nucleoprotein gene sequences.

    Science.gov (United States)

    Kuzmin, I V; Hughes, G J; Rupprecht, C E

    2006-08-01

    Partial nucleoprotein (N) gene sequences of the rhabdoviruses Obodhiang (OBOV), Kotonkon (KOTV), Rochambeau (RBUV), Kern canyon (KCV), Mount Elgon bat (MEBV), Kolongo (KOLV) and Sandjimba (SJAV) were generated and their phylogenetic positions within the family Rhabdoviridae were determined. Both OBOV and KOTV were placed within the genus Ephemerovirus. RBUV was joined to the same cluster, but more distantly. MEBV and KCV were grouped into a monophyletic cluster (putative genus) with Oita virus (OITAV). These three viruses, originating from different regions of the world, were all isolated from insectivorous bats and may be specific for these mammals. African avian viruses KOLV and SJAV were joined to each other and formed another clade at the genus level. Further, they were grouped with the recently characterized rhabdovirus Tupaia virus (TRV). Although the genetic distance was great, the grouping was supported by consistent bootstrap values. This observation suggests that viruses of this group may be distributed widely in the Old World. Non-synonymous/synonymous substitution ratio estimations (dN/dS) using a partial N gene fragment (241 codons) for the three rhabdovirus genera revealed contrasting patterns of evolution, where dN/dS values follow the pattern Ephemerovirus > Vesiculovirus > Lyssavirus. The magnitude of this ratio corresponds well with the number of negatively selected codons. The accumulation of dS appears evenly distributed along the gene fragment for all three genera. These estimations demonstrated clearly that lyssaviruses are subjected to the strongest constraints against amino acid substitutions, probably related to their particular niche and unique pathobiology.

  9. Hereditary spastic paraplegia in Greece: characterisation of a previously unexplored population using next-generation sequencing.

    Science.gov (United States)

    Lynch, David S; Koutsis, Georgios; Tucci, Arianna; Panas, Marios; Baklou, Markella; Breza, Marianthi; Karadima, Georgia; Houlden, Henry

    2016-06-01

    Hereditary Spastic Paraplegia (HSP) is a syndrome characterised by lower limb spasticity, occurring alone or in association with other neurological manifestations, such as cognitive impairment, seizures, ataxia or neuropathy. HSP occurs worldwide, with different populations having different frequencies of causative genes. The Greek population has not yet been characterised. The purpose of this study was to describe the clinical presentation and molecular epidemiology of the largest cohort of HSP in Greece, comprising 54 patients from 40 families. We used a targeted next-generation sequencing (NGS) approach to genetically assess a proband from each family. We made a genetic diagnosis in >50% of cases and identified 11 novel variants. Variants in SPAST and KIF5A were the most common causes of autosomal dominant HSP, whereas SPG11 and CYP7B1 were the most common cause of autosomal recessive HSP. We identified a novel variant in SPG11, which led to disease with later onset and may be unique to the Greek population and report the first nonsense mutation in KIF5A. Interestingly, the frequency of HSP mutations in the Greek population, which is relatively isolated, was very similar to other European populations. We confirm that NGS approaches are an efficient diagnostic tool and should be employed early in the assessment of HSP patients.

  10. Compilation of new and previously published geochemical and modal data for Mesoproterozoic igneous rocks of the St. Francois Mountains, southeast Missouri

    Science.gov (United States)

    du Bray, Edward A.; Day, Warren C.; Meighan, Corey J.

    2018-04-16

    The purpose of this report is to present recently acquired as well as previously published geochemical and modal petrographic data for igneous rocks in the St. Francois Mountains, southeast Missouri, as part of an ongoing effort to understand the regional geology and ore deposits of the Mesoproterozoic basement rocks of southeast Missouri, USA. The report includes geochemical data that is (1) newly acquired by the U.S. Geological Survey and (2) compiled from numerous sources published during the last fifty-five years. These data are required for ongoing petrogenetic investigations of these rocks. Voluminous Mesoproterozoic igneous rocks in the St. Francois Mountains of southeast Missouri constitute the basement buried beneath Paleozoic sedimentary rock that is over 600 meters thick in places. The Mesoproterozoic rocks of southeast Missouri represent a significant component of approximately 1.4 billion-year-old (Ga) igneous rocks that crop out extensively in North America along the southeast margin of Laurentia and subsequent researchers suggested that iron oxide-copper deposits in the St. Francois Mountains are genetically associated with ca. 1.4 Ga magmatism in this region. The geochemical and modal data sets described herein were compiled to support investigations concerning the tectonic setting and petrologic processes responsible for the associated magmatism.

  11. Technical Note: A novel leaf sequencing optimization algorithm which considers previous underdose and overdose events for MLC tracking radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Wisotzky, Eric, E-mail: eric.wisotzky@charite.de, E-mail: eric.wisotzky@ipk.fraunhofer.de; O’Brien, Ricky; Keall, Paul J., E-mail: paul.keall@sydney.edu.au [Radiation Physics Laboratory, Sydney Medical School, University of Sydney, Sydney, NSW 2006 (Australia)

    2016-01-15

    Purpose: Multileaf collimator (MLC) tracking radiotherapy is complex as the beam pattern needs to be modified due to the planned intensity modulation as well as the real-time target motion. The target motion cannot be planned; therefore, the modified beam pattern differs from the original plan and the MLC sequence needs to be recomputed online. Current MLC tracking algorithms use a greedy heuristic in that they optimize for a given time, but ignore past errors. To overcome this problem, the authors have developed and improved an algorithm that minimizes large underdose and overdose regions. Additionally, previous underdose and overdose events are taken into account to avoid regions with high quantity of dose events. Methods: The authors improved the existing MLC motion control algorithm by introducing a cumulative underdose/overdose map. This map represents the actual projection of the planned tumor shape and logs occurring dose events at each specific regions. These events have an impact on the dose cost calculation and reduce recurrence of dose events at each region. The authors studied the improvement of the new temporal optimization algorithm in terms of the L1-norm minimization of the sum of overdose and underdose compared to not accounting for previous dose events. For evaluation, the authors simulated the delivery of 5 conformal and 14 intensity-modulated radiotherapy (IMRT)-plans with 7 3D patient measured tumor motion traces. Results: Simulations with conformal shapes showed an improvement of L1-norm up to 8.5% after 100 MLC modification steps. Experiments showed comparable improvements with the same type of treatment plans. Conclusions: A novel leaf sequencing optimization algorithm which considers previous dose events for MLC tracking radiotherapy has been developed and investigated. Reductions in underdose/overdose are observed for conformal and IMRT delivery.

  12. A compendium of P- and S-wave velocities from surface-to-borehole logging; summary and reanalysis of previously published data and analysis of unpublished data

    Science.gov (United States)

    Boore, David M.

    2003-01-01

    For over 28 years, the U.S. Geological Survey (USGS) has been acquiring seismic velocity and geologic data at a number of locations in California, many of which were chosen because strong ground motions from earthquakes were recorded at the sites. The method for all measurements involves picking first arrivals of P- and S-waves from a surface source recorded at various depths in a borehole (as opposed to noninvasive methods, such as the SASW method [e.g., Brown et al., 2002]). The results from most of the sites are contained in a series of U.S. Geological Survey Open-File Reports (see References). Until now, none of the results have been available as computer files, and before 1992 the interpretation of the arrival times was in terms of piecemeal interval velocities, with no attempt to derive a layered model that would fit the travel times in an overall sense (the one exception is Porcella, 1984). In this report I reanalyze all of the arrival times in terms of layered models for P- and for S-wave velocities at each site, and I provide the results as computer files. In addition to the measurements reported in the open-file reports, I also include some borehole results from other reports, as well as some results never before published. I include data for 277 boreholes (at the time of this writing; more will be added to the web site as they are obtained), all in California (I have data from boreholes in Washington and Utah, but these will be published separately). I am also in the process of interpreting travel time data obtained using a seismic cone penetrometer at hundreds of sites; these data can be interpreted in the same way of those obtained from surface-to-borehole logging. When available, the data will be added to the web site (see below for information on obtaining data from the World Wide Web (WWW)). In addition to the basic borehole data and results, I provide information concerning strong-motion stations that I judge to be close enough to the boreholes

  13. Men without a sense of smell exhibit a strongly reduced number of sexual relationships, women exhibit reduced partnership security - a reanalysis of previously published data.

    Science.gov (United States)

    Croy, Ilona; Bojanowski, Viola; Hummel, Thomas

    2013-02-01

    Olfactory function influences social behavior. For instance, olfaction seems to play a key role in mate choice and helps detecting emotions in other people. In a previous study, we showed that people who were born without a sense of smell exhibit enhanced social insecurity. Based on the comments to this article we decided to have a closer look to whether the absence of the sense of smell affects men and women differently. Under this focus questionnaire data of 32 patients, diagnosed with isolated congenital anosmia (10 men, 22 women) and 36 age-matched healthy controls (15 men, 21 women) was reanalyzed. In result, men and women without a sense of smell reported enhanced social insecurity, but with different consequences: Men who were born without a sense of smell exhibit a strongly reduced number of sexual relationships and women are affected such that they feel less secure about their partner. This emphasizes the importance of the sense of smell for intimate relationships. Copyright © 2012 Elsevier B.V. All rights reserved.

  14. Draft Genome Sequence of Lactobacillus delbrueckii Strain #22 Isolated from a Patient with Short Bowel Syndrome and Previous d-Lactic Acidosis and Encephalopathy.

    Science.gov (United States)

    Domann, Eugen; Fischer, Florence; Glowatzki, Fabian; Fritzenwanker, Moritz; Hain, Torsten; Zechel-Gran, Silke; Giffhorn-Katz, Susanne; Neubauer, Bernd A

    2016-07-28

    d-Lactic acidosis with associated encephalopathy caused by overgrowth of intestinal lactic acid bacteria is a rarely diagnosed neurological complication of patients with short bowel syndrome. Here, we report the draft genome sequence of Lactobacillus delbrueckii strain #22 isolated from a patient with short bowel syndrome and previous d-lactic acidosis/encephalopathy. Copyright © 2016 Domann et al.

  15. De novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences.

    Directory of Open Access Journals (Sweden)

    Josephine A Reinhardt

    Full Text Available How non-coding DNA gives rise to new protein-coding genes (de novo genes is not well understood. Recent work has revealed the origins and functions of a few de novo genes, but common principles governing the evolution or biological roles of these genes are unknown. To better define these principles, we performed a parallel analysis of the evolution and function of six putatively protein-coding de novo genes described in Drosophila melanogaster. Reconstruction of the transcriptional history of de novo genes shows that two de novo genes emerged from novel long non-coding RNAs that arose at least 5 MY prior to evolution of an open reading frame. In contrast, four other de novo genes evolved a translated open reading frame and transcription within the same evolutionary interval suggesting that nascent open reading frames (proto-ORFs, while not required, can contribute to the emergence of a new de novo gene. However, none of the genes arose from proto-ORFs that existed long before expression evolved. Sequence and structural evolution of de novo genes was rapid compared to nearby genes and the structural complexity of de novo genes steadily increases over evolutionary time. Despite the fact that these genes are transcribed at a higher level in males than females, and are most strongly expressed in testes, RNAi experiments show that most of these genes are essential in both sexes during metamorphosis. This lethality suggests that protein coding de novo genes in Drosophila quickly become functionally important.

  16. Using the genome aggregation database, computational pathogenicity prediction tools, and patch clamp heterologous expression studies to demote previously published long QT syndrome type 1 mutations from pathogenic to benign.

    Science.gov (United States)

    Clemens, Daniel J; Lentino, Anne R; Kapplinger, Jamie D; Ye, Dan; Zhou, Wei; Tester, David J; Ackerman, Michael J

    2018-04-01

    Mutations in the KCNQ1-encoded Kv7.1 potassium channel cause long QT syndrome (LQTS) type 1 (LQT1). It has been suggested that ∼10%-20% of rare LQTS case-derived variants in the literature may have been published erroneously as LQT1-causative mutations and may be "false positives." The purpose of this study was to determine which previously published KCNQ1 case variants are likely false positives. A list of all published, case-derived KCNQ1 missense variants (MVs) was compiled. The occurrence of each MV within the Genome Aggregation Database (gnomAD) was assessed. Eight in silico tools were used to predict each variant's pathogenicity. Case-derived variants that were either (1) too frequently found in gnomAD or (2) absent in gnomAD but predicted to be pathogenic by ≤2 tools were considered potential false positives. Three of these variants were characterized functionally using whole-cell patch clamp technique. Overall, there were 244 KCNQ1 case-derived MVs. Of these, 29 (12%) were seen in ≥10 individuals in gnomAD and are demotable. However, 157 of 244 MVs (64%) were absent in gnomAD. Of these, 7 (4%) were predicted to be pathogenic by ≤2 tools, 3 of which we characterized functionally. There was no significant difference in current density between heterozygous KCNQ1-F127L, -P477L, or -L619M variant-containing channels compared to KCNQ1-WT. This study offers preliminary evidence for the demotion of 32 (13%) previously published LQT1 MVs. Of these, 29 were demoted because of their frequent sighting in gnomAD. Additionally, in silico analysis and in vitro functional studies have facilitated the demotion of 3 ultra-rare MVs (F127L, P477L, L619M). Copyright © 2017 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

  17. Published sequences do not support transfer of oseltamivir resistance mutations from avian to human influenza A virus strains.

    Science.gov (United States)

    Norberg, Peter; Lindh, Magnus; Olofsson, Sigvard

    2015-03-28

    Tamiflu (oseltamivir phosphate ester, OE) is a widely used antiviral active against influenza A virus. Its active metabolite, oseltamivir carboxylate (OC), is chemically stable and secreted into wastewater treatment plants. OC contamination of natural habitats of waterfowl might induce OC resistance in influenza viruses persistently infecting waterfowl, and lead to transfer of OC-resistance from avian to human influenza. The aim of this study was to evaluate whether such has occurred. A genomics approach including phylogenetic analysis and probability calculations for homologous recombination was applied on altogether 19,755 neuraminidase (N1 and N2) genes from virus sampled in humans and birds, with and without resistance mutations. No evidence for transfer of OE resistance mutations from avian to human N genes was obtained, and events suggesting recombination between human and avian influenza virus variants could not be traced in the sequence material studied. The results indicate that resistance in influenza viruses infecting humans is due to the selection pressure posed by the global OE administration in humans rather than transfer from avian influenza A virus strains carrying mutations induced by environmental exposure to OC.

  18. Desktop Publishing.

    Science.gov (United States)

    Stanley, Milt

    1986-01-01

    Defines desktop publishing, describes microcomputer developments and software tools that make it possible, and discusses its use as an instructional tool to improve writing skills. Reasons why students' work should be published, examples of what to publish, and types of software and hardware to facilitate publishing are reviewed. (MBR)

  19. Music publishing

    OpenAIRE

    Simões, Alberto; Almeida, J. J.

    2003-01-01

    Current music publishing in the Internet is mainly concerned with sound publishing. We claim that music publishing is not only to make sound available but also to define relations between a set of music objects like music scores, guitar chords, lyrics and their meta-data. We want an easy way to publish music in the Internet, to make high quality paper booklets and even to create Audio CD's. In this document we present a workbench for music publishing based on open formats, using open-source t...

  20. Comparison of nucleotide sequences of recent and previous lineages of peste-des-petits-ruminants viruses of sheep and goats in Nigeria

    Directory of Open Access Journals (Sweden)

    Samuel Mantip

    2016-08-01

    Full Text Available Peste-des-petits-ruminants virus (PPRV is a highly contagious, fatal and economically important viral disease of small ruminants that is still endemic and militates against the production of sheep and goats in endemic areas of the world. The aim of this study was to describe the viral strains within the country. This was carried out by collecting tissue and swab samples from sheep and goats in various agro-ecological zones of Nigeria. The phylogeny of archived PPRV strains or isolates and those circulating and causing recent outbreaks was determined by sequencing of the nucleoprotein (N-gene. Twenty tissue and swab samples from apparently healthy and sick sheep and goats were collected randomly from 18 states, namely 3 states in each of the 6 agro-ecological zones visited. A total of 360 samples were collected. A total of 35 samples of 360 (9.7% tested positive by reverse transcriptase–polymerase chain reaction, of which 25 were from oculo-nasal swabs and 10 were from tissue samples. Neighbour-joining phylogenetic analysis using Phylogenetic Analysis Using Parsimony (PAUP identified four different lineages, that is, lineages I, II, III and IV. Interestingly, the Nigerian strains described in this study grouped in two separate major lineages, that is, lineages II and IV. Strains from Sokoto, Oyo, Plateau and Ondo states grouped according to the historical distribution of PPRV together with the Nigerian 75/1 strain of lineage II, while other strains from Sokoto, Oyo, Plateau, Akwa-Ibom, Adamawa, Kaduna, Lagos, Bauchi, Niger and Kano states grouped together with the East African and Asian strains of lineage IV. This finding confirms that both lineage II and IV strains of PPRV are circulating in Nigeria. Previously, only strains of lineage II were found to be present in the country.

  1. Publisher Correction

    DEFF Research Database (Denmark)

    Turcot, Valérie; Lu, Yingchang; Highland, Heather M

    2018-01-01

    In the published version of this paper, the name of author Emanuele Di Angelantonio was misspelled. This error has now been corrected in the HTML and PDF versions of the article.......In the published version of this paper, the name of author Emanuele Di Angelantonio was misspelled. This error has now been corrected in the HTML and PDF versions of the article....

  2. Publisher Correction

    DEFF Research Database (Denmark)

    Bonàs-Guarch, Sílvia; Guindo-Martínez, Marta; Miguel-Escalada, Irene

    2018-01-01

    In the originally published version of this Article, the affiliation details for Santi González, Jian'an Luan and Claudia Langenberg were inadvertently omitted. Santi González should have been affiliated with 'Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB Research Program in Computatio......In the originally published version of this Article, the affiliation details for Santi González, Jian'an Luan and Claudia Langenberg were inadvertently omitted. Santi González should have been affiliated with 'Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB Research Program...

  3. Publisher Correction

    DEFF Research Database (Denmark)

    Stokholm, Jakob; Blaser, Martin J.; Thorsen, Jonathan

    2018-01-01

    The originally published version of this Article contained an incorrect version of Figure 3 that was introduced following peer review and inadvertently not corrected during the production process. Both versions contain the same set of abundance data, but the incorrect version has the children...

  4. Publisher Correction

    DEFF Research Database (Denmark)

    Turcot, Valérie; Lu, Yingchang; Highland, Heather M

    2018-01-01

    In the version of this article originally published, one of the two authors with the name Wei Zhao was omitted from the author list and the affiliations for both authors were assigned to the single Wei Zhao in the author list. In addition, the ORCID for Wei Zhao (Department of Biostatistics and E...

  5. Dear Publisher.

    Science.gov (United States)

    Chelton, Mary K.

    1992-01-01

    Addresses issues that concern the relationship between publishers and librarians, including differences between libraries and bookstores; necessary information for advertisements; out-of-stock designations and their effect on budgets; the role of distributors and vendors; direct mail for book promotions; unsolicited review copies; communications…

  6. Electronic Publishing.

    Science.gov (United States)

    Lancaster, F. W.

    1989-01-01

    Describes various stages involved in the applications of electronic media to the publishing industry. Highlights include computer typesetting, or photocomposition; machine-readable databases; the distribution of publications in electronic form; computer conferencing and electronic mail; collaborative authorship; hypertext; hypermedia publications;…

  7. Measurement errors in polymerase chain reaction are a confounding factor for a correct interpretation of 5-HTTLPR polymorphism effects on lifelong premature ejaculation: a critical analysis of a previously published meta-analysis of six studies.

    Science.gov (United States)

    Janssen, Paddy K C; Olivier, Berend; Zwinderman, Aeilko H; Waldinger, Marcel D

    2014-01-01

    To analyze a recently published meta-analysis of six studies on 5-HTTLPR polymorphism and lifelong premature ejaculation (PE). Calculation of fraction observed and expected genotype frequencies and Hardy Weinberg equilibrium (HWE) of cases and controls. LL,SL and SS genotype frequencies of patients were subtracted from genotype frequencies of an ideal population (LL25%, SL50%, SS25%, p = 1 for HWE). Analysis of PCRs of six studies and re-analysis of the analysis and Odds ratios (ORs) reported in the recently published meta-analysis. Three studies deviated from HWE in patients and one study deviated from HWE in controls. In three studies in-HWE the mean deviation of genotype frequencies from a theoretical population not-deviating from HWE was small: LL(1.7%), SL(-2.3%), SS(0.6%). In three studies not-in-HWE the mean deviation of genotype frequencies was high: LL(-3.3%), SL(-18.5%) and SS(21.8%) with very low percentage SL genotype concurrent with very high percentage SS genotype. The most serious PCR deviations were reported in the three not-in-HWE studies. The three in-HWE studies had normal OR. In contrast, the three not-in-HWE studies had a low OR. In three studies not-in-HWE and with very low OR, inadequate PCR analysis and/or inadequate interpretation of its gel electrophoresis resulted in very low SL and a resulting shift to very high SS genotype frequency outcome. Consequently, PCRs of these three studies are not reliable. Failure to note the inadequacy of PCR tests makes such PCRs a confounding factor in clinical interpretation of genetic studies. Currently, a meta-analysis can only be performed on three studies-in-HWE. However, based on the three studies-in-HWE with OR of about 1 there is not any indication that in men with lifelong PE the frequency of LL,SL and SS genotype deviates from the general male population and/or that the SL or SS genotype is in any way associated with lifelong PE.

  8. Measurement errors in polymerase chain reaction are a confounding factor for a correct interpretation of 5-HTTLPR polymorphism effects on lifelong premature ejaculation: a critical analysis of a previously published meta-analysis of six studies.

    Directory of Open Access Journals (Sweden)

    Paddy K C Janssen

    Full Text Available OBJECTIVE: To analyze a recently published meta-analysis of six studies on 5-HTTLPR polymorphism and lifelong premature ejaculation (PE. METHODS: Calculation of fraction observed and expected genotype frequencies and Hardy Weinberg equilibrium (HWE of cases and controls. LL,SL and SS genotype frequencies of patients were subtracted from genotype frequencies of an ideal population (LL25%, SL50%, SS25%, p = 1 for HWE. Analysis of PCRs of six studies and re-analysis of the analysis and Odds ratios (ORs reported in the recently published meta-analysis. RESULTS: Three studies deviated from HWE in patients and one study deviated from HWE in controls. In three studies in-HWE the mean deviation of genotype frequencies from a theoretical population not-deviating from HWE was small: LL(1.7%, SL(-2.3%, SS(0.6%. In three studies not-in-HWE the mean deviation of genotype frequencies was high: LL(-3.3%, SL(-18.5% and SS(21.8% with very low percentage SL genotype concurrent with very high percentage SS genotype. The most serious PCR deviations were reported in the three not-in-HWE studies. The three in-HWE studies had normal OR. In contrast, the three not-in-HWE studies had a low OR. CONCLUSIONS: In three studies not-in-HWE and with very low OR, inadequate PCR analysis and/or inadequate interpretation of its gel electrophoresis resulted in very low SL and a resulting shift to very high SS genotype frequency outcome. Consequently, PCRs of these three studies are not reliable. Failure to note the inadequacy of PCR tests makes such PCRs a confounding factor in clinical interpretation of genetic studies. Currently, a meta-analysis can only be performed on three studies-in-HWE. However, based on the three studies-in-HWE with OR of about 1 there is not any indication that in men with lifelong PE the frequency of LL,SL and SS genotype deviates from the general male population and/or that the SL or SS genotype is in any way associated with lifelong PE.

  9. Genome sequence analysis of five Canadian isolates of strawberry mottle virus reveals extensive intra-species diversity and a longer RNA2 with increased coding capacity compared to a previously characterized European isolate.

    Science.gov (United States)

    Bhagwat, Basdeo; Dickison, Virginia; Ding, Xinlun; Walker, Melanie; Bernardy, Michael; Bouthillier, Michel; Creelman, Alexa; DeYoung, Robyn; Li, Yinzi; Nie, Xianzhou; Wang, Aiming; Xiang, Yu; Sanfaçon, Hélène

    2016-06-01

    In this study, we report the genome sequence of five isolates of strawberry mottle virus (family Secoviridae, order Picornavirales) from strawberry field samples with decline symptoms collected in Eastern Canada. The Canadian isolates differed from the previously characterized European isolate 1134 in that they had a longer RNA2, resulting in a 239-amino-acid extension of the C-terminal region of the polyprotein. Sequence analysis suggests that reassortment and recombination occurred among the isolates. Phylogenetic analysis revealed that the Canadian isolates are diverse, grouping in two separate branches along with isolates from Europe and the Americas.

  10. Multilocus sequence typing of Pseudomonas syringae sensu lato confirms previously described genomospecies and permits rapid identification of P. syringae pv. coriandricola and P. syringae pv. apii causing bacterial leaf spot on parsley.

    Science.gov (United States)

    Bull, Carolee T; Clarke, Christopher R; Cai, Rongman; Vinatzer, Boris A; Jardini, Teresa M; Koike, Steven T

    2011-07-01

    Since 2002, severe leaf spotting on parsley (Petroselinum crispum) has occurred in Monterey County, CA. Either of two different pathovars of Pseudomonas syringae sensu lato were isolated from diseased leaves from eight distinct outbreaks and once from the same outbreak. Fragment analysis of DNA amplified between repetitive sequence polymerase chain reaction; 16S rDNA sequence analysis; and biochemical, physiological, and host range tests identified the pathogens as Pseudomonas syringae pv. apii and P. syringae pv. coriandricola. Koch's postulates were completed for the isolates from parsley, and host range tests with parsley isolates and pathotype strains demonstrated that P. syringae pv. apii and P. syringae pv. coriandricola cause leaf spot diseases on parsley, celery, and coriander or cilantro. In a multilocus sequence typing (MLST) approach, four housekeeping gene fragments were sequenced from 10 strains isolated from parsley and 56 pathotype strains of P. syringae. Allele sequences were uploaded to the Plant-Associated Microbes Database and a phylogenetic tree was built based on concatenated sequences. Tree topology directly corresponded to P. syringae genomospecies and P. syringae pv. apii was allocated appropriately to genomospecies 3. This is the first demonstration that MLST can accurately allocate new pathogens directly to P. syringae sensu lato genomospecies. According to MLST, P. syringae pv. coriandricola is a member of genomospecies 9, P. cannabina. In a blind test, both P. syringae pv. coriandricola and P. syringae pv. apii isolates from parsley were correctly identified to pathovar. In both cases, MLST described diversity within each pathovar that was previously unknown.

  11. Transition to electronic publishing

    Science.gov (United States)

    Bowning, Sam

    Previous communications have described some of the many changes that will occur in the next few months as AGU makes the transition to fully electronic publishing. With the advent of the new AGU electronic publishing system, manuscripts will be submitted, edited, reviewed, and published in electronic formats. This piece discusses how the electronic journals will differ from the print journals. Electronic publishing will require some adjustments to the ways we currently think about journals from our perspective of standard print versions. Visiting the Web site of AGU's Geochemistry, Geophysics, Geosystems (G-Cubed) is a great way to get familiar with the look and feel of electronic publishing. However, protocols, especially for citations of articles, are still evolving. Some of the biggest changes for users of AGU publications may be the lack of page numbers, the use of a unique identifier (DOI),and changes in citation style.

  12. Previously unknown species of Aspergillus.

    Science.gov (United States)

    Gautier, M; Normand, A-C; Ranque, S

    2016-08-01

    The use of multi-locus DNA sequence analysis has led to the description of previously unknown 'cryptic' Aspergillus species, whereas classical morphology-based identification of Aspergillus remains limited to the section or species-complex level. The current literature highlights two main features concerning these 'cryptic' Aspergillus species. First, the prevalence of such species in clinical samples is relatively high compared with emergent filamentous fungal taxa such as Mucorales, Scedosporium or Fusarium. Second, it is clearly important to identify these species in the clinical laboratory because of the high frequency of antifungal drug-resistant isolates of such Aspergillus species. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently been shown to enable the identification of filamentous fungi with an accuracy similar to that of DNA sequence-based methods. As MALDI-TOF MS is well suited to the routine clinical laboratory workflow, it facilitates the identification of these 'cryptic' Aspergillus species at the routine mycology bench. The rapid establishment of enhanced filamentous fungi identification facilities will lead to a better understanding of the epidemiology and clinical importance of these emerging Aspergillus species. Based on routine MALDI-TOF MS-based identification results, we provide original insights into the key interpretation issues of a positive Aspergillus culture from a clinical sample. Which ubiquitous species that are frequently isolated from air samples are rarely involved in human invasive disease? Can both the species and the type of biological sample indicate Aspergillus carriage, colonization or infection in a patient? Highly accurate routine filamentous fungi identification is central to enhance the understanding of these previously unknown Aspergillus species, with a vital impact on further improved patient care. Copyright © 2016 European Society of Clinical Microbiology and

  13. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  14. Publishing and Revising Content

    Science.gov (United States)

    Editors and Webmasters can publish content without going through a workflow. Publishing times and dates can be set, and multiple pages can be published in bulk. Making an edit to published content created a revision.

  15. Publishing with XML structure, enter, publish

    CERN Document Server

    Prost, Bernard

    2015-01-01

    XML is now at the heart of book publishing techniques: it provides the industry with a robust, flexible format which is relatively easy to manipulate. Above all, it preserves the future: the XML text becomes a genuine tactical asset enabling publishers to respond quickly to market demands. When new publishing media appear, it will be possible to very quickly make your editorial content available at a lower cost. On the downside, XML can become a bottomless pit for publishers attracted by its possibilities. There is a strong temptation to switch to audiovisual production and to add video and a

  16. An Electronic Publishing Model for Academic Publishers.

    Science.gov (United States)

    Gold, Jon D.

    1994-01-01

    Describes an electronic publishing model based on Standard Generalized Markup Language (SGML) and considers its use by an academic publisher. Highlights include how SGML is used to produce an electronic book, hypertext, methods of delivery, intellectual property rights, and future possibilities. Sample documents are included. (two references) (LRW)

  17. Human pro. cap alpha. 1(III) collagen: cDNA sequence for the 3' end

    Energy Technology Data Exchange (ETDEWEB)

    Mankoo, B S; Dalgleish, R

    1988-03-25

    The authors have previously isolated two overlapping cDNA clones, pIII-21 and pIII-33, which encode the C-terminal end of human type III procollagen. They now present the sequence of 2520 bases encoded in these cDNAs which overlaps other previously published sequences for the same gene. The sequence presented differs from previously published sequences at five positions.

  18. Getting Your Textbook Published.

    Science.gov (United States)

    Irwin, Armond J.

    1982-01-01

    Points to remember in getting a textbook published are examined: book idea, publisher's sales representatives, letter of inquiry, qualifications for authorship, author information form, idea proposal, reviews, marketing and sales, publishing agreement, author royalties, and copyright assignment. (CT)

  19. Plagiarism in scientific publishing.

    Science.gov (United States)

    Masic, Izet

    2012-12-01

    Scientific publishing is the ultimate product of scientist work. Number of publications and their quoting are measures of scientist success while unpublished researches are invisible to the scientific community, and as such nonexistent. Researchers in their work rely on their predecessors, while the extent of use of one scientist work, as a source for the work of other authors is the verification of its contributions to the growth of human knowledge. If the author has published an article in a scientific journal it cannot publish the article in any other journal h with a few minor adjustments or without quoting parts of the first article, which are used in another article. Copyright infringement occurs when the author of a new article with or without the mentioning the author used substantial portions of previously published articles, including tables and figures. Scientific institutions and universities should,in accordance with the principles of Good Scientific Practice (GSP) and Good Laboratory Practices (GLP) have a center for monitoring,security, promotion and development of quality research. Establish rules and compliance to rules of good scientific practice are the obligations of each research institutions,universities and every individual-researchers,regardless of which area of science is investigated. In this way, internal quality control ensures that a research institution such as a university, assume responsibility for creating an environment that promotes standards of excellence, intellectual honesty and legality. Although the truth should be the aim of scientific research, it is not guiding fact for all scientists. The best way to reach the truth in its study and to avoid the methodological and ethical mistakes is to consistently apply scientific methods and ethical standards in research. Although variously defined plagiarism is basically intended to deceive the reader's own scientific contribution. There is no general regulation of control of

  20. PLAGIARISM IN SCIENTIFIC PUBLISHING

    Science.gov (United States)

    Masic, Izet

    2012-01-01

    Scientific publishing is the ultimate product of scientist work. Number of publications and their quoting are measures of scientist success while unpublished researches are invisible to the scientific community, and as such nonexistent. Researchers in their work rely on their predecessors, while the extent of use of one scientist work, as a source for the work of other authors is the verification of its contributions to the growth of human knowledge. If the author has published an article in a scientific journal it cannot publish the article in any other journal h with a few minor adjustments or without quoting parts of the first article, which are used in another article. Copyright infringement occurs when the author of a new article with or without the mentioning the author used substantial portions of previously published articles, including tables and figures. Scientific institutions and universities should,in accordance with the principles of Good Scientific Practice (GSP) and Good Laboratory Practices (GLP) have a center for monitoring,security, promotion and development of quality research. Establish rules and compliance to rules of good scientific practice are the obligations of each research institutions,universities and every individual-researchers,regardless of which area of science is investigated. In this way, internal quality control ensures that a research institution such as a university, assume responsibility for creating an environment that promotes standards of excellence, intellectual honesty and legality. Although the truth should be the aim of scientific research, it is not guiding fact for all scientists. The best way to reach the truth in its study and to avoid the methodological and ethical mistakes is to consistently apply scientific methods and ethical standards in research. Although variously defined plagiarism is basically intended to deceive the reader’s own scientific contribution. There is no general regulation of control of

  1. Embracing Electronic Publishing.

    Science.gov (United States)

    Wills, Gordon

    1996-01-01

    Electronic publishing is the grandest revolution in the capture and dissemination of academic and professional knowledge since Caxton developed the printing press. This article examines electronic publishing, describes different electronic publishing scenarios (authors' cooperative, consolidator/retailer/agent oligopsony, publisher oligopoly), and…

  2. PUBLISHER'S ANNOUNCEMENT: Refereeing standards

    Science.gov (United States)

    Bender, C.; Scriven, N.

    2004-08-01

    On 1 January 2004 I will be assuming the position of Editor-in-Chief of Journal of Physics A: Mathematical and General (J. Phys. A). I am flattered at the confidence expressed in my ability to carry out this challenging job and I will try hard to justify this confidence. The previous Editor-in-Chief, Ed Corrigan, has worked tirelessly for the last five years and has done an excellent job for the journal. Everyone at the journal is profoundly grateful for his leadership and for his achievements. Before accepting the position of Editor-in-Chief, I visited the office of J. Phys. A to examine the organization and to assess its strengths and weaknesses. This office is located at the Institute of Physics Publishing (IOPP) headquarters in Bristol. J. Phys. A has been expanding rapidly and now publishes at the rate of nearly 1000 articles (or about 14,000 pages) per year. The entire operation of the journal is conducted in a very small space---about 15 square metres! Working in this space are six highly intelligent, talented, hard working, and dedicated people: Neil Scriven, Publisher; Mike Williams, Publishing Editor; Rose Gray and Sarah Nadin, Publishing Administrators; Laura Smith and Steve Richards, Production Editors. In this small space every day about eight submitted manuscripts are downloaded from the computer or received in the post. These papers are then processed and catalogued, referees are selected, and the papers are sent out for evaluation. In this small space the referees' reports are received, publication decisions are made, and accepted articles are then published quickly by IOPP. The whole operation is amazingly efficient. Indeed, one of the great strengths of J. Phys. A is the speed at which papers are processed. The average time between the receipt of a manuscript and an editorial decision is under sixty days. (Many distinguished journals take three to five times this amount of time.) This speed of publication is an extremely strong enticement for

  3. Copyright of Electronic Publishing.

    Science.gov (United States)

    Dong, Elaine; Wang, Bob

    2002-01-01

    Analyzes the importance of copyright, considers the main causes of copyright infringement in electronic publishing, discusses fair use of a copyrighted work, and suggests methods to safeguard copyrighted electronic publishing, including legislation, contracts, and technology. (Author/LRW)

  4. Publishing: The Creative Business.

    Science.gov (United States)

    Bohne, Harald; Van Ierssel, Harry

    This book offers guidelines to emerging and would-be publishers, whether they plan to enter publishing as a career, a sideline, or a diversion. It stresses the business aspects of publishing and emphasizes the major housekeeping functions encountered in the business, except methods of sales and distribution. Contents include "The Mechanics of…

  5. Academic Nightmares: Predatory Publishing

    Science.gov (United States)

    Van Nuland, Sonya E.; Rogers, Kem A.

    2017-01-01

    Academic researchers who seek to publish their work are confronted daily with a barrage of e-mails from aggressive marketing campaigns that solicit them to publish their research with a specialized, often newly launched, journal. Known as predatory journals, they often promise high editorial and publishing standards, yet their exploitive business…

  6. Desktop Publishing Made Simple.

    Science.gov (United States)

    Wentling, Rose Mary

    1989-01-01

    The author discusses the types of computer hardware and software necessary to set up a desktop publishing system, both for use in educational administration and for instructional purposes. Classroom applications of desktop publishing are presented. The author also provides guidelines for preparing to teach desktop publishing. (CH)

  7. Data Sharing & Publishing at Nature Publishing Group

    Science.gov (United States)

    VanDecar, J. C.; Hrynaszkiewicz, I.; Hufton, A. L.

    2015-12-01

    In recent years, the research community has come to recognize that upon-request data sharing has important limitations1,2. The Nature-titled journals feel that researchers have a duty to share data without undue qualifications, in a manner that allows others to replicate and build upon their published findings. Historically, the Nature journals have been strong supporters of data deposition in communities with existing data mandates, and have required data sharing upon request in all other cases. To help address some of the limitations of upon-request data sharing, the Nature titles have strengthened their existing data policies and forged a new partnership with Scientific Data, to promote wider data sharing in discoverable, citeable and reusable forms, and to ensure that scientists get appropriate credit for sharing3. Scientific Data is a new peer-reviewed journal for descriptions of research datasets, which works with a wide of range of public data repositories4. Articles at Scientific Data may either expand on research publications at other journals or may be used to publish new datasets. The Nature Publishing Group has also signed the Joint Declaration of Data Citation Principles5, and Scientific Data is our first journal to include formal data citations. We are currently in the process of adding data citation support to our various journals. 1 Wicherts, J. M., Borsboom, D., Kats, J. & Molenaar, D. The poor availability of psychological research data for reanalysis. Am. Psychol. 61, 726-728, doi:10.1037/0003-066x.61.7.726 (2006). 2 Vines, T. H. et al. Mandated data archiving greatly improves access to research data. FASEB J. 27, 1304-1308, doi:10.1096/fj.12-218164 (2013). 3 Data-access practices strengthened. Nature 515, 312, doi:10.1038/515312a (2014). 4 More bang for your byte. Sci. Data 1, 140010, doi:10.1038/sdata.2014.10 (2014). 5 Data Citation Synthesis Group: Joint Declaration of Data Citation Principles. (FORCE11, San Diego, CA, 2014).

  8. Publishing studies: what else?

    Directory of Open Access Journals (Sweden)

    Bertrand Legendre

    2015-07-01

    Full Text Available This paper intends to reposition “publishing studies” in the long process that goes from the beginning of book history to the current research on cultural industries. It raises questions about interdisciplinarity and the possibility of considering publishing independently of other sectors of the media and cultural offerings. Publishing is now included in a large range of industries and, at the same time, analyses tend to become more and more segmented according to production sectors and scientific fields. In addition to the problems created, from the professional point of view, by this double movement, this one requires a questioning of the concept of “publishing studies”.

  9. Laparoscopy After Previous Laparotomy

    Directory of Open Access Journals (Sweden)

    Zulfo Godinjak

    2006-11-01

    Full Text Available Following the abdominal surgery, extensive adhesions often occur and they can cause difficulties during laparoscopic operations. However, previous laparotomy is not considered to be a contraindication for laparoscopy. The aim of this study is to present that an insertion of Veres needle in the region of umbilicus is a safe method for creating a pneumoperitoneum for laparoscopic operations after previous laparotomy. In the last three years, we have performed 144 laparoscopic operations in patients that previously underwent one or two laparotomies. Pathology of digestive system, genital organs, Cesarean Section or abdominal war injuries were the most common causes of previouslaparotomy. During those operations or during entering into abdominal cavity we have not experienced any complications, while in 7 patients we performed conversion to laparotomy following the diagnostic laparoscopy. In all patients an insertion of Veres needle and trocar insertion in the umbilical region was performed, namely a technique of closed laparoscopy. Not even in one patient adhesions in the region of umbilicus were found, and no abdominal organs were injured.

  10. Publisher Correction to

    NARCIS (Netherlands)

    Barrio, Isabel C.; Lindén, Elin; Beest, Te Mariska; Olofsson, Johan; Rocha, Adrian; Soininen, Eeva M.; Alatalo, Juha M.; Andersson, Tommi; Asmus, Ashley; Boike, Julia; Bråthen, Kari Anne; Bryant, John P.; Buchwal, Agata; Bueno, C.G.; Christie, Katherine S.; Egelkraut, Dagmar; Ehrich, Dorothee; Fishback, Lee Ann; Forbes, Bruce C.; Gartzia, Maite; Grogan, Paul; Hallinger, Martin; Heijmans, Monique M.P.D.; Hik, David S.; Hofgaard, Annika; Holmgren, Milena; Høye, Toke T.; Huebner, Diane C.; Jónsdóttir, Ingibjörg Svala; Kaarlejärvi, Elina; Kumpula, Timo; Lange, Cynthia Y.M.J.G.; Lange, Jelena; Lévesque, Esther; Limpens, Juul; Macias-Fauria, Marc; Myers-Smith, Isla; Nieukerken, van Erik J.; Normand, Signe; Post, Eric S.; Schmidt, Niels Martin; Sitters, Judith; Skoracka, Anna; Sokolov, Alexander; Sokolova, Natalya; Speed, James D.M.; Street, Lorna E.; Sundqvist, Maja K.; Suominen, Otso; Tananaev, Nikita; Tremblay, Jean Pierre; Urbanowicz, Christine; Uvarov, Sergey A.; Watts, David; Wilmking, Martin; Wookey, Philip A.; Zimmermann, Heike H.; Zverev, Vitali; Kozlov, Mikhail V.

