Some methodological issues in the longitudinal analysis of demographic data.
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Demography↗
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Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
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e-Science and its implications.
After a definition of e-science and the Grid, the paper begins with an overview of the technological context of Grid developments. NASA's Information Power Grid is described as an early example of a 'prototype production Grid'. The discussion of e-science and the Grid is then set in the context of the UK e-Science Programme and is illustrated with reference to some UK e-science projects in science, engineering and medicine. The Open Standards approach to Grid middleware adopted by the community in the Global Grid Forum is described and compared with community-based standardization processes used for the Internet, MPI, Linux and the Web. Some implications of the imminent data deluge that will arise from the new generation of e-science experiments in terms of archiving and curation are then considered. The paper concludes with remarks about social and technological issues posed by Grid-enabled 'collaboratories' in both scientific and commercial contexts.
Archives↗
[Giovanni Botero and the impression that the population of Spain was diminishing during the first half of the seventeenth century].
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Data Collection↗
Health risk implications of magnetic field exposures.
Magnetic field exposures pose serious questions to the public. The science is not sufficiently clear or consistent to result in a consensus. Some scientists view the data as strongly suggestive and argue that if the association is true, the ubiquity of exposure may be resulting in a marked underestimation of the actual risk. Others argue that the inconsistencies in the data and the specific limitations of the studies suggest that there is no association and no reason for concern. The state of the science is such that a definitive resolution is unlikely in the next few years. In light of this uncertainty, I believe that the most prudent course of action is the prevention or limitation of exposure where feasible at limited cost and inconvenience. Be it at home or at work, prevention of exposure is simply good public health practice.
Environmental Exposure↗
Automatic registration of microarray images. I. Rectangular grid.
MOTIVATION: The analysis of high-throughput experiment data provided by microarrays becomes increasingly more and more important part of modern biological science. Microarrays allow to conduct genotyping or gene expression experiments on hundreds of thousands of test genes in parallel. Because of the large and constantly growing amount of experimental data the necessity of efficiency, robustness and complete automation of microarray image analysis algorithms is gaining significant attention in the field of microarray processing. RESULTS: The author presents here an efficient and completely automatic image registration algorithm (that is an algorithm for spots and blocks indexing) that allows to process a wide variety of microarray slides with different parameters of grid and block spacing as well as spot sizes. The algorithm scales linearly with the grid size, the time complexity is O(M), where M is number of rows x number of columns. It can successfully cope with local and global distortions of the grid, such as focal distortions and non-orthogonal transformations. The algorithm has been tested both on CCD and scanned images and showed very good performance-the processing time of a single slide with 44 blocks of 200 x 200 grid points (or 1 760 000 grid points total) was about 10 s. AVAILABILITY: The test implementation of the algorithm will be available upon request for academics. SUPPLEMENTARY INFORMATION: http://fleece.ucsd.edu/~vit/Registration_Supplement.pdf
Algorithms↗
The use of statistical methods in the analysis of clinical studies.
It is "standard" to analyze data from a clinical trial using a narrowly defined probabilistic mathematical model. This paper examines the ways in which mathematical models, in general, can be used in clinical research, the meaning of probability in the examination of clinical trials, and the philosophical flaws in the current "standard" method. An alternative formulation is proposed which is more flexible and which comes closer to meeting the needs of medical science. In this alternative formulation, significance tests are applied to the data from a study only as a first step to determine whether the data are worth further examination. After that, clinically relevant questions are answered with 50 and 95% confidence bounds. The initial significance test is tailored to be directed at a narrow class of hypotheses that, in turn, are dictated by clinical expectations.
Clinical Trials as Topic↗
A programming course in bioinformatics for computer and information science students.
