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PubMed2006

Ab initio phasing of X-ray powder diffraction patterns by charge flipping.

Determining crystal structures from powder X-ray diffraction data remains a challenging problem in materials science. By embedding a Le-Bail-like procedure within the recently discovered charge-flipping phasing algorithm, an extremely simple, fast and effective ab initio method has been developed to determine phases directly from indexed powder diffraction patterns. The algorithm solves the degeneracy problem by applying spherical averaging for overlapping Bragg reflections, while solving the phase problem by using the Oszlányi-Süto charge-flipping algorithm. The processes of peak decomposition and phasing are integrated within the same iteration, and a dynamic support is used. The Fienup hybrid input-output algorithm is also incorporated to minimize stagnation. The ability of the algorithm to find structure-factor phases rapidly is found to assist with the fundamental problem of degeneracy (overlapping reflections) which is intrinsic to powder diffraction data. Space-group and chemical-composition information are not needed as inputs, and can be determined from the result. The method is illustrated using several experimental powder patterns of indifferent quality.

Journal Article↗
PubMed1998

Antiretroviral drug resistance testing in adults with HIV infection: implications for clinical management. International AIDS Society--USA Panel.

OBJECTIVES: To review current knowledge of the biology and clinical implications of human immunodeficiency virus (HIV) resistance to antiretroviral drugs, describe assays for measuring resistance, and assess their use in clinical practice. PARTICIPANTS: The International AIDS Society-USA assembled a panel of 13 physicians with expertise in basic science, clinical research, and patient care relevant to HIV resistance to antiretroviral drugs. EVIDENCE: We reviewed available data from published reports and presented at national and international research conferences. Basic science research, clinical trial results, and expert opinions were used to form the basis of this report. Data on methods for and characteristics of specific genotypic and phenotypic assays were obtained from manufacturers and service providers. CONSENSUS PROCESS: The panel met regularly between October 1997 and April 1998. Panel subgroups developed and discussed different sections of the report before discussing them with the entire panel. Conclusions and suggested approaches to the use of resistance testing were determined by group consensus. CONCLUSIONS: Plasma HIV RNA level and CD4+ cell count are the primary values that should be used to guide the initiation of antiretroviral therapy and subsequent changes in therapy. Possible causes of treatment failure other than development of drug resistance that should be considered are adherence, drug potency, and pharmacokinetic issues. Genotypic and phenotypic testing for HIV resistance to antiretroviral drugs may prove useful for individual patient management. Assays under development need validation, standardization, and a clearer definition of their clinical roles. Possible current roles of resistance testing for choosing an initial regimen or changing antiretroviral therapy, as well as possible implications of the presence or absence of phenotypic resistance and genotypic changes, are discussed.

Anti-HIV Agents↗
PubMed2003

Normal tissue effects: reporting and analysis.

Any effective cancer therapy developed to date is associated with a spectrum of normal tissue effects of varying incidence and severity. With an increasing number of novel therapeutic approaches undergoing clinical testing and an increased effort to optimize the established treatment modalities, methods for reliable quantification of normal tissue effects have become a key element in advancing cancer care. Here, we present a review of many of the issues involved in reporting and analyzing clinical normal tissue effect data. A distinction is introduced between explorative (science-driven) and pragmatic (patient-centered) studies. The desirable properties of criteria for reporting and grading toxicity are discussed from a biological and clinical perspective. Validation of toxicity criteria and the statistical issues involved in analyzing this type of data are presented with special emphasis on descriptors of the time evolution of toxicity. Finally, we discuss surrogate markers for late effects, mechanistic studies, and the design of clinical studies with normal tissue endpoints as a primary outcome. It is concluded that a consensus is required on guidelines for the reporting of normal tissue effects to improve the comparability of published reports on treatment outcome.

Antineoplastic Agents↗
PubMed2002

Self-esteem and smoking in youth--muddying the waters?