    2018-01-01

    The above mentioned article was originally scheduled for publication in the special issue on Ecology of Tundra Arthropods with guest editors Toke T. Høye . Lauren E. Culler. Erroneously, the article was published in Polar Biology, Volume 40, Issue 11, November, 2017. The publisher sincerely

  11. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0258-252X. AJOL African Journals Online.

  12. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1596-6798. AJOL African Journals Online.

  13. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1115-2613. AJOL African Journals Online.

  14. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0047-651X. AJOL African Journals Online.

  15. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0856-7212. AJOL African Journals Online.

  16. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0378-4738. AJOL African Journals Online.

  17. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0254-2765. AJOL African Journals Online.

  18. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0850-3907. AJOL African Journals Online.

  19. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 2141-8322. AJOL African Journals Online.

  20. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0794-7410. AJOL African Journals Online.

  1. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 2078-6778. AJOL African Journals Online.

  2. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 2305-8862. AJOL African Journals Online.

  3. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1596-9819. AJOL African Journals Online.

  4. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0379-4350. AJOL African Journals Online.

  5. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 2408-8137. AJOL African Journals Online.

  6. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1029-5933. AJOL African Journals Online.

  7. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 2467-8252. AJOL African Journals Online.

  8. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0376-4753. AJOL African Journals Online.

  9. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1118-1028. AJOL African Journals Online.

  10. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1597-4292. AJOL African Journals Online.

  11. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0189-9686. AJOL African Journals Online.

  12. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 2360-994X. AJOL African Journals Online.

  13. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1595-1413. AJOL African Journals Online.

  14. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 2078-5151. AJOL African Journals Online.

  15. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1694-0423. AJOL African Journals Online.

  16. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0855-4307. AJOL African Journals Online.

  17. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1596-9827. AJOL African Journals Online.

  18. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0379-9069. AJOL African Journals Online.

  19. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1998-1279. AJOL African Journals Online.

  20. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1606-7479. AJOL African Journals Online.

  1. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1995-7262. AJOL African Journals Online.

  2. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0856-8960. AJOL African Journals Online.

  3. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0855-5591. AJOL African Journals Online.

  4. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1531-4065. AJOL African Journals Online.

  5. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1110-5607. AJOL African Journals Online.

  6. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 2076-7714. AJOL African Journals Online.

  7. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1858-554X. AJOL African Journals Online.

  8. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1994-8220. AJOL African Journals Online.

  9. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1596-6232. AJOL African Journals Online.

  10. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 2224-0020. AJOL African Journals Online.

  11. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0556-8641. AJOL African Journals Online.

  12. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1596-5414. AJOL African Journals Online.

  13. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 2305-2678. AJOL African Journals Online.

  14. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1119-3077. AJOL African Journals Online.

  15. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 2078-676X. AJOL African Journals Online.

  16. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1027-4332. AJOL African Journals Online.

  17. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1814-232X. AJOL African Journals Online.

  18. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1998-9881. AJOL African Journals Online.

  19. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0303-691X. AJOL African Journals Online.

  20. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0376-8902. AJOL African Journals Online.

  1. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 2507-7961. AJOL African Journals Online.

  2. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0189-5117. AJOL African Journals Online.

  3. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1012-2796. AJOL African Journals Online.

  4. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 2313-1799. AJOL African Journals Online.

  5. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1025-9848. AJOL African Journals Online.

  6. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 2449-108X. AJOL African Journals Online.

  7. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 2141-9884. AJOL African Journals Online.

  8. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1727-3781. AJOL African Journals Online.

  9. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 2090-7214. AJOL African Journals Online.

  10. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 2410-8936. AJOL African Journals Online.

  11. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0856-0714. AJOL African Journals Online.

  12. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1684-5374. AJOL African Journals Online.

  13. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1998-8125. AJOL African Journals Online.

  14. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1016-0728. AJOL African Journals Online.

  15. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1821-9241. AJOL African Journals Online.

  16. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1607-0011. AJOL African Journals Online.

  17. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. AJOL African Journals Online. HOW TO USE ...

  18. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 2591 6831. AJOL African Journals Online.

  19. Desktop Publishing for Counselors.

    Science.gov (United States)

    Lucking, Robert; Mitchum, Nancy

    1990-01-01

    Discusses the fundamentals of desktop publishing for counselors, including hardware and software systems and peripherals. Notes by using desktop publishing, counselors can produce their own high-quality documents without the expense of commercial printers. Concludes computers present a way of streamlining the communications of a counseling…

  20. Publishing: Alternatives and Economics.

    Science.gov (United States)

    Penchansky, Mimi; And Others

    The Library Association of the City University of New York presents an annotated bibliography on the subject of small and alternative publishing. In the first section directories, indexes, catalogs, and reviews are briefly described. Book distributors for small publishers are listed next. The major portion of the bibliography is a listing of books…

  1. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1999-7671. AJOL African Journals Online.

  2. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1110-6859. AJOL African Journals Online.

  3. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0794-4721. AJOL African Journals Online.

  4. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 2520–7997. AJOL African Journals Online.

  5. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 2072-6589. AJOL African Journals Online.

  6. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 0012-835X. AJOL African Journals Online.

  7. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1680-6905. AJOL African Journals Online.

  8. About this Publishing System

    African Journals Online (AJOL)

    This journal uses Open Journal Systems 2.4.3.0, which is open source journal management and publishing software developed, supported, and freely distributed by the Public Knowledge Project under the GNU General Public License. OJS Editorial and Publishing Process. ISSN: 1821-8148. AJOL African Journals Online.

  9. The Academic Publishing Industry

    DEFF Research Database (Denmark)

    Nell, Phillip Christopher; Wenzel, Tim Ole; Schmidt, Florian

    2014-01-01

    The case starts with introducing the outstanding profitability of academic journal publishers such as Elsevier and then dives into describing the research process from an idea to conducting research and to publishing the results in academic journals. Subsequently, demand and supply for scientific...... journals and papers are discussed including drivers and involved parties. Furthermore, the case describes competition between suppliers, customers, and publishers. In sum, the case study features a rich description of the industry’s many unusual attributes which allows for discussing the benefits...

  10. Elearning and digital publishing

    CERN Document Server

    Ching, Hsianghoo Steve; Mc Naught, Carmel

    2006-01-01

    ""ELearning and Digital Publishing"" will occupy a unique niche in the literature accessed by library and publishing specialists, and by university teachers and planners. It examines the interfaces between the work done by four groups of university staff who have been in the past quite separate from, or only marginally related to, each other - library staff, university teachers, university policy makers, and staff who work in university publishing presses. All four groups are directly and intimately connected with the main functions of universities - the creation, management and dissemination

  11. Desktop Publishing in Libraries.

    Science.gov (United States)

    Cisler, Steve

    1987-01-01

    Describes the components, costs, and capabilities of several desktop publishing systems, and examines their possible impact on work patterns within organizations. The text and graphics of the article were created using various microcomputer software packages. (CLB)

  12. Sisyphus desperately seeking publisher

    Indian Academy of Sciences (India)

    Antoinette Molinié

    The editors wield their Olympian authority by making today's scientists endlessly push their weighty boulders up ... since publishing has become a highly lucrative business. ... estimate that the richest 8.4 % own 83.3 % (see Global Wealth.

  13. Issues in Electronic Publishing.

    Science.gov (United States)

    Meadow, Charles T.

    1997-01-01

    Discusses issues related to electronic publishing. Topics include writing; reading; production, distribution, and commerce; copyright and ownership of intellectual property; archival storage; technical obsolescence; control of content; equality of access; and cultural changes. (Author/LRW)

  14. The Library as Publisher.

    Science.gov (United States)

    Field, Roy

    1979-01-01

    Presents a guide to for-profit library publishing of reprints, original manuscripts, and smaller items. Discussed are creation of a publications panel to manage finances and preparation, determining prices of items, and drawing up author contracts. (SW)

  15. The Book Publishing Industry

    OpenAIRE

    Jean-Paul Simon; Giuditta de Prato

    2012-01-01

    This report offers an in-depth analysis of the major economic developments in the book publishing industry. The analysis integrates data from a statistical report published earlier as part of this project. The report is divided into 4 main parts. Chapter 1, the introduction, puts the sector into an historical perspective. Chapter 2 introduces the markets at a global and regional level; describes some of the major EU markets (France, Germany, Italy, Spain and the United Kingdom). Chapter 3 ana...

  16. Open-Access Publishing

    Directory of Open Access Journals (Sweden)

    Nedjeljko Frančula

    2013-06-01

    Full Text Available Nature, one of the most prominent scientific journals dedicated one of its issues to recent changes in scientific publishing (Vol. 495, Issue 7442, 27 March 2013. Its editors stressed that words technology and revolution are closely related when it comes to scientific publishing. In addition, the transformation of research publishing is not as much a revolution than an attrition war in which all sides are buried. The most important change they refer to is the open-access model in which an author or an institution pays in advance for publishing a paper in a journal, and the paper is then available to users on the Internet free of charge.According to preliminary results of a survey conducted among 23 000 scientists by the publisher of Nature, 45% of them believes all papers should be published in open access, but at the same time 22% of them would not allow the use of papers for commercial purposes. Attitudes toward open access vary according to scientific disciplines, leading the editors to conclude the revolution still does not suit everyone.

  17. Publishers and repositories

    CERN Multimedia

    CERN. Geneva

    2007-01-01

    The impact of self-archiving on journals and publishers is an important topic for all those involved in scholarly communication. There is some evidence that the physics arXiv has had no impact on physics journals, while 'economic common sense' suggests that some impact is inevitable. I shall review recent studies of librarian attitudes towards repositories and journals, and place this in the context of IOP Publishing's experiences with arXiv. I shall offer some possible reasons for the mis-match between these perspectives and then discuss how IOP has linked with arXiv and experimented with OA publishing. As well as launching OA journals we have co-operated with Cornell and the arXiv on Eprintweb.org, a platform that offers new features to repository users. View Andrew Wray's biography

  18. Ethics in Scientific Publishing

    Science.gov (United States)

    Sage, Leslie J.

    2012-08-01

    We all learn in elementary school not turn in other people's writing as if it were our own (plagiarism), and in high school science labs not to fake our data. But there are many other practices in scientific publishing that are depressingly common and almost as unethical. At about the 20 percent level authors are deliberately hiding recent work -- by themselves as well as by others -- so as to enhance the apparent novelty of their most recent paper. Some people lie about the dates the data were obtained, to cover up conflicts of interest, or inappropriate use of privileged information. Others will publish the same conference proceeding in multiple volumes, or publish the same result in multiple journals with only trivial additions of data or analysis (self-plagiarism). These shady practices should be roundly condemned and stopped. I will discuss these and other unethical actions I have seen over the years, and steps editors are taking to stop them.

  19. Publisher Correction: Predicting unpredictability

    Science.gov (United States)

    Davis, Steven J.

    2018-06-01

    In this News & Views article originally published, the wrong graph was used for panel b of Fig. 1, and the numbers on the y axes of panels a and c were incorrect; the original and corrected Fig. 1 is shown below. This has now been corrected in all versions of the News & Views.

  20. Web Publishing Schedule

    Science.gov (United States)

    Section 207(f)(2) of the E-Gov Act requires federal agencies to develop an inventory and establish a schedule of information to be published on their Web sites, make those schedules available for public comment. To post the schedules on the web site.

  1. Hprints - Licence to publish

    DEFF Research Database (Denmark)

    Rabow, Ingegerd; Sikström, Marjatta; Drachen, Thea Marie

    2010-01-01

    realised the potential advantages for them. The universities have a role here as well as the libraries that manage the archives and support scholars in various aspects of the publishing processes. Libraries are traditionally service providers with a mission to facilitate the knowledge production...

  2. The Academic Publishing Industry

    DEFF Research Database (Denmark)

    Nell, Phillip Christopher; Wenzel, Tim Ole; Schmidt, Florian

    2014-01-01

    . The case is intended to be used as a basis for class discussion rather than to illustrate effective handling of a managerial situation. It is based on published sources, interviews, and personal experience. The authors have disguised some names and other identifying information to protect confidentiality....

  3. Desktop Publishing in Education.

    Science.gov (United States)

    Hall, Wendy; Layman, J.

    1989-01-01

    Discusses the state of desktop publishing (DTP) in education today and describes the weaknesses of the systems available for use in the classroom. Highlights include document design and layout; text composition; graphics; word processing capabilities; a comparison of commercial and educational DTP packages; and skills required for DTP. (four…

  4. Support open access publishing

    DEFF Research Database (Denmark)

    Ekstrøm, Jeannette

    2013-01-01

    Projektet Support Open Access Publishing har til mål at få opdateret Sherpa/Romeo databasen (www.sherpa.ac.uk/romeo) med fagligt relevante, danske tidsskrifter. Projektet skal endvidere undersøge mulighederne for at få udviklet en database, hvor forskere på tværs af relevante tidsskriftsinformati......Projektet Support Open Access Publishing har til mål at få opdateret Sherpa/Romeo databasen (www.sherpa.ac.uk/romeo) med fagligt relevante, danske tidsskrifter. Projektet skal endvidere undersøge mulighederne for at få udviklet en database, hvor forskere på tværs af relevante...

  5. Prepare to publish.

    Science.gov (United States)

    Price, P M

    2000-01-01

    "I couldn't possibly write an article." "I don't have anything worthwhile to write about." "I am not qualified to write for publication." Do any of these statements sound familiar? This article is intended to dispel these beliefs. You can write an article. You care for the most complex patients in the health care system so you do have something worthwhile to write about. Beside correct spelling and grammar there are no special skills, certificates or diplomas required for publishing. You are qualified to write for publication. The purpose of this article is to take the mystique out of the publication process. Each step of publishing an article will be explained, from idea formation to framing your first article. Practical examples and recommendations will be presented. The essential components of the APA format necessary for Dynamics: The Official Journal of the Canadian Association of Critical Care Nurses will be outlined and resources to assist you will be provided.

  6. Reclaiming Society Publishing

    Directory of Open Access Journals (Sweden)

    Philip E. Steinberg

    2015-07-01

    Full Text Available Learned societies have become aligned with commercial publishers, who have increasingly taken over the latter’s function as independent providers of scholarly information. Using the example of geographical societies, the advantages and disadvantages of this trend are examined. It is argued that in an era of digital publication, learned societies can offer leadership with a new model of open access that can guarantee high quality scholarly material whose publication costs are supported by society membership dues.

  7. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  8. RETRACTION: Publishers' Note

    Science.gov (United States)

    post="(Executive Editor">Graeme Watt,

    2010-06-01

    Withdrawal of the paper "Was the fine-structure constant variable over cosmological time?" by L. D. Thong, N. M. Giao, N. T. Hung and T. V. Hung (EPL, 87 (2009) 69002) This paper has been formally withdrawn on ethical grounds because the article contains extensive and repeated instances of plagiarism. EPL treats all identified evidence of plagiarism in the published articles most seriously. Such unethical behaviour will not be tolerated under any circumstance. It is unfortunate that this misconduct was not detected before going to press. My thanks to Editor colleagues from other journals for bringing this fact to my attention.

  9. Investigation of previously derived Hyades, Coma, and M67 reddenings

    International Nuclear Information System (INIS)

    Taylor, B.J.

    1980-01-01

    New Hyades polarimetry and field star photometry have been obtained to check the Hyades reddening, which was found to be nonzero in a previous paper. The new Hyades polarimetry implies essentially zero reddening; this is also true of polarimetry published by Behr (which was incorrectly interpreted in the previous paper). Four photometric techniques which are presumed to be insensitive to blanketing are used to compare the Hyades to nearby field stars; these four techniques also yield essentially zero reddening. When all of these results are combined with others which the author has previously published and a simultaneous solution for the Hyades, Coma, and M67 reddenings is made, the results are E (B-V) =3 +- 2 (sigma) mmag, -1 +- 3 (sigma) mmag, and 46 +- 6 (sigma) mmag, respectively. No support for a nonzero Hyades reddening is offered by the new results. When the newly obtained reddenings for the Hyades, Coma, and M67 are compared with results from techniques given by Crawford and by users of the David Dunlap Observatory photometric system, no differences between the new and other reddenings are found which are larger than about 2 sigma. The author had previously found that the M67 main-sequence stars have about the same blanketing as that of Coma and less blanketing than the Hyades; this conclusion is essentially unchanged by the revised reddenings

  10. PUBLISHER'S ANNOUNCEMENT: Editorial developments

    Science.gov (United States)

    2009-01-01

    We are delighted to announce that from January 2009, Professor Murray T Batchelor of the Australian National University, Canberra will be the new Editor-in-Chief of Journal of Physics A: Mathematical and Theoretical. Murray Batchelor has been Editor of the Mathematical Physics section of the journal since 2007. Prior to this, he served as a Board Member and an Advisory Panel member for the journal. His primary area of research is the statistical mechanics of exactly solved models. He holds a joint appointment in mathematics and physics and has held visiting positions at the Universities of Leiden, Amsterdam, Oxford and Tokyo. We very much look forward to working with Murray to continue to improve the journal's quality and interest to the readership. We would like to thank our outgoing Editor-in-Chief, Professor Carl M Bender. Carl has done a magnificent job as Editor-in-Chief and has worked tirelessly to improve the journal over the last five years. Carl has been instrumental in designing and implementing strategies that have enhanced the quality of papers published and service provided by Journal of Physics A: Mathematical and Theoretical. Notably, under his tenure, we have introduced the Fast Track Communications (FTC) section to the journal. This section provides a venue for outstanding short papers that report new and timely developments in mathematical and theoretical physics and offers accelerated publication and high visibility for our authors. During the last five years, we have raised the quality threshold for acceptance in the journal and now reject over 60% of submissions. As a result, papers published in Journal of Physics A: Mathematical and Theoretical are amongst the best in the field. We have also maintained and improved on our excellent receipt-to-first-decision times, which now average less than 50 days for papers. We have recently announced another innovation; the Journal of Physics A Best Paper Prize. These prizes will honour excellent papers

  11. Why publish with AGU?

    Science.gov (United States)

    Graedel, T. E.

    The most visible activity of the American Geophysical Union is its publication of scientific journals. There are eight of these: Journal of Geophysical Research—Space Physics (JGR I), Journal of Geophysical Research—Solid Earth (JGR II), Journal of Geophysical Research—Oceans and Atmospheres (JGR III), Radio Science (RS), Water Resources Research (WRR), Geophysical Research Letters (GRL), Reviews of Geophysics and Space Physics (RGSP), and the newest, Tectonics.AGU's journals have established solid reputations for scientific excellence over the years. Reputation is not sufficient to sustain a high quality journal, however, since other factors enter into an author's decision on where to publish his or her work. In this article the characteristics of AGU's journals are compared with those of its competitors, with the aim of furnishing guidance to prospective authors and a better understanding of the value of the products to purchasers.

  12. Development of simple sequence repeat (SSR) markers that are ...

    African Journals Online (AJOL)

    Simple sequence repeats (SSRs) markers were developed through data mining of 3,803 expressed sequence tags (ESTs) previously published. A total of 144 di- to penta-type SSRs were identified and they were screened for polymorphism between two turnip cultivars, 'Tsuda' and 'Yurugi Akamaru'. Out of 90 EST-SSRs for ...

  13. Standardized mortality in eating disorders--a quantitative summary of previously published and new evidence

    DEFF Research Database (Denmark)

    Nielsen, Søren; Møller-Madsen, S.; Isager, Torben

    2011-01-01

    strong evidence for an increase in SMR for anorexia nervosa (AN), whereas no firm conclusions could be drawn for bulimia nervosa (BN). Bias caused by loss to follow-up was quantified and found non-negligable in some samples (possible increase in SMR from 25% to 240%). We did not find a significant effect...

  14. Standardized mortality in eating disorders--a quantitative summary of previously published and new evidence

    DEFF Research Database (Denmark)

    Nielsen, Søren; Møller-Madsen, S.; Isager, Torben

    1998-01-01

    strong evidence for an increase in SMR for anorexia nervosa (AN), whereas no firm conclusions could be drawn for bulimia nervosa (BN). Bias caused by loss to follow-up was quantified and found non-negligable in some samples (possible increase in SMR from 25% to 240%). We did not find a significant effect...

  15. Leiomyosarcoma of the Prostate: Case Report and Review of 54 Previously Published Cases

    Directory of Open Access Journals (Sweden)

    Gerasimos P. Vandoros

    2008-01-01

    Full Text Available Prostate leiomyosarcoma is an extremely rare and highly aggressive neoplasm that accounts for less than 0.1% of primary prostate malignancies. We present a patient with primary leiomyosarcoma of the prostate and review 54 cases reported in the literature to discuss the clinical, diagnostic and therapeutic aspects of this uncommon tumor. Median survival was estimated at 17 months (95% C.I. 20.7–43.7 months and the 1-, 3-, and 5-year actuarial survival rates were 68%, 34%, and 26%, respectively. The only factors predictive of long-term survival were negative surgical margins and absence of metastatic disease at presentation. A multidisciplinary approach is necessary for appropriate management of this dire entity.

  16. Arbitrarily accurate twin composite π -pulse sequences

    Science.gov (United States)

    Torosov, Boyan T.; Vitanov, Nikolay V.

    2018-04-01

    We present three classes of symmetric broadband composite pulse sequences. The composite phases are given by analytic formulas (rational fractions of π ) valid for any number of constituent pulses. The transition probability is expressed by simple analytic formulas and the order of pulse area error compensation grows linearly with the number of pulses. Therefore, any desired compensation order can be produced by an appropriate composite sequence; in this sense, they are arbitrarily accurate. These composite pulses perform equally well as or better than previously published ones. Moreover, the current sequences are more flexible as they allow total pulse areas of arbitrary integer multiples of π .

  17. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Choosing the Right Desktop Publisher.

    Science.gov (United States)

    Eiser, Leslie

    1988-01-01

    Investigates the many different desktop publishing packages available today. Lists the steps to desktop publishing. Suggests which package to use with specific hardware available. Compares several packages for IBM, Mac, and Apple II based systems. (MVL)

  19. EPIC: Electronic Publishing is Cheaper.

    Science.gov (United States)

    Regier, Willis G.

    Advocates of inexpensive publishing confront a widespread complaint that there is already an overproduction of scholarship that electronic publishing will make worse. The costs of electronic publishing correlate to a clutch of choices: speeds of access, breadth and depth of content, visibility, flexibility, durability, dependability, definition of…

  20. International Marketing Developing Publishing Business

    Directory of Open Access Journals (Sweden)

    Eugenijus Chlivickas

    2015-05-01

    Full Text Available Lithuanian integration in the financial Eurozone and Lithuanian publishing business development in the European Union and outside it, becomes an important problem requiring a solution. Promoting the dissemination of printed books and literacy in Lithuania and beyond, to properly introduce the achievements of Lithuania in foreign countries, it is important to ensure Lithuanian letter, educational and scientific book publishing development. The article examines the characteristics of the international marketing publishing, the world and Lithuanian state publishing houses on the basis of foreign and Lithuanian scientists theoretical insights about the instruments of international marketing opportunities, developing proposals for publishing business integration of new economic conditions.

  1. What comes first? Publishing business or publishing studies?

    Directory of Open Access Journals (Sweden)

    Josipa Selthofer

    2015-07-01

    Full Text Available The aim of this paper is to analyze and compare publishing studies, their programmes at the undergraduate and graduate levels and scholars involved in the teaching of publishing courses at the top universities around the world and in Croatia. Since traditional publishing business is rapidly changing, new skills and new jobs are involved in it. The main research question is: Can modern publishing studies produce a modern publisher? Or, is it the other way around? The hypothesis of the paper is that scholars involved in the teaching of publishing courses at the top universities around the world have a background in publishing business. So, can they prepare their students for the future and can their students gain competencies they need to compete in a confusing world of digital authors and electronic books? The research methods used were content analysis and comparison. Research sample included 36 university publishing programmes at the undergraduate and graduate level worldwide (24 MA, 12 BA. The research sample was limited mainly to the English-speaking countries. In most non-English-speaking countries, it was difficult to analyse the programme curriculum in the native language because the programme and course description did not exit. In the data gathering phase, a customized web application was used for content analysis. The application has three main sections: a list of websites to evaluate, a visual representation of the uploaded website and a list of characteristics grouped by categories for quantifying data. About twenty years ago, publishing was not considered a separate scientific branch in Croatia. Publishing studies are therefore a new phenomenon to both scholars and publishers in Croatia. To create a new, ideal publishing course, can we simply copy global trends or is it better to create something of our own?

  2. THE QUALITY CRITERIA AND SELF-PUBLISHING IN SCIENTIFIC PUBLISHING

    Directory of Open Access Journals (Sweden)

    Almudena Mangas-Vega

    2015-11-01

    Full Text Available Self-publishing is a growing phenomenon in recent years. It is a process that goes beyond a simple change of leader in the publication, since it involves also a change of role of agents that were consolidated over time. A self-published work does not have to mean lack of quality, so it is important to define parameters and indicators that help its evaluation and identify who has the responsibility of those criteria. The article shows these aspects from the possibilities for cross-platform publishing and concludes with an analysis of the aspects that can be considered in assessing the quality of self-publishing.

  3. Thomas Jefferson, Page Design, and Desktop Publishing.

    Science.gov (United States)

    Hartley, James

    1991-01-01

    Discussion of page design for desktop publishing focuses on the importance of functional issues as opposed to aesthetic issues, and criticizes a previous article that stressed aesthetic issues. Topics discussed include balance, consistency in text structure, and how differences in layout affect the clarity of "The Declaration of…

  4. What Desktop Publishing Can Teach Professional Writing Students about Publishing.

    Science.gov (United States)

    Dobberstein, Michael

    1992-01-01

    Points out that desktop publishing is a metatechnology that allows professional writing students access to the production phase of publishing, giving students hands-on practice in preparing text for printing and in learning how that preparation affects the visual meaning of documents. (SR)

  5. E-publishing and multimodalities

    OpenAIRE

    Yngve Nordkvelle

    2008-01-01

    In the literature of e-publishing there has been a consistent call from the advent of e-publishing on, until now, to explore new ways of expressing ideas through the new media. It has been claimed that the Internet opens an alley of possibilities and opportunites for publishing that will change the ways of publishing once and for all. In the area of publication of e-journals, however, the call for changes has received very modest responds.The thing is, it appears, that the conventional paper ...

  6. Desktop Publishing in the University.

    Science.gov (United States)

    Burstyn, Joan N., Ed.

    Highlighting changes in the work of people within the university, this book presents nine essays that examine the effects of desktop publishing and electronic publishing on professors and students, librarians, and those who work at university presses and in publication departments. Essays in the book are: (1) "Introduction: The Promise of Desktop…

  7. The Decision to Publish Electronically.

    Science.gov (United States)

    Craig, Gary

    1983-01-01

    Argues that decision to publish a given intellectual product "electronically" is a business decision based on customer needs, available format alternatives, current business climate, and variety of already existing factors. Publishers are most influenced by customers' acceptance of new products and their own role as intermediaries in…

  8. Publishing in Open Access Journals

    International Development Research Centre (IDRC) Digital Library (Canada)

    mbrunet

    00054.x). • An ISSN (International Standard Serial Number e.g. 1234-5678) has ... Publisher uses direct and unsolicited marketing (i.e., spamming) or advertising is obtrusive (to publish articles or serve on editorial board). • No information is ...

  9. Comics, Copyright and Academic Publishing

    Directory of Open Access Journals (Sweden)

    Ronan Deazley

    2014-05-01

    Full Text Available This article considers the extent to which UK-based academics can rely upon the copyright regime to reproduce extracts and excerpts from published comics and graphic novels without having to ask the copyright owner of those works for permission. In doing so, it invites readers to engage with a broader debate about the nature, demands and process of academic publishing.

  10. Electronic Publishing: Baseline Data 1993.

    Science.gov (United States)

    Brock, Laurie

    1993-01-01

    Provides highlights of a report describing research conducted to analyze and compare publishers' and developers' current and planned involvement in electronic publishing. Topics include acceptance of new media, licensing issues, costs and other perceived obstacles, and CD-ROMs platforms. (EAM)

  11. The Evolution of Electronic Publishing.

    Science.gov (United States)

    Lancaster, F. W.

    1995-01-01

    Discusses the evolution of electronic publishing from the early 1960s when computers were used merely to produce conventional printed products to the present move toward networked scholarly publishing. Highlights include library development, periodicals on the Internet, online journals versus paper journals, problems, and the future of…

  12. The handbook of journal publishing

    CERN Document Server

    Morris, Sally; LaFrenier, Douglas; Reich, Margaret

    2013-01-01

    The Handbook of Journal Publishing is a comprehensive reference work written by experienced professionals, covering all aspects of journal publishing, both online and in print. Journals are crucial to scholarly communication, but changes in recent years in the way journals are produced, financed, and used make this an especially turbulent and challenging time for journal publishers - and for authors, readers, and librarians. The Handbook offers a thorough guide to the journal publishing process, from editing and production through marketing, sales, and fulfilment, with chapters on management, finances, metrics, copyright, and ethical issues. It provides a wealth of practical tools, including checklists, sample documents, worked examples, alternative scenarios, and extensive lists of resources, which readers can use in their day-to-day work. Between them, the authors have been involved in every aspect of journal publishing over several decades and bring to the text their experience working for a wide range of ...

  13. Developments in Publishing: The Potential of Digital Publishing

    OpenAIRE

    X. Tian

    2007-01-01

    This research aims to identify issues associated with the impact of digital technology on the publishing industry with a specific focus on aspects of the sustainability of existing business models in Australia. Based on the case studies, interviews and Australian-wide online surveys, the research presents a review of the traditional business models in book publishing for investigating their effectiveness in a digital environment. It speculates on how and what should be considered for construc...

  14. How libraries use publisher metadata

    Directory of Open Access Journals (Sweden)

    Steve Shadle

    2013-11-01

    Full Text Available With the proliferation of electronic publishing, libraries are increasingly relying on publisher-supplied metadata to meet user needs for discovery in library systems. However, many publisher/content provider staff creating metadata are unaware of the end-user environment and how libraries use their metadata. This article provides an overview of the three primary discovery systems that are used by academic libraries, with examples illustrating how publisher-supplied metadata directly feeds into these systems and is used to support end-user discovery and access. Commonly seen metadata problems are discussed, with recommendations suggested. Based on a series of presentations given in Autumn 2012 to the staff of a large publisher, this article uses the University of Washington Libraries systems and services as illustrative examples. Judging by the feedback received from these presentations, publishers (specifically staff not familiar with the big picture of metadata standards work would benefit from a better understanding of the systems and services libraries provide using the data that is created and managed by publishers.

  15. From protocol to published report

    DEFF Research Database (Denmark)

    Berendt, Louise; Callréus, Torbjörn; Petersen, Lene Grejs

    2016-01-01

    and published reports of academic clinical drug trials. METHODS: A comparison was made between study protocols and their corresponding published reports. We assessed the overall consistency, which was defined as the absence of discrepancy regarding study type (categorized as either exploratory or confirmatory...... in 1999, 2001, and 2003, 95 of which fulfilled the eligibility criteria and had at least one corresponding published report reporting data on trial subjects. Overall consistency was observed in 39% of the trials (95% CI: 29 to 49%). Randomized controlled trials (RCTs) constituted 72% (95% CI: 63 to 81......%) of the sample, and 87% (95% CI: 80 to 94%) of the trials were hospital based. CONCLUSIONS: Overall consistency between protocols and their corresponding published reports was low. Motivators for the inconsistencies are unknown but do not seem restricted to economic incentives....

  16. Desktop publishing com o scribus

    OpenAIRE

    Silva, Fabrício Riff; Uchôa, Kátia Cilene Amaral

    2015-01-01

    Este artigo apresenta um breve tutorial sobre Desktop Publishing, com ênfase no software livre Scribus, através da criação de um exemplo prático que explora algumas de suas principais funcionalidades.

  17. Publisher Correction: On our bookshelf

    Science.gov (United States)

    Karouzos, Marios

    2018-03-01

    In the version of this Books and Arts originally published, the book title Spectroscopy for Amateur Astronomy was incorrect; it should have read Spectroscopy for Amateur Astronomers. This has now been corrected.

  18. Published journal article with data

    Data.gov (United States)

    U.S. Environmental Protection Agency — published journal article. This dataset is associated with the following publication: Schumacher, B., J. Zimmerman, J. Elliot, and G. Swanson. The Effect of...

  19. Free Publishing Culture. Sustainable Models?

    Directory of Open Access Journals (Sweden)

    Silvia Nanclares Escudero

    2013-03-01

    Full Text Available As a result of the collective research on the possibilities for publishing production and distribution offered nowadays by the Free Culture scenario, we present here a mapping of symptoms in order to propose a transitory diagnostic of the question: Is it possible to generate an economically sustainable publishing model based on the uses and customs generated and provided by Free Culture? Data, intuitions, experiences and ideas attempt to back up our affirmative answer.

  20. THE TYPES OF PUBLISHING SLOGANS

    Directory of Open Access Journals (Sweden)

    Ryzhov Konstantin Germanovich

    2015-03-01

    Full Text Available The author of the article focuses his attention on publishing slogans which are posted on 100 present-day Russian publishing houses' official websites and have not yet been studied in the special literature. The author has developed his own classification of publishing slogans based on the results of analysis and considering the current scientific views on the classification of slogans. The examined items are classified into autonomous and text-dependent according to interrelationship with an advertising text; marketable, corporative and mixed according to a presentation subject; rational, emotional and complex depending on the method of influence upon a recipient; slogan-presentation, slogan-assurance, slogan-identifier, slogan-appraisal, slogan-appeal depending on the communicative strategy; slogans consisting of one sentence and of two or more sentences; Russian and foreign ones. The analysis of the slogans of all kinds presented in the actual material allowed the author to determine the dominant features of the Russian publishing slogan which is an autonomous sentence in relation to the advertising text. In spite of that, the slogan shows the publishing output, influences the recipient emotionally, actualizes the communicative strategy of publishing house presentation of its distinguishing features, gives assurance to the target audience and distinguishes the advertised subject among competitors.

  1. Draft genome sequence of the intestinal parasite Blastocystis subtype 4-isolate WR1

    NARCIS (Netherlands)

    Wawrzyniak, Ivan; Courtine, Damien; Osman, Marwan; Hubans-Pierlot, Christine; Cian, Amandine; Nourrisson, Céline; Chabe, Magali; Poirier, Philippe; Bart, Aldert; Polonais, Valérie; Delgado-Viscogliosi, Pilar; El Alaoui, Hicham; Belkorchia, Abdel; van Gool, Tom; Tan, Kevin S. W.; Ferreira, Stéphanie; Viscogliosi, Eric; Delbac, Frédéric

    2015-01-01

    (ST1-ST17) described to date. Only the whole genome of a human ST7 isolate was previously sequenced. Here we report the draft genome sequence of Blastocystis ST4-WR1 isolated from a laboratory rodent at Singapore. (C) 2015 The Authors. Published by Elsevier Inc

  2. pyPaSWAS : Python-based multi-core CPU and GPU sequence alignment

    NARCIS (Netherlands)

    Warris, Sven; Timal, N Roshan N; Kempenaar, Marcel; Poortinga, Arne M; van de Geest, Henri; Varbanescu, Ana L; Nap, Jan-Peter

    2018-01-01

    BACKGROUND: Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of

  3. The Aspergillus Mine - publishing bioinformatics

    DEFF Research Database (Denmark)

    Vesth, Tammi Camilla; Rasmussen, Jane Lind Nybo; Theobald, Sebastian

    Genome analysis is no longer a field reserved for specialists and experimental laboratories are doing groundbreaking research using genome sequencing and analysis. In this new era, it is essential that data, analysis and results are shared between scientists. But this can be a challenge, even mor...

  4. The Community Publishing Project: assisting writers to self-publish ...

    African Journals Online (AJOL)

    This article examines the need for a small project such as the Community Publishing Project in South Africa and explores its aims. The method of involving writers and community groups in the publication process is described and two completed projects are evaluated. Lessons learnt by the Centre for the Book in managing ...

  5. Web publishing today and tomorrow

    CERN Document Server

    Lie, Hakon W

    1999-01-01

    The three lectures will give participants the grand tour of the Web as we know it today, as well as peeks into the past and the future. Many three-letter acronyms will be expanded, and an overview will be provided to see how the various specifications work together. Web publishing is the common theme throughout the lectures and in the second lecture, special emphasis will be given to data formats for publishing, including HTML, XML, MathML and SMIL. In the last lectures, automatic document manipulation and presentation will be discussed, including CSS, DOM and XTL.

  6. A Course in Desktop Publishing.

    Science.gov (United States)

    Somerick, Nancy M.

    1992-01-01

    Describes "Promotional Publications," a required course for public relations majors, which teaches the basics of desktop publishing. Outlines how the course covers the preparation of publications used as communication tools in public relations, advertising, and organizations, with an emphasis upon design, layout, and technology. (MM)

  7. Improving Published Descriptions of Germplasm.

    Science.gov (United States)

    Published descriptions of new germplasm, such as in the Journal of Plant Registrations (JPR) and, prior to mid-2007, in Crop Science, are important vehicles for allowing researchers and other interested parties to learn about such germplasm and the methods used to generate them. Launched in 2007, JP...

  8. Publishing in Open Access Journals

    International Development Research Centre (IDRC) Digital Library (Canada)

    mbrunet

    While most open access journals are peer‐reviewed and high quality, there are a number of ... Publisher has a negative reputation (e.g., documented examples in Chronicle of Higher Education, ... A key part of Canada's aid program, IDRC supports research in developing countries to promote growth and development.

  9. FTP: Full-Text Publishing?

    Science.gov (United States)

    Jul, Erik

    1992-01-01

    Describes the use of file transfer protocol (FTP) on the INTERNET computer network and considers its use as an electronic publishing system. The differing electronic formats of text files are discussed; the preparation and access of documents are described; and problems are addressed, including a lack of consistency. (LRW)

  10. Library Networks and Electronic Publishing.

    Science.gov (United States)

    Olvey, Lee D.

    1995-01-01

    Provides a description of present and proposed plans and strategies of OCLC (Online Computer Library Center) and their relationship to electronic publishing. FirstSearch (end-user access to secondary information), GUIDON (electronic journals online) and FastDoc (document delivery) are emphasized. (JKP)

  11. cis sequence effects on gene expression

    Directory of Open Access Journals (Sweden)

    Jacobs Kevin

    2007-08-01

    Full Text Available Abstract Background Sequence and transcriptional variability within and between individuals are typically studied independently. The joint analysis of sequence and gene expression variation (genetical genomics provides insight into the role of linked sequence variation in the regulation of gene expression. We investigated the role of sequence variation in cis on gene expression (cis sequence effects in a group of genes commonly studied in cancer research in lymphoblastoid cell lines. We estimated the proportion of genes exhibiting cis sequence effects and the proportion of gene expression variation explained by cis sequence effects using three different analytical approaches, and compared our results to the literature. Results We generated gene expression profiling data at N = 697 candidate genes from N = 30 lymphoblastoid cell lines for this study and used available candidate gene resequencing data at N = 552 candidate genes to identify N = 30 candidate genes with sufficient variance in both datasets for the investigation of cis sequence effects. We used two additive models and the haplotype phylogeny scanning approach of Templeton (Tree Scanning to evaluate association between individual SNPs, all SNPs at a gene, and diplotypes, with log-transformed gene expression. SNPs and diplotypes at eight candidate genes exhibited statistically significant (p cis sequence effects in our study, respectively. Conclusion Based on analysis of our results and the extant literature, one in four genes exhibits significant cis sequence effects, and for these genes, about 30% of gene expression variation is accounted for by cis sequence variation. Despite diverse experimental approaches, the presence or absence of significant cis sequence effects is largely supported by previously published studies.

  12. Critical appraisal of published literature

    Science.gov (United States)

    Umesh, Goneppanavar; Karippacheril, John George; Magazine, Rahul

    2016-01-01

    With a large output of medical literature coming out every year, it is impossible for readers to read every article. Critical appraisal of scientific literature is an important skill to be mastered not only by academic medical professionals but also by those involved in clinical practice. Before incorporating changes into the management of their patients, a thorough evaluation of the current or published literature is an important step in clinical practice. It is necessary for assessing the published literature for its scientific validity and generalizability to the specific patient community and reader's work environment. Simple steps have been provided by Consolidated Standard for Reporting Trial statements, Scottish Intercollegiate Guidelines Network and several other resources which if implemented may help the reader to avoid reading flawed literature and prevent the incorporation of biased or untrustworthy information into our practice. PMID:27729695

  13. Critical appraisal of published literature

    Directory of Open Access Journals (Sweden)

    Goneppanavar Umesh

    2016-01-01

    Full Text Available With a large output of medical literature coming out every year, it is impossible for readers to read every article. Critical appraisal of scientific literature is an important skill to be mastered not only by academic medical professionals but also by those involved in clinical practice. Before incorporating changes into the management of their patients, a thorough evaluation of the current or published literature is an important step in clinical practice. It is necessary for assessing the published literature for its scientific validity and generalizability to the specific patient community and reader′s work environment. Simple steps have been provided by Consolidated Standard for Reporting Trial statements, Scottish Intercollegiate Guidelines Network and several other resources which if implemented may help the reader to avoid reading flawed literature and prevent the incorporation of biased or untrustworthy information into our practice.