We have created a course entitled "Representations and Algorithms for Computational Molecular Biology" with three specific goals in mind. First, we want to provide a technical introduction for computer science and medical information science students to the challenges of computing with molecular biology data, particularly the advantages of having easy access to real-world data sets. Second, we want to equip the students with the skills required of productive research assistants in molecular biology computing research projects. Finally, we want to provide a showcase for local investigators to describe their work in the context of a course that provide adequate background information. In order to achieve these goals, we have created a programming course, in which three major projects and six smaller assignments are assigned during the quarter. We stress fundamental representations and algorithms during the first part of the course in lectures given by the core faculty, and then have more focused lectures in which faculty research interests are highlighted. The course stressed issues of structural molecular biology, in order to better motivate the critical issues in sequence analysis. The culmination of the course was a challenge to the students to use a version of protein threading to predict which members of a set of unknown sequences were globins. The course was well received, and has been made a core requirement in the Medical Information Sciences program.
Algorithms↗
[The comparative role of computed tomography and magnetic resonance imaging in the diagnosis of extracapsular spread of malignant lymphomatous masses invading blood vessels].
Aim of the study was to search for an optimal method an of investigation in diagnosis of extracapsular spread of the malignant lymphomas and invading the blood vessels. In the period of 1998 to 2002, 81 patients with malignant lymphomas with coverage of neck and body areas were examined in the Department of Tomography of Kaunas University of Medicine Hospital. It was performed by computed tomography (CT) and magnetic resonance imaging (MRI), with or without iv. application of contrast media. The data were processed with SPSS 10.1 (Statistical package for Social Sciences 10.1 for Windows), including application of chi(2), t-test. Specificity, sensitivity and diagnostic accuracy of CT and MRI methods were calculated and compared according to recommendations by Gefland D. W. and Ott D. J., 1985. Diagnosis of extracapsular spread of the lymphomatous tissue and invading the blood vessels was best performed by MR method (specificity, sensitivity, accuracy in this case 91-95%). Bolus CT angiography because of low resolution in the range of soft tissues, insufficient opacification of blood vessels with contrast medium and differences in blood flow was not informative enough (specificity, sensitivity, accuracy in this case 80-85%).
Adolescent↗
Demand incidence of retinal detachment in Brazil.
AIM: To evaluate the epidemiological characteristics of retinal detachment in a defined urban population in the Southeast of Brazil. METHODS: A retrospective study of patients consulted at the Department of Ophthalmology, State University of Campinas, São Paulo, Brazil, with retinal detachment between June 1, 2003 and July 31, 2004. Data were entered into the Statistical Package for the Social Sciences (version 10.0). RESULTS: There were a total population of 3 389 294 in the 42 cities of Campinas catchment area. A total of 313 patients fitted the inclusion criteria. The overall demand incidence of retinal detachment was 9.2:100,000. The number of males peaked in the 50-79 age group, whereas that of the females peaked in the 60 to 80+ age group. The ages ranged from 4 months to 84 years (mean 49.3). The female-to-male ratio was 1:2.1. Nontraumatic phakic detachments had the highest demand incidence of 7.1:100,000. The demand incidence of nontraumatic aphakic detachments was very low at 0.09:100,000. Almost one third of all patients seeking treatment presented inoperable cases of retinal detachments. CONCLUSIONS: This is the first study of demand incidence of retinal detachment in Latin Americans. The age-specific demand incidence increases with age. Nontraumatic phakic detachments were the most common type of detachment. The incidence of the traumatic types of detachment was higher in males than that in females. Such data are important to plan and implement vitreoretinal services taking into account the population likely to be served.
Adolescent↗
Methodological and ethical issues in conducting qualitative research with children and young people: a literature review.
BACKGROUND: There is an increasing interest in involving children in research that has been influenced by the recognition of children's rights and by the reconceptualisation of children within the social sciences as active agents rather than as the objects of research. OBJECTIVES: To review the methodological and ethical issues involved in conducting qualitative research with children and to consider the implications for nursing research in light of recent debates within the social sciences. DESIGN: Narrative literature review using a systematic search of computerized databases. DATA SOURCES: Published papers, key texts, reports and policy documents that relate to the methodological and ethical issues in conducting qualitative research with children. RESULTS: There are three ethical issues in relation to conducting research with children: power relations, informed consent and confidentiality. Two key methodological issues are identifiable in relation to conducting research with children. One is epistemological and relates to the different cultures of childhood and adulthood and the second relates to the heterogenous nature of childhood itself. Novel techniques and task-based activities are being increasingly used to establish rapport and as a method of data collection. CONCLUSION: There are both differences and similarities in conducting qualitative research with children and with adults but often the similarities have been overlooked and the differences overstated. Nursing and other health-related researchers conducting research with adults could learn much from children's researchers, particularly in terms of sensitivity to ethical issues. Nursing research need to consider the methodological issues that have been debated in the social sciences and to critically reflect on the use of novel techniques in qualitative research.
