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Analysis of eggplant ( Solanum melongena)-related germplasm: morphological and AFLP data contribute to phylogenetic interpretations and germplasm utilization.

A total of 94 Solanum accessions, including eggplants and related species, were morphologically characterized based on greenhouse observations, and molecularly analysed by the AFLP technique. Morphological parameters were helpful in assessing similarities or differences among accessions, and molecular data were used to support morphological conclusions. A dendrogram was computed based on the Dice genetic distances using the neighbour-joining method. The analysis was efficient in the assignment of a species name for eight out of nine accessions that were not previously classified, and revealed that 14 further accessions were misnamed in the collection originally received. The results indicate that the taxonomy of Solanum sections and subgenera including several species should be reconsidered. The AFLP technique was revealed as an efficient tool in determining genetic relationships among species. In general, morphological observations were consistent with molecular data, indicating that both approaches complemented to define the phylogenetic status of a large genus like Solanum. In terms of eggplant breeding, the molecular analysis of the Melongena complex, and of the other sections of the subgenus Leptostemonum, establishes useful germplasm relationships in the gene pool available for the genetic improvement of the cultivated species. The results we have provided highlight an urgent necessity to include molecular parameters in handling and characterizing the genebank-deposited germplasm related to cultivated crops.

Breeding↗

The most efficient use of resources to identify those in need of antiretroviral treatment in Africa: empirical data from Côte d'Ivoire's Drug Access Initiative.

OBJECTIVE: To describe the cost and outcome associated with the use of CD4 cell count and viral load tests as part of screening strategies to identify persons eligible for subsidized antiretroviral therapy (ART) in Côte d'Ivoire. METHODS: Empirical data from the Drug Access Initiative in Côte d'Ivoire (DAI-CI) were used to describe the laboratory cost of patient screening using sequential clinical staging, CD4 cell count, and viral load and the proportion of screened patients identified as eligible for ART. We also estimated costs modelling a parallel screening algorithm, across a range of laboratory costs and with current international recommendations to assess treatment eligibility. Benefit was defined as being found eligible for ART. RESULTS: Of the 2138 HIV-positive, ART-naive, adults who presented to the DAI-CI between July 1998 and July 2000, median CD4 cell count was 172 x 10(6) cells/microl. DAI-CI criteria identified 2057 (96%) of these persons eligible for antiretroviral treatment. In a serial screening algorithm, 75% were eligible by CDC clinical stage B or C; 18% by CD4 cell count less than 500 x 10(6) cells/microl; and an estimated 3.9% by a viral load greater than 10 000 copies/ml. Use of the current US recommendations and a serial algorithm would have resulted in 1977 (92%) persons eligible for ART: 75% by CDC clinical stage B or C; 15% by CD4 cell count less than 350 x 10(6) cells/microl (including 8% < 200 x 10(6) cells/microl); and an estimated 3.6% due to viral load greater than 55 000 copies/ml. Using DAI-CI criteria and heavily subsidized laboratory test costs, the addition of CD4 cell count to clinical criteria cost US dollar 50 (serial algorithm) and US dollar 203 (parallel algorithm) to identify each additional eligible person. Modelling current recommendations with a serial algorithm, CD4 cell count cost an average US dollar 62/eligible person (US recommendations) and US dollar 109 (WHO recommendations). The addition of viral load cost between US dollar 108 (serial algorithm DAI) to US dollar 1700 (parallel algorithm DAI) to identify each additional eligible person. CONCLUSION: In the African context of scarce resources and the huge unmet demands for voluntary HIV testing and for ART, simple screening strategies are needed to identify those most in need of ART. Health personnel should be trained to identify and refer clinically symptomatic persons. Viral load testing is of high cost and dubious benefit and should not be part of screening algorithms for initiating ART.

Adolescent↗

PlasmoDB: An integrative database of the Plasmodium falciparum genome. Tools for accessing and analyzing finished and unfinished sequence data. The Plasmodium Genome Database Collaborative.

The PLASMODIUM: falciparum Genome Database (http://PlasmoDB.org) integrates sequence information, automated analyses and annotation data emerging from the P.falciparum genome sequencing consortium. To date, raw sequence coverage is available for >90% of the genome, and two chromosomes have been finished and annotated. Data in PlasmoDB are organized by chromosome (1-14), and can be accessed using a variety of tools for graphical and text-based browsing or downloaded in various file formats. The GUS (Genomics Unified Schema) implementation of PlasmoDB provides a multi-species genomic relational database, incorporating data from human and mouse, as well as P.falciparum. The relational schema uses a highly structured format to accommodate diverse data sets related to genomic sequence and gene expression. Tools have been designed to facilitate complex biological queries, including many that are specific to PLASMODIUM: parasites and malaria as a disease. Additional projects seek to integrate genomic information with the rich data sets now becoming available for RNA transcription, protein expression, metabolic pathways, genetic and physical mapping, antigenic and population diversity, and phylogenetic relationships with other apicomplexan parasites. The overall goal of PlasmoDB is to facilitate Internet- and CD-ROM-based access to both finished and unfinished sequence information by the global malaria research community.