  14. Bibliography of published papers, 1977

    International Nuclear Information System (INIS)

    1978-01-01

    Papers published by RERF (a cooperative Japan-U.S. research organization) personnel mainly in 1977 issues of journals are listed as bibliography giving the title, authors, etc. Mostly in both Japanese and English. The total of about 50 such cover areas as follows; Variety of diseases such as cancer and cardiovascular, dosimetry, genetics, pathology, radiation effects including such as diseases, and summary reports. (Mori, K.)

  15. Publisher Correction: Eternal blood vessels

    Science.gov (United States)

    Hindson, Jordan

    2018-05-01

    This article was originally published with an incorrect reference for the original article. The reference has been amended. Please see the correct reference below. Qiu, Y. et al. Microvasculature-on-a-chip for the long-term study of endothelial barrier dysfunction and microvascular obstruction in disease. Nat. Biomed. Eng. https://doi.org/10.1038/s41551-018-0224-z (2018)

  16. The Industrial Engineering publishing landscape

    OpenAIRE

    Claasen, Schalk

    2012-01-01

    Looking at the Industrial Engineering publishing landscape through the window of Google Search, an interesting panorama unfolds. The view that I took is actually just a peek and therefore my description of what I saw is not meant to be comprehensive. The African landscape is empty except for the South African Journal of Industrial Engineering (SAJIE). This is an extraordinary situation if compared to the South American continent where there are Industrial Engineering journals in at least ...

  17. Where is smoking research published?

    Science.gov (United States)

    Liguori, A.; Hughes, J. R.

    1996-01-01

    OBJECTIVE: To identify journals that have a focus on human nicotine/smoking research and to investigate the coverage of smoking in "high-impact" journals. DESIGN: The MEDLINE computer database was searched for English-language articles on human studies published in 1988-1992 using "nicotine", "smoking", "smoking cessation", "tobacco", or "tobacco use disorder" as focus descriptors. This search was supplemented with a similar search of the PSYCLIT computer database. Fifty-eight journals containing at least 20 nicotine/smoking articles over the five years were analysed for impact factor (IF; citations per article). RESULTS: Among the journals with the highest percentage of nicotine- or smoking-focused articles (that is, 9-39% of their articles were on nicotine/smoking), Addiction, American Journal of Public Health, Cancer Causes and Control, Health Psychology, and Preventive Medicine had the greatest IF (range = 1.3-2.6). Among the journals highest in impact factor (IF > 3), only American Journal of Epidemiology, American Review of Respiratory Disease, Journal of the National Cancer Institute, and Journal of the American Medical Association published more than 10 nicotine/smoking articles per year (3-5% of all articles). Of these, only Journal of the American Medical Association published a large number of nicotine/smoking articles (32 per year). CONCLUSIONS: Although smoking causes 20% of all mortality in developed countries, the topic is not adequately covered in high-impact journals. Most smoking research is published in low-impact journals. 




 PMID:8795857

  18. Books average previous decade of economic misery.

    Science.gov (United States)

    Bentley, R Alexander; Acerbi, Alberto; Ormerod, Paul; Lampos, Vasileios

    2014-01-01

    For the 20(th) century since the Depression, we find a strong correlation between a 'literary misery index' derived from English language books and a moving average of the previous decade of the annual U.S. economic misery index, which is the sum of inflation and unemployment rates. We find a peak in the goodness of fit at 11 years for the moving average. The fit between the two misery indices holds when using different techniques to measure the literary misery index, and this fit is significantly better than other possible correlations with different emotion indices. To check the robustness of the results, we also analysed books written in German language and obtained very similar correlations with the German economic misery index. The results suggest that millions of books published every year average the authors' shared economic experiences over the past decade.

  19. Books Average Previous Decade of Economic Misery

    Science.gov (United States)

    Bentley, R. Alexander; Acerbi, Alberto; Ormerod, Paul; Lampos, Vasileios

    2014-01-01

    For the 20th century since the Depression, we find a strong correlation between a ‘literary misery index’ derived from English language books and a moving average of the previous decade of the annual U.S. economic misery index, which is the sum of inflation and unemployment rates. We find a peak in the goodness of fit at 11 years for the moving average. The fit between the two misery indices holds when using different techniques to measure the literary misery index, and this fit is significantly better than other possible correlations with different emotion indices. To check the robustness of the results, we also analysed books written in German language and obtained very similar correlations with the German economic misery index. The results suggest that millions of books published every year average the authors' shared economic experiences over the past decade. PMID:24416159

  20. Open access to scientific publishing

    Directory of Open Access Journals (Sweden)

    Janne Beate Reitan

    2016-12-01

    Full Text Available Interest in open access (OA to scientific publications is steadily increasing, both in Norway and internationally. From the outset, FORMakademisk has been published as a digital journal, and it was one of the first to offer OA in Norway. We have since the beginning used Open Journal Systems (OJS as publishing software. OJS is part of the Public Knowledge Project (PKP, which was created by Canadian John Willinsky and colleagues at the Faculty of Education at the University of British Columbia in 1998. The first version of OJS came as an open source software in 2001. The programme is free for everyone to use and is part of a larger collective movement wherein knowledge is shared. When FORMakademisk started in 2008, we received much help from the journal Acta Didactic (n.d. at the University of Oslo, which had started the year before us. They had also translated the programme to Norwegian. From the start, we were able to publish in both Norwegian and English. Other journals have used FORMakademisk as a model and source of inspiration when starting or when converting from subscription-based print journals to electronic OA, including the Journal of Norwegian Media Researchers [Norsk medietidsskrift]. It is in this way that the movement around PKP works and continues to grow to provide free access to research. As the articles are OA, they are also easily accessible to non-scientists. We also emphasise that the language should be readily available, although it should maintain a high scientific quality. Often there may be two sides of the same coin. We on the editorial team are now looking forward to adopting the newly developed OJS 3 this spring, with many new features and an improved design for users, including authors, peer reviewers, editors and readers.

  1. Electronic publishing of SPE papers

    International Nuclear Information System (INIS)

    Perdue, J.M.

    1992-01-01

    This paper reports that the SPE is creating an electronic index to over 25,000 technical papers and will produce a CD-ROM as an initial product. This SPE CD-ROM Masterdisc will be available at the SPE Annual Meeting in Washington, D.C. on October 4-7, 1992. The SPE Board has appointed an Ad Hoc Committee on Electronic Publishing to coordinate and oversee this project and to recommend authoring standards for submitting SPE papers electronically in the future

  2. Common integration sites of published datasets identified using a graph-based framework

    Directory of Open Access Journals (Sweden)

    Alessandro Vasciaveo

    2016-01-01

    Full Text Available With next-generation sequencing, the genomic data available for the characterization of integration sites (IS has dramatically increased. At present, in a single experiment, several thousand viral integration genome targets can be investigated to define genomic hot spots. In a previous article, we renovated a formal CIS analysis based on a rigid fixed window demarcation into a more stretchy definition grounded on graphs. Here, we present a selection of supporting data related to the graph-based framework (GBF from our previous article, in which a collection of common integration sites (CIS was identified on six published datasets. In this work, we will focus on two datasets, ISRTCGD and ISHIV, which have been previously discussed. Moreover, we show in more detail the workflow design that originates the datasets.

  3. Open Access Publishing with Drupal

    Directory of Open Access Journals (Sweden)

    Nina McHale

    2011-10-01

    Full Text Available In January 2009, the Colorado Association of Libraries (CAL suspended publication of its print quarterly journal, Colorado Libraries, as a cost-saving measure in a time of fiscal uncertainty. Printing and mailing the journal to its 1300 members cost CAL more than $26,000 per year. Publication of the journal was placed on an indefinite hiatus until the editorial staff proposed an online, open access format a year later. The benefits to migrating to open access included: significantly lower costs; a green platform; instant availability of content; a greater level of access to users with disabilities; and a higher level of visibility of the journal and the association. The editorial staff chose Drupal, including the E-journal module, and while Drupal is notorious for its steep learning curve—which exacerbated delays to content that had been created before the publishing hiatus—the fourth electronic issue was published recently at coloradolibrariesjournal.org. This article will discuss both the benefits and challenges of transitioning to an open access model and the choice Drupal as a platform over other more established journal software options.

  4. E-publishing and multimodalities

    Directory of Open Access Journals (Sweden)

    Yngve Nordkvelle

    2008-12-01

    Full Text Available In the literature of e-publishing there has been a consistent call from the advent of e-publishing on, until now, to explore new ways of expressing ideas through the new media. It has been claimed that the Internet opens an alley of possibilities and opportunites for publishing that will change the ways of publishing once and for all. In the area of publication of e-journals, however, the call for changes has received very modest responds.The thing is, it appears, that the conventional paper journal has a solid grip on the accepted formats of publishing. In a published research paper Mayernik (2007 explaines some of the reasons for that. Although pioneers of e-publishing suggested various areas where academic publishing could be expanded on, the opportunities given are scarsely used. Mayernik outlines "Non-linearity", "Multimedia", "Multiple use", "Interactivity" and "Rapid Publication" as areas of expansion for the academic e-journal. (2007. The paper deserves a thorough reading in itself, and I will briefly quote from his conclusion: "It is likely that the traditional linear article will continue to be the prevalent format for scholarly journals, both print and electronic, for the foreseeable future, and while electronic features will garner more and more use as technology improves, they will continue to be used to supplement, and not supplant, the traditional article."This is a challenging situation. If we accept the present dominant style of presenting scientific literature, we would use our energy best in seeking a way of improving the efficiency of that communication style. The use of multimedia, non-linearity etc. would perfect the present state, but still keep the scientific article as the main template. It is very unlikely that scientific publication will substitute the scholarly article with unproven alternatives. What we face is a rather conservative style of remediation that blurs the impact of the new media, - or "transparency" if

  5. Publishing corruption discussion: predatory journalism.

    Science.gov (United States)

    Jones, James W; McCullough, Laurence B

    2014-02-01

    Dr Spock is a brilliant young vascular surgeon who is up for tenure next year. He has been warned by the chair of surgery that he needs to increase his list of publications to assure passage. He has recently had a paper reviewed by one of the top journals in his specialty, Journal X-special, with several suggestions for revision. He received an e-mail request for manuscript submission from a newly minted, open access, Journal of Vascular Disease Therapy, which promises a quick and likely favorable response for a fee. What should be done? A. Send the paper to another peer reviewed journal with the suggested revisions. B. Resubmit the paper to Journal X-special. C. Submit to the online journal as is to save time. D. Submit to the online journal and another regular journal. E. Look for another job. Copyright © 2014 Society for Vascular Surgery. Published by Mosby, Inc. All rights reserved.

  6. The IAEA as a publisher

    International Nuclear Information System (INIS)

    1965-01-01

    One of the largest publishing enterprises in Vienna has developed in then Agency, incidental to its function of disseminating scientific information. The Agency recently completed its sixth year of scientific publication of literature dealing with the peaceful uses of atomic energy. Quite early in the history of IAEA, this work grew to considerable dimensions. In 1959 the programme consisted of two volumes in the Proceedings series, one in the Safety series, and four Technical Directories, making a total in that year of 18 000 books, in addition to those prepared for free distribution. In the following year, as Agency meetings and other activities developed, the list was much longer consisting of six volumes in the Proceedings series, two in the Safety series, two in the Technical Directory series, eight in the Review series, two in the Bibliographical series, three panel reports, one volume in the legal series and the first issue of 'Nuclear Fusion'. The total number of volumes sold was 24 000, in addition to the large number for free distribution. Thereafter, there was some difficulty in keeping up with the expanding demands, and some arrears of contract printing began to accumulate. It was therefore decided to introduce internal printing of Agency publications. The adoption of the 'cold type' method in 1962 led to considerable savings and faster production. During 1963, printing and binding equipment was installed which rendered the Agency independent of contractual services. Current policy is to print and bind internally all IAEA publications except the journal, 'Nuclear Fusion', Average annual production now consists of about twenty volumes of the proceedings of scientific meetings, six technical directories (the Directory of Nuclear Reactors has been published in its fifth edition), several bibliographies and numerous technical reports

  7. Publishing perishing? Towards tomorrow's information architecture

    Directory of Open Access Journals (Sweden)

    Gerstein Mark B

    2007-01-01

    Full Text Available Abstract Scientific articles are tailored to present information in human-readable aliquots. Although the Internet has revolutionized the way our society thinks about information, the traditional text-based framework of the scientific article remains largely unchanged. This format imposes sharp constraints upon the type and quantity of biological information published today. Academic journals alone cannot capture the findings of modern genome-scale inquiry. Like many other disciplines, molecular biology is a science of facts: information inherently suited to database storage. In the past decade, a proliferation of public and private databases has emerged to house genome sequence, protein structure information, functional genomics data and more; these digital repositories are now a vital component of scientific communication. The next challenge is to integrate this vast and ever-growing body of information with academic journals and other media. To truly integrate scientific information we must modernize academic publishing to exploit the power of the Internet. This means more than online access to articles, hyperlinked references and web-based supplemental data; it means making articles fully computer-readable with intelligent markup and Structured Digital Abstracts. Here, we examine the changing roles of scholarly journals and databases. We present our vision of the optimal information architecture for the biosciences, and close with tangible steps to improve our handling of scientific information today while paving the way for an expansive central index in the future.

  8. ESTABLISHING A PUBLISHING OUTFIT IN NIGERIA EMENYONU ...

    African Journals Online (AJOL)

    CIU

    stakeholders in the publishing industry,the legal environment of publishing, ... retailers. Publishing is a peculiar form of business for which a special group of very .... The publisher should provide furniture and fittings for the staff and intended ...

  9. Sequence History Update Tool

    Science.gov (United States)

    Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

    2008-01-01

    The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

  10. A meditation on the use of hands. Previously published in Scandinavian Journal of Occupational Therapy 1995; 2: 153-166.

    Science.gov (United States)

    Kielhofner, G

    2014-01-01

    The theme of mind-body unity is fundamental to occupational therapy. Nonetheless, the field continues to embrace a dualism of mind and body. This dualism persists because the field views the body only as an object, ignoring how the body is lived. Drawing upon phenomenological discussions of bodily experience, this paper illustrates how the lived body is a locus of intelligence, intentionality, adaptiveness, and experience. It also considers the bodily ground of motivation and thought and discusses how the body constitutes and incorporates its world. Finally, the paper considers implications of the lived body for therapy.

  11. Outcome of unicompartmental knee arthroplasty in octogenarians with tricompartmental osteoarthritis: A longer followup of previously published report

    Directory of Open Access Journals (Sweden)

    Sanjiv KS Marya

    2013-01-01

    Full Text Available Background: Unicompartmental knee arthroplasty (UKA has specific indications, producing excellent results. It, however, has a limited lifespan and needs eventual conversion to total knee arthroplasty (TKA. It is, therefore, a temporizing procedure in select active young patients with advanced unicompartmental osteoarthritis (UCOA. Being a less morbid procedure it is suggested as an alternative in the very elderly patients with tricompartmental osteoarthritis (TCOA. We performed UKA in a series of 45 octogenarians with TCOA predominant medial compartment osteoarthritis (MCOA and analyzed the results. Materials and Methods: Forty five octogenarian patients with TCOA predominant MCOA underwent UKA (19 bilateral from January 2002 to January 2012. All had similar preoperative work-up, surgical approach, procedure, implants and postoperative protocol. Clinicoradiological assessment was done at 3-monthly intervals for the first year, then yearly till the last followup (average 72 months, range 8-128 months. Results were evaluated using the knee society scores (KSS, satisfaction index [using the visual analogue scale (VAS] and orthogonal radiographs (for loosening, subsidence, lysis or implant wear. Resurgery for any cause was considered failure. Results: Four patients (six knees died due to medical conditions, two patients (three knees were lost to followup, and these were excluded from the final analysis. Barring two failures, all the remaining patients were pain-free and performing well at the final followup. Indications for resurgery were: medial femoral condyle fracture needing fixation subsequent conversion to TKA at 2 years (n=1 and progression of arthritis and pain leading to revision TKA at 6 years (n=1. Conclusion: UKA has shown successful outcomes with regards to pain relief and function with 96.4% implant survival and 94.9% good or excellent outcomes. Due to lower demands, early rehabilitation, less morbidity, and relative short life expectancy, UKA can successfully manage TCOA in the octogenarians.

  12. Electrons, Electronic Publishing, and Electronic Display.

    Science.gov (United States)

    Brownrigg, Edwin B.; Lynch, Clifford A.

    1985-01-01

    Provides a perspective on electronic publishing by distinguishing between "Newtonian" publishing and "quantum-mechanical" publishing. Highlights include media and publishing, works delivered through electronic media, electronic publishing and the printed word, management of intellectual property, and recent copyright-law issues…

  13. Comparative genomic survey, exon-intron annotation and phylogenetic analysis of NAT-homologous sequences in archaea, protists, fungi, viruses, and invertebrates

    Science.gov (United States)

    We have previously published extensive genomic surveys [1-3], reporting NAT-homologous sequences in hundreds of sequenced bacterial, fungal and vertebrate genomes. We present here the results of our latest search of 2445 genomes, representing 1532 (70 archaeal, 1210 bacterial, 43 protist, 97 fungal,...

  14. Statistical assignment of DNA sequences using Bayesian phylogenetics

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Boomsma, Wouter Krogh; Huelsenbeck, John P.

    2008-01-01

    We provide a new automated statistical method for DNA barcoding based on a Bayesian phylogenetic analysis. The method is based on automated database sequence retrieval, alignment, and phylogenetic analysis using a custom-built program for Bayesian phylogenetic analysis. We show on real data...... that the method outperforms Blast searches as a measure of confidence and can help eliminate 80% of all false assignment based on best Blast hit. However, the most important advance of the method is that it provides statistically meaningful measures of confidence. We apply the method to a re......-analysis of previously published ancient DNA data and show that, with high statistical confidence, most of the published sequences are in fact of Neanderthal origin. However, there are several cases of chimeric sequences that are comprised of a combination of both Neanderthal and modern human DNA....

  15. Desktop Publishing Choices: Making an Appropriate Decision.

    Science.gov (United States)

    Crawford, Walt

    1991-01-01

    Discusses various choices available for desktop publishing systems. Four categories of software are described, including advanced word processing, graphics software, low-end desktop publishing, and mainstream desktop publishing; appropriate hardware is considered; and selection guidelines are offered, including current and future publishing needs,…

  16. MUCH Electronic Publishing Environment: Principles and Practices.

    Science.gov (United States)

    Min, Zheng; Rada, Roy

    1994-01-01

    Discusses the electronic publishing system called Many Using and Creating Hypermedia (MUCH). The MUCH system supports collaborative authoring; reuse; formatting and printing; management; hypermedia publishing and delivery; and interchange. This article examines electronic publishing environments; the MUCH environment; publishing activities; and…

  17. Self-Published Books: An Empirical "Snapshot"

    Science.gov (United States)

    Bradley, Jana; Fulton, Bruce; Helm, Marlene

    2012-01-01

    The number of books published by authors using fee-based publication services, such as Lulu and AuthorHouse, is overtaking the number of books published by mainstream publishers, according to Bowker's 2009 annual data. Little empirical research exists on self-published books. This article presents the results of an investigation of a random sample…

  18. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  19. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  20. The sequence specificity of UV-induced DNA damage in a systematically altered DNA sequence.

    Science.gov (United States)

    Khoe, Clairine V; Chung, Long H; Murray, Vincent

    2018-06-01

    The sequence specificity of UV-induced DNA damage was investigated in a specifically designed DNA plasmid using two procedures: end-labelling and linear amplification. Absorption of UV photons by DNA leads to dimerisation of pyrimidine bases and produces two major photoproducts, cyclobutane pyrimidine dimers (CPDs) and pyrimidine(6-4)pyrimidone photoproducts (6-4PPs). A previous study had determined that two hexanucleotide sequences, 5'-GCTC*AC and 5'-TATT*AA, were high intensity UV-induced DNA damage sites. The UV clone plasmid was constructed by systematically altering each nucleotide of these two hexanucleotide sequences. One of the main goals of this study was to determine the influence of single nucleotide alterations on the intensity of UV-induced DNA damage. The sequence 5'-GCTC*AC was designed to examine the sequence specificity of 6-4PPs and the highest intensity 6-4PP damage sites were found at 5'-GTTC*CC nucleotides. The sequence 5'-TATT*AA was devised to investigate the sequence specificity of CPDs and the highest intensity CPD damage sites were found at 5'-TTTT*CG nucleotides. It was proposed that the tetranucleotide DNA sequence, 5'-YTC*Y (where Y is T or C), was the consensus sequence for the highest intensity UV-induced 6-4PP adduct sites; while it was 5'-YTT*C for the highest intensity UV-induced CPD damage sites. These consensus tetranucleotides are composed entirely of consecutive pyrimidines and must have a DNA conformation that is highly productive for the absorption of UV photons. Crown Copyright © 2018. Published by Elsevier B.V. All rights reserved.

  1. Structure and navigation for electronic publishing

    Science.gov (United States)

    Tillinghast, John; Beretta, Giordano B.

    1998-01-01

    The sudden explosion of the World Wide Web as a new publication medium has given a dramatic boost to the electronic publishing industry, which previously was a limited market centered around CD-ROMs and on-line databases. While the phenomenon has parallels to the advent of the tabloid press in the middle of last century, the electronic nature of the medium brings with it the typical characteristic of 4th wave media, namely the acceleration in its propagation speed and the volume of information. Consequently, e-publications are even flatter than print media; Shakespeare's Romeo and Juliet share the same computer screen with a home-made plagiarized copy of Deep Throat. The most touted tool for locating useful information on the World Wide Web is the search engine. However, due to the medium's flatness, sought information is drowned in a sea of useless information. A better solution is to build tools that allow authors to structure information so that it can easily be navigated. We experimented with the use of ontologies as a tool to formulate structures for information about a specific topic, so that related concepts are placed in adjacent locations and can easily be navigated using simple and ergonomic user models. We describe our effort in building a World Wide Web based photo album that is shared among a small network of people.

  2. Types of Open Access Publishers in Scopus

    Directory of Open Access Journals (Sweden)

    David Solomon

    2013-05-01

    Full Text Available This study assessed characteristics of publishers who published 2010 open access (OA journals indexed in Scopus. Publishers were categorized into six types; professional, society, university, scholar/researcher, government, and other organizations. Type of publisher was broken down by number of journals/articles published in 2010, funding model, location, discipline and whether the journal was born or converted to OA. Universities and societies accounted for 50% of the journals and 43% of the articles published. Professional publisher accounted for a third of the journals and 42% of the articles. With the exception of professional and scholar/researcher publishers, most journals were originally subscription journals that made at least their digital version freely available. Arts, humanities and social science journals are largely published by societies and universities outside the major publishing countries. Professional OA publishing is most common in biomedicine, mathematics, the sciences and engineering. Approximately a quarter of the journals are hosted on national/international platforms, in Latin America, Eastern Europe and Asia largely published by universities and societies without the need for publishing fees. This type of collaboration between governments, universities and/or societies may be an effective means of expanding open access publications.

  3. What was hidden in the Publisher's Archive

    DEFF Research Database (Denmark)

    Mai, Anne-Marie

    2015-01-01

    On the Danish Author Elsa Gress and her correspondence on American Literature with the Publisher, K. E. Hermann, Arena.......On the Danish Author Elsa Gress and her correspondence on American Literature with the Publisher, K. E. Hermann, Arena....

  4. Desktop Publishing: Changing Technology, Changing Occupations.

    Science.gov (United States)

    Stanton, Michael

    1991-01-01

    Describes desktop publishing (DTP) and its place in corporations. Lists job titles of those working in desktop publishing and describes DTP as it is taught at secondary and postsecondary levels and by private trainers. (JOW)

  5. Making the Leap to Desktop Publishing.

    Science.gov (United States)

    Schleifer, Neal

    1986-01-01

    Describes one teacher's approach to desktop publishing. Explains how the Macintosh and LaserWriter were used in the publication of a school newspaper. Guidelines are offered to teachers for the establishment of a desktop publishing lab. (ML)

  6. Promises and Realities of Desktop Publishing.

    Science.gov (United States)

    Thompson, Patricia A.; Craig, Robert L.

    1991-01-01

    Examines the underlying assumptions of the rhetoric of desktop publishing promoters. Suggests four criteria to help educators provide insights into issues and challenges concerning desktop publishing technology that design students will face on the job. (MG)

  7. Electronic Journal Publishing: Observations from Inside.

    Science.gov (United States)

    Hunter, Karen

    1998-01-01

    Focuses on electronic scholarly-journal publishing. Discusses characteristics of current academic electronic publishing; effects of the World Wide Web; user needs and positions of academic libraries; costs; and decisions of research librarians that drive the industry. (AEF)

  8. Sequencing of the Hepatitis C Virus: A Systematic Review.

    Directory of Open Access Journals (Sweden)

    Brendan Jacka

    Full Text Available Since the identification of hepatitis C virus (HCV, viral sequencing has been important in understanding HCV classification, epidemiology, evolution, transmission clustering, treatment response and natural history. The length and diversity of the HCV genome has resulted in analysis of certain regions of the virus, however there has been little standardisation of protocols. This systematic review was undertaken to map the location and frequency of sequencing on the HCV genome in peer reviewed publications, with the aim to produce a database of sequencing primers and amplicons to inform future research. Medline and Scopus databases were searched for English language publications based on keyword/MeSH terms related to sequence analysis (9 terms or HCV (3 terms, plus "primer" as a general search term. Exclusion criteria included non-HCV research, review articles, duplicate records, and incomplete description of HCV sequencing methods. The PCR primer locations of accepted publications were noted, and purpose of sequencing was determined. A total of 450 studies were accepted from the 2099 identified, with 629 HCV sequencing amplicons identified and mapped on the HCV genome. The most commonly sequenced region was the HVR-1 region, often utilised for studies of natural history, clustering/transmission, evolution and treatment response. Studies related to genotyping/classification or epidemiology of HCV genotype generally targeted the 5'UTR, Core and NS5B regions, while treatment response/resistance was assessed mainly in the NS3-NS5B region with emphasis on the Interferon sensitivity determining region (ISDR region of NS5A. While the sequencing of HCV is generally constricted to certain regions of the HCV genome there is little consistency in the positioning of sequencing primers, with the exception of a few highly referenced manuscripts. This study demonstrates the heterogeneity of HCV sequencing, providing a comprehensive database of previously

  9. The Release 6 reference sequence of the Drosophila melanogaster genome.

    Science.gov (United States)

    Hoskins, Roger A; Carlson, Joseph W; Wan, Kenneth H; Park, Soo; Mendez, Ivonne; Galle, Samuel E; Booth, Benjamin W; Pfeiffer, Barret D; George, Reed A; Svirskas, Robert; Krzywinski, Martin; Schein, Jacqueline; Accardo, Maria Carmela; Damia, Elisabetta; Messina, Giovanni; Méndez-Lago, María; de Pablos, Beatriz; Demakova, Olga V; Andreyeva, Evgeniya N; Boldyreva, Lidiya V; Marra, Marco; Carvalho, A Bernardo; Dimitri, Patrizio; Villasante, Alfredo; Zhimulev, Igor F; Rubin, Gerald M; Karpen, Gary H; Celniker, Susan E

    2015-03-01

    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 and 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. Further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads. © 2015 Hoskins et al.; Published by Cold Spring Harbor Laboratory Press.

  10. Basics of Desktop Publishing. Second Edition.

    Science.gov (United States)

    Beeby, Ellen; Crummett, Jerrie

    This document contains teacher and student materials for a basic course in desktop publishing. Six units of instruction cover the following: (1) introduction to desktop publishing; (2) desktop publishing systems; (3) software; (4) type selection; (5) document design; and (6) layout. The teacher edition contains some or all of the following…

  11. The Changing Business of Scholarly Publishing.

    Science.gov (United States)

    Hunter, Karen

    1993-01-01

    Discussion of changes and trends in scholarly publishing highlights monographs; journals; user-centered publishing; electronic products and services, including adding value, marketing strategies, and new pricing systems; changing attitudes regarding copyright; trends in publishing industry reorganization; and impacts on research libraries. (LRW)

  12. Peer-review: An IOP Publishing Perspective

    Science.gov (United States)

    Smith, Timothy

    2015-03-01

    Online publishing is challenging, and potentially changing, the role of publishers in both managing the peer-review process and disseminating the work that they publish in meeting contrasting needs from diverse groups of research communities. Recognizing the value of peer-review as a fundamental service to authors and the research community, the underlying principles of managing the process for journals published by IOP Publishing remain unchanged and yet the potential and demand for alternative models exists. This talk will discuss the traditional approach to peer-review placed in the context of this changing demand.

  13. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  14. Preoperative screening: value of previous tests.

    Science.gov (United States)

    Macpherson, D S; Snow, R; Lofgren, R P

    1990-12-15

    To determine the frequency of tests done in the year before elective surgery that might substitute for preoperative screening tests and to determine the frequency of test results that change from a normal value to a value likely to alter perioperative management. Retrospective cohort analysis of computerized laboratory data (complete blood count, sodium, potassium, and creatinine levels, prothrombin time, and partial thromboplastin time). Urban tertiary care Veterans Affairs Hospital. Consecutive sample of 1109 patients who had elective surgery in 1988. At admission, 7549 preoperative tests were done, 47% of which duplicated tests performed in the previous year. Of 3096 previous results that were normal as defined by hospital reference range and done closest to the time of but before admission (median interval, 2 months), 13 (0.4%; 95% CI, 0.2% to 0.7%), repeat values were outside a range considered acceptable for surgery. Most of the abnormalities were predictable from the patient's history, and most were not noted in the medical record. Of 461 previous tests that were abnormal, 78 (17%; CI, 13% to 20%) repeat values at admission were outside a range considered acceptable for surgery (P less than 0.001, frequency of clinically important abnormalities of patients with normal previous results with those with abnormal previous results). Physicians evaluating patients preoperatively could safely substitute the previous test results analyzed in this study for preoperative screening tests if the previous tests are normal and no obvious indication for retesting is present.

  15. Structural Revision of Some Recently Published Iridoid Glucosides

    DEFF Research Database (Denmark)

    Jensen, Søren Rosendal; Calis, Ihsan; Gotfredsen, Charlotte Held

    2007-01-01

    ). Finally, two alleged iridoid galactosides from Buddleja crispa named buddlejosides A and B (12a and 12b) have been shown to be the corresponding glucosides; the former is identical to agnuside (13a) while the latter is 3,4-dihydroxybenzoylaucubin (13b), an iridoid glucoside not previously published...

  16. Augmenting Data with Published Results in Bayesian Linear Regression

    Science.gov (United States)

    de Leeuw, Christiaan; Klugkist, Irene

    2012-01-01

    In most research, linear regression analyses are performed without taking into account published results (i.e., reported summary statistics) of similar previous studies. Although the prior density in Bayesian linear regression could accommodate such prior knowledge, formal models for doing so are absent from the literature. The goal of this…

  17. Poet's Market, 1997: Where & How To Publish Your Poetry.

    Science.gov (United States)

    Martin, Christine, Ed.; Bentley, Chantelle, Ed.

    This directory provides 1700 listings and evaluations of poetry publishers--300 more than in the previous edition--along with complete submission and contact information. Listings include both domestic and international markets, from mass circulation and literary magazines to small presses and university quarterlies, and contain complete profiles…

  18. Automatic electromagnetic valve for previous vacuum

    International Nuclear Information System (INIS)

    Granados, C. E.; Martin, F.

    1959-01-01

    A valve which permits the maintenance of an installation vacuum when electric current fails is described. It also lets the air in the previous vacuum bomb to prevent the oil ascending in the vacuum tubes. (Author)

  19. Ethical issues in publishing in predatory journals.

    Science.gov (United States)

    Ferris, Lorraine E; Winker, Margaret A

    2017-06-15

    Predatory journals, or journals that charge an article processing charge (APC) to authors, yet do not have the hallmarks of legitimate scholarly journals such as peer review and editing, Editorial Boards, editorial offices, and other editorial standards, pose a number of new ethical issues in journal publishing. This paper discusses ethical issues around predatory journals and publishing in them. These issues include misrepresentation; lack of editorial and publishing standards and practices; academic deception; research and funding wasted; lack of archived content; and undermining confidence in research literature. It is important that the scholarly community, including authors, institutions, editors, and publishers, support the legitimate scholarly research enterprise, and avoid supporting predatory journals by not publishing in them, serving as their editors or on the Editorial Boards, or permitting faculty to knowingly publish in them without consequences.

  20. QlikView Server and Publisher

    CERN Document Server

    Redmond, Stephen

    2014-01-01

    This is a comprehensive guide with a step-by-step approach that enables you to host and manage servers using QlikView Server and QlikView Publisher.If you are a server administrator wanting to learn about how to deploy QlikView Server for server management,analysis and testing, and QlikView Publisher for publishing of business content then this is the perfect book for you. No prior experience with QlikView is expected.

  1. Strategic Brand Management Tools in Publishing

    OpenAIRE

    Pitsaki, Irini

    2011-01-01

    Further to the introduction of the brand concept evolution and theory, as well as the ways these operate in the publishing sector (see paper: Pitsaki, I. 2010), the present paper treats publishing strategies and the tools used to establish them. Publishers often base their brand strategy on classic marketing approaches, such as the marketing mix -product, price, promotion, placement and people. They also direct their products to specific market segments in regard to the type of content and te...

  2. Mergers, Acquisitions, and Access: STM Publishing Today

    Science.gov (United States)

    Robertson, Kathleen

    Electronic publishing is changing the fundamentals of the entire printing/delivery/archive system that has served as the distribution mechanism for scientific research over the last century and a half. The merger-mania of the last 20 years, preprint pools, and publishers' licensing and journals-bundling plans are among the phenomena impacting the scientific information field. Science-Technology-Medical (STM) publishing is experiencing a period of intense consolidation and reorganization. This paper gives an overview of the economic factors fueling these trends, the major STM publishers, and the government regulatory bodies that referee this industry in Europe, Canada, and the USA.

  3. An extended sequence specificity for UV-induced DNA damage.

    Science.gov (United States)

    Chung, Long H; Murray, Vincent

    2018-01-01

    The sequence specificity of UV-induced DNA damage was determined with a higher precision and accuracy than previously reported. UV light induces two major damage adducts: cyclobutane pyrimidine dimers (CPDs) and pyrimidine(6-4)pyrimidone photoproducts (6-4PPs). Employing capillary electrophoresis with laser-induced fluorescence and taking advantages of the distinct properties of the CPDs and 6-4PPs, we studied the sequence specificity of UV-induced DNA damage in a purified DNA sequence using two approaches: end-labelling and a polymerase stop/linear amplification assay. A mitochondrial DNA sequence that contained a random nucleotide composition was employed as the target DNA sequence. With previous methodology, the UV sequence specificity was determined at a dinucleotide or trinucleotide level; however, in this paper, we have extended the UV sequence specificity to a hexanucleotide level. With the end-labelling technique (for 6-4PPs), the consensus sequence was found to be 5'-GCTC*AC (where C* is the breakage site); while with the linear amplification procedure, it was 5'-TCTT*AC. With end-labelling, the dinucleotide frequency of occurrence was highest for 5'-TC*, 5'-TT* and 5'-CC*; whereas it was 5'-TT* for linear amplification. The influence of neighbouring nucleotides on the degree of UV-induced DNA damage was also examined. The core sequences consisted of pyrimidine nucleotides 5'-CTC* and 5'-CTT* while an A at position "1" and C at position "2" enhanced UV-induced DNA damage. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

  4. False gold: Safely navigating open access publishing to avoid predatory publishers and journals.

    Science.gov (United States)

    McCann, Terence V; Polacsek, Meg

    2018-04-01

    The aim of this study was to review and discuss predatory open access publishing in the context of nursing and midwifery and develop a set of guidelines that serve as a framework to help clinicians, educators and researchers avoid predatory publishers. Open access publishing is increasingly common across all academic disciplines. However, this publishing model is vulnerable to exploitation by predatory publishers, posing a threat to nursing and midwifery scholarship and practice. Guidelines are needed to help researchers recognize predatory journals and publishers and understand the negative consequences of publishing in them. Discussion paper. A literature search of BioMed Central, CINAHL, MEDLINE with Full Text and PubMed for terms related to predatory publishing, published in the period 2007-2017. Lack of awareness of the risks and pressure to publish in international journals, may result in nursing and midwifery researchers publishing their work in dubious open access journals. Caution should be taken prior to writing and submitting a paper, to avoid predatory publishers. The advantage of open access publishing is that it provides readers with access to peer-reviewed research as soon as it is published online. However, predatory publishers use deceptive methods to exploit open access publishing for their own profit. Clear guidelines are needed to help researchers navigate safely open access publishing. A deeper understanding of the risks of predatory publishing is needed. Clear guidelines should be followed by nursing and midwifery researchers seeking to publish their work in open access journals. © 2017 John Wiley & Sons Ltd.

  5. QTL analysis by sequencing of Water Use Efficiency (WUE) in potato

    DEFF Research Database (Denmark)

    Kaminski, Kacper Piotr; Sønderkær, Mads; Sørensen, Kirsten Kørup

    2013-01-01

    The traditional approach to potato breeding, the classical “mate and phenotype” approach is relatively costly and because phenotyping and growth capacity is limited, this are being slowly replaced by Marker Assisted Selection (MAS) breeding schemes. MAS is based on the presence of DNA polymorphic.......sparsipilum), phenotyped for water use efficiency. This population has also previously been phenotyped for the total glycoalkaloid (TGA) content....... and time consuming process. Here, a novel method for Quantitative Trait Locus (QTL) analysis has been developed, that allows for development of specific markers by use of genomic sequence reads and the recently published reference genome sequence for potato. Prior to sequencing the mapping population...

  6. Academic Publishing: Making the Implicit Explicit

    Directory of Open Access Journals (Sweden)

    Cecile Badenhorst

    2016-07-01

    Full Text Available For doctoral students, publishing in peer-reviewed journals is a task many face with anxiety and trepidation. The world of publishing, from choosing a journal, negotiating with editors and navigating reviewers’ responses is a bewildering place. Looking in from the outside, it seems that successful and productive academic writers have knowledge that is inaccessible to novice scholars. While there is a growing literature on writing for scholarly publication, many of these publications promote writing and publishing as a straightforward activity that anyone can achieve if they follow the rules. We argue that the specific and situated contexts in which academic writers negotiate publishing practices is more complicated and messy. In this paper, we attempt to make explicit our publishing processes to highlight the complex nature of publishing. We use autoethnographic narratives to provide discussion points and insights into the challenges of publishing peer reviewed articles. One narrative is by a doctoral student at the beginning of her publishing career, who expresses her desires, concerns and anxieties about writing for publication. The other narrative focuses on the publishing practices of a more experienced academic writer. Both are international scholars working in the Canadian context. The purpose of this paper is to explore academic publishing through the juxtaposition of these two narratives to make explicit some of the more implicit processes. Four themes emerge from these narratives. To publish successfully, academic writers need: (1 to be discourse analysts; (2 to have a critical competence; (3 to have writing fluency; and (4 to be emotionally intelligent.

  7. Publish or perish: authorship and peer review

    Science.gov (United States)

    Publish or perish is defined in Wikipedia as the pressure to publish work constantly to further or sustain one’s career in academia. This is an apt description given that refereed scientific publications are the currency of science and the primary means for broad dissemination of knowledge. Professi...

  8. Open Access Publishing: What Authors Want

    Science.gov (United States)

    Nariani, Rajiv; Fernandez, Leila

    2012-01-01

    Campus-based open access author funds are being considered by many academic libraries as a way to support authors publishing in open access journals. Article processing fees for open access have been introduced recently by publishers and have not yet been widely accepted by authors. Few studies have surveyed authors on their reasons for publishing…

  9. Publisher Correction: Invisible Trojan-horse attack

    DEFF Research Database (Denmark)

    Sajeed, Shihan; Minshull, Carter; Jain, Nitin

    2017-01-01

    A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper.......A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper....

  10. The cost of publishing in Danish astronomy

    DEFF Research Database (Denmark)

    Dorch, Bertil F.

    I investigate the cost of publishing in Danish astronomy on a fine scale, including all direct publication costs: The figures show how the annual number of publications with authors from Denmark in astronomy journals increased by a factor approximately four during 15 years (Elsevier’s Scopus...... database), and the increase of the corresponding potential (maximum) cost of publishing....

  11. Pages from the Desktop: Desktop Publishing Today.

    Science.gov (United States)

    Crawford, Walt

    1994-01-01

    Discusses changes that have made desktop publishing appealing and reasonably priced. Hardware, software, and printer options for getting started and moving on, typeface developments, and the key characteristics of desktop publishing are described. The author's notes on 33 articles from the personal computing literature from January-March 1994 are…

  12. Desktop Publishing for the Gifted/Talented.

    Science.gov (United States)

    Hamilton, Wayne

    1987-01-01

    Examines the nature of desktop publishing and how it can be used in the classroom for gifted/talented students. Characteristics and special needs of such students are identified, and it is argued that desktop publishing addresses those needs, particularly with regard to creativity. Twenty-six references are provided. (MES)

  13. Equity for open-access journal publishing.

    Directory of Open Access Journals (Sweden)

    Stuart M Shieber

    2009-08-01

    Full Text Available Open-access journals, which provide access to their scholarly articles freely and without limitations, are at a systematic disadvantage relative to traditional closed-access journal publishing and its subscription-based business model. A simple, cost-effective remedy to this inequity could put open-access publishing on a path to become a sustainable, efficient system.

  14. 20 CFR 902.3 - Published information.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 3 2010-04-01 2010-04-01 false Published information. 902.3 Section 902.3 Employees' Benefits JOINT BOARD FOR THE ENROLLMENT OF ACTUARIES RULES REGARDING AVAILABILITY OF INFORMATION § 902.3 Published information. (a) Federal Register. Pursuant to sections 552 and 553 of title 5 of the...

  15. Publishers' Sales Strategies: A Questionable Business.

    Science.gov (United States)

    Eaglen, Audrey B.