Adolescent↗
MEASUREMENT AND MECHANISATION IN MEDICINE.
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Artificial Limbs↗
Optimizing census geography: the separation of collection and output geographies.
"This paper reviews the changing way in which census geography has been treated with the increasing automation of census data processing. A four-stage model of modern census geography development is presented. In the context of this model, current practice is reviewed, and new opportunities for automated census geography design presented, culminating in a current prototype for the separation of purpose-designed data collection and output geographies. The narrative is presented primarily from a British perspective, but focuses on internationally relevant issues such as the implementation of census geography design, and the influence of census output geography on data analysis."
Censuses↗
Communication. Social values and the governance of science.
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Canada↗
Cause of death as a contemporary problem.
Four characteristics have been identified that affect the contemporary analysis of cause of death: (1) the increasing use of cause-of-death data for public policy; (2) the growing disjuncture between cause of death and cause of poor health; (3) the problem of specifying cause of death for the elderly, who constitute a growing proportion of the population and, accordingly, of mortality; and (4) the impact of technology and medical science on the temporal comparability of mortality statistics. With regard to the first issue, statistical data in general are being used with increasing sophistication throughout society. The public is exposed to all types of data by the media,and is increasingly educated in how to interpret statistics. Government at all levels increasingly uses data to help to help identify priorities, to choose among policy options, and to evaluate outcomes of decision making. Cause-of-death data are but a specific subset of information that are being used to understand social, economic, and health issues and to make more informed private and public choices regarding these issues. Increasing use of any data set is likely to result in better data simply because greater use results in closer scrutiny of data quality with resultant emphasis on evaluation and systematic efforts to improve quality. This is happening to cause-of-death data in the United States. The National Center for Health Statistics (NCHS) initiated major efforts through two national workshops in 1989 and 1991 to improve the quality of medical certification of death through better training of physicians, medical examiners, and coroners. While there is no clear evidence that the initiatives resulting from these workshops alone resulted in data quality improvement, the indicators used by NCHS to measure quality of medical certification point to continued gradual improvement in completeness and specificity in cause-of-death data. The gap between causes of morbidity and causes of mortality is growing because advances in medical science has essentially eliminated many infectious and communicable diseases that previously caused premature death and have considerably reduced the lethality of chronic conditions that previously caused death at earlier ages. As acute conditions have moved into the background, so to speak, a variety of disabilities and impairments have moved forward as sources of illness,pain, and diminished quality of life. As a consequence, the previously clear etching in mortality statistics of a society's health has become blurred by advances in medicine, healthcare, and prevention. Mortality data continue to have value per set and are important to social and medical knowledge because of their availability as a uniquely continuous data set. However, increasingly, a complete and contemporary profile of the health of a society requires data on both morbidity and mortality as complimentary indicators of health and social development. Not only do we need to know of what causes people to die, but also what health conditions aggravate and diminish their lives and, at an aggregate level, that conditions impose the greatest health costs on the community. Increasingly, these are debilitating conditions of the elderly that may diminish life but may not cause death. Medical description of the cause of death of an elderly person has probably never been easy; however, the contemporary extension of life has made the problem more visible and substantial than in earlier times. It is likely that the relatively few octogenarians of centuries past were also afflicted by concurrent medical conditions, and that even younger persons were prematurely afflicted by conditions that are now identified with advanced age. For these population groups, the description of cause of death, as a single and singular initiating event, is problematic.
Brain Neoplasms↗
[Geriatrics on the internet].