Animals↗

The Stanford Microarray Database accommodates additional microarray platforms and data formats.

The Stanford Microarray Database (SMD) (http://smd.stanford.edu) is a research tool for hundreds of Stanford researchers and their collaborators. In addition, SMD functions as a resource for the entire biological research community by providing unrestricted access to microarray data published by SMD users and by disseminating its source code. In addition to storing GenePix (Axon Instruments) and ScanAlyze output from spotted microarrays, SMD has recently added the ability to store, retrieve, display and analyze the complete raw data produced by several additional microarray platforms and image analysis software packages, so that we can also now accept data from Affymetrix GeneChips (MAS5/GCOS or dChip), Agilent Catalog or Custom arrays (using Agilent's Feature Extraction software) or data created by SpotReader (Niles Scientific). We have implemented software that allows us to accept MAGE-ML documents from array manufacturers and to submit MIAME-compliant data in MAGE-ML format directly to ArrayExpress and GEO, greatly increasing the ease with which data from SMD can be published adhering to accepted standards and also increasing the accessibility of published microarray data to the general public. We have introduced a new tool to facilitate data sharing among our users, so that datasets can be shared during, before or after the completion of data analysis. The latest version of the source code for the complete database package was released in November 2004 (http://smd.stanford.edu/download/), allowing researchers around the world to deploy their own installations of SMD.

California↗

Sex differences in access to coronary revascularization after cardiac catheterization: importance of detailed clinical data.

BACKGROUND: Although some studies suggest that access to cardiac procedures may differ by sex, others have found no evidence of gender bias in cardiac care. OBJECTIVE: To study rates of percutaneous coronary intervention (PCI) or coronary artery bypass graft (CABG) surgery in men and women after cardiac catheterization. DESIGN: Cohort study with prospective data collection. SETTING: Alberta, Canada. PATIENTS: Persons undergoing cardiac catheterization between 1 January 1995 and 31 December 1998 (n = 21 816). MEASUREMENTS: The occurrence of revascularization procedures (PCI or CABG) in the year after cardiac catheterization was measured. Unadjusted revascularization rates, partially adjusted rates (adjusted for clinical variables available in most databases, including administrative databases), and fully adjusted rates (additionally adjusted for extent of coronary artery disease and ejection fraction) were also evaluated. RESULTS: The unadjusted relative risk was 0.67 (95% CI, 0.65 to 0.71) for the end point of any revascularization in women relative to men. The relative risk increased to 0.69 (CI, 0.66 to 0.72) with partial adjustment and to 0.98 (CI, 0.94 to 1.03) with full adjustment, indicating equivalent access to revascularization for men and women. For PCI, the corresponding relative risks were 0.77 (CI, 0.73 to 0.82), 0.84 (CI, 0.80 to 0.89), and 1.02 (CI, 0.96 to 1.08). For CABG surgery, the relative risks were 0.54 (CI, 0.51 to 0.58), 0.51 (CI, 0.48 to 0.55), and 0.93 (CI, 0.87 to 1.01). CONCLUSIONS: In Alberta, Canada, clinical variables fully explain sex differences in rates of revascularization after cardiac catheterization, and misleading conclusions would arise without full adjustment for clinical differences between men and women. Extreme caution is needed in interpreting reports on access to care that use sparsely detailed clinical data sources.

Alberta↗

What the publisher can teach the patient: intellectual property and privacy in an era of trusted privication.