Longitudinal analysis by McGee and Williams (2000, Journal of Adolescence, 23, 569-582, doi: 10.1006/jado.2000.0344) indicates that global self-esteem is not related to substance use in early youth. In the case of tobacco use Glendinning and Inglis (1999, Journal of Adolescence, 22, 673-682, doi: 10.1006/jado.1999.0262) have looked at the "problem" of self-esteem in youth and its relevance for smoking, and they also note that the evidence from the survey literature has been inconclusive. However, rather than suggest that the survey methods and data have been inadequate, Glendinning and Inglis argue that an explanation is provided by looking at the relationship between global self-esteem and smoking in much greater detail, specifically within the peer context, and at peer culture, and the meanings that different groupings of young people attach to smoking or not smoking. That is, rather than a direct link between global self-esteem and smoking behaviour in youth, both are bound up with peer status and differentiation in early youth, although it must be said, not necessarily in the "expected" way. In the present study longitudinal data from the British Household Panel Study (BHPS, 2001, Economic & Social Science Research Council, Research Centre on Micro-Social Change. British Household Panel Survey Colchester, Essex: The Data Archive, 28 February 2001.SN: 4340.) confirm this more complex picture, and qualify the conclusions of McGee and Williams, in that global self-esteem year-on-year at around age 12-14-when young people take up smoking in increasing numbers-is clearly linked to experimentation and to smoking in subsequent years, in the shorter term. However, a longer-term linkage between self-esteem in early youth and smoking in later youth is less clear cut, and less compelling; but then, pursuing the longitudinal analysis still further, the findings lend force to the argument that putative links between self-esteem and smoking must be understood in context, specifically the peer context.

Adolescent↗
PubMedDate not supplied

Glucocorticoid use in rheumatoid arthritis: benefits, mechanisms, and risks.

Glucocorticoids have long been recognized to have beneficial effects in rheumatoid arthritis (RA) (1,2). Several clinical trials over the last decade have further documented the efficacy of glucocorticoids in relieving inflammation and in preventing radiographic erosions in early RA (3-5). Additionally, research has yielded new insights about the cellular mechanisms responsible for these perceived beneficial effects (6,7). Despite potential short term benefits, there is a lack of demonstrated long-term efficacy as well as concerns about short and long-term toxicity. Although these concerns have limited enthusiasm for glucocorticoids by many patients and practitioners, in the U.S. it is estimated that 44% to 75% of RA patients use glucocorticoids (8,9). Confusion and controversy may relate to the fact that toxicity reports are also limited by only modest data quality and quantity. Given growing clinical and basic science evidence supporting the efficacy of glucocorticoids for the treatment of rheumatoid arthritis, their use may further increase. In this review we will examine the latest data supporting the benefits and risks of glucocorticoid use in RA.

Anti-Inflammatory Agents, Non-Steroidal↗
PubMed2004

Survival after transfusion as assessed in a large multistate US cohort.

BACKGROUND: The only survival and mortality data on a general population of transfused patients in the United States is more than two decades old. More contemporary data are needed to reflect more current patient populations and transfusion practices. STUDY DESIGN AND METHODS: Data were extracted from Constella Health Strategies Sciences' managed-care administrative claims database that contains private health care claims. Patients were selected if they had at least one professional or facility claim indicating transfusion in 1995. Only the first transfusion in the time period was included so that each patient was counted only once and all claims were unduplicated. Survival for five years after transfusion was the primary outcome measure. RESULTS: A total of 6779 patients were included in the analysis. A total of 4658 (69%) patients were alive 1 year after transfusion, 4056 (60%) were alive at 2 years, and 3092 (46%) were alive 5 years after transfusion. Overall annual mortality was 31 percent in Year 1 after transfusion, 14 percent in Year 2, and 10 percent in each of Years 3 through 5. Transfusion mortality was much higher in recipients older than age 65 at the time of transfusion, who comprised 60 percent of transfused patients. CONCLUSION: These data from the mid 1990s can be used in models of the effectiveness of risk reduction interventions and in models of the disease consequences of infections transmitted through blood transfusions.

Adolescent↗
PubMed2005

A mixed-effects regression model for three-level ordinal response data.

Three-level data occur frequently in behaviour and medical sciences. For example, in a multi-centre trial, subjects within a given site are randomly assigned to treatments and then studied over time. In this example, the repeated observations (level-1) are nested within subjects (level-2) who are nested within sites (level-3). Similarly, in twin studies, repeated measurements (level-1) are taken on each twin (level-2) within each twin pair (level-3). A three-level mixed-effects regression model is described here. Random effects at the second and third level are included in the model. Additionally, both proportional odds and non-proportional odds models are developed. The latter allows the effects of explanatory variables to vary across the cumulative logits of the model. A maximum marginal likelihood (MML) solution is described and Gauss-Hermite numerical quadrature is used to integrate over the distribution of random effects. The random effects are normally distributed in this instance. Features of this model are illustrated using data from a school-based smoking prevention trial and an Alzheimer's disease clinical trial.