    1988-01-01

    Speed, fill rate, and discount are reasons why it is often preferable for libraries to order directly from publishers rather than through a distributor. Nevertheless, some publishers have decided not to accept orders from libraries and schools. This has had a deleterious effect on libraries and library collections. (MES)

  16. Scientific publishing: some food for thought

    Directory of Open Access Journals (Sweden)

    Vittorio Bo

    2007-03-01

    Full Text Available Scientific publishing, here to be considered in a broader sense, as publishing of both specialised scientific journals and science popularisation works addressed to a wider audience, has been sailing for some years on troubled waters. To gather some possible food for thought is the purpose of this brief article.

  17. Electronic Publishing in Science: Changes and Risks.

    Science.gov (United States)

    Kinne, Otto

    1999-01-01

    Discussion of the Internet and the guidance of the World Wide Web Consortium focuses on scientific communication and electronic publishing. Considers the speed of communicating and disseminating information; quality issues; cost; library subscriptions; publishers; and risks and concerns, including the role of editors and reviewers or referees.…

  18. Another Interface: Electronic Publishing and Technical Services.

    Science.gov (United States)

    Yamamoto, Rumi

    1986-01-01

    Discusses the problems of assimilating electronic publishing within the technical services area of academic libraries: whether to consider electronic journals as acquisitions; how to catalog them; whether to charge users for access to them; and how to preserve online publications for future research. Future trends in electronic publishing are…

  19. Electronic Publishing: Introduction to This Issue.

    Science.gov (United States)

    Siegel, Martin A.

    1994-01-01

    Provides an overview of this special issue that addresses the possibilities and implications of electronic publishing and information dissemination as key components of effective education. Highlights include the theory and framework of electronic publishing; differences between electronic text and print; development of new educational materials;…

  20. New journals for publishing medical case reports.

    Science.gov (United States)

    Akers, Katherine G

    2016-04-01

    Because they do not rank highly in the hierarchy of evidence and are not frequently cited, case reports describing the clinical circumstances of single patients are seldom published by medical journals. However, many clinicians argue that case reports have significant educational value, advance medical knowledge, and complement evidence-based medicine. Over the last several years, a vast number (∼160) of new peer-reviewed journals have emerged that focus on publishing case reports. These journals are typically open access and have relatively high acceptance rates. However, approximately half of the publishers of case reports journals engage in questionable or "predatory" publishing practices. Authors of case reports may benefit from greater awareness of these new publication venues as well as an ability to discriminate between reputable and non-reputable journal publishers.

  1. Open Access, data capitalism and academic publishing.

    Science.gov (United States)

    Hagner, Michael

    2018-02-16

    Open Access (OA) is widely considered a breakthrough in the history of academic publishing, rendering the knowledge produced by the worldwide scientific community accessible to all. In numerous countries, national governments, funding institutions and research organisations have undertaken enormous efforts to establish OA as the new publishing standard. The benefits and new perspectives, however, cause various challenges. This essay addresses several issues, including that OA is deeply embedded in the logic and practices of data capitalism. Given that OA has proven an attractive business model for commercial publishers, the key predictions of OA-advocates, namely that OA would liberate both scientists and tax payers from the chains of global publishing companies, have not become true. In its conclusion, the paper discusses the opportunities and pitfalls of non-commercial publishing.

  2. Exploring Digital News Publishing Business Models

    DEFF Research Database (Denmark)

    Lindskow, Kasper

    News publishers in the industrialized world are experiencing a fundamental challenge to their business models because of the changing modes of consumption, competition, and production of their offerings that are associated with the emergence of the networked information society. The erosion...... of the traditional business models poses an existential threat to news publishing and has given rise to a continuing struggle among news publishers to design digital business models that will be sustainable in the future. This dissertation argues that a central and underresearched aspect of digital news publishing...... business models concerns the production networks that support the co-production of digital news offerings. To fill this knowledge gap, this dissertation explores the strategic design of the digital news publishing production networks that are associated with HTML-based news offerings on the open Web...

  3. 77 FR 70176 - Previous Participation Certification

    Science.gov (United States)

    2012-11-23

    ... participants' previous participation in government programs and ensure that the past record is acceptable prior... information is designed to be 100 percent automated and digital submission of all data and certifications is... government programs and ensure that the past record is acceptable prior to granting approval to participate...

  4. On the Tengiz petroleum deposit previous study

    International Nuclear Information System (INIS)

    Nysangaliev, A.N.; Kuspangaliev, T.K.

    1997-01-01

    Tengiz petroleum deposit previous study is described. Some consideration about structure of productive formation, specific characteristic properties of petroleum-bearing collectors are presented. Recommendation on their detail study and using of experience on exploration and development of petroleum deposit which have analogy on most important geological and industrial parameters are given. (author)

  5. Subsequent pregnancy outcome after previous foetal death

    NARCIS (Netherlands)

    Nijkamp, J. W.; Korteweg, F. J.; Holm, J. P.; Timmer, A.; Erwich, J. J. H. M.; van Pampus, M. G.

    Objective: A history of foetal death is a risk factor for complications and foetal death in subsequent pregnancies as most previous risk factors remain present and an underlying cause of death may recur. The purpose of this study was to evaluate subsequent pregnancy outcome after foetal death and to

  6. High prevalence of genetic variants previously associated with Brugada syndrome in new exome data

    DEFF Research Database (Denmark)

    Risgaard, B; Jabbari, R; Refsgaard, L

    2013-01-01

    More than 300 variants in 12 genes have been associated with Brugada syndrome (BrS) which has a prevalence ranging between 1:2000 and 1:100,000. Until recently, there has been little knowledge regarding the distribution of genetic variations in the general population. This problem was partly solved......, when exome data from the NHLI GO Exome Sequencing Project (ESP) was published. In this study, we aimed to report the prevalence of previously BrS-associated variants in the ESP population. We performed a search in ESP for variants previously associated with BrS. In addition, four variants in ESP were...... to a surprisingly high genotype prevalence of 1:23 (274:6258). Genotyping the four common ESP-derived variants CACNA2D1 S709N, SCN5A F2004L, CACNB2 S143F, and CACNB2 T450I in the Danish controls, we found a genotype prevalence comparable with that found in ESP. We suggest that exome data are used in research...

  7. Amino-acid sequence of two trypsin isoinhibitors, ITD I and ITD III from squash seeds (Cucurbita maxima).

    Science.gov (United States)

    Wilusz, T; Wieczorek, M; Polanowski, A; Denton, A; Cook, J; Laskowski, M

    1983-01-01

    The amino-acid sequences of two trypsin isoinhibitors, ITD I and ITD III, from squash seeds (Cucurbita maxima) were determined. Both isoinhibitors contain 29 amino-acid residues, including 6 half cystine residues. They differ only by one amino acid. Lysine in position 9 of ITD III is substituted by glutamic acid in ITD I. Arginine in position 5 is present at the reactive site of both isoinhibitors. The previously published sequence of ITD III has been shown to be incorrect.

  8. Critical analysis of marketing in Croatian publishing

    Directory of Open Access Journals (Sweden)

    Silvija Gašparić

    2018-03-01

    Full Text Available Marketing is an inevitable part of today's modern lifestyle. The role that marketing plays is so big that it has become the most important part of business. Due to crisis that is still affecting publishers in Croatia, this paper emphasizes the power of advertising as a key ingredient in how to overcome this situation and upgrade the system of publishing in Croatia. The framework of the paper is based on marketing as a tool that leads to popularization of books and sales increase. Beside the experimental part which gives an insight into public's opinion about books, publishing and marketing, the first chapter gives the literature review and analysis conducted on the whole process of book publishing in Croatia with pointing out mistakes that Croatian publishers make. Also, benefits of foreign publishing will be mentioned and used for comparison and projection on to the problems of the native market. The aim of this analysis and this viewpoint paper is to contribute the comprehension of marketing strategies and activities and its use and gains in Croatian publishing.

  9. Navigating the heavy seas of online publishing

    DEFF Research Database (Denmark)

    Carpentier, Samuel; Dörry, Sabine; Lord, Sébastien

    2015-01-01

    Articulo – Journal of Urban Research celebrates its 10th anniversary! To celebrate this milestone, the current editors discuss the numerous changes and challenges related to publishing a peer-reviewed online journal. Since 2005, Articulo has progressively become more international, more professio......Articulo – Journal of Urban Research celebrates its 10th anniversary! To celebrate this milestone, the current editors discuss the numerous changes and challenges related to publishing a peer-reviewed online journal. Since 2005, Articulo has progressively become more international, more...... rough seas of online publishing in the future....

  10. Preparing and Publishing a Scientific Manuscript

    Directory of Open Access Journals (Sweden)

    Padma R Jirge

    2017-01-01

    Full Text Available Publishing original research in a peer-reviewed and indexed journal is an important milestone for a scientist or a clinician. It is an important parameter to assess academic achievements. However, technical and language barriers may prevent many enthusiasts from ever publishing. This review highlights the important preparatory steps for creating a good manuscript and the most widely used IMRaD (Introduction, Materials and Methods, Results, and Discussion method for writing a good manuscript. It also provides a brief overview of the submission and review process of a manuscript for publishing in a biomedical journal.

  11. [SciELO: method for electronic publishing].

    Science.gov (United States)

    Laerte Packer, A; Rocha Biojone, M; Antonio, I; Mayumi Takemaka, R; Pedroso García, A; Costa da Silva, A; Toshiyuki Murasaki, R; Mylek, C; Carvalho Reisl, O; Rocha F Delbucio, H C

    2001-01-01

    It describes the SciELO Methodology Scientific Electronic Library Online for electronic publishing of scientific periodicals, examining issues such as the transition from traditional printed publication to electronic publishing, the scientific communication process, the principles which founded the methodology development, its application in the building of the SciELO site, its modules and components, the tools use for its construction etc. The article also discusses the potentialities and trends for the area in Brazil and Latin America, pointing out questions and proposals which should be investigated and solved by the methodology. It concludes that the SciELO Methodology is an efficient, flexible and wide solution for the scientific electronic publishing.

  12. Open Access Publishing in the Electronic Age.

    Science.gov (United States)

    Kovács, Gábor L

    2014-10-01

    The principle of open-access (OA) publishing is more and more prevalent also on the field of laboratory medicine. Open-access journals (OAJs) are available online to the reader usually without financial, legal, or technical barriers. Some are subsidized, and some require payment on behalf of the author. OAJs are one of the two general methods for providing OA. The other one is self-archiving in a repository. The electronic journal of the IFCC (eJIFCC) is a platinum OAJ- i.e. there is no charge to read, or to submit to this journal. Traditionally, the author was required to transfer the copyright to the journal publisher. Publishers claimed this was necessary in order to protect author's rights. However, many authors found this unsatisfactory, and have used their influence to affect a gradual move towards a license to publish instead. Under such a system, the publisher has permission to edit, print, and distribute the article commercially, but the author(s) retain the other rights themselves. An OA mandate is a policy adopted by a research institution, research funder, or government which requires researchers to make their published, peer-reviewed journal articles and conference papers OA by self-archiving their peer-reviewed drafts in a repository ("green OA") or by publishing them in an OAJ ("gold OA"). Creative Commons (CC) is a nonprofit organization that enables the sharing and use of creativity and knowledge through free legal tools. The free, easy-to-use copyright licenses provide a simple, standardized way to give the public permission to share and use creative work. CC licenses let you easily change your copyright terms from the default of "all rights reserved" to "some rights reserved." OA publishing also raises a number of new ethical problems (e.g. predatory publishers, fake papers). Laboratory scientists are encouraged to publish their scientific results OA (especially in eJIFCC). They should, however, be aware of their rights, institutional mandate

  13. Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing

    Directory of Open Access Journals (Sweden)

    Li Kelvin

    2012-11-01

    Full Text Available Abstract Background In a high-throughput environment, to PCR amplify and sequence a large set of viral isolates from populations that are potentially heterogeneous and continuously evolving, the use of degenerate PCR primers is an important strategy. Degenerate primers allow for the PCR amplification of a wider range of viral isolates with only one set of pre-mixed primers, thus increasing amplification success rates and minimizing the necessity for genome finishing activities. To successfully select a large set of degenerate PCR primers necessary to tile across an entire viral genome and maximize their success, this process is best performed computationally. Results We have developed a fully automated degenerate PCR primer design system that plays a key role in the J. Craig Venter Institute’s (JCVI high-throughput viral sequencing pipeline. A consensus viral genome, or a set of consensus segment sequences in the case of a segmented virus, is specified using IUPAC ambiguity codes in the consensus template sequence to represent the allelic diversity of the target population. PCR primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the full length of the specified target region. As part of the tiling process, primer pairs are computationally screened to meet the criteria for successful PCR with one of two described amplification protocols. The actual sequencing success rates for designed primers for measles virus, mumps virus, human parainfluenza virus 1 and 3, human respiratory syncytial virus A and B and human metapneumovirus are described, where >90% of designed primer pairs were able to consistently successfully amplify >75% of the isolates. Conclusions Augmenting our previously developed and published JCVI Primer Design Pipeline, we achieved similarly high sequencing success rates with only minor software modifications. The recommended methodology for the construction of the consensus

  14. Subsequent childbirth after a previous traumatic birth.

    Science.gov (United States)

    Beck, Cheryl Tatano; Watson, Sue

    2010-01-01

    Nine percent of new mothers in the United States who participated in the Listening to Mothers II Postpartum Survey screened positive for meeting the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition criteria for posttraumatic stress disorder after childbirth. Women who have had a traumatic birth experience report fewer subsequent children and a longer length of time before their second baby. Childbirth-related posttraumatic stress disorder impacts couples' physical relationship, communication, conflict, emotions, and bonding with their children. The purpose of this study was to describe the meaning of women's experiences of a subsequent childbirth after a previous traumatic birth. Phenomenology was the research design used. An international sample of 35 women participated in this Internet study. Women were asked, "Please describe in as much detail as you can remember your subsequent pregnancy, labor, and delivery following your previous traumatic birth." Colaizzi's phenomenological data analysis approach was used to analyze the stories of the 35 women. Data analysis yielded four themes: (a) riding the turbulent wave of panic during pregnancy; (b) strategizing: attempts to reclaim their body and complete the journey to motherhood; (c) bringing reverence to the birthing process and empowering women; and (d) still elusive: the longed-for healing birth experience. Subsequent childbirth after a previous birth trauma has the potential to either heal or retraumatize women. During pregnancy, women need permission and encouragement to grieve their prior traumatic births to help remove the burden of their invisible pain.

  15. 18th International Conference on Electronic Publishing

    CERN Document Server

    Dobreva, Milena

    2014-01-01

    The ways in which research data is used and handled continue to capture public attention and are the focus of increasing interest. Electronic publishing is intrinsic to digital data management, and relevant to the fields of data mining, digital publishing and social networks, with their implications for scholarly communication, information services, e-learning, e-business and the cultural heritage sector. This book presents the proceedings of the 18th International Conference on Electronic Publishing (ELPUB), held in Thessaloniki, Greece, in June 2014. The conference brings together researchers and practitioners to discuss the many aspects of electronic publishing, and the theme this year is 'Let's put data to use: digital scholarship for the next generation'. As well as examining the role of cultural heritage and service organisations in the creation, accessibility, duration and long-term preservation of data, it provides a discussion forum for the appraisal, citation and licensing of research data and the n...

  16. Predatory publishing and cybercrime targeting academics.

    Science.gov (United States)

    Umlauf, Mary Grace; Mochizuki, Yuki

    2018-04-01

    The purpose of this report is to inform and warn academics about practices used by cybercriminals who seek to profit from unwary scholars and undermine the industry of science. This report describes the signs, symptoms, characteristics, and consequences of predatory publishing and related forms of consumer fraud. Methods to curb these cybercrimes include educating scholars and students about tactics used by predatory publishers; institutional changes in how faculty are evaluated using publications; soliciting cooperation from the industries that support academic publishing and indexing to curb incorporation of illegitimate journals; and taking an offensive position by reporting these consumer fraud crimes to the authorities. Over and above the problem of publishing good science in fraudulent journals, disseminating and citing poor-quality research threaten the credibility of science and of nursing. © 2018 John Wiley & Sons Australia, Ltd.

  17. Design Options for a Desktop Publishing Course.

    Science.gov (United States)

    Mayer, Kenneth R.; Nelson, Sandra J.

    1992-01-01

    Offers recommendations for development of an undergraduate desktop publishing course. Discusses scholastic level and prerequisites, purpose and objectives, instructional resources and methodology, assignments and evaluation, and a general course outline. (SR)

  18. Open Access publishing in physics gains momentum

    CERN Multimedia

    2006-01-01

    The first meeting of European particle physics funding agencies took place on 3 November at CERN to establish a consortium for Open Access publishing in particle physics, SCOAP3 (Sponsoring Consortium for Open Access Publishing in Particle Physics). Open Access could transform the academic publishing world, with a great impact on research. The traditional model of research publication is funded through reader subscriptions. Open Access will turn this model on its head by changing the funding structure of research results, without increasing the overall cost of publishing. Instead of demanding payment from readers, publications will be distributed free of charge, financed by funding agencies via laboratories and the authors. This new concept will bring greater benefits and broaden opportunities for researchers and funding agencies by providing unrestricted distribution of the results of publicly funded research. The meeting marked a positive step forward, with international support from laboratories, fundin...

  19. INNOVATION MANAGEMENT TOOLS IN PUBLISHING COMPANIES

    Directory of Open Access Journals (Sweden)

    A. Shegda

    2013-09-01

    Full Text Available This article is devoted to the highly topical issue of modern publishing business as innovation management. introduction of technological innovation, measured as a promising strategy for the development of a constructive industry. The paper deals with main problems in managing of publishing companies. The reference consider of innovation management tools. In the article are exams the problems of books trend decline which require publishers introducing innovative methods of production and distribution. It was found that while the tools can be used. The process of innovation management with the following basic tools like as marketing innovation bench marketing, franchising, engineering innovation. It was found that while the tools can be used. So, the aim of the article is to analyze the modern tools of innovation management in the publishing field.

  20. Monitoring Information By Industry - Printing and Publishing

    Science.gov (United States)

    Stationary source emissions monitoring is required to demonstrate that a source is meeting the requirements in Federal or state rules. This page is about control techniques used to reduce pollutant emissions in the printing and publishing industry.

  1. Printing and Publishing Industry Training Board

    Science.gov (United States)

    Industrial Training International, 1974

    1974-01-01

    Accounted is the supervisory training program currently in operation in the printing and publishing industry. The purpose of the training program is to increase managerial efficiency and to better prepare new supervisors. (DS)

  2. NSA Diana Wueger Published in Washington Quarterly

    OpenAIRE

    Grant, Catherine L.

    2016-01-01

    National Security Affairs (NSA) News NSA Faculty Associate for Research Diana Wueger has recently had an article titled “India’s Nuclear-Armed Submarines: Deterrence or Danger?” published in the Washington Quarterly.

  3. Decentralized provenance-aware publishing with nanopublications

    Directory of Open Access Journals (Sweden)

    Tobias Kuhn

    2016-08-01

    Full Text Available Publication and archival of scientific results is still commonly considered the responsability of classical publishing companies. Classical forms of publishing, however, which center around printed narrative articles, no longer seem well-suited in the digital age. In particular, there exist currently no efficient, reliable, and agreed-upon methods for publishing scientific datasets, which have become increasingly important for science. In this article, we propose to design scientific data publishing as a web-based bottom-up process, without top-down control of central authorities such as publishing companies. Based on a novel combination of existing concepts and technologies, we present a server network to decentrally store and archive data in the form of nanopublications, an RDF-based format to represent scientific data. We show how this approach allows researchers to publish, retrieve, verify, and recombine datasets of nanopublications in a reliable and trustworthy manner, and we argue that this architecture could be used as a low-level data publication layer to serve the Semantic Web in general. Our evaluation of the current network shows that this system is efficient and reliable.

  4. Electronic astronomical information handling and flexible publishing.

    Science.gov (United States)

    Heck, A.

    The current dramatic evolution in information technology is bringing major modifications in the way scientists work and communicate. The concept of electronic information handling encompasses the diverse types of information, the different media, as well as the various communication methodologies and technologies. It ranges from the very collection of data until the final publication of results and sharing of knowledge. New problems and challenges result also from the new information culture, especially on legal, ethical, and educational grounds. Electronic publishing will have to diverge from an electronic version of contributions on paper and will be part of a more general flexible-publishing policy. The benefits of private publishing are questioned. The procedures for validating published material and for evaluating scientific activities will have to be adjusted too. Provision of electronic refereed information independently from commercial publishers in now feasible. Scientists and scientific institutions have now the possibility to run an efficient information server with validated (refereed) material without the help of a commercial publishers.

  5. Electronic publishing and Acupuncture in Medicine.

    Science.gov (United States)

    White, Adrian

    2006-09-01

    The internet has fundamentally altered scientific publishing; this article discusses current models and how they affect this journal. The greatest innovation is a new range of open access journals published only on the internet, aimed at rapid publication and universal access. In most cases authors pay a publication charge for the overhead costs of the journal. Journals that are published by professional organisations primarily for their members have some functions other than publishing research, including clinical articles, conference reports and news items. A small number of these journals are permitting open access to their research reports. Commercial science publishing still exists, where profit for shareholders provides motivation in addition to the desire to spread knowledge for the benefit of all. A range of electronic databases now exists that offer various levels of listing and searching. Some databases provide direct links to journal articles, such as the LinkOut scheme in PubMed. Acupuncture in Medicine will continue to publish in paper format; all research articles will be available on open access, but non-subscribers will need to pay for certain other articles for the first 12 months after publication. All Acupuncture in Medicine articles will in future be included in the LinkOut scheme, and be presented to the databases electronically.

  6. Analysis of thirteen predatory publishers: a trap for eager-to-publish researchers.

    Science.gov (United States)

    Bolshete, Pravin

    2018-01-01

    To demonstrate a strategy employed by predatory publishers to trap eager-to-publish authors or researchers into submitting their work. This was a case study of 13 potential, possible, or probable predatory scholarly open-access publishers with similar characteristics. Eleven publishers were included from Beall's list and two additional publishers were identified from a Google web search. Each publisher's site was visited and its content analyzed. Publishers publishing biomedical journals were further explored and additional data was collected regarding their volumes, details of publications and editorial-board members. Overall, the look and feel of all 13 publishers was similar including names of publishers, website addresses, homepage content, homepage images, list of journals and subject areas, as if they were copied and pasted. There were discrepancies in article-processing charges within the publishers. None of the publishers identified names in their contact details and primarily included only email addresses. Author instructions were similar across all 13 publishers. Most publishers listed journals of varied subject areas including biomedical journals (12 publishers) covering different geographic locations. Most biomedical journals published none or very few articles. The highest number of articles published by any single biomedical journal was 28. Several editorial-board members were listed across more than one journals, with one member listed 81 times in different 69 journals (i.e. twice in 12 journals). There was a strong reason to believe that predatory publishers may have several publication houses with different names under a single roof to trap authors from different geographic locations.

  7. Image sequence analysis

    CERN Document Server

    1981-01-01

    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  8. Recently Published Lectures and Tutorials for ATLAS

    CERN Multimedia

    J. Herr

    2006-01-01

    As reported in the September 2004 ATLAS eNews, the Web Lecture Archive Project, a collaboration between the University of Michigan and CERN, has developed a synchronized system for recording and publishing educational multimedia presentations, using the Web as medium. The current system, including future developments for the project and the field in general, was recently presented at the CHEP 2006 conference in Mumbai, India. The relevant presentations and papers can be found here: The Web Lecture Archive Project A Web Lecture Capture System with Robotic Speaker Tracking This year, the University of Michigan team has been asked to record and publish all ATLAS Plenary sessions, as well as a large number of Physics and Computing tutorials. A significant amount of this material has already been published and can be accessed via the links below. All lectures can be viewed on any major platform with any common internet browser, either via streaming or local download (for limited bandwidth). Please enjoy the l...

  9. Recently Published Lectures and Tutorials for ATLAS

    CERN Multimedia

    Goldfarb, S.

    2006-01-01

    As reported in the September 2004 ATLAS eNews, the Web Lecture Archive Project, WLAP, a collaboration between the University of Michigan and CERN, has developed a synchronized system for recording and publishing educational multimedia presentations, using the Web as medium. The current system, including future developments for the project and the field in general, was recently presented at the CHEP 2006 conference in Mumbai, India. The relevant presentations and papers can be found here: The Web Lecture Archive Project. A Web Lecture Capture System with Robotic Speaker Tracking This year, the University of Michigan team has been asked to record and publish all ATLAS Plenary sessions, as well as a large number of Physics and Computing tutorials. A significant amount of this material has already been published and can be accessed via the links below. All lectures can be viewed on any major platform with any common internet browser, either via streaming or local download (for limited bandwidth). Please e...

  10. Electronic Publishing or Electronic Information Handling?

    Science.gov (United States)

    Heck, A.

    The current dramatic evolution in information technology is bringing major modifications in the way scientists communicate. The concept of 'electronic publishing' is too restrictive and has often different, sometimes conflicting, interpretations. It is thus giving way to the broader notion of 'electronic information handling' encompassing the diverse types of information, the different media, as well as the various communication methodologies and technologies. New problems and challenges result also from this new information culture, especially on legal, ethical, and educational grounds. The procedures for validating 'published material' and for evaluating scientific activities will have to be adjusted too. 'Fluid' information is becoming a common concept. Electronic publishing cannot be conceived without link to knowledge bases nor without intelligent information retrieval tools.

  11. Electronic publishing and intelligent information retrieval

    Science.gov (United States)

    Heck, A.

    1992-01-01

    Europeans are now taking steps to homogenize policies and standardize procedures in electronic publishing (EP) in astronomy and space sciences. This arose from an open meeting organized in Oct. 1991 at Strasbourg Observatory (France) and another business meeting held late Mar. 1992 with the major publishers and journal editors in astronomy and space sciences. The ultimate aim of EP might be considered as the so-called 'intelligent information retrieval' (IIR) or better named 'advanced information retrieval' (AIR), taking advantage of the fact that the material to be published appears at some stage in a machine-readable form. It is obvious that the combination of desktop and electronic publishing with networking and new structuring of knowledge bases will profoundly reshape not only our ways of publishing, but also our procedures of communicating and retrieving information. It should be noted that a world-wide survey among astronomers and space scientists carried out before the October 1991 colloquium on the various packages and machines used, indicated that TEX-related packages were already in majoritarian use in our community. It has also been stressed at each meeting that the European developments should be carried out in collaboration with what is done in the US (STELLAR project, for instance). American scientists and journal editors actually attended both meetings mentioned above. The paper will offer a review of the status of electronic publishing in astronomy and its possible contribution to advanced information retrieval in this field. It will also report on recent meetings such as the 'Astronomy from Large Databases-2 (ALD-2)' conference dealing with the latest developments in networking, in data, information, and knowledge bases, as well as in the related methodologies.

  12. Introduction to scientific publishing backgrounds, concepts, strategies

    CERN Document Server

    Öchsner, Andreas

    2013-01-01

    This book is a very concise introduction to the basic knowledge of scientific publishing. It  starts with the basics of writing a scientific paper, and recalls the different types of scientific documents. In gives an overview on the major scientific publishing companies and different business models. The book also introduces to abstracting and indexing services and how they can be used for the evaluation of science, scientists, and institutions. Last but not least, this short book faces the problem of plagiarism and publication ethics.

  13. Publishing activities improves undergraduate biology education.

    Science.gov (United States)

    Smith, Michelle K

    2018-06-01

    To improve undergraduate biology education, there is an urgent need for biology instructors to publish their innovative active-learning instructional materials in peer-reviewed journals. To do this, instructors can measure student knowledge about a variety of biology concepts, iteratively design activities, explore student learning outcomes and publish the results. Creating a set of well-vetted activities, searchable through a journal interface, saves other instructors time and encourages the use of active-learning instructional practices. For authors, these publications offer new opportunities to collaborate and can provide evidence of a commitment to using active-learning instructional techniques in the classroom.

  14. Publishing to become an 'ideal academic'

    DEFF Research Database (Denmark)

    Lund, Rebecca

    2012-01-01

    over a two-year period in a recently merged Finnish university. I focus specifically on how a translocal discourse of competitive performance measurement and standards of academic excellence are accomplished in the local construction of the “ideal academic” as a person who publishes articles in A level...... journals. While the construct is hard for anyone to live up to, it would seem to be more difficult for some people than for others. The current obsession with getting published in top journals place those women, who are heavily engaged in teaching activities and with responsibilities besides academic work...

  15. Advances in semantic authoring and publishing

    CERN Document Server

    Groza, T

    2012-01-01

    Dissemination can be seen as a communication process between scientists. Over the course of several publications, they expose and support their findings, while discussing stated claims. Such discourse structures are trapped within the content of the publications, thus making the semantics discoverable only by humans. In addition, the lack of advances in scientific publishing, where electronic publications are still used as simple projections of paper documents, combined with the current growth in the amount of scientific research being published, transforms the process of finding relevant lite

  16. Publish Subscribe Systems Design and Principles

    CERN Document Server

    Tarkoma, Sasu

    2012-01-01

    This book offers an unified treatment of the problems solved by publish/subscribe, how to design and implement the solutions In this book, the author provides an insight into the publish/subscribe technology including the design, implementation, and evaluation of new systems based on the technology.  The book also addresses the basic design patterns and solutions, and discusses their application in practical application scenarios. Furthermore, the author examines current standards and industry best practices as well as recent research proposals in the area. Finally, necessary content ma

  17. Scholarly publishing depends on peer reviewers.

    Science.gov (United States)

    Fernandez-Llimos, Fernando

    2018-01-01

    The peer-review crisis is posing a risk to the scholarly peer-reviewed journal system. Journals have to ask many potential peer reviewers to obtain a minimum acceptable number of peers accepting reviewing a manuscript. Several solutions have been suggested to overcome this shortage. From reimbursing for the job, to eliminating pre-publication reviews, one cannot predict which is more dangerous for the future of scholarly publishing. And, why not acknowledging their contribution to the final version of the article published? PubMed created two categories of contributors: authors [AU] and collaborators [IR]. Why not a third category for the peer-reviewer?

  18. Scholarly publishing depends on peer reviewers

    Directory of Open Access Journals (Sweden)

    Fernandez-Llimos F

    2018-03-01

    Full Text Available The peer-review crisis is posing a risk to the scholarly peer-reviewed journal system. Journals have to ask many potential peer reviewers to obtain a minimum acceptable number of peers accepting reviewing a manuscript. Several solutions have been suggested to overcome this shortage. From reimbursing for the job, to eliminating pre-publication reviews, one cannot predict which is more dangerous for the future of scholarly publishing. And, why not acknowledging their contribution to the final version of the article published? PubMed created two categories of contributors: authors [AU] and collaborators [IR]. Why not a third category for the peer-reviewer?

  19. [Trends of electronic publishing in medicine and life sciences].

    Science.gov (United States)

    Strelski-Waisman, Neta; Waisman, Dan

    2005-09-01

    Scientific publication in the electronic media is gaining popularity in academic libraries, research institutions and commercial organizations. The electronic journal may shorten the processes of writing and publication, decrease publication and distribution costs, and enable access from any location in the world. Electronic publications have unique advantages: it is possible to search them, to create hyperlinks to references and footnotes, as well as to information on the web and to include graphics and photographs at a very low cost. Audio, video and tri-dimensional images may also be included. Electronic publishing may also speed up review and publication processes and enable the writer to receive immediate feedback through the web. However, in spite of the advantages, there are certain points that must be considered: accessibility to previously published material is not guaranteed as databases are not always stable and coverage may change without notice. In addition, the price that commercial publishers charge for their services may be very high or be subject to the purchase of a packaged deal that may include unwanted databases. Many issues of copyright and the use of published material are not yet finalized. In this review we discuss the advantages and disadvantages of the electronic scientific publication, the feasibility of keeping appropriate quality and peer-review process, the stability and accessibility of databases managed by the publishers and the acceptance of the electronic format by scientists and clinicians.

  20. Evolution of developmental sequences in lepidosaurs

    Directory of Open Access Journals (Sweden)

    Tomasz Skawiński

    2017-04-01

    Full Text Available Background Lepidosaurs, a group including rhynchocephalians and squamates, are one of the major clades of extant vertebrates. Although there has been extensive phylogenetic work on this clade, its interrelationships are a matter of debate. Morphological and molecular data suggest very different relationships within squamates. Despite this, relatively few studies have assessed the utility of other types of data for inferring squamate phylogeny. Methods We used developmental sequences of 20 events in 29 species of lepidosaurs. These sequences were analysed using event-pairing and continuous analysis. They were transformed into cladistic characters and analysed in TNT. Ancestral state reconstructions were performed on two main phylogenetic hypotheses of squamates (morphological and molecular. Results Cladistic analyses conducted using characters generated by these methods do not resemble any previously published phylogeny. Ancestral state reconstructions are equally consistent with both morphological and molecular hypotheses of squamate phylogeny. Only several inferred heterochronic events are common to all methods and phylogenies. Discussion Results of the cladistic analyses, and the fact that reconstructions of heterochronic events show more similarities between certain methods rather than phylogenetic hypotheses, suggest that phylogenetic signal is at best weak in the studied developmental events. Possibly the developmental sequences analysed here evolve too quickly to recover deep divergences within Squamata.

  1. Educational Systems Design Implications of Electronic Publishing.

    Science.gov (United States)

    Romiszowski, Alexander J.

    1994-01-01

    Discussion of electronic publishing focuses on the four main purposes of media in general: communication, entertainment, motivation, and education. Highlights include electronic journals and books; hypertext; user control; computer graphics and animation; electronic games; virtual reality; multimedia; electronic performance support;…

  2. Hypertext Publishing and the Revitalization of Knowledge.

    Science.gov (United States)

    Louie, Steven; Rubeck, Robert F.

    1989-01-01

    Discusses the use of hypertext for publishing and other document control activities in higher education. Topics discussed include a model of hypertext, called GUIDE, that is used at the University of Arizona Medical School; the increase in the number of scholarly publications; courseware development by faculty; and artificial intelligence. (LRW)

  3. Open Access Publishing in Particle Physics

    CERN Document Server

    2007-01-01

    Particle Physics, often referred to as High Energy Physics (HEP), spearheaded the Open Access dissemination of scientific results with the mass mailing of preprints in the pre-Web era and with the launch of the arXiv preprint system at the dawn of the '90s. The HEP community is now ready for a further push to Open Access while retaining all the advantages of the peerreview system and, at the same time, bring the spiralling cost of journal subscriptions under control. I will present a plan for the conversion to Open Access of HEP peer-reviewed journals, through a consortium of HEP funding agencies, laboratories and libraries: SCOAP3 (Sponsoring Consortium for Open Access Publishing in Particle Physics). SCOAP3 will engage with scientific publishers towards building a sustainable model for Open Access publishing, which is as transparent as possible for HEP authors. The current system in which journals income comes from subscription fees is replaced with a scheme where SCOAP3 compensates publishers for the costs...

  4. Publishing Qualitative Research in Counseling Journals

    Science.gov (United States)

    Hunt, Brandon

    2011-01-01

    This article focuses on the essential elements to be included when developing a qualitative study and preparing the findings for publication. Using the sections typically found in a qualitative article, the author describes content relevant to each section, with additional suggestions for publishing qualitative research.

  5. Publisher Correction: Geometric constraints during epithelial jamming

    Science.gov (United States)

    Atia, Lior; Bi, Dapeng; Sharma, Yasha; Mitchel, Jennifer A.; Gweon, Bomi; Koehler, Stephan A.; DeCamp, Stephen J.; Lan, Bo; Kim, Jae Hun; Hirsch, Rebecca; Pegoraro, Adrian F.; Lee, Kyu Ha; Starr, Jacqueline R.; Weitz, David A.; Martin, Adam C.; Park, Jin-Ah; Butler, James P.; Fredberg, Jeffrey J.

    2018-06-01

    In the version of this Article originally published, the Supplementary Movies were linked to the wrong descriptions. These have now been corrected. Additionally, the authors would like to note that co-authors James P. Butler and Jeffrey J. Fredberg contributed equally to this Article; this change has now been made.

  6. Doing Publishable Research with Undergraduate Students

    Science.gov (United States)

    Fenn, Aju J.; Johnson, Daniel K. N.; Smith, Mark Griffin; Stimpert, J. L.

    2010-01-01

    Many economics majors write a senior thesis. Although this experience can be the pinnacle of their education, publication is not the common standard for undergraduates. The authors describe four approaches that have allowed students to get their work published: (1) identify a topic, such as competitive balance in sports, and have students work on…

  7. Desktop publishing: a useful tool for scientists.

    Science.gov (United States)

    Lindroth, J R; Cooper, G; Kent, R L

    1994-01-01

    Desktop publishing offers features that are not available in word processing programs. The process yields an impressive and professional-looking document that is legible and attractive. It is a simple but effective tool to enhance the quality and appearance of your work and perhaps also increase your productivity.

  8. Desktop Publishing as a Learning Resources Service.

    Science.gov (United States)

    Drake, David

    In late 1988, Midland College in Texas implemented a desktop publishing service to produce instructional aids and reduce and complement the workload of the campus print shop. The desktop service was placed in the Media Services Department of the Learning Resource Center (LRC) for three reasons: the LRC was already established as a campus-wide…

  9. Desktop Publishing: Things Gutenberg Never Taught You.

    Science.gov (United States)

    Bowman, Joel P.; Renshaw, Debbie A.

    1989-01-01

    Provides a desktop publishing (DTP) overview, including: advantages and disadvantages; hardware and software requirements; and future development. Discusses cost-effectiveness, confidentiality, credibility, effects on volume of paper-based communication, and the need for training in layout and design which DTP creates. Includes a glossary of DTP…

  10. Basics of Desktop Publishing. Teacher Edition.

    Science.gov (United States)

    Beeby, Ellen

    This color-coded teacher's guide contains curriculum materials designed to give students an awareness of various desktop publishing techniques before they determine their computer hardware and software needs. The guide contains six units, each of which includes some or all of the following basic components: objective sheet, suggested activities…

  11. Reconfiguration Service for Publish/Subscribe Middleware

    NARCIS (Netherlands)

    Zieba, Bogumil; Glandrup, Maurice; van Sinderen, Marten J.; Wegdam, M.

    2006-01-01

    Mission-critical, distributed systems are often designed as a set of distributed, components that interact using publish/subscribe middleware. Currently, in these systems, software components are usually statically allocated to the nodes to fulfil predictability, reliability requirements. However, a

  12. Awareness and Perceptions of Published Osteoporosis Clinical ...

    African Journals Online (AJOL)

    Awareness and Perceptions of Published Osteoporosis Clinical Guidelines-a Survey of Primary Care Practitioners in the Cape Town Metropolitan Area. ... Further attention needs to be focused on developing implementation and dissemination strategies of evidence-based guidelines in South Africa. South African Journal of ...

  13. Librarians and Libraries Supporting Open Access Publishing

    Science.gov (United States)

    Richard, Jennifer; Koufogiannakis, Denise; Ryan, Pam

    2009-01-01

    As new models of scholarly communication emerge, librarians and libraries have responded by developing and supporting new methods of storing and providing access to information and by creating new publishing support services. This article will examine the roles of libraries and librarians in developing and supporting open access publishing…

  14. 12 CFR 271.3 - Published information.

    Science.gov (United States)

    2010-01-01

    ... preceding year upon all matters of policy relating to open market operations, showing the reasons underlying... information relating to open market operations of the Federal Reserve Banks is published in the Federal... Banks and Banking FEDERAL RESERVE SYSTEM (CONTINUED) FEDERAL OPEN MARKET COMMITTEE RULES REGARDING...

  15. Electronic Publishing and The American Astronomical Society

    Science.gov (United States)

    Milkey, R. W.

    1999-12-01

    Electronic Publishing has created, and will continue to create, new opportunities and challenges for representing scientific work in new media and formats. The AAS will position itself to take advantage of these, both for newly created works and for improved representation of works already published. It is the view of the AAS that we hold the works that we publish in trust for our community and are obligated to protect the integrity of these works and to assure that they continue to be available to the research community. Assignment of copyright to the AAS by the author plays a central role in the preservation of the integrity and accessability of the literature published by the American Astronomical Society. In return for such assignment the AAS allows the author to freely use the work for his/her own purpose and to control the grant of permission to third parties to use such materials. The AAS retains the right to republish the work in whatever format or medium, and to retain the rights after the author's death. Specific advantages to this approach include: Assurance of the continued availability of the materials to the research and educational communities; A guarantee of the intellectual integrity of the materials in the archive; Stimulation of the development of new means of presentation or of access to the archival literature; and Provision of a uniformity of treatment for copyright issues and to relieve the individual authors of much of the administrative work.

  16. Open access publishing in physics gains momentum

    CERN Multimedia

    2006-01-01

    "The first meeting of European particle physics funding agencies took place today at CERN to establish a consortium for Open Access publishing in particle physics, SCOAP3. This is the first time an antire scientific field is exploring the conversion of its reader-paid journals into an author-paid Open Access format." (1 page)

  17. [Medical publishing in Norway 1905-2005].

    Science.gov (United States)

    Nylenna, Magne; Larsen, Øivind

    2005-06-02

    The nation-building process in Norway took mainly place before the Norwegian-Swedish union came to a close in 1905. This was not a dramatic change, though the end of the union did bring a lift to Norwegian national consciousness. In 1905 there were three general medical journals in Norway and approximately 1200 doctors. German was the most important language of international science, but most scientific publishing was done in Norwegian. After the Second World War, English became the dominating language of scientific communication. Twentieth-century medicine and medical publishing was an era of specialisation and internationalisation. Norwegian medicine has to a large extent been internationalised through Nordic cooperation, with the Nordic specialist journals being of particular importance. With increasing professionalism in research, international English-language journals have become the major channels of communication, though several Norwegian-language journals (on paper or on the internet) have been established and are of crucial importance to a national identity within medical specialties. In 2005 there is only one general medical journal in Norwegian, in a country with approximately 20,000 doctors. A national identity related to medical publishing is not given much attention, though national medicine is still closely tied in with national culture. Good clinical practice should be based on a firm knowledge of local society and local tradition. This is a challenge in contemporary medical publishing.