This article begins with a premise that intellectual property and privacy have something significant and yet understated in common: both are about balancing a creator's desire to control a particular set of data with consumers' desires to access and redistribute that data. Both law and technology influence such balancing, making it more or less palatable to use data for particular purposes--whether one is an individual making a copy of a popular song for a friend, or a hospital selling a list of maternity ward patients to a day care service. In the shadow of the Internet's rapid development and concomitant easing of barriers to data sharing, holders of intellectual property are pairing increased legal protection with the technologies of "trusted systems." I describe how these technologies might allow more thorough mass distribution of data, while allowing publishers to retain unprecedented control over their wares. For instance, an e-Book seller might charge one price for a read-only copy that could not be printed or forwarded and charge an additional fee for each copy or printout made. Taking up the case of medical privacy, I then suggest that those who worry about the confidentiality of medical records, particularly as they are digitized by recent congressional mandate, might seek to augment comparatively paltry legal protections with trusted systems technologies. For instance, a trusted system could allow a patient to specify how and by whom her records could be used; within limits, she could allow full access to her primary care physician, while allowing only time-limited access to emergency care providers, non-personally identifiable access to medical researchers, and no access at all for marketing purposes. These technologies could allow for new kinds of privacy protection, without sacrificing the legitimate interests of the consumers of medical records.

Humans↗

In-house access to PACS images and related data through World Wide Web.

The development of a hospital wide PACS is in progress at the University Hospital of Geneva and several archive modules are operational since 1992. This PACS is intended for wide distribution of images to clinical wards. As the PACS project and the number of archived images grow rapidly in the hospital, it was necessary to provide an easy, more widely accessible and convenient access to the PACS database for the clinicians in the different wards and clinical units of the hospital. An innovative solution has been developed using tools such as Netscape navigator and NCSA World Wide Web server as an alternative to conventional database query and retrieval software. These tools present the advantages of providing a user interface which is the same, independent of the platform being used (e.g. Mac, Windows, UNIX), and an easy integration of different types of documents (e.g. text, images). A strict access control has been added to this interface. It allows user identification and access rights checking, as defined by the in-house hospital information system, before allowing the navigation through patient data records.

Computer Communication Networks↗

Standardization of therapy machine interface for treatment monitoring.

Computerized monitoring of radiation treatments is an effective tool in detecting and preventing errors in treatment delivery. Most manufacturers now supply optional treatment monitoring (Record and Verify) systems. These differ significantly in their features and are, in general, incompatible with each other. Based on our examination of four different commercial systems, we believe that these commercial and individualized systems are not adequate and are difficult to use. In a radiation therapy facility with more than one treatment machine, it is highly desirable, for a variety of reasons, that such a system be implemented on a central computer which monitors all machines. A centralized record and verify system which allows the storage of all data on a long term basis in an on-line common data base permits much easier access to individual patient data as well as useful data analysis and reports. Every patient's demographic, prescription and treatment data are then available on all treatment machines. This is particularly useful for cases in which a patient may be transferred from one machine to the other. Such a system is also easier to operate. The development of such a treatment monitoring system requires that the protocol of communication between the therapy machine and the computer, and the data describing therapy machine settings transmitted to the computer be standardized. We propose that every manufacturer supply an optional interface meeting this standard. A description of the proposed standard evolved in four years of our work in this field is given.

Computers↗

Integrating biological databases.

Recent years have seen an explosion in the amount of available biological data. More and more genomes are being sequenced and annotated, and protein and gene interaction data are accumulating. Biological databases have been invaluable for managing these data and for making them accessible. Depending on the data that they contain, the databases fulfil different functions. But, although they are architecturally similar, so far their integration has proved problematic.

Animals↗

A skeletal gene database.

Systematic organization of documented data coupled with ready accessibility is of great value to research. Catalogs and databases are created specifically to meet this purpose. The Skeletal Gene Database evolves as part of the Skeletal Genome Anatomy Project (SGAP), an ongoing multi-institute collaborative effort, to study the functional genome of bone and other skeletal tissues. The primary objective of the Skeletal Gene Database is to create a contemporary list of skeletal-related genes, offering the following information for each gene: gene name, protein name, cellular function, disease(s) caused by mutation of the corresponding gene, chromosomal location, LocusLink number, gene size, exon/intron numbers, messenger RNA (mRNA) coding region size, protein size/molecular weight, Online Mendelian Inheritance in Man (OMIM) number of the gene, UniGene assignment, and PubMed reference. The database includes genes already known and published in the literature as well as novel genes not yet characterized but known to be expressed in skeletal tissue. It will be posted on the web for easy access and swift referencing. The data will be updated in tempo with current and future research, thereby providing an invaluable service to the scientific community interested in obtaining information on bone-related genes.

Bone and Bones↗

[HeiDATAProViT--a universal software tool for evaluating biomedical data].

Evaluation of large sets of biomedical data can be divided into three universal stages: 1. archiving of clinical data together with data obtained from measurements, 2. processing of numerical data using signal processing algorithms and 3. visualizing the results. In this paper a software is presented which tightly integrates a data base under MS Access and the possibilities for data processing and visualization offered by Matlab. This software tool provides an interface between a data base containing large sets of biomedical data and an extensible pool of evaluation and visualization procedures. It can serve both as an instrument for data processing in clinical routine and an important component for evaluation of measurement data in any medical research project.

