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PubMed2005

Communication and re-use of chemical information in bioscience.

The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture at proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective.

Archives↗
PubMed2005

NemaFootPrinter: a web based software for the identification of conserved non-coding genome sequence regions between C. elegans and C. briggsae.

BACKGROUND: NemaFootPrinter (Nematode Transcription Factor Scan Through Philogenetic Footprinting) is a web-based software for interactive identification of conserved, non-exonic DNA segments in the genomes of C. elegans and C. briggsae. It has been implemented according to the following project specifications:a) Automated identification of orthologous gene pairs. b) Interactive selection of the boundaries of the genes to be compared. c) Pairwise sequence comparison with a range of different methods. d) Identification of putative transcription factor binding sites on conserved, non-exonic DNA segments. RESULTS: Starting from a C. elegans or C. briggsae gene name or identifier, the software identifies the putative ortholog (if any), based on information derived from public nematode genome annotation databases. The investigator can then retrieve the genome DNA sequences of the two orthologous genes; visualize graphically the genes' intron/exon structure and the surrounding DNA regions; select, through an interactive graphical user interface, subsequences of the two gene regions. Using a bioinformatics toolbox (Blast2seq, Dotmatcher, Ssearch and connection to the rVista database) the investigator is able at the end of the procedure to identify and analyze significant sequences similarities, detecting the presence of transcription factor binding sites corresponding to the conserved segments. The software automatically masks exons. DISCUSSION: This software is intended as a practical and intuitive tool for the researchers interested in the identification of non-exonic conserved sequence segments between C. elegans and C. briggsae. These sequences may contain regulatory transcriptional elements since they are conserved between two related, but rapidly evolving genomes. This software also highlights the power of genome annotation databases when they are conceived as an open resource and the possibilities offered by seamless integration of different web services via the http protocol. AVAILABILITY: The program is freely available at http://bio.ifom-firc.it/NTFootPrinter.

Animals↗
PubMed2022

A custom library construction method for super-resolution ribosome profiling in Arabidopsis.

BACKGROUND: Ribosome profiling, also known as Ribo-seq, is a powerful technique to study genome-wide mRNA translation. It reveals the precise positions and quantification of ribosomes on mRNAs through deep sequencing of ribosome footprints. We previously optimized the resolution of this technique in plants. However, several key reagents in our original method have been discontinued, and thus, there is an urgent need to establish an alternative protocol. RESULTS: Here we describe a step-by-step protocol that combines our optimized ribosome footprinting in plants with available custom library construction methods established in yeast and bacteria. We tested this protocol in 7-day-old Arabidopsis seedlings and evaluated the quality of the sequencing data regarding ribosome footprint length, mapped genomic features, and the periodic properties corresponding to actively translating ribosomes through open resource bioinformatic tools. We successfully generated high-quality Ribo-seq data comparable with our original method. CONCLUSIONS: We established a custom library construction method for super-resolution Ribo-seq in Arabidopsis. The experimental protocol and bioinformatic pipeline should be readily applicable to other plant tissues and species.

3-nt periodicity↗
PubMedDate not supplied

Persuasion: getting your points across.

Leaders have many options and resources open to them when they try to motivate their followers. These include forcing, ordering, manipulating, cajoling, threatening, and persuading. Of all these options, perhaps the most useful and powerful is persuasion. Every effective leader persuades, even when other options are open and available. Leaders persuade as a means to getting the maximum commitment from their followers, in pursuit of the objectives of the organization or for personal objectives. Force, threat, and manipulation too often lead to follower involvement ("I'm here, but that's all") but rarely to a personal commitment. Yet motivation experts suggest that the most productive behavior results when employees are committed to the organization, its clients, customers, and goals. It's been suggested that the difference between "commitment" and "involvement" is the difference between a ham-and-eggs breakfast: a chicken was involved in your meal, but a pig was committed to it. We persuade to raise our employee's involvement in their jobs to some greater level of commitment. This article will examine some of the latest persuasion research and how it applies to better management. In doing so, we'll frequently use the jargon of persuasion, referring to the persuaders as "sellers," and those being persuaded as "buyers."

Humans↗
PubMed2002

Large-scale open bioinformatics data resources.

The data explosion in bioinformatics is relentless. More and more genomes are being sequenced and many new types of datasets are being generated in large-scale projects. Integration and true open access to the data are still difficult issues, although they are gradually being addressed. Notably, certain fields have good standardization and interoperability, while others lag behind. This review summarizes the latest developments in genome and sequences databases, transcriptomics data (ESTs, ORESTES, full-length cDNAs), proteomics data (protein databases, protein structures, family and domain classification) as well as loosely integrated fields, such as microarray experiments, mutation databases and databases of regulatory regions and elements. The review attempts to resist simply summarizing what data are available, and aims to provide a critical look at some of the integration and access issues associated with several of these resources.