Alzheimer Disease↗
PubMed1997

Profile of the graduate student population in U.S. medical schools.

The Association of American Medical Colleges (AAMC) sponsored surveys of accredited U.S. medical schools in 1994-95 and in 1995-96 to gather enough data to determine an accurate profile of the population of students enrolled in and/or graduated from biomedical PhD and MD-PhD programs at these institutions. Previously collected data on the graduate student population at medical schools often did not distinguish between PhD students at the medical school and graduate students in other parts of the university. The AAMC surveys defined a medical school PhD- or MD-PhD-trained student as one whose major professor holds his or her primary appointment in a department of the medical school. The data were the result of census-taking by the responding schools on October 1, 1994, and October 1, 1995. There were 81 responses to each of the two surveys. Overall, 104 medical schools supplied data in either one or both of the survey years. When the data are extrapolated from the sample to the total population of 122 medical schools that award graduate degrees, a number of interesting estimates emerge. (1) When compared with the 1995 data for 18 biomedically-related biological science disciplines from the National Research Council's Survey of Earned Doctorates, the AAMC survey indicates that approximately 60% of the 4,000 PhDs awarded were earned by students studying at U.S. medical schools. (2) The total enrollment of PhD students in U.S. medical schools is approximately 18,600, a number that is about 25-30% of the number of medical students currently enrolled at all accredited U.S. medical schools. In some institutions, the number of graduate students rivals the number of medical students. (3) PhD students are enrolled in a wide variety of programs bearing titles reflective of a trend toward "interdisciplinary" rather than "departmental" degrees. (4) At a given time, the number of students supported by National Institutes of Health (NIH) research grants is nearly twice that provided for by NIH traineeships. In addition, all forms of institutional support provide for more than one-third of the PhD students in U.S. medical schools. (5) Approximately 24% of enrolled students are international students on temporary or permanent visas. (6) The data obtained from the two surveys of graduate programs within medical schools are relatively consistent, enabling more confidence in the reliability and accuracy of findings presented in this report.

Education, Medical, Graduate↗
PubMed2005

Comparison of amount of biomedical research originating from the European Union and the United States.

OBJECTIVE: To examine and compare the research productivity of the European Union, the four "candidate" countries (those currently waiting to join the EU), and the United States in several fields of biomedical sciences. DESIGN: A retrospective observational study-bibliometric analysis. DATA SOURCES: Manuscripts published by authors from each country separately and from each group of countries for the period 1994 to 2004 and included in the Essential Science Indicators database of the Institute of Scientific Information. MAIN OUTCOME MEASURES: Number of published articles and number of citations, adjusted for gross domestic product and population size. RESULTS: 1,485,749 articles were published by authors from the EU compared with 1,356,805 from the US. The research productivity of the first 15 countries to join the EU, adjusted for population, was lower (76%) than that of the US-and even lower (66%) when the 10 newest EU countries were included in the analysis. CONCLUSION: The newest EU members and the EU candidate countries need further help and resources to increase their productivity, thereby improving the productivity of the EU as a whole.

Biomedical Research↗
PubMed2006

qPCR-DAMS: a database tool to analyze, manage, and store both relative and absolute quantitative real-time PCR data.

Quantitative real-time PCR is an important high-throughput method in the biomedical sciences. However, existing software has limitations in handling both relative and absolute quantification. We designed quantitative PCR data analysis and management system (qPCR-DAMS), a database tool based on Access 2003, to deal with such shortcomings by the addition of integrated mathematical procedures. qPCR-DAMS allows a user to choose among four methods for data processing within a single software package: 1) ratio relative quantification, 2) absolute level, 3) normalized absolute expression, and 4) ratio absolute quantification. qPCR-DAMS also provides a tool for multiple reference gene normalization. qPCR-DAMS has three quality control steps and a data display system to monitor data variation. In summary, qPCR-DAMS is a handy tool for real-time PCR users.

Database Management Systems↗
PubMed1994

Reflections on the principle of life, medical theory and ethics, and the limitations of science.

The knowledge of modern science is based on and limited to data from the material world. It does not cover all levels of reality. Its achievements have been striking. It continues to amass at an ever increasing pace information about the physical basis of "life" in respect of its essential structures and their functions. Nonetheless there are questions which it cannot answer. The idea of the "vital spirit", according to Greek and Medieval philosophers and theologians the principle that imbues mortal flesh with life, transcends the limits of its empirical thinking, as do questions about traditional values and ethical issues, like the topical problems in medicine brought to the fore by recent and ongoing developments in molecular genetics. Their resolution will require vision wider than the empiric and knowledge broader than the exclusively scientific.