Algorithms↗

[Electronic medical record, confidentiality and safeguarding of privacy].

An electronic patient file is expected to contribute to individual health care, as well as to policy goals. For acceptance by doctors and patients, some conditions have to be fulfilled. Among them is the appropriate specification of the right of the patient to medical secrecy and privacy. Reference is made to new legal requirements (Wet Bescherming Persoonsgegevens (Act on the protection of personal data)), which e.g. regulate when access to personal medical data is lawful, when consent is required and in what form, in addition to a number of other conditions. The current information and communication technology must not be allowed to dictate the possibilities and limitations of legally applicable standards, but the technical implementation of the electronic patient file must be made to suit and assure the legal standards of medical professional secrecy and patient privacy. Otherwise the advantages of an electronic patient file will be out-weighed by patients withholding important information from their physician and by their being less inclined to consent to their data being used for e.g. scientific investigations.

Confidentiality↗

[The computer in radiology. findings obtained by the text rail].

As a dedicated solution for professional classification, the COMRAD (COMputer in RADiology) system makes available a "dialog system" that enables the fully integrated processing of operational layouts or word processing and administration of medical practice. The dialog system is based on data files which enable direct access to all stored data as well as the storage of new data, thus avoiding a multiple input and storage. The operational layout of text processing which is to be introduced by this paper, permits radiological findings to be prepared in a flow text, strictly observing a division of the analysis into a descriptive and a evaluative report. The synthesis of the findings is reached through a dialed description of a pathological condition, which is automatically supplemented for assessment by the pertinent evaluation text including its variables. In contrary of assembling text modules the texts of all not directly dialed findings without pathological changes are automatically incorporated both into the description and into the assessment. The variables may be standard attributes, free attributes and pairing attributes.

Computers↗

[Methods of feeding and illness in infants in the first six months of life].

UNLABELLED: There is now a general agreement, that breast feeding prevents infantile gastrointestinal infections and non-gastrointestinal infections in all settings. In this study, we tried to pay attention to Kovar et al. who suggested that studies to detect the effects of breast feeding on health should be undertaken for other reasons and should include the collection of related information as part of the study. METHODS: Data collection. The population consisted of all infants born in the community of Krushevac in 1994. After at least 36 weeks of pregnancy their weight was 2500 g or more. The babies were selected by a modified cluster sampling. Data were collected by access to health cards where data of systematic medical examination of infants after the first, third and sixth month of life were recorded. Feeding method. Breast feeding was defined as the period of breast feeding from birth until the infant was totally weaned, even if other food was offered. The term bottle feeding referred to no breast feeding but to an infant formula or cow milk. Each infant was classified every month into either a breast feeding group or a bottle feeding group. Infectious diseases. We studied gastrointestinal and respiratory diseases, and all other illnesses except trauma were included in the third category. Statistical analysis. Every infant was classified each month as breast or bottle fed and thus was included in a 6-month observation. An episode of illness was associated either with breast feeding or bottle feeding according to the method of feeding in the month during which the episode occurred. The incidence density of diseases in breast fed infants was computed as follows: The rate numerator corresponded to the total number of episodes of diseases reported while infants were breast fed. The denominator was the number of month of breast feeding of all infants. The rate of diseases in bottle fed infants was obtained in the similar way. To compare the rates of illnesses in breast fed and bottle fed infants, we computed the incidence density ratio (IDR). So, when less than one, the IDR indicated a protective effect of breast feeding. RESULTS: Figure 1 illustrates the distribution of infants by the method of feeding at each age in months. Sixty four percent of babies were breast fed at the end of the first month, 43 percent at the end of the third month and 37.8 percent at the end of the sixth month. A total of 305 episodes of diseases were observed in 448 infants. An approximate incidence density analysis revealed the significant protective effect of breast feeding in relation to the total number of illnesses during the first sixth months of life (Table 1). The incidence density for gastrointestinal diseases was 49 percent lower in breast fed infants than in bottle fed infants (IDR = 0.51). The protective effect of breast feeding on gastrointestinal diseases persisted after individual adjustment according to the infant's age (Table 2). The rough incidence density for respiratory diseases was 38 percent lower in breast fed infants than in bottle fed infants (IDR = 0.62)(Table 1). The protective effect of breast feeding on respiratory diseases persisted after individual adjustment according to the infant's age (Table 3). DISCUSSION: The results of this retrospective cohort study revealed protective effects of breast feeding in relation to respiratory illnesses as well as gastrointestinal diseases during the first six months of life. The statistical analysis based on Person-time methods best emphasizes the common problems that arise in such studies, because it takes in account the fact that (1) the outcome may be recurrent in one individual; (2) the duration of breast feeding is associated with the infant's age, and (3) the incidence is also age related. We conclude that breast feeding was protective against respiratory illnesses including ear infection and against gastrointestinal diseases. The study thus reinforces the benefits of breast feeding for

Bottle Feeding↗

Web servlet-assisted, dial-in flow cytometry data analysis.