Computational Biology↗
PubMed2007

hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.

Complete sets of cloned protein-encoding open reading frames (ORFs), or ORFeomes, are essential tools for large-scale proteomics and systems biology studies. Here we describe human ORFeome version 3.1 (hORFeome v3.1), currently the largest publicly available resource of full-length human ORFs (available at ). Generated by Gateway recombinational cloning, this collection contains 12,212 ORFs, representing 10,214 human genes, and corresponds to a 51% expansion of the original hORFeome v1.1. An online human ORFeome database, hORFDB, was built and serves as the central repository for all cloned human ORFs (http://horfdb.dfci.harvard.edu). This expansion of the original ORFeome resource greatly increases the potential experimental search space for large-scale proteomics studies, which will lead to the generation of more comprehensive datasets.

Animals↗
PubMed1996

Effects of open marsh water management on selected tidal marsh resources: a review.

Open Marsh Water Management (OMWM) is a method of salt-marsh mosquito control that advocates source reduction and biological control through selective pond creation and ditching in mosquito breeding areas. This method has been used as an alternative to chemical insecticides in coastal wetlands for 30 years. This paper reviews the effects of OMWM on hydrology, topography, vegetation, mosquitoes, invertebrates, fishes, birds, mammals, and water quality. Other source reduction techniques and the economics of OMWM are also discussed.

Animals↗
PubMedDate not supplied

Uncensored open access gastroscopy--limited resources--unlimited demand.

In the first 3 yr of an uncensored open access gastroscopy service in a County Hospital, 891 patients attended for first gastroscopy. The data on these patients is presented and compared with a randomly selected group who attended for gastroscopy in the yr prior to the establishment of the service having come to the normal Consultant clinics. In the open access group the gastroscopy examination was normal in 29 per cent (32 per cent comparator group), 31 per cent had major abnormalities (33 per cent comparator group) and 40 per cent had minor abnormalities (35 per cent comparator group). Delay time from referral to endoscopy was 37 days for open access patients (45 days comparator group). Only 6 per cent of open access patients were brought back to O.P.D. (47 per cent comparator group) and 72 per cent of open access patients returned directly to their family doctor (28 per cent comparator group). A comparison of the Clonmel findings with British centres reporting their results shows a broadly similar picture. It is concluded that almost 1,300 unnecessary clinic visits were avoided by the provision of the open access service, some reduction in delay time to gastroscopy was achieved, the family doctor maintained control of patient management in the great majority of patients, the pattern of referral was not inappropriate and compared very well with the comparator group. Over the 3 yr there was a large increase in the number of gastroscopies performed which caused resource difficulties. It is recommended that adequate planning of these requirements should be carried out before an open access service is started. At least 1 additional dedicated gastroscopy only endoscopy service per week would be required.

Gastroscopy↗
PubMed2006

An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes.

Two collections of oligonucleotides have been designed for preparing pangenomic human and mouse microarrays. A total of 148,993 and 121,703 oligonucleotides were designed against human and mouse transcripts. Quality scores were created in order to select 25,342 human and 24,109 mouse oligonucleotides. They correspond to: (i) a BLAST-specificity score; (ii) the number of expressed sequence tags matching each probe; (iii) the distance to the 3' end of the target mRNA. Scores were also used to compare in silico the two microarrays with commercial microarrays. The sets described here, called RNG/MRC collections, appear at least as specific and sensitive as those from the commercial platforms. The RNG/MRC collections have now been used by an Anglo-French consortium to distribute more than 3500 microarrays to the academic community. Ad hoc identification of tissue-specific transcripts and a approximately 80% correlation with hybridizations performed on Affymetrix GeneChiptrade mark suggest that the RNG/MRC microarrays perform well. This work provides a comprehensive open resource for investigators working on human and mouse transcriptomes, as well as a generic method to generate new microarray collections in other organisms. All information related to these probes, as well as additional information about commercial microarrays have been stored in a freely-accessible database called MEDIANTE.

Animals↗
PubMed2002

Determinants of costs and resource utilization associated with open heart surgery.