  18. Humanists, Libraries, Electronic Publishing, and the Future.

    Science.gov (United States)

    Sweetland, James H.

    1992-01-01

    Discusses the impact of computerization on humanists and libraries. Highlights include a lack of relevant databases; a reliance on original text; vocabulary and language issues; lack of time pressure; research style; attitudes of humanists toward technology; trends in electronic publishing; hypertext; collection development; electronic mail;…

  19. Evolving Digital Publishing Opportunities across Composition Studies

    Science.gov (United States)

    Hawishler, Gail E.; Selfe, Cynthia L.

    2014-01-01

    In this article, the authors report since the early 1980s, the profession has seen plenty of changes in the arena of digital scholarly publishing: during this time, while the specific challenges have seldom remained the same, the presence and the pressures of rapid technological change endure. In fact, as an editorial team that has, in part,…

  20. Electronic Publishing in Library and Information Science.

    Science.gov (United States)

    Lee, Joel M.; And Others

    1988-01-01

    Discusses electronic publishing as it refers to machine-readable databases. Types of electronic products and services are described and related topics considered: (1) usage of library and information science databases; (2) production and distribution of databases; (3) trends and projections in the electronic information industry; and (4)…

  1. Publisher Correction: The price of fast fashion

    Science.gov (United States)

    2018-02-01

    In the version of this Editorial originally published, the rate of clothing disposal to landfill was incorrectly given as `one rubbish truck per day'; it should have read `one rubbish truck per second'. This has now been corrected in the online versions of the Editorial.

  2. Data Publishing - View from the Front

    Science.gov (United States)

    Carlson, David; Pfeiffenberger, Hans

    2014-05-01

    As data publishing journals - Earth System Science Data (ESSD, Copernicus, since 2009), Geophysical Data Journal (GDJ, Wiley, recent) and Scientific Data (SD, Nature Publishing Group, anticipated from May 2014) - expose data sets, implement data description and data review practices, and develop partnerships with data centres and data providers, we anticipate substantial benefits for the broad earth system and environmental research communities but also substantial challenges for all parties. A primary advantage emerges from open access to convergent data: subsurface hydrographic data near Antarctica, for example, now available for combination and comparison with nearby atmospheric data (both documented in ESSD), basin-scale precipitation data (accessed through GDJ) for comparison and interpolation with long-term global precipitation records (accessed from ESSD), or, imagining not too far into the future, stomach content and abundance data for European fish (from ESSD) linked to genetic or nutritional data (from SD). In addition to increased opportunity for discovery and collaboration, we also notice parallel developments of new tools for (published) data visualization and display and increasing acceptance of data publication as a useful and anticipated dissemination step included in project- and institution-based data management plans. All parties - providers, publishers and users - will benefit as various indexing services (SCI, SCOPUS, DCI etc.) acknowledge the creative, intellectual and meritorious efforts of data preparation and data provision. The challenges facing data publication, in most cases very familiar to the data community but made more acute by the advances in data publishing, include diverging metadata standards (among biomedical, green ocean modeling and meteorological communities, for example), adhering to standards and practices for permanent identification while also accommodating 'living' data, and maintaining prompt but rigorous review and

  3. Mutations in Genes Encoding Cardiac Ion Channels Previously Associated With Sudden Infant Death Syndrome (SIDS) Are Present With High Frequency in New Exome Data

    DEFF Research Database (Denmark)

    Andreasen, Charlotte Hartig; Refsgaard, Lena; Nielsen, Jonas B

    2013-01-01

    National Heart, Lung, and Blood Institute Grand Opportunity (NHLBI GO) Exome Sequencing Project (ESP) provided important knowledge on genetic variation in the background population. Our aim was to identify all variants previously associated with SIDS in ESP to improve the discrimination between plausible......Sudden infant death syndrome (SIDS) is the leading cause of death in the first 6 months after birth in the industrialized world. The genetic contribution to SIDS has been investigated intensively and to date, 14 cardiac channelopathy genes have been associated with SIDS. Newly published data from...

  4. Underestimation of Severity of Previous Whiplash Injuries

    Science.gov (United States)

    Naqui, SZH; Lovell, SJ; Lovell, ME

    2008-01-01

    INTRODUCTION We noted a report that more significant symptoms may be expressed after second whiplash injuries by a suggested cumulative effect, including degeneration. We wondered if patients were underestimating the severity of their earlier injury. PATIENTS AND METHODS We studied recent medicolegal reports, to assess subjects with a second whiplash injury. They had been asked whether their earlier injury was worse, the same or lesser in severity. RESULTS From the study cohort, 101 patients (87%) felt that they had fully recovered from their first injury and 15 (13%) had not. Seventy-six subjects considered their first injury of lesser severity, 24 worse and 16 the same. Of the 24 that felt the violence of their first accident was worse, only 8 had worse symptoms, and 16 felt their symptoms were mainly the same or less than their symptoms from their second injury. Statistical analysis of the data revealed that the proportion of those claiming a difference who said the previous injury was lesser was 76% (95% CI 66–84%). The observed proportion with a lesser injury was considerably higher than the 50% anticipated. CONCLUSIONS We feel that subjects may underestimate the severity of an earlier injury and associated symptoms. Reasons for this may include secondary gain rather than any proposed cumulative effect. PMID:18201501

  5. [Electronic cigarettes - effects on health. Previous reports].

    Science.gov (United States)

    Napierała, Marta; Kulza, Maksymilian; Wachowiak, Anna; Jabłecka, Katarzyna; Florek, Ewa

    2014-01-01

    Currently very popular in the market of tobacco products have gained electronic cigarettes (ang. E-cigarettes). These products are considered to be potentially less harmful in compared to traditional tobacco products. However, current reports indicate that the statements of the producers regarding to the composition of the e- liquids not always are sufficient, and consumers often do not have reliable information on the quality of the product used by them. This paper contain a review of previous reports on the composition of e-cigarettes and their impact on health. Most of the observed health effects was related to symptoms of the respiratory tract, mouth, throat, neurological complications and sensory organs. Particularly hazardous effects of the e-cigarettes were: pneumonia, congestive heart failure, confusion, convulsions, hypotension, aspiration pneumonia, face second-degree burns, blindness, chest pain and rapid heartbeat. In the literature there is no information relating to passive exposure by the aerosols released during e-cigarette smoking. Furthermore, the information regarding to the use of these products in the long term are not also available.

  6. Consortium Negotiations with Publishers - Past and Future

    Directory of Open Access Journals (Sweden)

    Pierre Carbone

    2007-09-01

    Full Text Available Since the mid nineties, with the development of online access to information (journals, databases, e-books, libraries strengthened their cooperation. They set up consortia at different levels around the world, generally with the support of the public authorities, for negotiating collectively with the publishers and information providers general agreements for access to these resources. This cooperation has been reinforced at the international level with the exchange of experiences and the debates in the ICOLC seminars and statements. So did the French consortium Couperin, which is now gathering more than 200 academic and research institutions. The level of access and downloading from these resources is growing with geometrical progression, and reaches a scale with no comparison to ILL or access to printed documents, but the costs did not reduce and the libraries budgets did not increase. At first, agreements with the major journal publishers were based on cross-access, and evolved rapidly to the access at a large bundle of titles in the so-called Big deal. After experiencing the advantages of the Big deal, the libraries are now more sensitive to the limits and lack of flexibility and to cost-effectiveness. These Big deals were based on a model where online access fee is built on the cost of print subscriptions, and the problem for the consortia and for the publishers is now to evolve from this print plus online model to an e-only model, no more based on the historical amount of the print subscriptions, to a new deal. In many European countries, VAT legislation is an obstacle to e-only, and this problem must be discussed at the European level. This change to e-only takes place at a moment where changes in the scientific publishing world are important (mergers of publishing houses, growth of research and of scientific publishing in the developing countries, open access and open archives movement. The transition to e-only leads also the library

  7. Publishing Landscape Archaeology in the Digital World

    Directory of Open Access Journals (Sweden)

    Howry Jeffrey C.

    2017-12-01

    Full Text Available The challenge of presenting micro- and macro-scale scale data in landscape archaeology studies is facilitated by a diversity of GIS technologies. Specific to scholarly research is the need to selectively share certain types of data with collaborators and academic researchers while also publishing general information in the public domain. This article presents a general model for scholarly online collaboration and teaching while providing examples of the kinds of landscape archaeology that can be published online. Specifically illustrated is WorldMap, an interactive mapping platform based upon open-source software which uses browsers built to open source standards. The various features of this platform allow tight user viewing control, views with URL referencing, commenting and certification of layers, as well as user annotation. Illustration of WorldMap features and its value for scholarly research and teaching is provided in the context of landscape archaeology studies.

  8. Springer Publishing Booth | 4-5 October

    CERN Multimedia

    2016-01-01

    In the spirit of continuation of the CERN Book Fairs of the past years, Springer Nature will be present with a book and journal booth on October 4th and 5th, located as usual in the foyer of the Main Building. Some of the latest titles in particle physics and related fields will be on sale.   You are cordially invited to come to the booth to meet Heike Klingebiel (Licensing Manager / Library Sales), Hisako Niko (Publishing Editor) and Christian Caron (Publishing Editor). In particular, information about the new Nano database – nanomaterial and device profiles from high-impact journals and patents, manually abstracted, curated and updated by nanotechnology experts – will be available. The database is accessible here: http://nano.nature.com/. 

  9. Publishing priorities of biomedical research funders

    Science.gov (United States)

    Collins, Ellen

    2013-01-01

    Objectives To understand the publishing priorities, especially in relation to open access, of 10 UK biomedical research funders. Design Semistructured interviews. Setting 10 UK biomedical research funders. Participants 12 employees with responsibility for research management at 10 UK biomedical research funders; a purposive sample to represent a range of backgrounds and organisation types. Conclusions Publicly funded and large biomedical research funders are committed to open access publishing and are pleased with recent developments which have stimulated growth in this area. Smaller charitable funders are supportive of the aims of open access, but are concerned about the practical implications for their budgets and their funded researchers. Across the board, biomedical research funders are turning their attention to other priorities for sharing research outputs, including data, protocols and negative results. Further work is required to understand how smaller funders, including charitable funders, can support open access. PMID:24154520

  10. The Open Data Repositorys Data Publisher

    Science.gov (United States)

    Stone, N.; Lafuente, B.; Downs, R. T.; Blake, D.; Bristow, T.; Fonda, M.; Pires, A.

    2015-01-01

    Data management and data publication are becoming increasingly important components of researcher's workflows. The complexity of managing data, publishing data online, and archiving data has not decreased significantly even as computing access and power has greatly increased. The Open Data Repository's Data Publisher software strives to make data archiving, management, and publication a standard part of a researcher's workflow using simple, web-based tools and commodity server hardware. The publication engine allows for uploading, searching, and display of data with graphing capabilities and downloadable files. Access is controlled through a robust permissions system that can control publication at the field level and can be granted to the general public or protected so that only registered users at various permission levels receive access. Data Publisher also allows researchers to subscribe to meta-data standards through a plugin system, embargo data publication at their discretion, and collaborate with other researchers through various levels of data sharing. As the software matures, semantic data standards will be implemented to facilitate machine reading of data and each database will provide a REST application programming interface for programmatic access. Additionally, a citation system will allow snapshots of any data set to be archived and cited for publication while the data itself can remain living and continuously evolve beyond the snapshot date. The software runs on a traditional LAMP (Linux, Apache, MySQL, PHP) server and is available on GitHub (http://github.com/opendatarepository) under a GPLv2 open source license. The goal of the Open Data Repository is to lower the cost and training barrier to entry so that any researcher can easily publish their data and ensure it is archived for posterity.

  11. Publisher Correction: Local sourcing in astronomy

    Science.gov (United States)

    2018-06-01

    In the version of this Editorial originally published, we mistakenly wrote that `the NAOJ ... may decommission Subaru in favour of other priorities'. In fact, the National Astronomical Observatory of Japan is committed to the long-term operation of the Subaru telescope. In the corrected version that whole sentence has been replaced with: `It will be critical to maintain such smaller telescopes in the age of the ELTs.'

  12. Electronic pre-publishing for worldwide access

    International Nuclear Information System (INIS)

    Dallman, D.; Draper, M.; Schwarz, S.

    1994-01-01

    In High Energy Physics, as in other areas of research, paper preprints have traditionally been the primary method of communication, before publishing in a journal. Electronic bulletin boards (EBBs) are now taking over as the dominant medium. While fast and readily available EBBs do not constitute electronic journals as they bypass the referee system crucial for prestigious research journals, although this too may be achieved electronically in time. (UK)

  13. The Open Data Repository's Data Publisher

    Science.gov (United States)

    Stone, N.; Lafuente, B.; Downs, R. T.; Bristow, T.; Blake, D. F.; Fonda, M.; Pires, A.

    2015-12-01

    Data management and data publication are becoming increasingly important components of research workflows. The complexity of managing data, publishing data online, and archiving data has not decreased significantly even as computing access and power has greatly increased. The Open Data Repository's Data Publisher software (http://www.opendatarepository.org) strives to make data archiving, management, and publication a standard part of a researcher's workflow using simple, web-based tools and commodity server hardware. The publication engine allows for uploading, searching, and display of data with graphing capabilities and downloadable files. Access is controlled through a robust permissions system that can control publication at the field level and can be granted to the general public or protected so that only registered users at various permission levels receive access. Data Publisher also allows researchers to subscribe to meta-data standards through a plugin system, embargo data publication at their discretion, and collaborate with other researchers through various levels of data sharing. As the software matures, semantic data standards will be implemented to facilitate machine reading of data and each database will provide a REST application programming interface for programmatic access. Additionally, a citation system will allow snapshots of any data set to be archived and cited for publication while the data itself can remain living and continuously evolve beyond the snapshot date. The software runs on a traditional LAMP (Linux, Apache, MySQL, PHP) server and is available on GitHub (http://github.com/opendatarepository) under a GPLv2 open source license. The goal of the Open Data Repository is to lower the cost and training barrier to entry so that any researcher can easily publish their data and ensure it is archived for posterity. We gratefully acknowledge the support for this study by the Science-Enabling Research Activity (SERA), and NASA NNX11AP82A

  14. Promising Products for Printing and Publishing Market

    Directory of Open Access Journals (Sweden)

    Renata Činčikaitė

    2011-04-01

    Full Text Available The article surveys printing and publishing market and its strong and weak aspects. The concept of a new product is described as well as its lifetime and the necessity of its introduction to the market. The enterprise X operating on the market is analyzed, its strong and weak characteristics are presented. The segmentation of the company consumers is performed. On the basis of the performed analysis the potential promising company products are defined.Article in Lithuanian

  15. Redressing the inverted pyramid of scientific publishing

    Science.gov (United States)

    Caux, Jean-Sébastien

    2017-11-01

    Scientific publishing is currently undergoing a progressively rapid transformation away from the traditional subscription model. With the Open Access movement in full swing, existing business practices and future plans are coming under increasing scrutiny, while new "big deals" are being made at breakneck speed. Scientists can rightfully ask themselves if all these changes are going the right way, and if not, what can be done about it.

  16. Open Access publishing in physics gains momentum

    CERN Multimedia

    2006-01-01

    "As if inventing the World-Wide Web were not revolutionary enough, the European Organisation for Nuclear Research (CERN) is now on its way to unleashing a paradigm shift in the world of academic publishing. For the first time ever, an entire scientific field is exploring the possibility of converting its reader-paid journals into an author-pai Open Access format." (1 page)

  17. The BiPublishers ranking: Main results and methodological problems when constructing rankings of academic publishers

    Directory of Open Access Journals (Sweden)

    Torres-Salinas, Daniel

    2015-12-01

    Full Text Available We present the results of the Bibliometric Indicators for Publishers project (also known as BiPublishers. This project represents the first attempt to systematically develop bibliometric publisher rankings. The data for this project was derived from the Book Citation Index and the study time period was 2009-2013. We have developed 42 rankings: 4 by fields and 38 by disciplines. We display six indicators for publishers divided into three types: output, impact and publisher’s profile. The aim is to capture different characteristics of the research performance of publishers. 254 publishers were processed and classified according to publisher type: commercial publishers and university presses. We present the main publishers by field and then discuss the principal challenges presented when developing this type of tool. The BiPublishers ranking is an on-going project which aims to develop and explore new data sources and indicators to better capture and define the research impact of publishers.Presentamos los resultados del proyecto Bibliometric Indicators for Publishers (BiPublishers. Es el primer proyecto que desarrolla de manera sistemática rankings bibliométricos de editoriales. La fuente de datos empleada es el Book Citation Index y el periodo de análisis 2009-2013. Se presentan 42 rankings: 4 por áreas y 38 por disciplinas. Mostramos seis indicadores por editorial divididos según su tipología: producción, impacto y características editoriales. Se procesaron 254 editoriales y se clasificaron según el tipo: comerciales y universitarias. Se presentan las principales editoriales por áreas. Después, se discuten los principales retos a superar en el desarrollo de este tipo de herramientas. El ranking Bipublishers es un proyecto en desarrollo que persigue analizar y explorar nuevas fuentes de datos e indicadores para captar y definir el impacto de las editoriales académicas.

  18. Recently Published Lectures and Tutorials for ATLAS

    CERN Multimedia

    Herr, J.

    2006-01-01

    As reported in the September 2004 ATLAS eNews, the Web Lecture Archive Project, WLAP, a collaboration between the University of Michigan and CERN, has developed a synchronized system for recording and publishing educational multimedia presentations, using the Web as medium. This year, the University of Michigan team has been asked to record and publish all ATLAS Plenary sessions, as well as a large number of Physics and Computing tutorials. A significant amount of this material has already been published and can be accessed via the links below. The WLAP model is spreading. This summer, the CERN's High School Teachers program has used WLAP's system to record several physics lectures directed toward a broad audience. And a new project called MScribe, which is essentially the WLAP system coupled with an infrared tracking camera, is being used by the University of Michigan to record several University courses this academic year. All lectures can be viewed on any major platform with any common internet browser...

  19. The ethics of open access publishing.

    Science.gov (United States)

    Parker, Michael

    2013-03-22

    Should those who work on ethics welcome or resist moves to open access publishing? This paper analyses arguments in favour and against the increasing requirement for open access publishing and considers their implications for bioethics research. In the context of biomedical science, major funders are increasingly mandating open access as a condition of funding and such moves are also common in other disciplines. Whilst there has been some debate about the implications of open-access for the social sciences and humanities, there has been little if any discussion about the implications of open access for ethics. This is surprising given both the central role of public reason and critique in ethics and the fact that many of the arguments made for and against open access have been couched in moral terms. In what follows I argue that those who work in ethics have a strong interest in supporting moves towards more open publishing approaches which have the potential both to inform and promote richer and more diverse forms of public deliberation and to be enriched by them. The importance of public deliberation in practical and applied ethics suggests that ethicists have a particular interest in the promotion of diverse and experimental forms of publication and debate and in supporting new, more creative and more participatory approaches to publication.

  20. Applied and implied semantics in crystallographic publishing

    Directory of Open Access Journals (Sweden)

    McMahon Brian

    2012-08-01

    Full Text Available Abstract Background Crystallography is a data-rich, software-intensive scientific discipline with a community that has undertaken direct responsibility for publishing its own scientific journals. That community has worked actively to develop information exchange standards allowing readers of structure reports to access directly, and interact with, the scientific content of the articles. Results Structure reports submitted to some journals of the International Union of Crystallography (IUCr can be automatically validated and published through an efficient and cost-effective workflow. Readers can view and interact with the structures in three-dimensional visualization applications, and can access the experimental data should they wish to perform their own independent structure solution and refinement. The journals also layer on top of this facility a number of automated annotations and interpretations to add further scientific value. Conclusions The benefits of semantically rich information exchange standards have revolutionised the scholarly publishing process for crystallography, and establish a model relevant to many other physical science disciplines.

  1. Open Access Publishing - Strengths and Strategies

    Science.gov (United States)

    Rasmussen, Martin

    2010-05-01

    The journal crisis and the demand for free accessibility to the results of publicly funded research were the main drivers of the Open Access movement since the late 1990's. Besides many academic institutions that support the different ways of Open Access publishing, there is a growing number of publishing houses that are specialized on this new access and business model of scholarly literature. The lecture provides an overview of the different kinds of Open Access publishing, discusses the variety of underlying business models, names the advantages and potentials for researches and the public, and overcomes some objections against Open Access. Besides the increased visibility and information supply, the topic of copyrights and exploitation rights will be discussed. Furthermore, it is a central aim of the presentation to show that Open Access does not only support full peer-review, but also provides the potential for even enhanced quality assurance. The financing of business models based on open accessible literature is another important part to be outlined in the lecture.

  2. Publisher Correction: Optimal compressed representation of high throughput sequence data via light assembly.

    Science.gov (United States)

    Ginart, Antonio A; Hui, Joseph; Zhu, Kaiyuan; Numanagić, Ibrahim; Courtade, Thomas A; Sahinalp, S Cenk; Tse, David N

    2018-04-26

    The original version of this Article contained errors in the affiliations of the authors Ibrahim Numanagić and Thomas A. Courtade, which were incorrectly given as 'Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA' and 'Computer Science & Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA', respectively. Also, the hyperlink for the source code in the Data Availability section was incorrectly given as https://github.iu.edu/kzhu/assembltrie , which links to a page that is not publicly accessible. The source code is publicly accessible at https://github.com/kyzhu/assembltrie . Furthermore, in the PDF version of the Article, the right-hand side of Figure 3 was inadvertently cropped. These errors have now been corrected in both the PDF and HTML versions of the Article.

  3. Publishing bioethics and bioethics--reflections on academic publishing by a journal editor.

    Science.gov (United States)

    Schüklenk, Udo

    2011-02-01

    This article by one of the Editors of Bioethics, published in the 25th anniversary issue of the journal, describes some of the revolutionary changes academic publishing has undergone during the last decades. Many humanities journals went from typically small print-runs, counting by the hundreds, to on-line availability in thousands of university libraries worldwide. Article up-take by our subscribers can be measured efficiently. The implications of this and other changes to academic publishing are discussed. Important ethical challenges need to be addressed in areas such as the enforcement of plagiarism-related policies, the so-called 'impact factor' and its impact on academic integrity, and the question of whether on-line only publishing can currently guarantee the integrity of academic publishing histories. © 2010 Blackwell Publishing Ltd.

  4. Reinvention of publishers' revenue model: expectations of advertisers towards publishers' products

    OpenAIRE

    Koller, Hans; Dennstedt, Bianca

    2017-01-01

    Publishers have to reconsider their revenue model. Facing a massive decline in the circulation of newspapers and magazines over the past years, publishers have lost not only readers but also many advertisers. Thus, publishers are faced with both changed customer expectations as well as difficulty in generating profit. Users are increasingly less willing to pay for digital products and their expectations of digital content have changed: They would like to contribute their own content as well a...

  5. Serine Protease Variants Encoded by Echis ocellatus Venom Gland cDNA: Cloning and Sequencing Analysis

    Directory of Open Access Journals (Sweden)

    S. S. Hasson

    2010-01-01

    Full Text Available Envenoming by Echis saw-scaled viper is the leading cause of death and morbidity in Africa due to snake bite. Despite its medical importance, there have been few investigations into the toxin composition of the venom of this viper. Here, we report the cloning of cDNA sequences encoding four groups or isoforms of the haemostasis-disruptive Serine protease proteins (SPs from the venom glands of Echis ocellatus. All these SP sequences encoded the cysteine residues scaffold that form the 6-disulphide bonds responsible for the characteristic tertiary structure of venom serine proteases. All the Echis ocellatus EoSP groups showed varying degrees of sequence similarity to published viper venom SPs. However, these groups also showed marked intercluster sequence conservation across them which were significantly different from that of previously published viper SPs. Because viper venom SPs exhibit a high degree of sequence similarity and yet exert profoundly different effects on the mammalian haemostatic system, no attempt was made to assign functionality to the new Echis ocellatus EoSPs on the basis of sequence alone. The extraordinary level of interspecific and intergeneric sequence conservation exhibited by the Echis ocellatus EoSPs and analogous serine proteases from other viper species leads us to speculate that antibodies to representative molecules should neutralise (that we will exploit, by epidermal DNA immunization the biological function of this important group of venom toxins in vipers that are distributed throughout Africa, the Middle East, and the Indian subcontinent.

  6. PUBLISHER'S ANNOUNCEMENT: Editorial developments Editorial developments

    Science.gov (United States)

    2010-01-01

    I am delighted to inform you that from January 2010 Professor Alfred K Louis of the University of Saarland, Germany, will be the new Editor-in-Chief of Inverse Problems. Alfred joins us with a wealth of experience and a great deal of respect from the community. He has served the journal in a number of ways as an Editorial Board member, outstanding reviewer and author. We very much look forward to working with him to continue to publish the highest quality articles in the field and build on our extremely successful special section and topical review programmes. Whilst welcoming Alfred to the position, we are also keen to thank our outgoing Editor-in-Chief, Professor Bill Symes, for the fabulous job that he has done over the past five years. Under Bill's direction, Inverse Problems has gone from strength to strength. In fact, in the last year we have taken the step of moving from six to 12 issues a year, reflecting the increased number of high-quality papers submitted to the journal. During the last five years we have published a wide range of fantastic special sections and topical reviews, including a celebration of the journal's 25th year (issue 12 2009), in which Bill played a pivotal role. We are very much looking forward to 2010 and will be celebrating our 25th birthday further with a selection of highlighted articles chosen from the past 25 years. We hope that you will continue to enjoy reading the journal. If you have any feedback, comments or questions, please do not hesitate to contact us at ip@iop.org. Zoë Crossman Publisher

  7. Scientific Publishing and the Data Deluge (Invited)

    Science.gov (United States)

    Hanson, B.

    2010-12-01

    The ability to collect and analyze huge data sets is changing and revolutionizing many aspects of science, including scientific publishing. Policies and practices with respect to data management and archiving have been evolving at journals, but many outstanding problems and challenges have emerged and some are growing. Journals have an evolving mission including a traditional role in advancing science and an increasingly important role of accrediting peer-reviewed research used in public policy and the legal and regulatory systems. Publishing is increasingly responsible for assuring the reliability and transparency of data for both uses, and policies have been evolving to meet these goals. Most journals now include data supplements and have strengthened sharing and archiving requirements. For example, Science now requires all references to be available (published) at publication, and to the extent possible, supporting data to be archived in online supplements. Many problems remain and are growing: Journals cannot handle some of the large data sets routinely being produced now, and must rely on public databases. Of these, too many do not have reliable funding, and others (e.g., personal or institutional WWW sites) are not reliably curated. Much usable data is being discarded. Journals are in the role of monitoring and in too many cases enforcing deposition and sharing of data. Presentation and visualization of data requires new tools that are challenging to standardize and maintain, and to represent within traditional formats still used by most users. Much data is being archived in a minimally usable form (PDF) without common metadata. A growing burden is being placed on reviewers and editors as papers are longer and more complex, and many journals are seeing large growths in submissions. In some disciplines, huge private data sets, third-party data, or privacy issues are increasingly important, and scientists and journals may be unaware of use restrictions. It is

  8. Conceiving, Writing and Publishing a Scientific Paper

    Directory of Open Access Journals (Sweden)

    Marta Christina Suciu

    2018-02-01

    Full Text Available I consider that the second edition of the book “Conceiving, Writing and Publishing a Scientific Paper. An approach in the context of economic research” is a work of high scientific standing, excellently documented, addressed to knowledgeable readers but also to the new generations of PhD students and researchers interested in attaining the highest academic and scientific performances in the field of Economics. From my point of view, both editions of the book are highly useful for the academic environment. I especially appreciate the authors’ efforts to improve and expand the second edition. This fact is due to the changes occurred in the evolution of scientometric indicators, to the feedback received from readers, but also as the result of the desire to include multiple networks and platforms that take into account professional and institutional profiles, such as to facilitate the researchers’ dissemination of their results obtained in the scientific research activity. The authors benefit on an unanimous recognition and are highly appreciated., fact proven for example by the ten existing reviews of the book’s first edition, published in journals indexed in Web of Science, Scopus and other international databases. I am mostly impressed by the authors’ permanent concern to improve their book’s scientific content. The first edition was awarded the distinction “The Best Book in the Field of Economics” published in 2016 in Romania by the Association of Romanian Economic Faculties, but also by The Association of Cultural-Educational Cooperation from Suceava (ACCES prize in 2016

  9. XML Publishing with Adobe InDesign

    CERN Document Server

    Hoskins, Dorothy

    2010-01-01

    From Adobe InDesign CS2 to InDesign CS5, the ability to work with XML content has been built into every version of InDesign. Some of the useful applications are importing database content into InDesign to create catalog pages, exporting XML that will be useful for subsequent publishing processes, and building chunks of content that can be reused in multiple publications. In this Short Cut, we'll play with the contents of a college course catalog and see how we can use XML for course descriptions, tables, and other content. Underlying principles of XML structure, DTDs, and the InDesign namesp

  10. Tackling Tumblr Web Publishing Made Simple

    CERN Document Server

    Hedengren, Thord Daniel

    2011-01-01

    A comprehensive guide to the popular web publishing site Tumblr The popularity of Tumblr is growing by leaps and bounds, as it continues to make a name for itself as a reliable, accessible blogging platform. Yet, there is very little documentation on Tumblr, leaving newcomers confused as to where to start. That's where this helpful book comes in. Written by well-respected author Thord Hedengren, this step-by-step guide is an ideal starting point for Tumblr newcomers as well as web designers who want to take their Tumblblogs to the next level. You'll learn how to maximize the full potential of

  11. Astronomical Publishing: Yesterday, Today and Tomorrow

    Science.gov (United States)

    Huchra, John

    Just in the last few years scientific publishing has moved rapidly away from the modes that served it well for over two centuries. As "digital natives" take over the field and rapid and open access comes to dominate the way we communicate, both scholarly journals and libraries need to adopt new business models to serve their communities. This is best done by identifying new "added value" such as databases, full text searching, full cross indexing while at the same time retaining the high quality of peer reviewed publication.

  12. Pioneers, publishers and the dissemination of archaeological knowledge: A study of publishing in British archaeology 1816-1851

    Directory of Open Access Journals (Sweden)

    Sarah Scott

    2013-08-01

    Full Text Available The first half of the nineteenth century was a formative period in the development of archaeology as a discipline and archaeological publishing played a key role in this. Libraries were an essential marker of social and intellectual status and there now exists a considerable body of scholarship on the most impressive publications of the day and on the factors influencing their presentation; for example, in relation to the publication of Mediterranean classical antiquities. The crucial role which publishers played in the selection and dissemination of scholarship has been addressed in recent studies of the history of the book, and there is a growing literature on the role of publishers in the dissemination of scientific knowledge, but there has to date been very limited evaluation of the role of publishers in the selection and dissemination of archaeological knowledge in Britain in this period. This study will investigate the extent to which the publication and dissemination of archaeological knowledge, and hence the discipline itself, was shaped by the intellectual and/or commercial concerns of publishers, with a view to providing a more nuanced understanding of the ways in which knowledge was filtered and the impact that this had. Key trends in archaeological publishing in the period 1816-51 will be identified, based on the London Catalogue of Books, and will show how and why this kind of study should be seen as an essential component of any research which considers the history of the discipline. Selected case studies will show the immense, and previously unacknowledged, importance of decisions made during the publication process on the development of archaeology in Britain, and directions for further study will be identified.

  13. Desktop Publishing: A Brave New World and Publishing from the Desktop.

    Science.gov (United States)

    Lormand, Robert; Rowe, Jane J.

    1988-01-01

    The first of two articles presents basic selection criteria for desktop publishing software packages, including discussion of expectations, required equipment, training costs, publication size, desired software features, additional equipment needed, and quality control. The second provides a brief description of desktop publishing using the Apple…

  14. Scientific Journal Publishing in India: Promoting electronic publishing of scholarly journals in India

    OpenAIRE

    Abraham, Thomas; Minj, Suvarsha

    2007-01-01

    Provides a report about the Scientific Journal Publishing in India (SJPI) Project which promotes electronic publishing of scholarly journals. It covers briefly the objectives, implementation and outcomes of the Project. Open Journal Systems and Open Archives Harvester were used to achieve the goals of the Project.

  15. Entomological journals and publishing in Japan.

    Science.gov (United States)

    Fukatsu, Takema

    Here I present an overview of entomological journals and publishing in Japan, thereby providing a convenient portal to the valuable scientific resources for the world's entomological researchers and scientific communities. Currently, except for several international journals published fully in English such as Applied Entomology and Zoology and Entomological Science , many entomological and entomology-related journals in Japan are not indexed by major scientific databases like Web of Science, and therefore they are neither conveniently recognizable nor accessible for the world's entomological communities. However, I point out that many of the contents of such journals are freely available via Japan's public platforms for electronic scientific literature, Japan Science and Technology Information Aggregator, Electronic (J-stage) or Citation Information by National Institute of Informatics (CiNii). Here I list 32 entomological and entomology-related societies and their 45 journals, the majority of which belong to either the Union of Japanese Societies for Insect Sciences (UJSIS), the Union of the Japanese Societies for Systematic Biology (UJSSB), the Union of Japanese Societies for Natural History (UJSNH), or the Union of Japanese Societies for Biological Science (UJSBS), with their respective URL and open-access availability.

  16. Open meeting on changing the publishing model

    CERN Multimedia

    2005-01-01

    The Director-General is calling all CERN editors and authors to a meeting to contribute to the discussion on the direction that CERN should take in its experimentation with new publishing models. The current subscription-funded publishing model for journal articles (where access to a particular journal is granted upon payment of a subscription, often arranged by the institutional library) has been the status quo for many years. However, new evidence suggests that removing this subscription barrier gives access to a greater number of readers and so leads to a higher citation rate and therefore greater impact. New so-called Open Access models are emerging but these require the support of authors and editors to be successful. A number of presentations have been solicited which will explain the background to the current situation and Chief Scientific Officer, Jos Engelen, will lead a discussion about the pros and cons of CERN following a particular model. Your input and support is crucial to the success of suc...

  17. Copyright case a victory for science publishing

    Science.gov (United States)

    Cole, Stephen

    An important victory for the financial health and future of scientific journals was won July 23 when Judge Pierre Leval of the Federal District Court in New York handed down his decision on the copyright infringement suit, American Geophysical Union, et al. v. Texaco Inc. Leval ruled that profit-making companies cannot photocopy copyrighted journal articles without permission and without compensating the copyright holder.The class action suit was brought in 1985 by AGU and six other scientific publishers on behalf of 8500 publishers worldwide who make their titles available for legal copying under licenses granted by the Copyright Clearance Center, Inc. This licensing system was designed in cooperation with major corporations to facilitate compliance with the 1976 Copyright Act. Although more than 200 companies now use the center, some corporations, such as Texaco, have not. The suit was initiated to force compliance with copyright law. The current decision is very important because it establishes legal precedents on the “fair use” issue.

  18. Publish or perish: tools for survival

    Directory of Open Access Journals (Sweden)

    Quan SF

    2017-02-01

    Full Text Available No abstract available. Article truncated at 150 words. Success in one’s chosen profession is often predicated upon meeting a profession-wide standard of excellence or productivity. In the corporate world, the metric might be sales volume and in clinical medicine it may be patient satisfaction and/or number of patients seen. In academic medicine, including the fields of Pulmonary and Critical Care Medicine, the “coin of the realm” is demonstrable written scholarship. In large part, this is determined by the number and quality of publications in scientific journals. Unfortunately, the skills required to navigate the complexities of how to publish in the scientific literature rarely are taught in either medical school or postgraduate training. To assist the inexperienced academic physician or scientist, the Writing for Scholarship Interest Group of the Harvard Medical School Academy recently published “A Writer’s Toolkit” (1. This comprehensive monograph provides valuable information on all phases of the writing process ranging from conceptualization of a manuscript to …

  19. AAS Publishing News: Astronomical Software Citation Workshop

    Science.gov (United States)

    Kohler, Susanna

    2015-07-01

    Do you write code for your research? Use astronomical software? Do you wish there were a better way of citing, sharing, archiving, or discovering software for astronomy research? You're not alone! In April 2015, AAS's publishing team joined other leaders in the astronomical software community in a meeting funded by the Sloan Foundation, with the purpose of discussing these issues and potential solutions. In attendance were representatives from academic astronomy, publishing, libraries, for-profit software sharing platforms, telescope facilities, and grantmaking institutions. The goal of the group was to establish “protocols, policies, and platforms for astronomical software citation, sharing, and archiving,” in the hopes of encouraging a set of normalized standards across the field. The AAS is now collaborating with leaders at GitHub to write grant proposals for a project to develop strategies for software discoverability and citation, in astronomy and beyond. If this topic interests you, you can find more details in this document released by the group after the meeting: http://astronomy-software-index.github.io/2015-workshop/ The group hopes to move this project forward with input and support from the broader community. Please share the above document, discuss it on social media using the hashtag #astroware (so that your conversations can be found!), or send private comments to julie.steffen@aas.org.

  20. [Reconstruction of the phylogenetic position of larch (Larix sukaczewii Dylis) by sequencing data for the trnK intron of chloroplast DNA].

    Science.gov (United States)

    Bashalkhanov, S I; Konstantinov, Iu M; Verbitskiĭ, D S; Kobzev, V F

    2003-10-01

    To reconstruct the systematic relationships of larch Larix sukaczewii, we used the chloroplast trnK intron sequences of L. decidua, L. sukaczewii, L. sibirica, L. czekanovskii, and L. gmelinii. Analysis of phylogenetic trees constructed using the maximum parsimony and maximum likelihood methods showed a clear divergence of the trnK intron sequences between L. sukaczewii and L. sibirica. This divergence reaches intraspecific level, which supports a previously published hypothesis on the taxonomic isolation of L. sukaczewii.

  1. An automated annotation tool for genomic DNA sequences using

    Indian Academy of Sciences (India)

    Genomic sequence data are often available well before the annotated sequence is published. We present a method for analysis of genomic DNA to identify coding sequences using the GeneScan algorithm and characterize these resultant sequences by BLAST. The routines are used to develop a system for automated ...

  2. PUBLISHER'S ANNOUNCEMENT: Editorial developments Editorial developments

    Science.gov (United States)

    Gillan, Rebecca

    2009-01-01

    We are delighted to announce that from January 2009, Professor Murray T Batchelor of the Australian National University, Canberra will be the new Editor-in-Chief of Journal of Physics A: Mathematical and Theoretical. Murray Batchelor has been Editor of the Mathematical Physics section of the journal since 2007. Prior to this, he served as a Board Member and an Advisory Panel member for the journal. His primary area of research is the statistical mechanics of exactly solved models. He holds a joint appointment in mathematics and physics and has held visiting positions at the Universities of Leiden, Amsterdam, Oxford and Tokyo. We very much look forward to working with Murray to continue to improve the journal's quality and interest to the readership. We would like to thank our outgoing Editor-in-Chief, Professor Carl M Bender. Carl has done a magnificent job as Editor-in-Chief and has worked tirelessly to improve the journal over the last five years. Carl has been instrumental in designing and implementing strategies that have enhanced the quality of papers published and service provided by Journal of Physics A: Mathematical and Theoretical. Notably, under his tenure, we have introduced the Fast Track Communications (FTC) section to the journal. This section provides a venue for outstanding short papers that report new and timely developments in mathematical and theoretical physics and offers accelerated publication and high visibility for our authors. During the last five years, we have raised the quality threshold for acceptance in the journal and now reject over 60% of submissions. As a result, papers published in Journal of Physics A: Mathematical and Theoretical are amongst the best in the field. We have also maintained and improved on our excellent receipt-to-first-decision times, which now average less than 50 days for papers. We have recently announced another innovation; the Journal of Physics A Best Paper Prize. These prizes will honour excellent papers

  3. Predictive effects of previous episodes on the risk of recurrence in depressive and bipolar disorders

    DEFF Research Database (Denmark)

    Kessing, Lars Vedel; Andersen, Per Kragh

    2005-01-01

    Findings from several studies have suggested that the risk of recurrence increases with the number of previous episodes in depressive and bipolar disorders. However, a comprehensive and critical review of the literature published during the past century shows that in several previous studies...

  4. Webmail: an Automated Web Publishing System

    Science.gov (United States)

    Bell, David

    A system for publishing frequently updated information to the World Wide Web will be described. Many documents now hosted by the NOAO Web server require timely posting and frequent updates, but need only minor changes in markup or are in a standard format requiring only conversion to HTML. These include information from outside the organization, such as electronic bulletins, and a number of internal reports, both human and machine generated. Webmail uses procmail and Perl scripts to process incoming email messages in a variety of ways. This processing may include wrapping or conversion to HTML, posting to the Web or internal newsgroups, updating search indices or links on related pages, and sending email notification of the new pages to interested parties. The Webmail system has been in use at NOAO since early 1997 and has steadily grown to include fourteen recipes that together handle about fifty messages per week.