BACKGROUND: The obvious benefits of centralized data storage notwithstanding, the size of modern flow cytometry data files discourages their transmission over commonly used telephone modem connections. The proposed solution is to install at the central location a web servlet that can extract compact data arrays, of a form dependent on the requested display type, from the stored files and transmit them to a remote client computer program for display. METHODS: A client program and a web servlet, both written in the Java programming language, were designed to communicate over standard network connections. The client program creates familiar numerical and graphical display types and allows the creation of gates from combinations of user-defined regions. Data compression techniques further reduce transmission times for data arrays that are already much smaller than the data file itself. RESULTS: For typical data files, network transmission times were reduced more than 700-fold for extraction of one-dimensional (1-D) histograms, between 18 and 120-fold for 2-D histograms, and 6-fold for color-coded dot plots. Numerous display formats are possible without further access to the data file. CONCLUSIONS: This scheme enables telephone modem access to centrally stored data without restricting flexibility of display format or preventing comparisons with locally stored files.

Computer Communication Networks↗

A Grid-based HIV expert system.

OBJECTIVES: This paper addresses Grid-based integration and access of distributed data from infectious disease patient databases, literature on in-vitro and in-vivo pharmaceutical data, mutation databases, clinical trials, simulations and medical expert knowledge. METHODS: Multivariate analyses combined with rule-based fuzzy logic are applied to the integrated data to provide ranking of patient-specific drugs. In addition, cellular automata-based simulations are used to predict the drug behaviour over time. Access to and integration of data is done through existing Internet servers and emerging Grid-based frameworks like Globus. Data presentation is done by standalone PC based software, Web-access and PDA roaming WAP access. The experiments were carried out on the DAS2, a Dutch Grid testbed. RESULTS: The output of the problem-solving environment (PSE) consists of a prediction of the drug sensitivity of the virus, generated by comparing the viral genotype to a relational database which contains a large number of phenotype-genotype pairs. CONCLUSIONS: Artificial Intelligence and Grid technology are effectively used to abstract knowledge from the data and provide the physicians with adaptive interactive advice on treatment applied to drug resistant HIV. An important aspect of our research is to use a variety of statistical and numerical methods to identify relationships between HIV genetic sequences and antiviral resistance to investigate consistency of results.

Biometry↗

Public access for teaching genomics, proteomics, and bioinformatics.

When the human genome project was conceived, its leaders wanted all researchers to have equal access to the data and associated research tools. Their vision of equal access provides an unprecedented teaching opportunity. Teachers and students have free access to the same databases that researchers are using. Furthermore, the recent movement to deliver scientific publications freely has presented a second source of current information for teaching. I have developed a genomics course that incorporates many of the public-domain databases, research tools, and peer-reviewed journals. These online resources provide students with exciting entree into the new fields of genomics, proteomics, and bioinformatics. In this essay, I outline how these fields are especially well suited for inclusion in the undergraduate curriculum. Assessment data indicate that my students were able to utilize online information to achieve the educational goals of the course and that the experience positively influenced their perceptions of how they might contribute to biology.

Computational Biology↗

An organized pilot program promoting web access to picture archiving and communications system data: emphasis on offices outside the host institution.

A formal Pilot Program for Web-based access to a host picture archiving and communication system (PACS) can augment the transition to filmless radiology. Beyond the technical issues of PCs and networks, appropriate legal input and documentation is necessary. While it is important to be in line with overall institutional priorities with regard to online access strategies, it is important to recognize that the Radiology Department has the greatest stake in successfully going filmless, and that it is incumbent upon the Radiology Department itself to take on outreach efforts to the medical community at large. The MMC Web Access Pilot Project has been successful in helping key non-MMC offices overcome the issues associated with preparing for and mastering Web access to PACS images. The benefit has been mutual, and MMC is now able to provide better advice to new offices that are coming online, as well as sharpening its focus on logistical issues that need to be resolved if we are to eliminate film from medical practice.

Humans↗