National and international data networks for data transfer and communication are playing an increasingly important role in science and medicine. These networks already exist on a regional, national and international scale. The biggest international network, the Internet, offers more than 300 sites referring to "aging", which lead to a great number of other related pages. The access to the Internet and some examples of the information on aging available are presented here. This is to give the reader an impression of the present state of this worldwide data network, which may be useful for his professional use. At this stage, the author has the impression that conventional media such as journals, books and especially personal contacts are still sufficient to satisfy the need for professional information, and opinion that may well have to be reconsidered soon. In view of the future, however, it seems useful for medical societies to be represented on the Internet as soon as possible.
Aged↗
On achieving strong inference in prehension research.
Smeets and Brenner have suggested that it may be time to abandon Jeannerod's "classical approach" to studying human prehension, and have presented a mathematical model as an alternative. We argue that this model provides insufficient grounds for widespread acceptance, and questions whether or not such an approach furthers the science of motor control.
Data Interpretation, Statistical↗
Environmental health: flow cytometric methods to assess our water world.
Flow cytometry/cell sorting in aquatic sciences has been driven in two directions. The frontier directions are on shipboard and shore-based. On the one hand, the rapid analytical technique has been taken on shipboard to provide a real-time assessment of the particles and phytoplankton in water masses. These data also give information on the amount of vertical mixing and advection, and denote fronts between two or more water masses. There is an optical characterization (based on sizes, numbers, and pigment groups) of the individual primary producers, as well as detritus and suspended sediments. An optical-closure question is being addressed: "Does the total optical signal equal the sum of the parts?" Additionally, associations with chemical and physical oceanographic features are readily accomplished. A "census" of thousands of phytoplankton cells is obtained and can be mapped. Scientists are able to identify "who is where?" Such data are critical to understand the optical-feedback loop or the so-called photon-budget-in-the-sea, which in turn controls the rates at which growth processes occur in nature. On the other hand, an in-depth understanding is sought as to how particle size, shape, refractive index, nutritional status (nutrient and/or light limitation), growth dynamics, and cell cycle combine to control the optics (light scatter and fluorescence at the moment, and ideally absorption as well) or the photon-budget-of-the-cell. For this purpose, a shore-based facility associated with a diverse collection of phytoplankton is ideal. The development at Bigelow Laboratory of the Jane J. MacIsaac Facility is to provide services for the oceanographic community. Association and co-location with the Provasoli-Guillard Center for Culture of Marine Phytoplankton is key. Visitors are trained and given access to state-of-the-art instrumentation. Visiting investigators have available "the tropical, temperate, and polar seas" in concentrated form, as marine phytoplankton isolated worldwide and maintained as living clonal cultures. In this way, frontline cell biology questions can be addressed. The relentless exploration of standards and controls appropriate for the aquatic community must be continued. An intercalibration effort is a vital step. It is only with the widespread acceptance of particular reference materials and uniform optical filters among research groups utilizing FCM that comparable data sets describing aquatic particle distributions will be possible. For a global science, this strategy is imperative.
Colorimetry↗
Prognostic value of nodal ratios in node-positive breast cancer.
PURPOSE: The American Joint Committee on Cancer staging system for breast cancer was recently updated to reflect the impact of increasing the absolute number of positive lymph nodes on prognosis. However, numerous studies suggest that nodal ratios (absolute number of involved nodes-number of nodes resected) may have greater prognostic value than absolute numbers of involved nodes. Here we examine the data supporting the use of nodal ratios in breast cancer prognosis and consider the potential advantages and disadvantages of including nodal ratios in breast cancer staging. METHODS: A systematic review of the literature was conducted using the following search engines: http://www.google.com; Thomson's ISI Web of Science; PubMed. RESULTS: In multiple reports from both prospective and retrospectively collected data sets, nodal ratios have been shown to be significant predictors of outcome, including locoregional recurrence and overall survival. These studies span all stages of breast cancer and include various treatments as well as various statistical approaches. CONCLUSION: There is considerable data supporting the use of nodal ratios in breast cancer prognosis. A thorough and methodological evaluation of the potential prognostic importance of nodal ratios in large multicenter data sets is merited and is currently being undertaken by the International Nodal Ratio Working Group.
Breast Neoplasms↗