  5. A Learned Society's Perspective on Publishing.

    Science.gov (United States)

    Suzuki, Kunihiko; Edelson, Alan; Iversen, Leslie L; Hausmann, Laura; Schulz, Jörg B; Turner, Anthony J

    2016-10-01

    Scientific journals that are owned by a learned society, like the Journal of Neurochemistry (JNC), which is owned by the International Society for Neurochemistry (ISN), benefit the scientific community in that a large proportion of the income is returned to support the scientific mission of the Society. The income generated by the JNC enables the ISN to organize conferences as a platform for members and non-members alike to share their research, supporting researchers particularly in developing countries by travel grants and other funds, and promoting education in student schools. These direct benefits and initiatives for ISN members and non-members distinguish a society journal from pure commerce. However, the world of scholarly publishing is changing rapidly. Open access models have challenged the business model of traditional journal subscription and hence provided free access to publicly funded scientific research. In these models, the manuscript authors pay a publication cost after peer review and acceptance of the manuscript. Over the last decade, numerous new open access journals have been launched and traditional subscription journals have started to offer open access (hybrid journals). However, open access journals follow the general scheme that, of all participating parties, the publisher receives the highest financial benefit. The income is generated by researchers whose positions and research are mostly financed by taxpayers' or funders' money, and by reviewers and editors, who frequently are not reimbursed. Last but not least, the authors pay for the publication of their work after a rigorous and sometimes painful review process. JNC itself has an open access option, at a significantly reduced cost for Society members as an additional benefit. This article provides first-hand insights from two former Editors-in-Chief, Kunihiko Suzuki and Leslie Iversen, about the history of JNC's ownership and about the difficulties and battles fought along the way to

  6. Promotion and monetization in publishing mobile applications

    Directory of Open Access Journals (Sweden)

    Fernando Peinado Miguel

    2016-07-01

    Full Text Available The road to new technologies and digital systems of transmission of the message produce unpublished business channels to support the media management current. And the printed media can benefit since they can find greater advantages in this new channel of increasing consumption: mobile greater advantages in this new channel of increasing consumption: mobile applications. The modern editor coexists with these new technologies, scheduled or native applications on web languages that offer multiple possibilities of loyalty, monetization, distribution and synergies with the channels already considered classics. The study of apps to generate revenue in the media can be the new contextual paradigm of the Periodismo and establish the key factors for a better profitability of the participants this industry, increasingly weakened financially and business by the accelerated arrival of technology in publishing groups accustomed to changes of slow evolution.

  7. Next-generation sequencing can reveal in vitro-generated PCR crossover products: some artifactual sequences correspond to HLA alleles in the IMGT/HLA database.

    Science.gov (United States)

    Holcomb, C L; Rastrou, M; Williams, T C; Goodridge, D; Lazaro, A M; Tilanus, M; Erlich, H A

    2014-01-01

    The high-resolution human leukocyte antigen (HLA) genotyping assay that we developed using 454 sequencing and Conexio software uses generic polymerase chain reaction (PCR) primers for DRB exon 2. Occasionally, we observed low abundance DRB amplicon sequences that resulted from in vitro PCR 'crossing over' between DRB1 and DRB3/4/5. These hybrid sequences, revealed by the clonal sequencing property of the 454 system, were generally observed at a read depth of 5%-10% of the true alleles. They usually contained at least one mismatch with the IMGT/HLA database, and consequently, were easily recognizable and did not cause a problem for HLA genotyping. Sometimes, however, these artifactual sequences matched a rare allele and the automatic genotype assignment was incorrect. These observations raised two issues: (1) could PCR conditions be modified to reduce such artifacts? and (2) could some of the rare alleles listed in the IMGT/HLA database be artifacts rather than true alleles? Because PCR crossing over occurs during late cycles of PCR, we compared DRB genotypes resulting from 28 and (our standard) 35 cycles of PCR. For all 21 cell line DNAs amplified for 35 cycles, crossover products were detected. In 33% of the cases, these hybrid sequences corresponded to named alleles. With amplification for only 28 cycles, these artifactual sequences were not detectable. To investigate whether some rare alleles in the IMGT/HLA database might be due to PCR artifacts, we analyzed four samples obtained from the investigators who submitted the sequences. In three cases, the sequences were generated from true alleles. In one case, our 454 sequencing revealed an error in the previously submitted sequence. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  8. Issues in Science Publishing. What's Hot and What's not?

    Directory of Open Access Journals (Sweden)

    Jaime A. Teixeira da Silva

    2015-06-01

    Full Text Available Science is in crisis: a crisis of trust, and a crisis of values. Yet, this is an opportune moment for scientists to examine the issues that underly science to discover how they may be of use, beyond their laboratory or field experience, to improve the research and publishing landscapes to create an environment that suits their needs more. Traditionally, the science publishing landscape had been controlled by the science, technology and medicine publishers, who have always taunted their peer review systems as being fail-safe. Yet, considerable moss has been gathered by the post-publication peer review (PPPR movement over the past few years, indicating that the voice of the average scientist now carries more weight, and more value, than ever before. Despite this, most scientists are unaware of their potential power of opinion. Especially when it comes to commenting on, and correcting, the already published literature. Commenting by name, or anonymously, is the new PPPR publishing reality. There needs to also be a concomitant movement away from artificial metrics, such as the impact factor, which serve only as ego-boosting parameters, and which distract the wider readership from the weaknesses of the traditional peer review system currently in place. Increasing cases of the abuse of peer review, such as the creation of fake identities, affiliations or e-mail addresses further highlights the need for scientists to be vigilant, without necessairly being vigilantes. The discovery, within a matter of years, that the literature is more corrupted than was previously thought, in some cases caused by clear cases of editorial cronyism, or abuse, has resulted in a need for scientists to exceed their functions as mere scientists to evolve into whistle-blowers. Some ethical guidelines are in place, such as those by COPE, yet what is being increasingly witnessed, is a discrepancy between preached values by select COPE member journals, and the literature that

  9. Biomedical informatics: we are what we publish.

    Science.gov (United States)

    Elkin, P L; Brown, S H; Wright, G

    2013-01-01

    This article is part of a For-Discussion-Section of Methods of Information in Medicine on "Biomedical Informatics: We are what we publish". It is introduced by an editorial and followed by a commentary paper with invited comments. In subsequent issues the discussion may continue through letters to the editor. Informatics experts have attempted to define the field via consensus projects which has led to consensus statements by both AMIA. and by IMIA. We add to the output of this process the results of a study of the Pubmed publications with abstracts from the field of Biomedical Informatics. We took the terms from the AMIA consensus document and the terms from the IMIA definitions of the field of Biomedical Informatics and combined them through human review to create the Health Informatics Ontology. We built a terminology server using the Intelligent Natural Language Processor (iNLP). Then we downloaded the entire set of articles in Medline identified by searching the literature by "Medical Informatics" OR "Bioinformatics". The articles were parsed by the joint AMIA / IMIA terminology and then again using SNOMED CT and for the Bioinformatics they were also parsed using HGNC Ontology. We identified 153,580 articles using "Medical Informatics" and 20,573 articles using "Bioinformatics". This resulted in 168,298 unique articles and an overlap of 5,855 articles. Of these 62,244 articles (37%) had titles and abstracts that contained at least one concept from the Health Informatics Ontology. SNOMED CT indexing showed that the field interacts with most all clinical fields of medicine. Further defining the field by what we publish can add value to the consensus driven processes that have been the mainstay of the efforts to date. Next steps should be to extract terms from the literature that are uncovered and create class hierarchies and relationships for this content. We should also examine the high occurring of MeSH terms as markers to define Biomedical Informatics

  10. Sequencing BPS spectra

    Energy Technology Data Exchange (ETDEWEB)

    Gukov, Sergei [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Max-Planck-Institut für Mathematik,Vivatsgasse 7, D-53111 Bonn (Germany); Nawata, Satoshi [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Centre for Quantum Geometry of Moduli Spaces, University of Aarhus,Nordre Ringgade 1, DK-8000 (Denmark); Saberi, Ingmar [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Stošić, Marko [CAMGSD, Departamento de Matemática, Instituto Superior Técnico,Av. Rovisco Pais, 1049-001 Lisbon (Portugal); Mathematical Institute SANU,Knez Mihajlova 36, 11000 Belgrade (Serbia); Sułkowski, Piotr [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland)

    2016-03-02

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  11. Sequencing BPS spectra

    International Nuclear Information System (INIS)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-01-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  12. Bioinformatics for whole-genome shotgun sequencing of microbial communities.

    Directory of Open Access Journals (Sweden)

    Kevin Chen

    2005-07-01

    Full Text Available The application of whole-genome shotgun sequencing to microbial communities represents a major development in metagenomics, the study of uncultured microbes via the tools of modern genomic analysis. In the past year, whole-genome shotgun sequencing projects of prokaryotic communities from an acid mine biofilm, the Sargasso Sea, Minnesota farm soil, three deep-sea whale falls, and deep-sea sediments have been reported, adding to previously published work on viral communities from marine and fecal samples. The interpretation of this new kind of data poses a wide variety of exciting and difficult bioinformatics problems. The aim of this review is to introduce the bioinformatics community to this emerging field by surveying existing techniques and promising new approaches for several of the most interesting of these computational problems.

  13. The past, present and future of mitochondrial genomics: have we sequenced enough mtDNAs?

    Science.gov (United States)

    Smith, David Roy

    2016-01-01

    The year 2014 saw more than a thousand new mitochondrial genome sequences deposited in GenBank-an almost 15% increase from the previous year. Hundreds of peer-reviewed articles accompanied these genomes, making mitochondrial DNAs (mtDNAs) the most sequenced and reported type of eukaryotic chromosome. These mtDNA data have advanced a wide range of scientific fields, from forensics to anthropology to medicine to molecular evolution. But for many biological lineages, mtDNAs are so well sampled that newly published genomes are arguably no longer contributing significantly to the progression of science, and in some cases they are tying up valuable resources, particularly journal editors and referees. Is it time to acknowledge that as a research community we have published enough mitochondrial genome papers? Here, I address this question, exploring the history, milestones and impacts of mitochondrial genomics, the benefits and drawbacks of continuing to publish mtDNAs at a high rate and what the future may hold for such an important and popular genetic marker. I highlight groups for which mtDNAs are still poorly sampled, thus meriting further investigation, and recommend that more energy be spent characterizing aspects of mitochondrial genomes apart from the DNA sequence, such as their chromosomal and transcriptional architectures. Ultimately, one should be mindful before writing a mitochondrial genome paper. Consider perhaps sending the sequence directly to GenBank instead, and be sure to annotate it correctly before submission. © The Author 2015. Published by Oxford University Press.

  14. Publisher Correction: Measuring progress from nationally determined contributions to mid-century strategies

    Science.gov (United States)

    Iyer, Gokul; Ledna, Catherine; Clarke, Leon; Edmonds, James; McJeon, Haewon; Kyle, Page; Williams, James H.

    2018-03-01

    In the version of this Article previously published, technical problems led to the wrong summary appearing on the homepage, and an incorrect Supplementary Information file being uploaded. Both errors have now been corrected.

  15. A second chance for authors of hijacked journals to publish in legitimate journals.

    Science.gov (United States)

    Jalalian, Mehrdad

    2015-01-01

    This article proposes the republication of articles that have previously been published in counterfeit websites of hijacked journals. The paper also discusses the technical and ethical aspects of republishing such articles.

  16. Determination of genetic relatedness from low-coverage human genome sequences using pedigree simulations.

    Science.gov (United States)

    Martin, Michael D; Jay, Flora; Castellano, Sergi; Slatkin, Montgomery

    2017-08-01

    We develop and evaluate methods for inferring relatedness among individuals from low-coverage DNA sequences of their genomes, with particular emphasis on sequences obtained from fossil remains. We suggest the major factors complicating the determination of relatedness among ancient individuals are sequencing depth, the number of overlapping sites, the sequencing error rate and the presence of contamination from present-day genetic sources. We develop a theoretical model that facilitates the exploration of these factors and their relative effects, via measurement of pairwise genetic distances, without calling genotypes, and determine the power to infer relatedness under various scenarios of varying sequencing depth, present-day contamination and sequencing error. The model is validated by a simulation study as well as the analysis of aligned sequences from present-day human genomes. We then apply the method to the recently published genome sequences of ancient Europeans, developing a statistical treatment to determine confidence in assigned relatedness that is, in some cases, more precise than previously reported. As the majority of ancient specimens are from animals, this method would be applicable to investigate kinship in nonhuman remains. The developed software grups (Genetic Relatedness Using Pedigree Simulations) is implemented in Python and freely available. © 2017 John Wiley & Sons Ltd.

  17. IAEA publishes first health and safety manual

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1959-01-15

    A 'Manual on the Safe Handling of Radioisotopes' was published in English on 15 Dec ember 1958 by the International Atomic Energy Agency. This is a comprehensive handbook of internationally compiled recommendations for users of radioisotopes. It covers organizational, medical and technical aspects of radiation safety practices. It is also the Agency's first technical publication. French, Russian and Spanish editions will appear shortly. The Manual should prove useful to all users of radioisotopes in industry, medicine, research, etc., but is directed mainly to small scale users who may not have access to other sources of information. The recommendations apply only to radioactivity surpassing the limit of 0,002 microcurie concentration per gram of material; or a total activity of more than 0,1 microcuries in the working areas; this limit is based on the most dangerous radioisotopes. The experts state that the limiting level might be higher for less dangerous isotopes, but recommend that all be treated as potentially dangerous. This would have educational value and avoid accidents caused by misidentification. The Manual also stressed that good radiation safety practices depend on effective organization and warns that even very competent workers sometimes ignore or forget important health and safety requirements.

  18. History of attempts to publish a paper

    International Nuclear Information System (INIS)

    Kowalski, Ludwik

    2006-01-01

    A paper reviewing recent cold fusion claim, written by the author in 2004, has been rejected (without sending it to referees and without offering any criticism) by editors of seven journals, namely, Physics Today (USA), American Scientist (USA), Scientific American (USA), Nature (UK), New Scientist (UK), The Physics Teacher (USA), Science (USA). The present paper has the following contents: 1. Here is how my paper was introduced to the editor of one of the above journals. Other accompanied letters were similar; 2. In rejecting my paper the editor of Physics Today wrote; 3. And here how the editor of American Scientist responded to my submission; 4. Responding to the above I wrote; 5. Seek not the golden egg, seek the goose; 6. In a subsequent reply I wrote; 7. The manuscript was submitted to Scientific American; 8. I then tried to publish the paper in Nature; 9. I then tried another UK journal, New Scientist; 10. My immediate reply; 11. The manuscript was then submitted to the Editor in chief of Science

  19. History of attempts to publish a paper

    Energy Technology Data Exchange (ETDEWEB)

    Kowalski, Ludwik [Department of Mathematical Sciences, Montclair State University, 341, Brook Avenue, Passaic NJ, 07055 (United States)

    2006-07-01

    A paper reviewing recent cold fusion claim, written by the author in 2004, has been rejected (without sending it to referees and without offering any criticism) by editors of seven journals, namely, Physics Today (USA), American Scientist (USA), Scientific American (USA), Nature (UK), New Scientist (UK), The Physics Teacher (USA), Science (USA). The present paper has the following contents: 1. Here is how my paper was introduced to the editor of one of the above journals. Other accompanied letters were similar; 2. In rejecting my paper the editor of Physics Today wrote; 3. And here how the editor of American Scientist responded to my submission; 4. Responding to the above I wrote; 5. Seek not the golden egg, seek the goose; 6. In a subsequent reply I wrote; 7. The manuscript was submitted to Scientific American; 8. I then tried to publish the paper in Nature; 9. I then tried another UK journal, New Scientist; 10. My immediate reply; 11. The manuscript was then submitted to the Editor in chief of Science.

  20. New developments in publishing related to authorship.

    Science.gov (United States)

    Donev, Doncho

    2014-01-01

    To present the inappropriate types of authorship and practice, and the most recent developments related to basic principles and criteria to a fair system for allocating authorship in scientific publications. An analysis of relevant materials and documents, sources from the internet and published literature and personal experience and observations of the author. Working in multidisciplinary teams is a common feature of modern research processes. The most sensitive question is how to decide on who to acknowledge as author of a multi-authored publication. The pertinence of this question is growing with the increasing importance of individual scientists' publication records for professional status and career. However, discussions about authorship allocation might lead to serious conflicts and disputes among coworkers which could even endanger cooperation and successful completion of a research project. It seems that discussion and education about ethical standards and practical guidelines for fairly allocating authorship are insufficient and the question of ethical practices related to authorship in multi-authored publications remains generally unresolved. It is necessary to work for raising awareness about the importance and need for education about principles of scientific communication and fair allocation of authorship, ethics of research and publication of results. The use of various forms of education in the scientific community, especially young researchers and students, in order to create an ethical environment, is one of the most effective ways to prevent the emergence of scientific and publication dishonesty and fraud, including pathology of authorship.

  1. IAEA publishes first health and safety manual

    International Nuclear Information System (INIS)

    1959-01-01

    A 'Manual on the Safe Handling of Radioisotopes' was published in English on 15 Dec ember 1958 by the International Atomic Energy Agency. This is a comprehensive handbook of internationally compiled recommendations for users of radioisotopes. It covers organizational, medical and technical aspects of radiation safety practices. It is also the Agency's first technical publication. French, Russian and Spanish editions will appear shortly. The Manual should prove useful to all users of radioisotopes in industry, medicine, research, etc., but is directed mainly to small scale users who may not have access to other sources of information. The recommendations apply only to radioactivity surpassing the limit of 0,002 microcurie concentration per gram of material; or a total activity of more than 0,1 microcuries in the working areas; this limit is based on the most dangerous radioisotopes. The experts state that the limiting level might be higher for less dangerous isotopes, but recommend that all be treated as potentially dangerous. This would have educational value and avoid accidents caused by misidentification. The Manual also stressed that good radiation safety practices depend on effective organization and warns that even very competent workers sometimes ignore or forget important health and safety requirements

  2. Publishing integrity and good practices in editing in biomedicine.

    Science.gov (United States)

    Polenakovic, Momir; Gucev, Zoran

    2014-01-01

    accept reports which support the reviewer's concepts of thinking and, like Procrustes, cutting everything else out. Authorship is often a contentious issue, as undeserved authors appear on the list of authors. Some principles are now a norm in academic publishing. This applies to the declaration of a conflict of interest, the consent of the patient and the approval of the Ethical Board of the institution. This global informational technological revolution has, unfortunately, led to largely widespread and increasingly sophisticated deviations: plagiarism, data fabrication and data falsification as forms of scientific misconduct. Those events are now more widespread than in the past. Luckily new tools to track them are much better than previously. The race for perfect publishing integrity and for the best good practices in editing in biomedicine is on. New and old challenges will be met. The benevolent and caring society, educated professionals and an enlightened public remain essential preconditions. The wealth of nations depends on R&D and consequently on academic publishing.

  3. Why should we publish Linked Data?

    Science.gov (United States)

    Blower, Jon; Riechert, Maik; Koubarakis, Manolis; Pace, Nino

    2016-04-01

    We use the Web every day to access information from all kinds of different sources. But the complexity and diversity of scientific data mean that discovering accessing and interpreting data remains a large challenge to researchers, decision-makers and other users. Different sources of useful information on data, algorithms, instruments and publications are scattered around the Web. How can we link all these things together to help users to better understand and exploit earth science data? How can we combine scientific data with other relevant data sources, when standards for describing and sharing data vary so widely between communities? "Linked Data" is a term that describes a set of standards and "best practices" for sharing data on the Web (http://www.w3.org/standards/semanticweb/data). These principles can be summarised as follows: 1. Create unique and persistent identifiers for the important "things" in a community (e.g. datasets, publications, algorithms, instruments). 2. Allow users to "look up" these identifiers on the web to find out more information about them. 3. Make this information machine-readable in a community-neutral format (such as RDF, Resource Description Framework). 4. Within this information, embed links to other things and concepts and say how these are related. 5. Optionally, provide web service interfaces to allow the user to perform sophisticated queries over this information (using a language such as SPARQL). The promise of Linked Data is that, through these techniques, data will be more discoverable, more comprehensible and more usable by different communities, not just the community that produced the data. As a result, many data providers (particularly public-sector institutions) are now publishing data in this way. However, this area is still in its infancy in terms of real-world applications. Data users need guidance and tools to help them use Linked Data. Data providers need reassurance that the investments they are making in

  4. Data publishing - visions of the future

    Science.gov (United States)

    Schäfer, Leonie; Klump, Jens; Bertelmann, Roland; Klar, Jochen; Enke, Harry; Rathmann, Torsten; Koudela, Daniela; Köhler, Klaus; Müller-Pfefferkorn, Ralph; van Uytvanck, Dieter; Strathmann, Stefan; Engelhardt, Claudia

    2013-04-01

    This poster describes future scenarios of information infrastructures in science and other fields of research. The scenarios presented are based on practical experience resulting from interaction with research data in a research center and its library, and further enriched by the results of a baseline study of existing data repositories and data infrastructures. The baseline study was conducted as part of the project "Requirements for a multi-disciplinary research data infrastructure (Radieschen)", which is funded by the German Research Foundation (DFG). Current changes in information infrastructures pose new challenges to libraries and scientific journals, which both act as information service providers, facilitating access to digital media, support publications of research data and enable their long-term archiving. Digital media and research data open new aspects in the field of activity of libraries and scientific journals. What will a library of the future look like? Will a library purely serve as interface to data centres? Will libraries and data centres merge into a new service unit? Will a future library be the interface to academic cloud services? Scientific journals already converted from mostly print editions to print and e-journals. What type of journals will emerge in the future? Is there a role for data-centred journals? Will there be journals to publish software code to make this type of research result citable and a part of the record of science? Just as users evolve from being consumers of information into producers, the role of information service providers, such as libraries, changes from a purely supporting to a contributing role. Furthermore, the role of the library changes from a central point of access for the search of publications to an important link in the value-adding chain from author to publication. Journals for software publication might be another vision for the future in data publishing. Software forms the missing link between big

  5. Utility-preserving anonymization for health data publishing.

    Science.gov (United States)

    Lee, Hyukki; Kim, Soohyung; Kim, Jong Wook; Chung, Yon Dohn

    2017-07-11

    Publishing raw electronic health records (EHRs) may be considered as a breach of the privacy of individuals because they usually contain sensitive information. A common practice for the privacy-preserving data publishing is to anonymize the data before publishing, and thus satisfy privacy models such as k-anonymity. Among various anonymization techniques, generalization is the most commonly used in medical/health data processing. Generalization inevitably causes information loss, and thus, various methods have been proposed to reduce information loss. However, existing generalization-based data anonymization methods cannot avoid excessive information loss and preserve data utility. We propose a utility-preserving anonymization for privacy preserving data publishing (PPDP). To preserve data utility, the proposed method comprises three parts: (1) utility-preserving model, (2) counterfeit record insertion, (3) catalog of the counterfeit records. We also propose an anonymization algorithm using the proposed method. Our anonymization algorithm applies full-domain generalization algorithm. We evaluate our method in comparison with existence method on two aspects, information loss measured through various quality metrics and error rate of analysis result. With all different types of quality metrics, our proposed method show the lower information loss than the existing method. In the real-world EHRs analysis, analysis results show small portion of error between the anonymized data through the proposed method and original data. We propose a new utility-preserving anonymization method and an anonymization algorithm using the proposed method. Through experiments on various datasets, we show that the utility of EHRs anonymized by the proposed method is significantly better than those anonymized by previous approaches.

  6. Civility in scientific publishing: The glyphosate paper.

    Science.gov (United States)

    Blaylock, Russell Lane

    2015-01-01

    In recent years, we have witnessed a decline in civility in the public arena when various socially sensitive issues are being presented. Those of us engaged in the publishing of scientific papers and in our comments on these papers, need to be cognizant of the social graces, courteous demeanor, and chivalry. Debates are essential to our learning and in being able to ferret out the essentials of various scientific issues that are of value. Because of the amount of time and effort connected with analyzing the complex problems and the years invested in such endeavors, we often resort to the behavior, that is, contentious and at times even quite insulting to our opponents during our defense. This is the part of human nature but as civilized human beings, we must strive to maintain the courtesy and a calm demeanor during such discussions and debates. I have yielded to such temptations myself but am striving to repent of my sins. The medical and scientific history should have taught us that in defending our ideas we learn and sometimes come to the realization that our paradigm or hypothesis is wrong, either in part or whole. Such debates allow us to fine tune our ideas and correct our errors in thinking, which are easily, consciously, or subconsciously sublimated by our enthusiasm. The glyphosate papers presented ideas that, while well supported by the scientific studies and logical conclusions, also contained some possible errors in its suppositions. Dr. Miguel Faria challenged some of these concepts and was met with some degree of derision by one of the authors. This editorial comment is in response to these issues.

  7. Mediastinal involvement in lymphangiomatosis: a previously unreported MRI sign

    Energy Technology Data Exchange (ETDEWEB)

    Shah, Vikas; Shah, Sachit; Barnacle, Alex; McHugh, Kieran [Great Ormond Street Hospital for Children, Department of Radiology, London (United Kingdom); Sebire, Neil J. [Great Ormond Street Hospital for Children, Department of Histopathology, London (United Kingdom); Brock, Penelope [Great Ormond Street Hospital for Children, Department of Oncology, London (United Kingdom); Harper, John I. [Great Ormond Street Hospital for Children, Department of Dermatology, London (United Kingdom)

    2011-08-15

    Multifocal lymphangiomatosis is a rare systemic disorder affecting children. Due to its rarity and wide spectrum of clinical, histological and imaging features, establishing the diagnosis of multifocal lymphangiomatosis can be challenging. The purpose of this study was to describe a new imaging sign in this disorder: paraspinal soft tissue and signal abnormality at MRI. We retrospectively reviewed the imaging, clinical and histopathological findings in a cohort of eight children with thoracic involvement from this condition. Evidence of paraspinal chest disease was identified at MRI and CT in all eight of these children. The changes comprise heterogeneous intermediate-to-high signal parallel to the thoracic vertebrae on T2-weighted sequences at MRI, with abnormal paraspinal soft tissue at CT and plain radiography. Multifocal lymphangiomatosis is a rare disorder with a broad range of clinicopathological and imaging features. MRI allows complete evaluation of disease extent without the use of ionising radiation and has allowed us to describe a previously unreported imaging sign in this disorder, namely, heterogeneous hyperintense signal in abnormal paraspinal tissue on T2-weighted images. (orig.)

  8. Mixed media : feminist presses and publishing politics in twentieth-century Britain

    OpenAIRE

    Murray, S. E.

    1999-01-01

    The high cultural profile of contemporary feminist publishing in Britain has previously met with a curiously evasive response from those spheres of academic discourse in which it might be expected to figure: women's studies, while asserting the innate politicality of all communication, has tended to overlook the subject of publishing in favour of less materialist cultural modes; while publishing studies has conventionally overlooked the significance of gender as a differential ...

  9. HEART TRANSPLANTATION IN PATIENTS WITH PREVIOUS OPEN HEART SURGERY

    Directory of Open Access Journals (Sweden)

    R. Sh. Saitgareev

    2016-01-01

    Full Text Available Heart Transplantation (HTx to date remains the most effective and radical method of treatment of patients with end-stage heart failure. The defi cit of donor hearts is forcing to resort increasingly to the use of different longterm mechanical circulatory support systems, including as a «bridge» to the follow-up HTx. According to the ISHLT Registry the number of recipients underwent cardiopulmonary bypass surgery increased from 40% in the period from 2004 to 2008 to 49.6% for the period from 2009 to 2015. HTx performed in repeated patients, on the one hand, involves considerable technical diffi culties and high risks; on the other hand, there is often no alternative medical intervention to HTx, and if not dictated by absolute contradictions the denial of the surgery is equivalent to 100% mortality. This review summarizes the results of a number of published studies aimed at understanding the immediate and late results of HTx in patients, previously underwent open heart surgery. The effect of resternotomy during HTx and that of the specifi c features associated with its implementation in recipients previously operated on open heart, and its effects on the immediate and long-term survival were considered in this review. Results of studies analyzing the risk factors for perioperative complications in repeated recipients were also demonstrated. Separately, HTx risks after implantation of prolonged mechanical circulatory support systems were examined. The literature does not allow to clearly defi ning the impact factor of earlier performed open heart surgery on the course of perioperative period and on the prognosis of survival in recipients who underwent HTx. On the other hand, subject to the regular fl ow of HTx and the perioperative period the risks in this clinical situation are justifi ed as a long-term prognosis of recipients previously conducted open heart surgery and are comparable to those of patients who underwent primary HTx. Studies

  10. Nonlinear deterministic structures and the randomness of protein sequences

    CERN Document Server

    Huang Yan Zhao

    2003-01-01

    To clarify the randomness of protein sequences, we make a detailed analysis of a set of typical protein sequences representing each structural classes by using nonlinear prediction method. No deterministic structures are found in these protein sequences and this implies that they behave as random sequences. We also give an explanation to the controversial results obtained in previous investigations.

  11. Music Consumption and Publishing in Todays Music Industry : Music publishing for an independent record label

    OpenAIRE

    Pienimäki, Kristian

    2015-01-01

    For the last two decades the changes in music technology and music consumption have affected music publishing as well as its viability. Much due to music digitalization and the overall decline in physical sales, the music industry has been forced to re-evaluate the means of publishing. The topic of the thesis is of current interest since the music industry is still in the state of change and new research is important. The thesis was assigned by an independent record label called Meiän Mu...

  12. Behind the Spam: A ``Spectral Analysis'' of Predatory Publishers

    Science.gov (United States)

    Beall, Jeffrey

    2016-10-01

    Most researchers today are bombarded with spam email solicitations from questionable scholarly publishers. These emails solicit article manuscripts, editorial board service, and even ad hoc peer reviews. These ``predatory'' publishers exploit the scholarly publishing process, patterning themselves after legitimate scholarly publishers yet performing little or no peer review and quickly accepting submitted manuscripts and collecting fees from submitting authors. These counterfeit publishers and journals have published much junk science? especially in the field of cosmology? threatening the integrity of the academic record. This paper examines the current state of predatory publishing and advises researchers how to navigate scholarly publishing to best avoid predatory publishers and other scholarly publishing-related perils.

  13. Urethrotomy has a much lower success rate than previously reported.

    Science.gov (United States)

    Santucci, Richard; Eisenberg, Lauren

    2010-05-01

    We evaluated the success rate of direct vision internal urethrotomy as a treatment for simple male urethral strictures. A retrospective chart review was performed on 136 patients who underwent urethrotomy from January 1994 through March 2009. The Kaplan-Meier method was used to analyze stricture-free probability after the first, second, third, fourth and fifth urethrotomy. Patients with complex strictures (36) were excluded from the study for reasons including previous urethroplasty, neophallus or previous radiation, and 24 patients were lost to followup. Data were available for 76 patients. The stricture-free rate after the first urethrotomy was 8% with a median time to recurrence of 7 months. For the second urethrotomy stricture-free rate was 6% with a median time to recurrence of 9 months. For the third urethrotomy stricture-free rate was 9% with a median time to recurrence of 3 months. For procedures 4 and 5 stricture-free rate was 0% with a median time to recurrence of 20 and 8 months, respectively. Urethrotomy is a popular treatment for male urethral strictures. However, the performance characteristics are poor. Success rates were no higher than 9% in this series for first or subsequent urethrotomy during the observation period. Most of the patients in this series will be expected to experience failure with longer followup and the expected long-term success rate from any (1 through 5) urethrotomy approach is 0%. Urethrotomy should be considered a temporizing measure until definitive curative reconstruction can be planned. 2010 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

  14. Places, Publishers and Personal Ties; the relational qualities of urban environments for book publishers

    NARCIS (Netherlands)

    Heebels, B.; van Aalst, I.; Atzema, O.A.L.C.

    2014-01-01

    Book publishers act as cultural mediators. Personal networks and face-to-face contacts with authors, booksellers, colleagues and people from the press are crucial for their business. This is in accordance with the literature on cultural entrepreneurship, which emphasizes the importance of informal

  15. Efficient error correction for next-generation sequencing of viral amplicons.

    Science.gov (United States)

    Skums, Pavel; Dimitrova, Zoya; Campo, David S; Vaughan, Gilberto; Rossi, Livia; Forbi, Joseph C; Yokosawa, Jonny; Zelikovsky, Alex; Khudyakov, Yury

    2012-06-25

    Next-generation sequencing allows the analysis of an unprecedented number of viral sequence variants from infected patients, presenting a novel opportunity for understanding virus evolution, drug resistance and immune escape. However, sequencing in bulk is error prone. Thus, the generated data require error identification and correction. Most error-correction methods to date are not optimized for amplicon analysis and assume that the error rate is randomly distributed. Recent quality assessment of amplicon sequences obtained using 454-sequencing showed that the error rate is strongly linked to the presence and size of homopolymers, position in the sequence and length of the amplicon. All these parameters are strongly sequence specific and should be incorporated into the calibration of error-correction algorithms designed for amplicon sequencing. In this paper, we present two new efficient error correction algorithms optimized for viral amplicons: (i) k-mer-based error correction (KEC) and (ii) empirical frequency threshold (ET). Both were compared to a previously published clustering algorithm (SHORAH), in order to evaluate their relative performance on 24 experimental datasets obtained by 454-sequencing of amplicons with known sequences. All three algorithms show similar accuracy in finding true haplotypes. However, KEC and ET were significantly more efficient than SHORAH in removing false haplotypes and estimating the frequency of true ones. Both algorithms, KEC and ET, are highly suitable for rapid recovery of error-free haplotypes obtained by 454-sequencing of amplicons from heterogeneous viruses.The implementations of the algorithms and data sets used for their testing are available at: http://alan.cs.gsu.edu/NGS/?q=content/pyrosequencing-error-correction-algorithm.

  16. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  17. New population-based exome data are questioning the pathogenicity of previously cardiomyopathy-associated genetic variants

    DEFF Research Database (Denmark)

    Andreasen, Charlotte Hartig; Nielsen, Jonas B; Refsgaard, Lena

    2013-01-01

    Cardiomyopathies are a heterogeneous group of diseases with various etiologies. We focused on three genetically determined cardiomyopathies: hypertrophic (HCM), dilated (DCM), and arrhythmogenic right ventricular cardiomyopathy (ARVC). Eighty-four genes have so far been associated with these card......Cardiomyopathies are a heterogeneous group of diseases with various etiologies. We focused on three genetically determined cardiomyopathies: hypertrophic (HCM), dilated (DCM), and arrhythmogenic right ventricular cardiomyopathy (ARVC). Eighty-four genes have so far been associated...... with these cardiomyopathies, but the disease-causing effect of reported variants is often dubious. In order to identify possible false-positive variants, we investigated the prevalence of previously reported cardiomyopathy-associated variants in recently published exome data. We searched for reported missense and nonsense...... variants in the NHLBI-Go Exome Sequencing Project (ESP) containing exome data from 6500 individuals. In ESP, we identified 94 variants out of 687 (14%) variants previously associated with HCM, 58 out of 337 (17%) variants associated with DCM, and 38 variants out of 209 (18%) associated with ARVC...

  18. Social participation: redesign of education, research, and practice in occupational therapy. Previously published in Scandinavian Journal of Occupational Therapy 2013; 20: 2-8.

    Science.gov (United States)

    Piškur, Barbara

    2014-01-01

    There is growing attention to participation and social participation in literature and policy reports. Occupational therapists strongly believe that creating coherence between the person's occupations and environment will facilitate participation of each individual. Nowadays, societal developments such as "health literacy and self-management", "Web 2.0 social media", "empowering communities", and "Nothing About Us Without Us" increase opportunities for people to interact on different levels of social participation. Social participation can be used as an outcome, though it can also be seen as a means to change society and to develop solutions for barriers experienced by people with chronic diseases or disabilities. Societal developments will have an impact on social participation in terms of supporting each other and contributing to society. Additionally, these changes will have a major influence on the way we educate, conduct research, and deliver occupational therapy practice.

  19. Population-based Neisseria gonorrhoeae, Chlamydia trachomatis and Trichomonas vaginalis Prevalence Using Discarded, Deidentified Urine Specimens Previously Collected for Drug Testing (Open Access Publisher’s Version)

    Science.gov (United States)

    2017-10-24

    trichomonas vaginalis testing, Melinda Balansay-ames, chris Myers and gary Brice for Pcr- based sex determination testing, and Kimberly De Vera for...2017-053355 rEFErEnCEs 1 torrone e , Papp J, Weinstock H. centers for Disease control and Prevention (cDc). Prevalence of Chlamydia trachomatis genital...infection among persons aged 14-39 years-United States, 2007-2012. MMWR Morb Mortal Wkly Rep 2014;63:834–7. 2 rietmeijer ca, Hopkins e , geisler WM

  20. δ-dependency for privacy-preserving XML data publishing.

    Science.gov (United States)

    Landberg, Anders H; Nguyen, Kinh; Pardede, Eric; Rahayu, J Wenny

    2014-08-01

    An ever increasing amount of medical data such as electronic health records, is being collected, stored, shared and managed in large online health information systems and electronic medical record systems (EMR) (Williams et al., 2001; Virtanen, 2009; Huang and Liou, 2007) [1-3]. From such rich collections, data is often published in the form of census and statistical data sets for the purpose of knowledge sharing and enabling medical research. This brings with it an increasing need for protecting individual people privacy, and it becomes an issue of great importance especially when information about patients is exposed to the public. While the concept of data privacy has been comprehensively studied for relational data, models and algorithms addressing the distinct differences and complex structure of XML data are yet to be explored. Currently, the common compromise method is to convert private XML data into relational data for publication. This ad hoc approach results in significant loss of useful semantic information previously carried in the private XML data. Health data often has very complex structure, which is best expressed in XML. In fact, XML is the standard format for exchanging (e.g. HL7 version 3(1)) and publishing health information. Lack of means to deal directly with data in XML format is inevitably a serious drawback. In this paper we propose a novel privacy protection model for XML, and an algorithm for implementing this model. We provide general rules, both for transforming a private XML schema into a published XML schema, and for mapping private XML data to the new privacy-protected published XML data. In addition, we propose a new privacy property, δ-dependency, which can be applied to both relational and XML data, and that takes into consideration the hierarchical nature of sensitive data (as opposed to "quasi-identifiers"). Lastly, we provide an implementation of our model, algorithm and privacy property, and perform an experimental analysis

  1. Next generation sequencing and its applications in forensic genetics.

    Science.gov (United States)

    Børsting, Claus; Morling, Niels

    2015-09-01

    It has been almost a decade since the first next generation sequencing (NGS) technologies emerged and quickly changed the way genetic research is conducted. Today, full genomes are mapped and published almost weekly and with ever increasing speed and decreasing costs. NGS methods and platforms have matured during the last 10 years, and the quality of the sequences has reached a level where NGS is used in clinical diagnostics of humans. Forensic genetic laboratories have also explored NGS technologies and especially in the last year, there has been a small explosion in the number of scientific articles and presentations at conferences with forensic aspects of NGS. These contributions have demonstrated that NGS offers new possibilities for forensic genetic case work. More information may be obtained from unique samples in a single experiment by analyzing combinations of markers (STRs, SNPs, insertion/deletions, mRNA) that cannot be analyzed simultaneously with the standard PCR-CE methods used today. The true variation in core forensic STR loci has been uncovered, and previously unknown STR alleles have been discovered. The detailed sequence information may aid mixture interpretation and will increase the statistical weight of the evidence. In this review, we will give an introduction to NGS and single-molecule sequencing, and we will discuss the possible applications of NGS in forensic genetics. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  2. Towards mainstreaming of biodiversity data publishing: recommendations of the GBIF Data Publishing Framework Task Group.

    Science.gov (United States)

    Moritz, Tom; Krishnan, S; Roberts, Dave; Ingwersen, Peter; Agosti, Donat; Penev, Lyubomir; Cockerill, Matthew; Chavan, Vishwas

    2011-01-01

    Data are the evidentiary basis for scientific hypotheses, analyses and publication, for policy formation and for decision-making. They are essential to the evaluation and testing of results by peer scientists both present and future. There is broad consensus in the scientific and conservation communities that data should be freely, openly available in a sustained, persistent and secure way, and thus standards for 'free' and 'open' access to data have become well developed in recent years. The question of effective access to data remains highly problematic. Specifically with respect to scientific publishing, the ability to critically evaluate a published scientific hypothesis or scientific report is contingent on the examination, analysis, evaluation - and if feasible - on the re-generation of data on which conclusions are based. It is not coincidental that in the recent 'climategate' controversies, the quality and integrity of data and their analytical treatment were central to the debate. There is recent evidence that even when scientific data are requested for evaluation they may not be available. The history of dissemination of scientific results has been marked by paradigm shifts driven by the emergence of new technologies. In recent decades, the advance of computer-based technology linked to global communications networks has created the potential for broader and more consistent dissemination of scientific information and data. Yet, in this digital era, scientists and conservationists, organizations and institutions have often been slow to make data available. Community studies suggest that the withholding of data can be attributed to a lack of awareness, to a lack of technical capacity, to concerns that data should be withheld for reasons of perceived personal or organizational self interest, or to lack of adequate mechanisms for attribution. There is a clear need for institutionalization of a 'data publishing framework' that can address sociocultural

  3. Towards mainstreaming of biodiversity data publishing: recommendations of the GBIF Data Publishing Framework Task Group

    Directory of Open Access Journals (Sweden)

    Moritz Tom

    2011-12-01

    Full Text Available Abstract Background Data are the evidentiary basis for scientific hypotheses, analyses and publication, for policy formation and for decision-making. They are essential to the evaluation and testing of results by peer scientists both present and future. There is broad consensus in the scientific and conservation communities that data should be freely, openly available in a sustained, persistent and secure way, and thus standards for 'free' and 'open' access to data have become well developed in recent years. The question of effective access to data remains highly problematic. Discussion Specifically with respect to scientific publishing, the ability to critically evaluate a published scientific hypothesis or scientific report is contingent on the examination, analysis, evaluation - and if feasible - on the re-generation of data on which conclusions are based. It is not coincidental that in the recent 'climategate' controversies, the quality and integrity of data and their analytical treatment were central to the debate. There is recent evidence that even when scientific data are requested for evaluation they may not be available. The history of dissemination of scientific results has been marked by paradigm shifts driven by the emergence of new technologies. In recent decades, the advance of computer-based technology linked to global communications networks has created the potential for broader and more consistent dissemination of scientific information and data. Yet, in this digital era, scientists and conservationists, organizations and institutions have often been slow to make data available. Community studies suggest that the withholding of data can be attributed to a lack of awareness, to a lack of technical capacity, to concerns that data should be withheld for reasons of perceived personal or organizational self interest, or to lack of adequate mechanisms for attribution. Conclusions There is a clear need for institutionalization of a

  4. Toxoplasma gondii and schizophrenia: a review of published RCTs.

    Science.gov (United States)

    Chorlton, Sam D

    2017-07-01

    Over the last 60 years, accumulating evidence has suggested that acute, chronic, and maternal Toxoplasma gondii infections predispose to schizophrenia. More recent evidence suggests that chronically infected patients with schizophrenia present with more severe disease. After acute infection, parasites form walled cysts in the brain, leading to lifelong chronic infection and drug resistance to commonly used antiparasitics. Chronic infection is the most studied and closely linked with development and severity of schizophrenia. There are currently four published randomized controlled trials evaluating antiparasitic drugs, specifically azithromycin, trimethoprim, artemisinin, and artemether, in patients with schizophrenia. No trials have demonstrated a change in psychopathology with adjunctive treatment. Published trials have either selected drugs without evidence against chronic infection or used them at doses too low to reduce brain cyst burden. Furthermore, trials have failed to achieve sufficient power or account for confounders such as previous antipsychotic treatment, sex, age, or rhesus status on antiparasitic effect. There are currently no ongoing trials of anti-Toxoplasma therapy in schizophrenia despite ample evidence to justify further testing.