AIMS: This study sought to determine the patient- and the therapy-related determinants of in-hospital costs for patients undergoing heart surgery at the University Hospital in Zurich. METHODS AND RESULTS: We performed a retrospective analysis of all adult cardiac surgical patients from the canton St. Gallen who were covered by a fixed fee arrangement (29,500 Swiss francs (19,470 Euro)) and referred to our institution during 1998. A total of 201 patients (143 (71%) male) with basic insurance were hospitalized in 1998 under the fixed fee arrangement. The mean age of the patients was 61.4 years (95% confidence intervals (CI): 60; 63). With the help of univariate analysis, the following pre-operative characteristics were found to be significantly associated with cost: age (P<0.001), pre-operative cardiac diagnosis (coronary vs valvular heart disease) (P<0.001) and EuroSCORE (P<0.0001). A significant correlation was also found between intra-operative variables and costs (P<0.0001) as well as between postoperative variables and costs (P<0.0001). A linear regression model based on EuroSCORE, operation time and postoperative infection status is able to predict costs for patients (all P -values <0.0001, except for P<0.05 for operation time, R(2)=0.565). CONCLUSIONS: These results suggest that both pre-operative (patient related) and intra-operative (therapy- and patient-related) variables are predictors of costs in cardiac surgical patients.

Analysis of Variance↗
PubMed2003

OpenGALEN: open source medical terminology and tools.

The GALEN programme of research into medical terminology began in 1991. In 1999 OpenGALEN was formed to provide an open source route both for disseminating the results of that programme and as a framework for its future development. Currently available open source resources include a sophisticated ontology development environment and a large open source description logic-based ontology for the medical domain.

Intellectual Property↗
PubMed1993

ENB--resource and careers department.

The English National Board for Nursing, Midwifery and Health Visiting is aware that, in the current climate of change, a range of information is required by nurses, midwives and health visitors to enable them to update their professional knowledge and plan their careers. In response to this need the Board offers a comprehensive range of services through the Resource and Careers Department based in Sheffield. I will describe in detail the services provided by the Resource Section and then give a brief overview of the role and functions of the other sections, i.e. Publications, Careers Service and Projects. The Resource Section comprises three separate but interactive parts. These are the Health Care Database, Open Learning Resource and Reference Room and ENB Campus.

Databases, Factual↗
PubMed1992

The community bioethics committee: a unique pathway out of bioethical dilemmas.

We believe that most bioethics committees as well as individual ethics consultants have major shortcomings in that they are unlikely to be open to serving the widest number of citizens who may need their services when facing bioethical dilemmas. The HDCC serves as a community resource, is open to all citizens, is free standing, and provides a wide variety of perspectives which can assist patients, their families, and healthcare providers to explore a range of values and options. The HDCC serves as a model for communities that seek to establish a bioethics resource. Further, the HDCC model permits the further exploration of ways in which important healthcare issues can be faced. AHD believes, in keeping with its mission, that the creation of the HDCC can increase the public's awareness of and involvement in healthcare issues. As B. Jennings reminds us, The mission of community health decisions projects is to stimulate a well-informed conversation where many voices are heard and all reasonable perspectives given due consideration. They not only inform, but also enable responsible civic participation and thoughtful health care decisionmaking. The HDCC model can serve to bring discussions on bioethical dilemmas out of secrecy into safer, yet more open, community fora.

Arizona↗
PubMed2002

The origins of sexual dimorphism in body size in ungulates.

Jarman (1974) proposed a series of relationships between habitat use, food dispersion, and social behavior and hypothesized a series of evolutionary steps leading to sexual dimorphism in body size through sexual selection in African antelope species. The hypothesis states that sexual size dimorphism evolved in a three-step process. Initially, ancestral monomorphic and monogamous ungulate species occupying closed habitats radiated into open grassland habitats. Polygynous mating systems then rapidly evolved in response to the aggregation of males and females, perhaps in relation to the clumped distribution of food resources in open habitats. Subsequently, size dimorphism evolved in those species occupying open habitats, but not in species that remained in closed habitats or retained monogamy. This hypothesis has played an important role in explaining the origins of sexual dimorphism in mammals. However, the temporal sequence of the events that Jarman proposed has never been demonstrated. Here we use a phylogeny of extant ungulate species, along with maximum-likelihood statistical techniques, to provide a test of Jarman's hypothesis.

Animals↗
PubMed1990

National Practitioner Data Bank; announcement of opening date--PHS. Notice of opening.

The Health Resources and Services Administration, Public Health Service, Department of Health and Human Services (DHSS), is announcing the opening date of the National Practitioner Data Bank (Data Bank), as authorized by the Health Care Quality Improvement Act of 1986 (the Act), title IV of Public Law 99-660 as amended (42 U.S.C. 11101 et seq.).

Information Systems↗
PubMed1991

Pay-as-you-go social security in a changing environment.

"In this paper, we examine the optimal pay-as-you-go social security scheme which reallocates resources across generations in a changing environment, that is, with fluctuations in population growth rates and in productivity levels. We use an overlapping generations model along with a social welfare function consisting of the sum of generational utilities either unweighted or weighted by population size and a discount factor. We show how intergenerational resource sharing can be used to improve social welfare even though the extent of intergenerational redistribution is hampered by payroll tax deadweight losses...." The authors also consider the effects of an economy's openness on resource sharing. The geographical focus is on developed countries.

Demography↗