Biological Science Disciplines↗
PubMed2003

Implications of pharmacogenetics for individualizing drug treatment and for study design.

Adverse drug reactions and ineffective drug treatment are responsible for a large health care burden. Considerable variability in drug response makes the prediction of the individual reaction difficult. Pharmacogenetics can help to individualize drug treatment in accordance with the genetic make-up of the patient. Drug response is best understood as a complex interplay between pharmacokinetics, pharmacodynamics, and other disease-associated factors. There are a large number of genetic variants in the enzymes of phase I and phase II drug metabolism, in drug transporters, and drug targets, all of which account for differences in drug response. The polymorphisms in the cytochrome P450 enzyme system have been investigated most extensively. Genotype-based dose adjustment which should ensure "bioequivalent" drug concentrations in all patients has been derived from pharmacokinetic parameters, but this approach will have to be verified in prospective studies. Drug transport has recently been recognized as a further crucial determinant in pharmacokinetics. The effect of genetics on disease susceptibility and drug treatment has been studied quite extensively; however, hardly any of this progress is at present reflected in routine health care. The integration of pharmacogenetic factors in clinical trials requires novel considerations for study design and data interpretation. It is to be hoped that the new science bioinformatics will (a) help us identify the contribution of genetics to disease and treatment response and will (b) create data-processing devices which help the physician in the face of the enormously expanding scientific knowledge in selecting the best individually adapted treatment for the patient.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1995

A caveat concerning independence estimating equations with multivariate binary data.

Clustered binary data occur commonly in both the biomedical and health sciences. In this paper, we consider logistic regression models for multivariate binary responses, where the association between the responses is largely regarded as a nuisance characteristic of the data. In particular, we consider the estimator based on independence estimating equations (IEE), which assumes that the responses are independent. This estimator has been shown to be nearly efficient when compared with maximum likelihood (ML) and generalized estimating equations (GEE) in a variety of settings. The purpose of this paper is to highlight a circumstance where assuming independence can lead to quite substantial losses of efficiency. In particular, when the covariate design includes within-cluster covariates, assuming independence can lead to a considerable loss of efficiency in estimating the regression parameters associated with those covariates.

Biometry↗
PubMed2003

Ultrasonic locating devices for central venous cannulation: meta-analysis.

OBJECTIVES: To assess the evidence for the clinical effectiveness of ultrasound guided central venous cannulation. DATA SOURCES: 15 electronic bibliographic databases, covering biomedical, science, social science, health economics, and grey literature. DESIGN: Systematic review and meta-analysis of randomised controlled trials. Populations Patients scheduled for central venous access. INTERVENTION REVIEWED: Guidance using real time two dimensional ultrasonography or Doppler needles and probes compared with the anatomical landmark method of cannulation. DATA EXTRACTION: Risk of failed catheter placement (primary outcome), risk of complications from placement, risk of failure on first attempt at placement, number of attempts to successful catheterisation, and time (seconds) to successful catheterisation. DATA SYNTHESIS: 18 trials (1646 participants) were identified. Compared with the landmark method, real time two dimensional ultrasound guidance for cannulating the internal jugular vein in adults was associated with a significantly lower failure rate both overall (relative risk 0.14, 95% confidence interval 0.06 to 0.33) and on the first attempt (0.59, 0.39 to 0.88). Limited evidence favoured two dimensional ultrasound guidance for subclavian vein and femoral vein procedures in adults (0.14, 0.04 to 0.57 and 0.29, 0.07 to 1.21, respectively). Three studies in infants confirmed a higher success rate with two dimensional ultrasonography for internal jugular procedures (0.15, 0.03 to 0.64). Doppler guided cannulation of the internal jugular vein in adults was more successful than the landmark method (0.39, 0.17 to 0.92), but the landmark method was more successful for subclavian vein procedures (1.48, 1.03 to 2.14). No significant difference was found between these techniques for cannulation of the internal jugular vein in infants. An indirect comparison of relative risks suggested that two dimensional ultrasonography would be more successful than Doppler guidance for subclavian vein procedures in adults (0.09, 0.02 to 0.38). CONCLUSIONS: Evidence supports the use of two dimensional ultrasonography for central venous cannulation.

Adult↗