  5. Perception of Key Barriers in Using and Publishing Open Data

    Directory of Open Access Journals (Sweden)

    Martin Beno

    2017-12-01

    Full Text Available TThere is a growing body of literature recognizing the benefits of Open Data. However, many potential data providers are unwilling to publish their data and at the same time, data users are often faced with difficulties when attempting to use Open Data in practice. Despite various barriers in using and publishing Open Data still being present, studies which systematically collect and assess these barriers are rare. Based on this observation we present a review on prior literature on barriers and the results of an empirical study aimed at assessing both the users’ and publishers’ views on obstacles regarding Open Data adoption. We collected data with an online survey in Austria and internationally. Using a sample of 183 participants, we draw conclusions about the relative importance of the barriers reported in the literature. In comparison to a previous conference paper presented at the conference for E-Democracy and Open Government, this article includes new additional data from participants outside Austria, reports new analyses, and substantially extends the discussion of results and of possible strategies for the mitigation of Open Data barriers.

  6. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  7. Publishing for Learned Societies: The Secret Life of a Scholarly Publisher

    Science.gov (United States)

    Nicholson, David

    Wiley-Blackwell was formed in February 2007 as a result of the acquisition of Blackwell Publishing Ltd. by John Wiley & Sons, Inc. and the merger between Blackwell and Wiley's Scientific, Technical, and Medical business. Wiley-Blackwell publishes approximately 1,250 scholarly peer-reviewed journals including Monthly Notices of the Royal Astronomical Society and Astronomische Nachrichten, and has relationships with over 800 learned societies. The "secret life" of the article's title refers to the two broad areas of activity we undertake for our society partners, namely practical assistance and strategic advice. One of our goals at Wiley-Blackwell is to set the standard for both areas, and this article illustrates how we are doing this with a series of tangible examples.

  8. Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data.

    Directory of Open Access Journals (Sweden)

    Can Alkan

    2007-09-01

    Full Text Available The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%-5% of sequence generated as part of primate genome sequencing projects consists of this material, which is fragmented or not assembled as part of published genome sequences due to its highly repetitive nature. Here, we develop computational methods to rapidly recover and categorize alpha-satellite sequences from previously uncharacterized whole-genome shotgun sequence data. We present an algorithm to computationally predict potential higher-order array structure based on paired-end sequence data and then experimentally validate its organization and distribution by experimental analyses. Using whole-genome shotgun data from the human, chimpanzee, and macaque genomes, we examine the phylogenetic relationship of these sequences and provide further support for a model for their evolution and mutation over the last 25 million years. Our results confirm fundamental differences in the dispersal and evolution of centromeric satellites in the Old World monkey and ape lineages of evolution.

  9. kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets

    Science.gov (United States)

    Fletez-Brant, Christopher; Lee, Dongwon; McCallion, Andrew S.; Beer, Michael A.

    2013-01-01

    Massively parallel sequencing technologies have made the generation of genomic data sets a routine component of many biological investigations. For example, Chromatin immunoprecipitation followed by sequence assays detect genomic regions bound (directly or indirectly) by specific factors, and DNase-seq identifies regions of open chromatin. A major bottleneck in the interpretation of these data is the identification of the underlying DNA sequence code that defines, and ultimately facilitates prediction of, these transcription factor (TF) bound or open chromatin regions. We have recently developed a novel computational methodology, which uses a support vector machine (SVM) with kmer sequence features (kmer-SVM) to identify predictive combinations of short transcription factor-binding sites, which determine the tissue specificity of these genomic assays (Lee, Karchin and Beer, Discriminative prediction of mammalian enhancers from DNA sequence. Genome Res. 2011; 21:2167–80). This regulatory information can (i) give confidence in genomic experiments by recovering previously known binding sites, and (ii) reveal novel sequence features for subsequent experimental testing of cooperative mechanisms. Here, we describe the development and implementation of a web server to allow the broader research community to independently apply our kmer-SVM to analyze and interpret their genomic datasets. We analyze five recently published data sets and demonstrate how this tool identifies accessory factors and repressive sequence elements. kmer-SVM is available at http://kmersvm.beerlab.org. PMID:23771147

  10. Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data.

    Science.gov (United States)

    Alkan, Can; Ventura, Mario; Archidiacono, Nicoletta; Rocchi, Mariano; Sahinalp, S Cenk; Eichler, Evan E

    2007-09-01

    The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%-5% of sequence generated as part of primate genome sequencing projects consists of this material, which is fragmented or not assembled as part of published genome sequences due to its highly repetitive nature. Here, we develop computational methods to rapidly recover and categorize alpha-satellite sequences from previously uncharacterized whole-genome shotgun sequence data. We present an algorithm to computationally predict potential higher-order array structure based on paired-end sequence data and then experimentally validate its organization and distribution by experimental analyses. Using whole-genome shotgun data from the human, chimpanzee, and macaque genomes, we examine the phylogenetic relationship of these sequences and provide further support for a model for their evolution and mutation over the last 25 million years. Our results confirm fundamental differences in the dispersal and evolution of centromeric satellites in the Old World monkey and ape lineages of evolution.

  11. Revision of Begomovirus taxonomy based on pairwise sequence comparisons

    KAUST Repository

    Brown, Judith K.

    2015-04-18

    Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.

  12. Revision of Begomovirus taxonomy based on pairwise sequence comparisons

    KAUST Repository

    Brown, Judith K.; Zerbini, F. Murilo; Navas-Castillo, Jesú s; Moriones, Enrique; Ramos-Sobrinho, Roberto; Silva, José C. F.; Fiallo-Olivé , Elvira; Briddon, Rob W.; Herná ndez-Zepeda, Cecilia; Idris, Ali; Malathi, V. G.; Martin, Darren P.; Rivera-Bustamante, Rafael; Ueda, Shigenori; Varsani, Arvind

    2015-01-01

    Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.

  13. The GBIF integrated publishing toolkit: facilitating the efficient publishing of biodiversity data on the internet.

    Directory of Open Access Journals (Sweden)

    Tim Robertson

    Full Text Available The planet is experiencing an ongoing global biodiversity crisis. Measuring the magnitude and rate of change more effectively requires access to organized, easily discoverable, and digitally-formatted biodiversity data, both legacy and new, from across the globe. Assembling this coherent digital representation of biodiversity requires the integration of data that have historically been analog, dispersed, and heterogeneous. The Integrated Publishing Toolkit (IPT is a software package developed to support biodiversity dataset publication in a common format. The IPT's two primary functions are to 1 encode existing species occurrence datasets and checklists, such as records from natural history collections or observations, in the Darwin Core standard to enhance interoperability of data, and 2 publish and archive data and metadata for broad use in a Darwin Core Archive, a set of files following a standard format. Here we discuss the key need for the IPT, how it has developed in response to community input, and how it continues to evolve to streamline and enhance the interoperability, discoverability, and mobilization of new data types beyond basic Darwin Core records. We close with a discussion how IPT has impacted the biodiversity research community, how it enhances data publishing in more traditional journal venues, along with new features implemented in the latest version of the IPT, and future plans for more enhancements.

  14. k-Degree Anonymity Model for Social Network Data Publishing

    Directory of Open Access Journals (Sweden)

    MACWAN, K. R.

    2017-11-01

    Full Text Available Publicly accessible platform for social networking has gained special attraction because of its easy data sharing. Data generated on such social network is analyzed for various activities like marketing, social psychology, etc. This requires preservation of sensitive attributes before it becomes easily accessible. Simply removing the personal identities of the users before publishing data is not enough to maintain the privacy of the individuals. The structure of the social network data itself reveals much information regarding its users and their connections. To resolve this problem, k-degree anonymous method is adopted. It emphasizes on the modification of the graph to provide at least k number of nodes that contain the same degree. However, this approach is not efficient on a huge amount of social data and the modification of the original data fails to maintain data usefulness. In addition to this, the current anonymization approaches focus on a degree sequence-based graph model which leads to major modification of the graph topological properties. In this paper, we have proposed an improved k-degree anonymity model that retain the social network structural properties and also to provide privacy to the individuals. Utility measurement approach for community based graph model is used to verify the performance of the proposed technique.

  15. Technical Writing Teachers and the Challenges of Desktop Publishing.

    Science.gov (United States)

    Kalmbach, James

    1988-01-01

    Argues that technical writing teachers must understand desktop publishing. Discusses the strengths that technical writing teachers bring to desktop publishing, and the impact desktop publishing will have on technical writing courses and programs. (ARH)

  16. Writing and Publishing Books in Counseling: A Survey of Authors.

    Science.gov (United States)

    Seligman, Linda; Kelly, Shirley C.

    1990-01-01

    Presents data and ideas from 74 authors who published books in counseling field. Reviews writing and publishing process. Provides information on timetables, book contracts, and remuneration as well as suggestions on publisher selection and contract negotiation. (Author/CM)

  17. Establishing a publishing outfit in Nigeria | Emenyonu | International ...

    African Journals Online (AJOL)

    Journal Home > Vol 12, No 1 (2017) > ... The paper examines the steps in establishing a publishing firm in the Nigerian environment. ... to follow in establishing a publishing company, networking with stakeholders in the publishing industry,the ...

  18. Persistent seropositivity for yellow fever in a previously vaccinated autologous hematopoietic stem cell transplantation recipient.

    Science.gov (United States)

    Hayakawa, Kayoko; Takasaki, Tomohiko; Tsunemine, Hiroko; Kanagawa, Shuzo; Kutsuna, Satoshi; Takeshita, Nozomi; Mawatari, Momoko; Fujiya, Yoshihiro; Yamamoto, Kei; Ohmagari, Norio; Kato, Yasuyuki

    2015-08-01

    The duration of a protective level of yellow fever antibodies after autologous hematopoietic stem cell transplantation in a previously vaccinated person is unclear. The case of a patient who had previously been vaccinated for yellow fever and who remained seropositive for 22 months after autologous peripheral blood stem cell transplantation for malignant lymphoma is described herein. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  19. Characterization and sequence analysis of cysteine and glycine-rich ...

    African Journals Online (AJOL)

    Primers specific for CSRP3 were designed using known cDNA sequences of Bos taurus published in database with different accession numbers. Polymerase chain reaction (PCR) was performed and products were purified and sequenced. Sequence analysis and alignment were carried out using CLUSTAL W (1.83).

  20. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

    Science.gov (United States)

    de Souza, Sandro J.; Camargo, Anamaria A.; Briones, Marcelo R. S.; Costa, Fernando F.; Nagai, Maria Aparecida; Verjovski-Almeida, Sergio; Zago, Marco A.; Andrade, Luis Eduardo C.; Carrer, Helaine; El-Dorry, Hamza F. A.; Espreafico, Enilza M.; Habr-Gama, Angelita; Giannella-Neto, Daniel; Goldman, Gustavo H.; Gruber, Arthur; Hackel, Christine; Kimura, Edna T.; Maciel, Rui M. B.; Marie, Suely K. N.; Martins, Elizabeth A. L.; Nóbrega, Marina P.; Paçó-Larson, Maria Luisa; Pardini, Maria Inês M. C.; Pereira, Gonçalo G.; Pesquero, João Bosco; Rodrigues, Vanderlei; Rogatto, Silvia R.; da Silva, Ismael D. C. G.; Sogayar, Mari C.; de Fátima Sonati, Maria; Tajara, Eloiza H.; Valentini, Sandro R.; Acencio, Marcio; Alberto, Fernando L.; Amaral, Maria Elisabete J.; Aneas, Ivy; Bengtson, Mário Henrique; Carraro, Dirce M.; Carvalho, Alex F.; Carvalho, Lúcia Helena; Cerutti, Janete M.; Corrêa, Maria Lucia C.; Costa, Maria Cristina R.; Curcio, Cyntia; Gushiken, Tsieko; Ho, Paulo L.; Kimura, Elza; Leite, Luciana C. C.; Maia, Gustavo; Majumder, Paromita; Marins, Mozart; Matsukuma, Adriana; Melo, Analy S. A.; Mestriner, Carlos Alberto; Miracca, Elisabete C.; Miranda, Daniela C.; Nascimento, Ana Lucia T. O.; Nóbrega, Francisco G.; Ojopi, Élida P. B.; Pandolfi, José Rodrigo C.; Pessoa, Luciana Gilbert; Rahal, Paula; Rainho, Claudia A.; da Ro's, Nancy; de Sá, Renata G.; Sales, Magaly M.; da Silva, Neusa P.; Silva, Tereza C.; da Silva, Wilson; Simão, Daniel F.; Sousa, Josane F.; Stecconi, Daniella; Tsukumo, Fernando; Valente, Valéria; Zalcberg, Heloisa; Brentani, Ricardo R.; Reis, Luis F. L.; Dias-Neto, Emmanuel; Simpson, Andrew J. G.

    2000-01-01

    Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1,181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. Of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTES coincided with DNA regions predicted as encoding exons by genscan. (http://genes.mit.edu/GENSCAN.html). PMID:11070084

  1. Diagnostic yield of molecular autopsy in patients with sudden arrhythmic death syndrome using targeted exome sequencing

    DEFF Research Database (Denmark)

    Nunn, Laurence M; Lopes, Luis R; Syrris, Petros

    2016-01-01

    AIMS: The targeted genetic screening of Sudden Arrhythmic Death Syndrome (SADS) probands in a molecular autopsy has a diagnostic yield of up to 35%. Exome sequencing has the potential to improve this yield. The primary aim of this study is to examine the feasibility and diagnostic utility...... of targeted exome screening in SADS victims, utilizing familial clinical screening whenever possible. METHODS AND RESULTS: To determine the feasibility and diagnostic yield of targeted exome sequencing deoxyribonucleic acid (DNA) was isolated from 59 SADS victims (mean age 25 years, range 1-51 years...... previously published rare (0.02-0.5%) candidate mutations-a total yield of 29%. Co-segregation fully confirmed two private SCN5A Na channel mutations. Variants of unknown significance were detected in a further 34% of probands. CONCLUSION: Molecular autopsy using targeted exome sequencing has a relatively...

  2. ‘‘Blind'' mapping of genic DNA sequence polymorphisms in Lolium perenne L. by high resolution melting curve analysis

    DEFF Research Database (Denmark)

    Studer, Bruno; Jensen, Louise Bach; Fiil, Alice

    2009-01-01

    High resolution melting curve analysis (HRM) measures dissociation of double stranded DNA of a PCR product amplified in the presence of a saturating fluorescence dye. Recently, HRM proved successful to genotype DNA sequence polymorphisms such as SSRs and SNPs based on the shape of the melting...... curves. In this study, HRM was used for simultaneous screening and genotyping of genic DNA sequence polymorphisms identified in the Lolium perenne F2 mapping population VrnA. Melting profiles of PCR products amplified from previously published gene loci and from a novel gene putatively involved...

  3. PURA syndrome: clinical delineation and genotype-phenotype study in 32 individuals with review of published literature

    Science.gov (United States)

    Reijnders, Margot R F; Janowski, Robert; Alvi, Mohsan; Self, Jay E; van Essen, Ton J; Vreeburg, Maaike; Rouhl, Rob P W; Stevens, Servi J C; Stegmann, Alexander P A; Schieving, Jolanda; Pfundt, Rolph; van Dijk, Katinke; Smeets, Eric; Stumpel, Connie T R M; Bok, Levinus A; Cobben, Jan Maarten; Engelen, Marc; Mansour, Sahar; Whiteford, Margo; Chandler, Kate E; Douzgou, Sofia; Cooper, Nicola S; Tan, Ene-Choo; Foo, Roger; Lai, Angeline H M; Rankin, Julia; Green, Andrew; Lönnqvist, Tuula; Isohanni, Pirjo; Williams, Shelley; Ruhoy, Ilene; Carvalho, Karen S; Dowling, James J; Lev, Dorit L; Sterbova, Katalin; Lassuthova, Petra; Neupauerová, Jana; Waugh, Jeff L; Keros, Sotirios; Clayton-Smith, Jill; Smithson, Sarah F; Brunner, Han G; van Hoeckel, Ceciel; Anderson, Mel; Clowes, Virginia E; Siu, Victoria Mok; DDD study, The; Selber, Paulo; Leventer, Richard J; Nellaker, Christoffer; Niessing, Dierk; Hunt, David; Baralle, Diana

    2018-01-01

    Background De novo mutations in PURA have recently been described to cause PURA syndrome, a neurodevelopmental disorder characterised by severe intellectual disability (ID), epilepsy, feeding difficulties and neonatal hypotonia. Objectives To delineate the clinical spectrum of PURA syndrome and study genotype-phenotype correlations. Methods Diagnostic or research-based exome or Sanger sequencing was performed in individuals with ID. We systematically collected clinical and mutation data on newly ascertained PURA syndrome individuals, evaluated data of previously reported individuals and performed a computational analysis of photographs. We classified mutations based on predicted effect using 3D in silico models of crystal structures of Drosophila-derived Pur-alpha homologues. Finally, we explored genotype-phenotype correlations by analysis of both recurrent mutations as well as mutation classes. Results We report mutations in PURA (purine-rich element binding protein A) in 32 individuals, the largest cohort described so far. Evaluation of clinical data, including 22 previously published cases, revealed that all have moderate to severe ID and neonatal-onset symptoms, including hypotonia (96%), respiratory problems (57%), feeding difficulties (77%), exaggerated startle response (44%), hypersomnolence (66%) and hypothermia (35%). Epilepsy (54%) and gastrointestinal (69%), ophthalmological (51%) and endocrine problems (42%) were observed frequently. Computational analysis of facial photographs showed subtle facial dysmorphism. No strong genotype-phenotype correlation was identified by subgrouping mutations into functional classes. Conclusion We delineate the clinical spectrum of PURA syndrome with the identification of 32 additional individuals. The identification of one individual through targeted Sanger sequencing points towards the clinical recognisability of the syndrome. Genotype-phenotype analysis showed no significant correlation between mutation classes and

  4. The Applied Development of a Tiered Multilocus Sequence Typing (MLST) Scheme for Dichelobacter nodosus.

    Science.gov (United States)

    Blanchard, Adam M; Jolley, Keith A; Maiden, Martin C J; Coffey, Tracey J; Maboni, Grazieli; Staley, Ceri E; Bollard, Nicola J; Warry, Andrew; Emes, Richard D; Davies, Peers L; Tötemeyer, Sabine

    2018-01-01

    Dichelobacter nodosus ( D. nodosus ) is the causative pathogen of ovine footrot, a disease that has a significant welfare and financial impact on the global sheep industry. Previous studies into the phylogenetics of D. nodosus have focused on Australia and Scandinavia, meaning the current diversity in the United Kingdom (U.K.) population and its relationship globally, is poorly understood. Numerous epidemiological methods are available for bacterial typing; however, few account for whole genome diversity or provide the opportunity for future application of new computational techniques. Multilocus sequence typing (MLST) measures nucleotide variations within several loci with slow accumulation of variation to enable the designation of allele numbers to determine a sequence type. The usage of whole genome sequence data enables the application of MLST, but also core and whole genome MLST for higher levels of strain discrimination with a negligible increase in experimental cost. An MLST database was developed alongside a seven loci scheme using publically available whole genome data from the sequence read archive. Sequence type designation and strain discrimination was compared to previously published data to ensure reproducibility. Multiple D. nodosus isolates from U.K. farms were directly compared to populations from other countries. The U.K. isolates define new clades within the global population of D. nodosus and predominantly consist of serogroups A, B and H, however serogroups C, D, E, and I were also found. The scheme is publically available at https://pubmlst.org/dnodosus/.

  5. 44 CFR 5.21 - Effect of failure to publish.

    Science.gov (United States)

    2010-10-01

    ... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Effect of failure to publish... failure to publish. 5 U.S.C. 552(a)(1) provides that, except to the extent that a person has actual and... adversely affected by, a matter required to be published in the Federal Register and not so published. ...

  6. 22 CFR 212.11 - Materials to be published.

    Science.gov (United States)

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Materials to be published. 212.11 Section 212... Federal Register § 212.11 Materials to be published. (a) USAID separately states and currently publishes... section. (b) USAID Public Notice No. 1 and the USAID Regulations published in chapter II of Title 22 and...

  7. 15 CFR 10.13 - Withdrawal of a published standard.

    Science.gov (United States)

    2010-01-01

    ...) Before withdrawing a standard published under these procedures, the Director will review the relative... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Withdrawal of a published standard. 10... DEVELOPMENT OF VOLUNTARY PRODUCT STANDARDS § 10.13 Withdrawal of a published standard. (a) Standards published...

  8. The Ins and the Outs of Electronic Publishing.

    Science.gov (United States)

    Wills, Mathew; Wills, Gordon

    1996-01-01

    Examines electronic publishing for academic and professional publishers. Discusses benefits of electronic publishing to authors and readers, argues that the hard sell and product-driven mindsets will not work in a customer-focused communications medium, and outlines characteristics of electronic publishing that must be incorporated in successful…

  9. Behind the Spam: A "Spectral Analysis" of Predatory Publishers

    Science.gov (United States)

    Beall, Jeffrey

    2015-08-01

    Most researchers today are bombarded with spam email solicitations from questionable scholarly publishers. These emails solicit article manuscripts, editorial board service, and even ad hoc peer reviews. These "predatory" publishers exploit the scholarly publishing process, patterning themselves after legitimate scholarly publishers yet performing little or no peer review and quickly accepting submitted manuscripts and collecting fees from submitting authors. These counterfeit publishers and journals have published much junk science — especially in the field of cosmology — threatening the integrity of the academic record. This presentation examines the current state of predatory publishing and related scams such as fake impact factors and advises researchers how to navigate scholarly publishing to best avoid predatory publishers and other scholarly publishing-related perils.

  10. EDITORIAL: Roberts Prize for the best paper published in 2010 Roberts Prize for the best paper published in 2010

    Science.gov (United States)

    Webb, Steve; Harris, Simon

    2011-08-01

    The publishers of Physics in Medicine and Biology (PMB), IOP Publishing, in association with the journal owners, the Institute of Physics and Engineering in Medicine (IPEM), jointly award an annual prize for the best paper published in PMB during the previous year. The procedure for deciding the winner has been made as thorough as possible, to try to ensure that an outstanding paper wins the prize. We started off with a shortlist of the 10 research papers published in 2010 which were rated the best based on the referees' quality assessments. Following the submission of a short 'case for winning' document by each of the shortlisted authors, an IPEM college of jurors of the status of FIPEM assessed and rated these 10 papers in order to choose a winner, which was then endorsed by the Editorial Board. We have much pleasure in advising readers that the Roberts Prize for the best paper published in 2010 is awarded to M M Paulides et al from Erasmus MC, Rotterdam, The Netherlands, for their paper on hyperthermia treatment: The clinical feasibility of deep hyperthermia treatment in the head and neck: new challenges for positioning and temperature measurement M M Paulides, J F Bakker, M Linthorst, J van der Zee, Z Rijnen, E Neufeld, P M T Pattynama, P P Jansen, P C Levendag and G C van Rhoon 2010 Phys. Med. Biol. 55 2465 Our congratulations go to these authors. Of course all of the shortlisted papers were of great merit, and the full top-10 is listed below (in alphabetical order). Steve Webb Editor-in-Chief Simon Harris Publisher References Alonzo-Proulx O, Packard N, Boone J M, Al-Mayah A, Brock K K, Shen S Z and Yaffe M J 2010 Validation of a method for measuring the volumetric breast density from digital mammograms Phys. Med. Biol. 55 3027 Bian J, Siewerdsen J H, Han X, Sidky E Y, Prince J L, Pelizzari C A and Pan X 2010 Evaluation of sparse-view reconstruction from flat-panel-detector cone-beam CT Phys. Med. Biol. 55 6575 Brun M-A, Formanek F, Yasuda A, Sekine M, Ando N

  11. Quality assessment of published health economic analyses from South America.

    Science.gov (United States)

    Machado, Márcio; Iskedjian, Michael; Einarson, Thomas R

    2006-05-01

    Health economic analyses have become important to healthcare systems worldwide. No studies have previously examined South America's contribution in this area. To survey the literature with the purpose of reviewing, quantifying, and assessing the quality of published South American health economic analyses. A search of MEDLINE (1990-December 2004), EMBASE (1990-December 2004), International Pharmaceutical Abstracts (1990-December 2004), Literatura Latino-Americana e do Caribe em Ciências da Saúde (1982-December 2004), and Sistema de Informacion Esencial en Terapéutica y Salud (1980-December 2004) was completed using the key words cost-effectiveness analysis (CEA), cost-utility analysis (CUA), cost-minimization analysis (CMA), and cost-benefit analysis (CBA); abbreviations CEA, CUA, CMA, and CBA; and all South American country names. Papers were categorized by type and country by 2 independent reviewers. Quality was assessed using a 12 item checklist, characterizing scores as 4 (good), 3 (acceptable), 2 (poor), 1 (unable to judge), and 0 (unacceptable). To be included in our investigation, studies needed to have simultaneously examined costs and outcomes. We retrieved 25 articles; one duplicate article was rejected, leaving 24 (CEA = 15, CBA = 6, CMA = 3; Brazil = 9, Argentina = 5, Colombia = 3, Chile = 2, Ecuador = 2, 1 each from Peru, Uruguay, Venezuela). Variability between raters was less than 0.5 point on overall scores (OS) and less than 1 point on all individual items. Mean OS was 2.6 (SD 1.0, range 1.4-3.8). CBAs scored highest (OS 2.8, SD 0.8), CEAs next (OS 2.7, SD 0.7), and CMAs lowest (OS 2.0, SD 0.5). When scored by type of question, definition of study aim scored highest (OS 3.0, SD 0.8), while ethical issues scored lowest (OS 1.5, SD 0.9). By country, Peru scored highest (mean OS 3.8) and Uruguay had the lowest scores (mean OS 2.2). A nonsignificant time trend was noted for OS (R2 = 0.12; p = 0.104). Quality scores of health economic analyses

  12. Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data.

    Directory of Open Access Journals (Sweden)

    Lauren Coombe

    Full Text Available The linked read sequencing library preparation platform by 10X Genomics produces barcoded sequencing libraries, which are subsequently sequenced using the Illumina short read sequencing technology. In this new approach, long fragments of DNA are partitioned into separate micro-reactions, where the same index sequence is incorporated into each of the sequencing fragment inserts derived from a given long fragment. In this study, we exploited this property by using reads from index sequences associated with a large number of reads, to assemble the chloroplast genome of the Sitka spruce tree (Picea sitchensis. Here we report on the first Sitka spruce chloroplast genome assembled exclusively from P. sitchensis genomic libraries prepared using the 10X Genomics protocol. We show that the resulting 124,049 base pair long genome shares high sequence similarity with the related white spruce and Norway spruce chloroplast genomes, but diverges substantially from a previously published P. sitchensis- P. thunbergii chimeric genome. The use of reads from high-frequency indices enabled separation of the nuclear genome reads from that of the chloroplast, which resulted in the simplification of the de Bruijn graphs used at the various stages of assembly.

  13. "The devil's in the detail": Release of an expanded, enhanced and dynamically revised forensic STR Sequence Guide.

    Science.gov (United States)

    Phillips, C; Gettings, K Butler; King, J L; Ballard, D; Bodner, M; Borsuk, L; Parson, W

    2018-05-01

    The STR sequence template file published in 2016 as part of the considerations from the DNA Commission of the International Society for Forensic Genetics on minimal STR sequence nomenclature requirements, has been comprehensively revised and audited using the latest GRCh38 genome assembly. The list of forensic STRs characterized was expanded by including supplementary autosomal, X- and Y-chromosome microsatellites in less common use for routine DNA profiling, but some likely to be adopted in future massively parallel sequencing (MPS) STR panels. We outline several aspects of sequence alignment and annotation that required care and attention to detail when comparing sequences to GRCh37 and GRCh38 assemblies, as well as the necessary matching of MPS-based allele descriptions to previously established repeat region structures described in initial sequencing studies of the less well known forensic STRs. The revised sequence guide is now available in a dynamically updated FTP format from the STRidER website with a date-stamped change log to allow users to explore their own MPS data with the most up-to-date forensic STR sequence information compiled in a simple guide. Copyright © 2018 Elsevier B.V. All rights reserved.

  14. Impact of previously disadvantaged land-users on sustainable ...

    African Journals Online (AJOL)

    Impact of previously disadvantaged land-users on sustainable agricultural ... about previously disadvantaged land users involved in communal farming systems ... of input, capital, marketing, information and land use planning, with effect on ...

  15. Nonparametric combinatorial sequence models.

    Science.gov (United States)

    Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa

    2011-11-01

    This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.

  16. 22 CFR 40.91 - Certain aliens previously removed.

    Science.gov (United States)

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Certain aliens previously removed. 40.91... IMMIGRANTS UNDER THE IMMIGRATION AND NATIONALITY ACT, AS AMENDED Aliens Previously Removed § 40.91 Certain aliens previously removed. (a) 5-year bar. An alien who has been found inadmissible, whether as a result...

  17. Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing.

    Directory of Open Access Journals (Sweden)

    Sarah M Hykin

    Full Text Available For 150 years or more, specimens were routinely collected and deposited in natural history collections without preserving fresh tissue samples for genetic analysis. In the case of most herpetological specimens (i.e. amphibians and reptiles, attempts to extract and sequence DNA from formalin-fixed, ethanol-preserved specimens-particularly for use in phylogenetic analyses-has been laborious and largely ineffective due to the highly fragmented nature of the DNA. As a result, tens of thousands of specimens in herpetological collections have not been available for sequence-based phylogenetic studies. Massively parallel High-Throughput Sequencing methods and the associated bioinformatics, however, are particularly suited to recovering meaningful genetic markers from severely degraded/fragmented DNA sequences such as DNA damaged by formalin-fixation. In this study, we compared previously published DNA extraction methods on three tissue types subsampled from formalin-fixed specimens of Anolis carolinensis, followed by sequencing. Sufficient quality DNA was recovered from liver tissue, making this technique minimally destructive to museum specimens. Sequencing was only successful for the more recently collected specimen (collected ~30 ybp. We suspect this could be due either to the conditions of preservation and/or the amount of tissue used for extraction purposes. For the successfully sequenced sample, we found a high rate of base misincorporation. After rigorous trimming, we successfully mapped 27.93% of the cleaned reads to the reference genome, were able to reconstruct the complete mitochondrial genome, and recovered an accurate phylogenetic placement for our specimen. We conclude that the amount of DNA available, which can vary depending on specimen age and preservation conditions, will determine if sequencing will be successful. The technique described here will greatly improve the value of museum collections by making many formalin-fixed specimens

  18. Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing.

    Science.gov (United States)

    Hykin, Sarah M; Bi, Ke; McGuire, Jimmy A

    2015-01-01

    For 150 years or more, specimens were routinely collected and deposited in natural history collections without preserving fresh tissue samples for genetic analysis. In the case of most herpetological specimens (i.e. amphibians and reptiles), attempts to extract and sequence DNA from formalin-fixed, ethanol-preserved specimens-particularly for use in phylogenetic analyses-has been laborious and largely ineffective due to the highly fragmented nature of the DNA. As a result, tens of thousands of specimens in herpetological collections have not been available for sequence-based phylogenetic studies. Massively parallel High-Throughput Sequencing methods and the associated bioinformatics, however, are particularly suited to recovering meaningful genetic markers from severely degraded/fragmented DNA sequences such as DNA damaged by formalin-fixation. In this study, we compared previously published DNA extraction methods on three tissue types subsampled from formalin-fixed specimens of Anolis carolinensis, followed by sequencing. Sufficient quality DNA was recovered from liver tissue, making this technique minimally destructive to museum specimens. Sequencing was only successful for the more recently collected specimen (collected ~30 ybp). We suspect this could be due either to the conditions of preservation and/or the amount of tissue used for extraction purposes. For the successfully sequenced sample, we found a high rate of base misincorporation. After rigorous trimming, we successfully mapped 27.93% of the cleaned reads to the reference genome, were able to reconstruct the complete mitochondrial genome, and recovered an accurate phylogenetic placement for our specimen. We conclude that the amount of DNA available, which can vary depending on specimen age and preservation conditions, will determine if sequencing will be successful. The technique described here will greatly improve the value of museum collections by making many formalin-fixed specimens available for

  19. Similar Ratios of Introns to Intergenic Sequence across Animal Genomes.

    Science.gov (United States)

    Francis, Warren R; Wörheide, Gert

    2017-06-01

    One central goal of genome biology is to understand how the usage of the genome differs between organisms. Our knowledge of genome composition, needed for downstream inferences, is critically dependent on gene annotations, yet problems associated with gene annotation and assembly errors are usually ignored in comparative genomics. Here, we analyze the genomes of 68 species across 12 animal phyla and some single-cell eukaryotes for general trends in genome composition and transcription, taking into account problems of gene annotation. We show that, regardless of genome size, the ratio of introns to intergenic sequence is comparable across essentially all animals, with nearly all deviations dominated by increased intergenic sequence. Genomes of model organisms have ratios much closer to 1:1, suggesting that the majority of published genomes of nonmodel organisms are underannotated and consequently omit substantial numbers of genes, with likely negative impact on evolutionary interpretations. Finally, our results also indicate that most animals transcribe half or more of their genomes arguing against differences in genome usage between animal groups, and also suggesting that the transcribed portion is more dependent on genome size than previously thought. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  20. Substrate sequence selectivity of APOBEC3A implicates intra-DNA interactions.

    Science.gov (United States)

    Silvas, Tania V; Hou, Shurong; Myint, Wazo; Nalivaika, Ellen; Somasundaran, Mohan; Kelch, Brian A; Matsuo, Hiroshi; Kurt Yilmaz, Nese; Schiffer, Celia A

    2018-05-14

    The APOBEC3 (A3) family of human cytidine deaminases is renowned for providing a first line of defense against many exogenous and endogenous retroviruses. However, the ability of these proteins to deaminate deoxycytidines in ssDNA makes A3s a double-edged sword. When overexpressed, A3s can mutate endogenous genomic DNA resulting in a variety of cancers. Although the sequence context for mutating DNA varies among A3s, the mechanism for substrate sequence specificity is not well understood. To characterize substrate specificity of A3A, a systematic approach was used to quantify the affinity for substrate as a function of sequence context, length, secondary structure, and solution pH. We identified the A3A ssDNA binding motif as (T/C)TC(A/G), which correlated with enzymatic activity. We also validated that A3A binds RNA in a sequence specific manner. A3A bound tighter to substrate binding motif within a hairpin loop compared to linear oligonucleotide, suggesting A3A affinity is modulated by substrate structure. Based on these findings and previously published A3A-ssDNA co-crystal structures, we propose a new model with intra-DNA interactions for the molecular mechanism underlying A3A sequence preference. Overall, the sequence and structural preferences identified for A3A leads to a new paradigm for identifying A3A's involvement in mutation of endogenous or exogenous DNA.

  1. DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments.

    Science.gov (United States)

    Kelly, Steven; Maini, Philip K

    2013-01-01

    The rapidly growing availability of genome information has created considerable demand for both fast and accurate phylogenetic inference algorithms. We present a novel method called DendroBLAST for reconstructing phylogenetic dendrograms/trees from protein sequences using BLAST. This method differs from other methods by incorporating a simple model of sequence evolution to test the effect of introducing sequence changes on the reliability of the bipartitions in the inferred tree. Using realistic simulated sequence data we demonstrate that this method produces phylogenetic trees that are more accurate than other commonly-used distance based methods though not as accurate as maximum likelihood methods from good quality multiple sequence alignments. In addition to tests on simulated data, we use DendroBLAST to generate input trees for a supertree reconstruction of the phylogeny of the Archaea. This independent analysis produces an approximate phylogeny of the Archaea that has both high precision and recall when compared to previously published analysis of the same dataset using conventional methods. Taken together these results demonstrate that approximate phylogenetic trees can be produced in the absence of multiple sequence alignments, and we propose that these trees will provide a platform for improving and informing downstream bioinformatic analysis. A web implementation of the DendroBLAST method is freely available for use at http://www.dendroblast.com/.

  2. Non-codingRNA sequence variations in human chronic lymphocytic leukemia and colorectal cancer.

    Science.gov (United States)

    Wojcik, Sylwia E; Rossi, Simona; Shimizu, Masayoshi; Nicoloso, Milena S; Cimmino, Amelia; Alder, Hansjuerg; Herlea, Vlad; Rassenti, Laura Z; Rai, Kanti R; Kipps, Thomas J; Keating, Michael J; Croce, Carlo M; Calin, George A

    2010-02-01

    Cancer is a genetic disease in which the interplay between alterations in protein-coding genes and non-coding RNAs (ncRNAs) plays a fundamental role. In recent years, the full coding component of the human genome was sequenced in various cancers, whereas such attempts related to ncRNAs are still fragmentary. We screened genomic DNAs for sequence variations in 148 microRNAs (miRNAs) and ultraconserved regions (UCRs) loci in patients with chronic lymphocytic leukemia (CLL) or colorectal cancer (CRC) by Sanger technique and further tried to elucidate the functional consequences of some of these variations. We found sequence variations in miRNAs in both sporadic and familial CLL cases, mutations of UCRs in CLLs and CRCs and, in certain instances, detected functional effects of these variations. Furthermore, by integrating our data with previously published data on miRNA sequence variations, we have created a catalog of DNA sequence variations in miRNAs/ultraconserved genes in human cancers. These findings argue that ncRNAs are targeted by both germ line and somatic mutations as well as by single-nucleotide polymorphisms with functional significance for human tumorigenesis. Sequence variations in ncRNA loci are frequent and some have functional and biological significance. Such information can be exploited to further investigate on a genome-wide scale the frequency of genetic variations in ncRNAs and their functional meaning, as well as for the development of new diagnostic and prognostic markers for leukemias and carcinomas.

  3. DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments.

    Directory of Open Access Journals (Sweden)

    Steven Kelly

    Full Text Available The rapidly growing availability of genome information has created considerable demand for both fast and accurate phylogenetic inference algorithms. We present a novel method called DendroBLAST for reconstructing phylogenetic dendrograms/trees from protein sequences using BLAST. This method differs from other methods by incorporating a simple model of sequence evolution to test the effect of introducing sequence changes on the reliability of the bipartitions in the inferred tree. Using realistic simulated sequence data we demonstrate that this method produces phylogenetic trees that are more accurate than other commonly-used distance based methods though not as accurate as maximum likelihood methods from good quality multiple sequence alignments. In addition to tests on simulated data, we use DendroBLAST to generate input trees for a supertree reconstruction of the phylogeny of the Archaea. This independent analysis produces an approximate phylogeny of the Archaea that has both high precision and recall when compared to previously published analysis of the same dataset using conventional methods. Taken together these results demonstrate that approximate phylogenetic trees can be produced in the absence of multiple sequence alignments, and we propose that these trees will provide a platform for improving and informing downstream bioinformatic analysis. A web implementation of the DendroBLAST method is freely available for use at http://www.dendroblast.com/.

  4. Population diversity of Diaphorina citri (Hemiptera: Liviidae) in China based on whole mitochondrial genome sequences.

    Science.gov (United States)

    Wu, Fengnian; Jiang, Hongyan; Beattie, G Andrew C; Holford, Paul; Chen, Jianchi; Wallis, Christopher M; Zheng, Zheng; Deng, Xiaoling; Cen, Yijing

    2018-04-24

    Diaphorina citri (Asian citrus psyllid; ACP) transmits 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing (HLB). ACP has been reported in 11 provinces/regions in China, yet its population diversity remains unclear. In this study, we evaluated ACP population diversity in China using representative whole mitochondrial genome (mitogenome) sequences. Additional mitogenome sequences outside China were also acquired and evaluated. The sizes of the 27 ACP mitogenome sequences ranged from 14 986 to 15 030 bp. Along with three previously published mitogenome sequences, the 30 sequences formed three major mitochondrial groups (MGs): MG1, present in southwestern China and occurring at elevations above 1000 m; MG2, present in southeastern China and Southeast Asia (Cambodia, Indonesia, Malaysia, and Vietnam) and occurring at elevations below 180 m; and MG3, present in the USA and Pakistan. Single nucleotide polymorphisms in five genes (cox2, atp8, nad3, nad1 and rrnL) contributed mostly in the ACP diversity. Among these genes, rrnL had the most variation. Mitogenome sequences analyses revealed two major phylogenetic groups of ACP present in China as well as a possible unique group present currently in Pakistan and the USA. The information could have significant implications for current ACP control and HLB management. © 2018 Society of Chemical Industry. © 2018 Society of Chemical Industry.

  5. Electronic publishing in radiology: economics and the future.

    Science.gov (United States)

    Chew, Felix S; Llewellyn, Kevin T; Olsen, Kathryn M

    2004-11-01

    Scholarly publishing is a large market involving thousands of peer-reviewed journals but a decreasing number of publishers. An economic model can be described in which authors give their work to publishers who then sell access to this work. Because each published article is a unique work with few if any substitutes, publishers have some degree of monopoly power and can price their products accordingly. The advent of desktop publishing using personal computers made it possible for individuals to publish material without publishers, an activity that gained momentum when the publishing medium shifted from paper to electronic, and from electronic publishing to the Internet. This activity destabilized the industry, and in the rush to gain market share by providing free content, unsustainable business models were created. Scholarly publishing is now dominated by a small number of multinational corporations that acquired many smaller publishing operations. As these companies have exercised their monopoly power, an open access movement has gained traction in which authors (or their institutions) initially pay for publication, but readers have free and open access to the published articles. This movement is in diametric opposition to the commercial publishing model, and it remains to be seen whether and how well the two can coexist in the future.

  6. Determining root correspondence between previously and newly detected objects

    Science.gov (United States)

    Paglieroni, David W.; Beer, N Reginald

    2014-06-17

    A system that applies attribute and topology based change detection to networks of objects that were detected on previous scans of a structure, roadway, or area of interest. The attributes capture properties or characteristics of the previously detected objects, such as location, time of detection, size, elongation, orientation, etc. The topology of the network of previously detected objects is maintained in a constellation database that stores attributes of previously detected objects and implicitly captures the geometrical structure of the network. A change detection system detects change by comparing the attributes and topology of new objects detected on the latest scan to the constellation database of previously detected objects.

  7. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  8. Structural revision of some recently published iridoid glucosides.

    Science.gov (United States)

    Jensen, Søren R; Caliş, Ihsan; Gotfredsen, Charlotte H; Søtofte, Inger

    2007-01-01

    The structures of six different iridoid glucosides have been revised. Three compounds isolated from Eremostachys glabra and designated 6,9-epi-8-O-acetylshanziside (1), 5,9-epi-penstemoside (2), and 5,9-epi-7,8-didehydropenstemoside (3) have been shown to be identical to the known iridoids barlerin (4, 8-O-acetylshanziside), penstemoside (5), and 7,8-didehydropenstemoside (6), respectively. Another compound named harpagoside-B, isolated from Scrophularia deserti and proposed to be 9-epi-6-O-methylharpagoside (11), was demonstrated from the spectroscopic data given to be the known harpagoside (10b). Finally, two alleged iridoid galactosides from Buddleja crispa named buddlejosides A and B (12a and 12b) have been shown to be the corresponding glucosides; the former is identical to agnuside (13a), while the latter is 3,4-dihydroxybenzoylaucubin (13b), an iridoid glucoside not previously published. This clearly showed that care should be taken with the interpretation of NOEs involving bridgehead protons in iridoid structures because they can be capricious and lead to erroneous structural assignments.

  9. Deep whole-genome sequencing of 90 Han Chinese genomes.

    Science.gov (United States)

    Lan, Tianming; Lin, Haoxiang; Zhu, Wenjuan; Laurent, Tellier Christian Asker Melchior; Yang, Mengcheng; Liu, Xin; Wang, Jun; Wang, Jian; Yang, Huanming; Xu, Xun; Guo, Xiaosen

    2017-09-01

    Next-generation sequencing provides a high-resolution insight into human genetic information. However, the focus of previous studies has primarily been on low-coverage data due to the high cost of sequencing. Although the 1000 Genomes Project and the Haplotype Reference Consortium have both provided powerful reference panels for imputation, low-frequency and novel variants remain difficult to discover and call with accuracy on the basis of low-coverage data. Deep sequencing provides an optimal solution for the problem of these low-frequency and novel variants. Although whole-exome sequencing is also a viable choice for exome regions, it cannot account for noncoding regions, sometimes resulting in the absence of important, causal variants. For Han Chinese populations, the majority of variants have been discovered based upon low-coverage data from the 1000 Genomes Project. However, high-coverage, whole-genome sequencing data are limited for any population, and a large amount of low-frequency, population-specific variants remain uncharacterized. We have performed whole-genome sequencing at a high depth (∼×80) of 90 unrelated individuals of Chinese ancestry, collected from the 1000 Genomes Project samples, including 45 Northern Han Chinese and 45 Southern Han Chinese samples. Eighty-three of these 90 have been sequenced by the 1000 Genomes Project. We have identified 12 568 804 single nucleotide polymorphisms, 2 074 210 short InDels, and 26 142 structural variations from these 90 samples. Compared to the Han Chinese data from the 1000 Genomes Project, we have found 7 000 629 novel variants with low frequency (defined as minor allele frequency genome. Compared to the 1000 Genomes Project, these Han Chinese deep sequencing data enhance the characterization of a large number of low-frequency, novel variants. This will be a valuable resource for promoting Chinese genetics research and medical development. Additionally, it will provide a valuable supplement to the 1000

  10. EDITORIAL: Roberts Prize for the best paper published in 2009 Roberts Prize for the best paper published in 2009

    Science.gov (United States)

    Webb, Steve; Harris, Simon

    2010-07-01

    The publishers of Physics in Medicine and Biology (PMB), IOP Publishing, in association with the journal owners, the Institute of Physics and Engineering in Medicine (IPEM), jointly award an annual prize for the best paper published in PMB during the previous year. The procedure for deciding the winner has been made as thorough as possible, to try to ensure that an outstanding paper wins the prize. We started off with a shortlist of the 10 research papers published in 2009 which were rated the best based on the referees' quality assessments. Following the submission of a short 'case for winning' document by each of the shortlisted authors, an IPEM college of jurors of the status of FIPEM assessed and rated these 10 papers in order to choose a winner, which was then endorsed by the Editorial Board. We have a clear, and very worthy, winner this year. We have much pleasure in advising readers that the 2009 Roberts Prize is awarded to E Z Zhang et al from University College London for their paper on photoacoustic tomography. In vivo high resolution 3D photoacoustic imaging of superficial vascular anatomy E Z Zhang, J G Laufer, R B Pedley and P C Beard 2009 Phys. Med. Biol. 54 1035-46 Our congratulations go to these authors. Of course all of the shortlisted papers were of great merit, and the full top-10 is listed below (in alphabetical order). Steve Webb Editor-in-Chief Simon Harris Publisher References Cheng Y-C N , Neelavalli J and Haacke E M 2009 Limitations of calculating field distributions and magnetic susceptibilities in MRI using a Fourier based method Phys. Med. Biol. 54 1169-89 Cho S, Ahn S, Li Q and Leahy R M 2009 Exact and approximate Fourier rebinning of PET data from time-of-flight to non time-of-flight 2009 Phys. Med. Biol. 54 467-84 Davidson S R H, Weersink R A, Haider M A, Gertner M R, Bogaards A, Giewercer D, Scherz A, Sherar M D, Elhilali M, Chin J L, Trachtenberg J and Wilson B C 2009 Treatment planning and dose analysis for interstitial

  11. Snake Genome Sequencing: Results and Future Prospects.

    Science.gov (United States)

    Kerkkamp, Harald M I; Kini, R Manjunatha; Pospelov, Alexey S; Vonk, Freek J; Henkel, Christiaan V; Richardson, Michael K

    2016-12-01

    Snake genome sequencing is in its infancy-very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

  12. Snake Genome Sequencing: Results and Future Prospects

    Directory of Open Access Journals (Sweden)

    Harald M. I. Kerkkamp

    2016-12-01

    Full Text Available Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

  13. Long sequence correlation coprocessor

    Science.gov (United States)

    Gage, Douglas W.

    1994-09-01

    A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.

  14. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  15. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  16. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  17. sequenceMiner algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  18. Exploring new frontiers of electronic publishing in biomedical science.

    Science.gov (United States)

    Ng, K H

    2009-03-01

    Publishing is a hallmark of good scientific research. The aim of publishing is to disseminate new research knowledge and findings as widely as possible in a timely and efficient manner. Scientific publishing has evolved over the years with the advent of new technologies and demands. This paper presents a brief discussion on the history and status of electronic publishing. The Open Access Initiative was created with the aim of overcoming various limitations faced by traditional publishing access models. Innovations have opened up possibilities for electronic publishing to increase the accessibility, visibility, interactivity and usability of research. A glimpse of the future publishing landscape has revealed that scientific communication and research will not remain the same. The internet and advances in information technology will have an impact on the research landscape, scholarly publishing, research policy and funding, dissemination of knowledge, and the progress of science as a whole.

  19. Tracking TCRβ sequence clonotype expansions during antiviral therapy using high-throughput sequencing of the hypervariable region

    Directory of Open Access Journals (Sweden)

    Mark W Robinson

    2016-04-01

    Full Text Available To maintain a persistent infection viruses such as hepatitis C virus (HCV employ a range of mechanisms that subvert protective T cell responses. The suppression of antigen-specific T cell responses by HCV hinders efforts to profile T cell responses during chronic infection and antiviral therapy. Conventional methods of detecting antigen-specific T cells utilise either antigen stimulation (e.g. ELISpot, proliferation assays, cytokine production or antigen-loaded tetramer staining. This limits the ability to profile T cell responses during chronic infection due to suppressed effector function and the requirement for prior knowledge of antigenic viral peptide sequences. Recently high-throughput sequencing (HTS technologies have been developed for the analysis of T cell repertoires. In the present study we have assessed the feasibility of HTS of the TCRβ complementarity determining region (CDR3 to track T cell expansions in an antigen-independent manner. Using sequential blood samples from HCV-infected individuals undergoing anti-viral therapy we were able to measure the population frequencies of >35,000 TCRβ sequence clonotypes in each individual over the course of 12 weeks. TRBV/TRBJ gene segment usage varied markedly between individuals but remained relatively constant within individuals across the course of therapy. Despite this stable TRBV/TRBJ gene segment usage, a number of TCRβ sequence clonotypes showed dramatic changes in read frequency. These changes could not be linked to therapy outcomes in the present study however the TCRβ CDR3 sequences with the largest fold changes did include sequences with identical TRBV/TRBJ gene segment usage and high joining region homology to previously published CDR3 sequences from HCV-specific T cells targeting the HLA-B*0801-restricted 1395HSKKKCDEL1403 and HLA-A*0101–restricted 1435ATDALMTGY1443 epitopes. The pipeline developed in this proof of concept study provides a platform for the design of

  20. Microbial species delineation using whole genome sequences.

    Science.gov (United States)

    Varghese, Neha J; Mukherjee, Supratim; Ivanova, Natalia; Konstantinidis, Konstantinos T; Mavrommatis, Kostas; Kyrpides, Nikos C; Pati, Amrita

    2015-08-18

    Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotide Identity (gANI) metric, which is widely acknowledged as a robust measure of genomic relatedness. In this work, we demonstrate that the combination of gANI and the alignment fraction (AF) between two genomes accurately reflects their genomic relatedness. We introduce an efficient implementation of AF,gANI and discuss its successful application to 86.5M genome pairs between 13,151 prokaryotic genomes assigned to 3032 species. Subsequently, by comparing the genome clusters obtained from complete linkage clustering of these pairs to existing taxonomy, we observed that nearly 18% of all prokaryotic species suffer from anomalies in species definition. Our results can be used to explore central questions such as whether microorganisms form a continuum of genetic diversity or distinct species represented by distinct genetic signatures. We propose that this precise and objective AF,gANI-based species definition: the MiSI (Microbial Species Identifier) method, be used to address previous inconsistencies in species classification and as the primary guide for new taxonomic species assignment, supplemented by the traditional polyphasic approach, as required. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. Publishing and Alternative Licensing Model of Africa (PALM Africa ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Africa depends on learning materials published elsewhere, and has serious difficulty acquiring, producing and distributing them. In order to facilitate citizen access to these materials, the publishing sector in Africa needs to explore new business models and technologies. Publishing and Alternative Licensing Model of Africa ...

  2. 76 FR 30952 - Published Privacy Impact Assessments on the Web

    Science.gov (United States)

    2011-05-27

    ... DEPARTMENT OF HOMELAND SECURITY Office of the Secretary Published Privacy Impact Assessments on... the Department. These assessments were approved and published on the Privacy Office's web site between..., 2011 and March 31, 2011, the Chief Privacy Officer of the DHS approved and published sixteen Privacy...

  3. 46 CFR 503.11 - Materials to be published.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 9 2010-10-01 2010-10-01 false Materials to be published. 503.11 Section 503.11... in the Federal Register § 503.11 Materials to be published. The Commission shall separately state and concurrently publish the following materials in the Federal Register for the guidance of the public: (a...

  4. 76 FR 58814 - Published Privacy Impact Assessments on the Web

    Science.gov (United States)

    2011-09-22

    ... DEPARTMENT OF HOMELAND SECURITY Office of the Secretary Published Privacy Impact Assessments on... DHS. These assessments were approved and published on the Privacy Office's Web site between June 1... 31, 2011, the Chief Privacy Officer of the DHS approved and published twenty-six Privacy Impact...

  5. 76 FR 78934 - Published Privacy Impact Assessments on the Web

    Science.gov (United States)

    2011-12-20

    ... DEPARTMENT OF HOMELAND SECURITY Office of the Secretary Published Privacy Impact Assessments on.... These assessments were approved and published on the Privacy Office's web site between September 1, 2011... November 30, 2011, the Chief Privacy Officer of the DHS approved and published seven Privacy Impact...

  6. 77 FR 46100 - Published Privacy Impact Assessments on the Web

    Science.gov (United States)

    2012-08-02

    ... DEPARTMENT OF HOMELAND SECURITY Office of the Secretary Published Privacy Impact Assessments on... published on the Privacy Office's Web site between March 1, 2012 and May 31, 2012. DATES: The PIAs will be... approved and published fifteen Privacy Impact Assessments (PIAs) on the DHS Privacy Office Web site, www...

  7. 76 FR 37823 - Published Privacy Impact Assessments on the Web

    Science.gov (United States)

    2011-06-28

    ... DEPARTMENT OF HOMELAND SECURITY Office of the Secretary Published Privacy Impact Assessments on... Department. These assessments were approved and published on the Privacy Office's Web site between March 31... 31, 2011, the Chief Privacy Officer of the DHS approved and published ten Privacy Impact Assessments...

  8. Publishing in Educational Psychology Journals: Comments from Editors

    Science.gov (United States)

    Nihalani, Priya K.; Mayrath, Michael C.

    2008-01-01

    The following paper emphasizes the importance of publishing and learning how to publish in educational psychology journals. We have compiled a set of recommendations based on advice from editors in the field and several other sources on how to publish. Additionally, this paper provides a step-by-step guide that graduate students and junior faculty…

  9. Royalty Fees Part I: The Copyright Clearance Center and Publishers.

    Science.gov (United States)

    Eiblum, Paula; Ardito, Stephanie C.

    1998-01-01

    Discussion of copyrights, royalty fees, and intellectual property focuses on the Copyright Clearance Center and publishers. Topics include results of a survey of library and information science journal publishers; how users verify royalty fees; how publishers determine fees; royalty fee reporting; and terms and conditions imposed on electronic…

  10. The ethical hole at the centre of 'publish or perish'

    Czech Academy of Sciences Publication Activity Database

    Kravjar, J.; Hladík, Marek

    2016-01-01

    Roč. 430, 30 September 2016 (2016) ISSN 1756-297X Institutional support: RVO:68081758 Keywords : scholarly open-access publishing * predatory publishing * peer-review * publishing ethics Subject RIV: AC - Archeology, Anthropology, Ethnology http://www.universityworldnews.com/article.php?story=20160921112724448

  11. Performance of Nigerian Publishers as Innovation agents to ...

    African Journals Online (AJOL)

    There have been arguments suggesting that the low rate of adoption of digital publishing innovations in Nigeria could be attributed to the conservative activities of local publishers. This study, therefore, set out to investigate the role played by local Nigerian Publishers towards the acquisition and adoption of digital resources ...

  12. Small "p" Publishing: A Networked Blogging Approach to Academic Discourse

    Science.gov (United States)

    Martin, Julia W.; Hughes, Brian

    2012-01-01

    This article highlights a middle ground for academic publishing between formal peer-reviewed journals and informal blogging that we call "Small "p" Publishing." Having implemented and tested a publishing network that illustrates this middle ground, we describe its unique contributions to scholars and learning communities. Three features that…

  13. Publishing in Open Access Education Journals: The Authors' Perspectives

    Science.gov (United States)

    Coonin, Bryna; Younce, Leigh M.

    2010-01-01

    Open access publishing is now an accepted method of scholarly communication. However, the greatest traction for open access publishing thus far has been in the sciences. Penetration of open access publishing has been much slower among the social sciences. This study surveys 309 authors from recent issues of open access journals in education to…

  14. Technical Services in the Age of Electronic Publishing.

    Science.gov (United States)

    Brownrigg, Edwin; And Others

    1984-01-01

    Examination of the traditional library technical services functions and how they may change with the advent of widespread computer-based electronic publishing emphasizes ways in which technical services will have to adapt in electronic publishing environment. Implications of electronic publishing for library management and budgeting are explored.…

  15. Publishing scientific papers in scholarly journals | Ayensu | Journal ...

    African Journals Online (AJOL)

    The rigorous demand of peer review has been emphasized to illustrate the academic nature of scholarly publishing. The quality attributes of a manuscript in terms of ... The rules, norms, ethics and standards of publishing in relation to copyrights and plagiarism are discussed. The published paper is recognized as the ...

  16. Publishing Systems Same for J-Schools and Small Papers.

    Science.gov (United States)

    Oates, William R.

    1987-01-01

    Discusses how professional publishing software allows journalism education programs to accurately create the publishing environment students will encounter at small and medium-sized newspapers. Claims that the laser jet printer is the key ingredient that is turning the personal computer revolution into a newspaper publishing revolution, describing…

  17. Rapid and Accurate Sequencing of Enterovirus Genomes Using MinION Nanopore Sequencer.

    Science.gov (United States)

    Wang, Ji; Ke, Yue Hua; Zhang, Yong; Huang, Ke Qiang; Wang, Lei; Shen, Xin Xin; Dong, Xiao Ping; Xu, Wen Bo; Ma, Xue Jun

    2017-10-01

    Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. In this proof-of-concept study using Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Within the first minute (min) of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min (on average), 99% identity was achieved for 10 CA16 strains in a single run. MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use. Copyright © 2017 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

  18. Genomics dataset on unclassified published organism (patent US 7547531

    Directory of Open Access Journals (Sweden)

    Mohammad Mahfuz Ali Khan Shawan

    2016-12-01

    Full Text Available Nucleotide (DNA sequence analysis provides important clues regarding the characteristics and taxonomic position of an organism. With the intention that, DNA sequence analysis is very crucial to learn about hierarchical classification of that particular organism. This dataset (patent US 7547531 is chosen to simplify all the complex raw data buried in undisclosed DNA sequences which help to open doors for new collaborations. In this data, a total of 48 unidentified DNA sequences from patent US 7547531 were selected and their complete sequences were retrieved from NCBI BioSample database. Quick response (QR code of those DNA sequences was constructed by DNA BarID tool. QR code is useful for the identification and comparison of isolates with other organisms. AT/GC content of the DNA sequences was determined using ENDMEMO GC Content Calculator, which indicates their stability at different temperature. The highest GC content was observed in GP445188 (62.5% which was followed by GP445198 (61.8% and GP445189 (59.44%, while lowest was in GP445178 (24.39%. In addition, New England BioLabs (NEB database was used to identify cleavage code indicating the 5, 3 and blunt end and enzyme code indicating the methylation site of the DNA sequences was also shown. These data will be helpful for the construction of the organisms’ hierarchical classification, determination of their phylogenetic and taxonomic position and revelation of their molecular characteristics.

  19. Gene discovery by chemical mutagenesis and whole-genome sequencing in Dictyostelium.

    Science.gov (United States)

    Li, Cheng-Lin Frank; Santhanam, Balaji; Webb, Amanda Nicole; Zupan, Blaž; Shaulsky, Gad

    2016-09-01

    Whole-genome sequencing is a useful approach for identification of chemical-induced lesions, but previous applications involved tedious genetic mapping to pinpoint the causative mutations. We propose that saturation mutagenesis under low mutagenic loads, followed by whole-genome sequencing, should allow direct implication of genes by identifying multiple independent alleles of each relevant gene. We tested the hypothesis by performing three genetic screens with chemical mutagenesis in the social soil amoeba Dictyostelium discoideum Through genome sequencing, we successfully identified mutant genes with multiple alleles in near-saturation screens, including resistance to intense illumination and strong suppressors of defects in an allorecognition pathway. We tested the causality of the mutations by comparison to published data and by direct complementation tests, finding both dominant and recessive causative mutations. Therefore, our strategy provides a cost- and time-efficient approach to gene discovery by integrating chemical mutagenesis and whole-genome sequencing. The method should be applicable to many microbial systems, and it is expected to revolutionize the field of functional genomics in Dictyostelium by greatly expanding the mutation spectrum relative to other common mutagenesis methods. © 2016 Li et al.; Published by Cold Spring Harbor Laboratory Press.

  20. Ichnology applied to sequence stratigraphic analysis of Siluro-Devonian mud-dominated shelf deposits, Paraná Basin, Brazil

    Science.gov (United States)

    Sedorko, Daniel; Netto, Renata G.; Savrda, Charles E.

    2018-04-01

    Previous studies of the Paraná Supersequence (Furnas and Ponta Grossa formations) of the Paraná Basin in southern Brazil have yielded disparate sequence stratigraphic interpretations. An integrated sedimentological, paleontological, and ichnological model was created to establish a refined sequence stratigraphic framework for this succession, focusing on the Ponta Grossa Formation. Twenty-nine ichnotaxa are recognized in the Ponta Grossa Formation, recurring assemblages of which define five trace fossil suites that represent various expressions of the Skolithos, Glossifungites and Cruziana ichnofacies. Physical sedimentologic characteristics and associated softground ichnofacies provide the basis for recognizing seven facies that reflect a passive relationship to bathymetric gradients from shallow marine (shoreface) to offshore deposition. The vertical distribution of facies provides the basis for dividing the Ponta Grossa Formation into three major (3rd-order) depositional sequences- Siluro-Devonian and Devonian I and II-each containing a record of three to seven higher-order relative sea-level cycles. Major sequence boundaries, commonly coinciding with hiatuses recognized from previously published biostratigraphic data, are locally marked by firmground Glossifungites Ichnofacies associated with submarine erosion. Maximum transgressive horizons are prominently marked by unbioturbated or weakly bioturbated black shales. By integrating observations of the Ponta Grossa Formation with those recently made on the underlying marginal- to shallow-marine Furnas Formation, the entire Paraná Supersequence can be divided into four disconformity-bound sequences: a Lower Silurian (Llandovery-Wenlock) sequence, corresponding to lower and middle units of the Furnas; a Siluro-Devonian sequence (?Pridoli-Early Emsian), and Devonian sequences I (Late Emsian-Late Eifelian) and II (Late Eifelian-Early Givetian). Stratigraphic positions of sequence boundaries generally coincide with

  1. SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing.

    Science.gov (United States)

    Tsuchiya, Mariko; Amano, Kojiro; Abe, Masaya; Seki, Misato; Hase, Sumitaka; Sato, Kengo; Sakakibara, Yasubumi

    2016-06-15

    Deep sequencing of the transcripts of regulatory non-coding RNA generates footprints of post-transcriptional processes. After obtaining sequence reads, the short reads are mapped to a reference genome, and specific mapping patterns can be detected called read mapping profiles, which are distinct from random non-functional degradation patterns. These patterns reflect the maturation processes that lead to the production of shorter RNA sequences. Recent next-generation sequencing studies have revealed not only the typical maturation process of miRNAs but also the various processing mechanisms of small RNAs derived from tRNAs and snoRNAs. We developed an algorithm termed SHARAKU to align two read mapping profiles of next-generation sequencing outputs for non-coding RNAs. In contrast with previous work, SHARAKU incorporates the primary and secondary sequence structures into an alignment of read mapping profiles to allow for the detection of common processing patterns. Using a benchmark simulated dataset, SHARAKU exhibited superior performance to previous methods for correctly clustering the read mapping profiles with respect to 5'-end processing and 3'-end processing from degradation patterns and in detecting similar processing patterns in deriving the shorter RNAs. Further, using experimental data of small RNA sequencing for the common marmoset brain, SHARAKU succeeded in identifying the significant clusters of read mapping profiles for similar processing patterns of small derived RNA families expressed in the brain. The source code of our program SHARAKU is available at http://www.dna.bio.keio.ac.jp/sharaku/, and the simulated dataset used in this work is available at the same link. Accession code: The sequence data from the whole RNA transcripts in the hippocampus of the left brain used in this work is available from the DNA DataBank of Japan (DDBJ) Sequence Read Archive (DRA) under the accession number DRA004502. yasu@bio.keio.ac.jp Supplementary data are available

  2. Magazine Publishing Innovation: Two Case Studies on Managing Creativity

    Directory of Open Access Journals (Sweden)

    Simon Das

    2016-06-01

    Full Text Available This paper aims to highlight a link between publishing business innovation and how editors manage creativity in the digital era. Examining the changing industrial and historical business context for the U.K. magazine publishing industry, two case studies are analyzed as representatives of different ends of the publishing company spectrum (one a newly launched magazine published by a major, the other an independent ‘magazine’ website start-up. Qualitative data analysis on publishing innovation and managing creativity is presented as a springboard for further research on magazine media management.

  3. Historian: accurate reconstruction of ancestral sequences and evolutionary rates.

    Science.gov (United States)

    Holmes, Ian H

    2017-04-15

    Reconstruction of ancestral sequence histories, and estimation of parameters like indel rates, are improved by using explicit evolutionary models and summing over uncertain alignments. The previous best tool for this purpose (according to simulation benchmarks) was ProtPal, but this tool was too slow for practical use. Historian combines an efficient reimplementation of the ProtPal algorithm with performance-improving heuristics from other alignment tools. Simulation results on fidelity of rate estimation via ancestral reconstruction, along with evaluations on the structurally informed alignment dataset BAliBase 3.0, recommend Historian over other alignment tools for evolutionary applications. Historian is available at https://github.com/evoldoers/historian under the Creative Commons Attribution 3.0 US license. ihholmes+historian@gmail.com. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  4. 49 CFR 173.23 - Previously authorized packaging.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 2 2010-10-01 2010-10-01 false Previously authorized packaging. 173.23 Section... REQUIREMENTS FOR SHIPMENTS AND PACKAGINGS Preparation of Hazardous Materials for Transportation § 173.23 Previously authorized packaging. (a) When the regulations specify a packaging with a specification marking...

  5. 28 CFR 10.5 - Incorporation of papers previously filed.

    Science.gov (United States)

    2010-07-01

    ... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Incorporation of papers previously filed... CARRYING ON ACTIVITIES WITHIN THE UNITED STATES Registration Statement § 10.5 Incorporation of papers previously filed. Papers and documents already filed with the Attorney General pursuant to the said act and...

  6. 75 FR 76056 - FEDERAL REGISTER CITATION OF PREVIOUS ANNOUNCEMENT:

    Science.gov (United States)

    2010-12-07

    ... SECURITIES AND EXCHANGE COMMISSION Sunshine Act Meeting FEDERAL REGISTER CITATION OF PREVIOUS ANNOUNCEMENT: STATUS: Closed meeting. PLACE: 100 F Street, NE., Washington, DC. DATE AND TIME OF PREVIOUSLY ANNOUNCED MEETING: Thursday, December 9, 2010 at 2 p.m. CHANGE IN THE MEETING: Time change. The closed...

  7. The Impact of Electronic Commerce on the Publishing Industry: Towards a Business Value Complementarity Framework of Electronic Publishing.

    Science.gov (United States)

    Scupola, Ada

    1999-01-01

    Discussion of the publishing industry and its use of information and communication technologies focuses on the way in which electronic-commerce technologies are changing and could change the publishing processes, and develops a business complementarity model of electronic publishing to maximize profitability and improve the competitive position.…

  8. The pathogenicity of genetic variants previously associated with left ventricular non-compaction

    DEFF Research Database (Denmark)

    Abbasi, Yeganeh; Jabbari, Javad; Jabbari, Reza

    2016-01-01

    BACKGROUND: Left ventricular non-compaction (LVNC) is a rare cardiomyopathy. Many genetic variants have been associated with LVNC. However, the number of the previous LVNC-associated variants that are common in the background population remains unknown. The aim of this study was to provide...... an updated list of previously reported LVNC-associated variants with biologic description and investigate the prevalence of LVNC variants in healthy general population to find false-positive LVNC-associated variants. METHODS AND RESULTS: The Human Gene Mutation Database and PubMed were systematically...... searched to identify all previously reported LVNC-associated variants. Thereafter, the Exome Sequencing Project (ESP) and the Exome Aggregation Consortium (ExAC), that both represent the background population, was searched for all variants. Four in silico prediction tools were assessed to determine...

  9. Genomic sequencing of Pleistocene cave bears

    Energy Technology Data Exchange (ETDEWEB)

    Noonan, James P.; Hofreiter, Michael; Smith, Doug; Priest, JamesR.; Rohland, Nadin; Rabeder, Gernot; Krause, Johannes; Detter, J. Chris; Paabo, Svante; Rubin, Edward M.

    2005-04-01

    Despite the information content of genomic DNA, ancient DNA studies to date have largely been limited to amplification of mitochondrial DNA due to technical hurdles such as contamination and degradation of ancient DNAs. In this study, we describe two metagenomic libraries constructed using unamplified DNA extracted from the bones of two 40,000-year-old extinct cave bears. Analysis of {approx}1 Mb of sequence from each library showed that, despite significant microbial contamination, 5.8 percent and 1.1 percent of clones in the libraries contain cave bear inserts, yielding 26,861 bp of cave bear genome sequence. Alignment of this sequence to the dog genome, the closest sequenced genome to cave bear in terms of evolutionary distance, revealed roughly the expected ratio of cave bear exons, repeats and conserved noncoding sequences. Only 0.04 percent of all clones sequenced were derived from contamination with modern human DNA. Comparison of cave bear with orthologous sequences from several modern bear species revealed the evolutionary relationship of these lineages. Using the metagenomic approach described here, we have recovered substantial quantities of mammalian genomic sequence more than twice as old as any previously reported, establishing the feasibility of ancient DNA genomic sequencing programs.

  10. No discrimination against previous mates in a sexually cannibalistic spider

    Science.gov (United States)

    Fromhage, Lutz; Schneider, Jutta M.

    2005-09-01

    In several animal species, females discriminate against previous mates in subsequent mating decisions, increasing the potential for multiple paternity. In spiders, female choice may take the form of selective sexual cannibalism, which has been shown to bias paternity in favor of particular males. If cannibalistic attacks function to restrict a male's paternity, females may have little interest to remate with males having survived such an attack. We therefore studied the possibility of female discrimination against previous mates in sexually cannibalistic Argiope bruennichi, where females almost always attack their mate at the onset of copulation. We compared mating latency and copulation duration of males having experienced a previous copulation either with the same or with a different female, but found no evidence for discrimination against previous mates. However, males copulated significantly shorter when inserting into a used, compared to a previously unused, genital pore of the female.

  11. Implant breast reconstruction after salvage mastectomy in previously irradiated patients.

    Science.gov (United States)

    Persichetti, Paolo; Cagli, Barbara; Simone, Pierfranco; Cogliandro, Annalisa; Fortunato, Lucio; Altomare, Vittorio; Trodella, Lucio

    2009-04-01

    The most common surgical approach in case of local tumor recurrence after quadrantectomy and radiotherapy is salvage mastectomy. Breast reconstruction is the subsequent phase of the treatment and the plastic surgeon has to operate on previously irradiated and manipulated tissues. The medical literature highlights that breast reconstruction with tissue expanders is not a pursuable option, considering previous radiotherapy a contraindication. The purpose of this retrospective study is to evaluate the influence of previous radiotherapy on 2-stage breast reconstruction (tissue expander/implant). Only patients with analogous timing of radiation therapy and the same demolitive and reconstructive procedures were recruited. The results of this study prove that, after salvage mastectomy in previously irradiated patients, implant reconstruction is still possible. Further comparative studies are, of course, advisable to draw any conclusion on the possibility to perform implant reconstruction in previously irradiated patients.

  12. Perception Enhancement using Visual Attributes in Sequence Motif Visualization

    OpenAIRE

    Oon, Yin; Lee, Nung; Kok, Wei

    2016-01-01

    Sequence logo is a well-accepted scientific method to visualize the conservation characteristics of biological sequence motifs. Previous studies found that using sequence logo graphical representation for scientific evidence reports or arguments could seriously cause biases and misinterpretation by users. This study investigates on the visual attributes performance of a sequence logo in helping users to perceive and interpret the information based on preattentive theories and Gestalt principl...

  13. Nonlinear analysis of sequence repeats of multi-domain proteins

    Energy Technology Data Exchange (ETDEWEB)

    Huang Yanzhao [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Li Mingfeng [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Xiao Yi [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China)]. E-mail: lmf_bill@sina.com

    2007-11-15

    Many multi-domain proteins have repetitive three-dimensional structures but nearly-random amino acid sequences. In the present paper, by using a modified recurrence plot proposed by us previously, we show that these amino acid sequences have hidden repetitions in fact. These results indicate that the repetitive domain structures are encoded by the repetitive sequences. This also gives a method to detect the repetitive domain structures directly from amino acid sequences.

  14. [Parathyroid cancer in a patient with previous history of hypernephroma: a clinical case].

    Science.gov (United States)

    Martín Navarro, J; Mendoza, E; Mateos, P; Cereceda, A; Coca, S

    2007-01-01

    We report the clinical case of a 55 year-old male patient, with a previous history of nephrectomy by hypernephroma sixteen years ago, first presenting hypercalcemia and rising of intact parathyroid hormone (iPTH) levels. A localization study revealed an intrathyroid nodule with cystic appearance. After undergoing a hemi-thyroidectomy, the patient is diagnosed with parathyroid carcinoma. This article analyzes previously published cases presenting parathyroidal pathologies associated with hypernephroma. A broader differential diagnosis--including the screening of parathyroidal pathologies should be considered in patients with hypercalcemia and hypernephroma.

  15. Construction and sequencing of an infectious clone of the human parvovirus B19

    International Nuclear Information System (INIS)

    Zhi Ning; Zadori, Zoltan; Brown, Kevin E.; Tijssen, Peter

    2004-01-01

    Human parvovirus B19 has a nonenveloped, icosahedral capsid packaging a linear single-stranded DNA genome of 5.6 kb with long inverted terminal repeats (ITR) at both the 5' and 3' end. Previous attempts to construct a full-length B19 clone were unsuccessful due to deletions in the ITR sequences. We cloned the complete parvovirus B19 genome with intact ITRs from an aplastic crisis patient. Sequence analysis of the complete viral genome indicated that both 5' and 3' ITRs have two sequence configurations and several base changes within the ITRs compared to previous published sequences. After transfection of the plasmid into permissive cells, spliced and non-spliced viral transcripts and viral capsid proteins could be detected. Southern blot analysis of the DNA purified from the plasmid-transfected cells confirmed parvovirus B19 DNA replication. Production of infectious virus by the B19 plasmid was shown by inoculation of cell lysate derived from transfected cells into fresh cells. Together, these results indicate the first successful production of an infectious clone for parvovirus B19 virus

  16. Sequencing Cyclic Peptides by Multistage Mass Spectrometry

    Science.gov (United States)

    Mohimani, Hosein; Yang, Yu-Liang; Liu, Wei-Ting; Hsieh, Pei-Wen; Dorrestein, Pieter C.; Pevzner, Pavel A.

    2012-01-01

    Some of the most effective antibiotics (e.g., Vancomycin and Daptomycin) are cyclic peptides produced by non-ribosomal biosynthetic pathways. While hundreds of biomedically important cyclic peptides have been sequenced, the computational techniques for sequencing cyclic peptides are still in their infancy. Previous methods for sequencing peptide antibiotics and other cyclic peptides are based on Nuclear Magnetic Resonance spectroscopy, and require large amount (miligrams) of purified materials that, for most compounds, are not possible to obtain. Recently, development of mass spectrometry based methods has provided some hope for accurate sequencing of cyclic peptides using picograms of materials. In this paper we develop a method for sequencing of cyclic peptides by multistage mass spectrometry, and show its advantages over single stage mass spectrometry. The method is tested on known and new cyclic peptides from Bacillus brevis, Dianthus superbus and Streptomyces griseus, as well as a new family of cyclic peptides produced by marine bacteria. PMID:21751357

  17. Strategies and guidelines for scholarly publishing of biodiversity data

    Directory of Open Access Journals (Sweden)

    Lyubomir Penev

    2017-02-01

    Full Text Available The present paper describes policies and guidelines for scholarly publishing of biodiversity and biodiversity-related data, elaborated and updated during the Framework Program 7 EU BON project, on the basis of an earlier version published on Pensoft's website in 2011. The document discusses some general concepts, including a definition of datasets, incentives to publish data and licenses for data publishing. Further, it defines and compares several routes for data publishing, namely as (1 supplementary files to research articles, which may be made available directly by the publisher, or (2 published in a specialized open data repository with a link to it from the research article, or (3 as a data paper, i.e., a specific, stand-alone publication describing a particular dataset or a collection of datasets, or (4 integrated narrative and data publishing through online import/download of data into/from manuscripts, as provided by the Biodiversity Data Journal. The paper also contains detailed instructions on how to prepare and peer review data intended for publication, listed under the Guidelines for Authors and Reviewers, respectively. Special attention is given to existing standards, protocols and tools to facilitate data publishing, such as the Integrated Publishing Toolkit of the Global Biodiversity Information Facility (GBIF IPT and the DarwinCore Archive (DwC-A. A separate section describes most leading data hosting/indexing infrastructures and repositories for biodiversity and ecological data.

  18. Comparing gender discrimination and inequality in indie and traditional publishing.

    Science.gov (United States)

    Weinberg, Dana B; Kapelner, Adam

    2018-01-01

    In traditional publishing, female authors' titles command nearly half (45%) the price of male authors' and are underrepresented in more prestigious genres, and books are published by publishing houses, which determined whose books get published, subject classification, and retail price. In the last decade, the growth of digital technologies and sales platforms have enabled unprecedented numbers of authors to bypass publishers to publish and sell books. The rise of indie publishing (aka self-publishing) reflects the growth of the "gig" economy, where the influence of firms has diminished and workers are exposed more directly to external markets. Encompassing the traditional and the gig economy, the book industry illuminates how the gig economy may disrupt, replicate, or transform the gender discrimination mechanisms and inequality found in the traditional economy. In a natural experiment spanning from 2002 to 2012 and including over two million book titles, we compare discrimination mechanisms and inequality in indie and traditional publishing. We find that indie publishing, though more egalitarian, largely replicates traditional publishing's gender discrimination patterns, showing an unequal distribution of male and female authors by genre (allocative discrimination), devaluation of genres written predominantly by female authors (valuative discrimination), and lower prices within genres for books by female authors (within-job discrimination). However, these discrimination mechanisms are associated with far less price inequality in indie, only 7%, in large part due to the smaller and lower range of prices in indie publishing compared to traditional publishing. We conclude that, with greater freedom, workers in the gig economy may be inclined to greater equality but will largely replicate existing labor market segmentation and the lower valuation of female-typical work and of female workers. Nonetheless, price setting for work may be more similar for workers in the

  19. EGNAS: an exhaustive DNA sequence design algorithm

    Directory of Open Access Journals (Sweden)

    Kick Alfred

    2012-06-01

    Full Text Available Abstract Background The molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exhaustive DNA sequence design algorithm that allows to generate sets containing a maximum number of sequences with defined properties. EGNAS (Exhaustive Generation of Nucleic Acid Sequences offers the possibility of controlling both interstrand and intrastrand properties. The guanine-cytosine content can be adjusted. Sequences can be forced to start and end with guanine or cytosine. This option reduces the risk of “fraying” of DNA strands. It is possible to limit cross hybridizations of a defined length, and to adjust the uniqueness of sequences. Self-complementarity and hairpin structures of certain length can be avoided. Sequences and subsequences can optionally be forbidden. Furthermore, sequences can be designed to have minimum interactions with predefined strands and neighboring sequences. Results The algorithm is realized in a C++ program. TAG sequences can be generated and combined with primers for single-base extension reactions, which were described for multiplexed genotyping of single nucleotide polymorphisms. Thereby, possible foldback through intrastrand interaction of TAG-primer pairs can be limited. The design of sequences for specific attachment of molecular constructs to DNA origami is presented. Conclusions We developed a new software tool called EGNAS for the design of unique nucleic acid sequences. The presented exhaustive algorithm allows to generate greater sets of sequences than with previous software and equal constraints. EGNAS is freely available for noncommercial use at http://www.chm.tu-dresden.de/pc6/EGNAS.

  20. Adverse obstetric outcomes in women with previous cesarean for dystocia in second stage of labor.

    Science.gov (United States)

    Jastrow, Nicole; Demers, Suzanne; Gauthier, Robert J; Chaillet, Nils; Brassard, Normand; Bujold, Emmanuel

    2013-03-01

    To evaluate obstetric outcomes in women undergoing a trial of labor (TOL) after a previous cesarean for dystocia in second stage of labor. A retrospective cohort study of women with one previous low transverse cesarean undergoing a first TOL was performed. Women with previous cesarean for dystocia in first stage and those with previous dystocia in second stage were compared with those with previous cesarean for nonrecurrent reasons (controls). Multivariable regressions analyses were performed. Of 1655 women, those with previous dystocia in second stage of labor (n = 204) had greater risks than controls (n = 880) to have an operative delivery [odds ratio (OR): 1.5; 95% confidence intervals (CI) 1.1 to 2.2], shoulder dystocia (OR: 2.9; 95% CI 1.1 to 8.0), and uterine rupture in the second stage of labor (OR: 4.9; 95% CI 1.1 to 23), and especially in case of fetal macrosomia (OR: 29.6; 95% CI 4.4 to 202). The median second stage of labor duration before uterine rupture was 2.5 hours (interquartile range: 1.5 to 3.2 hours) in these women. Previous cesarean for dystocia in the second stage of labor is associated with second-stage uterine rupture at next delivery, especially in cases of suspected fetal macrosomia and prolonged second stage of labor. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.