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PubMed2006

Bioinformatics and its applications in plant biology.

Bioinformatics plays an essential role in today's plant science. As the amount of data grows exponentially, there is a parallel growth in the demand for tools and methods in data management, visualization, integration, analysis, modeling, and prediction. At the same time, many researchers in biology are unfamiliar with available bioinformatics methods, tools, and databases, which could lead to missed opportunities or misinterpretation of the information. In this review, we describe some of the key concepts, methods, software packages, and databases used in bioinformatics, with an emphasis on those relevant to plant science. We also cover some fundamental issues related to biological sequence analyses, transcriptome analyses, computational proteomics, computational metabolomics, bio-ontologies, and biological databases. Finally, we explore a few emerging research topics in bioinformatics.

Computational Biology↗

PubMed2025

A decentralized future for the open-science databases.

The continuous and reliable open access to curated biological data repositories is indispensable for accelerating rigorous scientific inquiry and fostering reproducible research outcomes. However, the current paradigm, which relies heavily on centralized infrastructure for the storage and distribution of foundational biomedical datasets, inherently introduces significant vulnerabilities. This centralized model is susceptible to single points of failure, including cyberattacks, technical malfunctions, natural disasters, and even political or funding uncertainties. Such disruptions can lead to widespread data unavailability, data loss, integrity compromises, and substantial delays in critical research, ultimately impeding scientific progress. The downstream effect of such interruptions can be the widespread paralysis of diverse research activities, including computational, clinical, molecular, and climate studies. This scenario vividly illustrates the inherent dangers of consolidating essential scientific resources within a single geopolitical or institutional locus. As data generation is accelerating and the global landscape continues to fluctuate, the sustainability of centralized models must be critically re-evaluated. A shift toward federated and decentralized architectures may offer a robust and forward-looking approach to enhancing the resilience of scientific data infrastructures by reducing exposure to governance instability, infrastructural fragility, and funding volatility, while also promoting equity and global accessibility. Inspired by established models such as ELIXIR's federated infrastructure and the policy and funding frameworks developed by CODATA and the Global Biodata Coalition (GBC), emerging Decentralized Science (DeSci) initiatives can contribute to building more resilient, fair, and incentive-aligned data ecosystems. The future of open science depends on integrating these complementary approaches to establish a globally distributed, economically sustainable, and institutionally robust infrastructure that safeguards scientific data as a public good, further ensuring continued accessibility, interoperability, and preservation for generations to come. Here, we examine the structural limitations of centralized repositories, evaluate federated and decentralized models, and propose a hybrid framework for resilient, fair, and sustainable scientific data stewardship.

data accessibility↗

PubMed2006

Bridging the divide: the need for translational informatics.

Translational science promises to deliver real benefit to the pharmaceutical industry, reducing attrition and affording high quality, efficacious medicines. The development and use of biomarkers aims to reduce drug development risks and generate a better understanding of disease. Informatics is an essential component of the translational science toolkit; researchers must be able to work effectively with biomarker data, and the capture and reuse of knowledge is vital for long-term success. An analysis of current data and knowledge management practices in the translational science area is presented.

Humans↗

PubMed2005

Rinsing with chlorhexidine may reduce incidence of dry socket after third molar surgery.

DATA SOURCES: Medline and the Science Citation Index were used and searches were made by hand for studies published in any language. STUDY SELECTION: Studies included were human clinical trials evaluating the effect of a chlorhexidine (CHX) rinse on the incidence of alveolar osteitis (AO), following extraction of mandibular third molars, if they randomly assigned individuals to control and CHX rinse groups that used similar criteria to diagnose AO. DATA EXTRACTION AND SYNTHESIS: Studies were screened by three examiners independently. Due to protocol differences, studies were separated into two groups. Group 1 included studies that evaluated subjects who rinsed with CHX only on the day of surgery and Group 2 studies that evaluated patients who used multiple rinses with CHX. RESULTS: The relative risk for the single-rinse group was 1.36 (95% confidence interval (CI), 0.80-2.33; P>0.05), whereas for the multiple-rinse group, relative risk was 1.90 (95% CI, 1.46-2.47, P<0.05). CONCLUSIONS: It was not possible to determine if a single rinse with CHX on the day of surgery significantly reduced the incidence of AO. The results of this study do, however, support the conclusion that rinsing at least on the day of surgery and for several days following the removal of the teeth reduces the incidence of AO associated with the extraction of mandibular third molars. The minimum number of days of rinsing needed to produce this effect could not be determined by this analysis. Further studies using a standard definition for AO, and stratification of patients by gender, difficulty of extraction, smoking etc., are needed to determine the best use for CHX rinses in subjects having the mandibular third molar removed.

Comment↗

PubMed2000

Relationship of CD4+ T cell counts and HIV type 1 viral loads in untreated, infected adolescents. Adolescent Medicine HIV/AIDS Research Network.

The REACH Project (Reaching for Excellence in Adolescent Care and Health) of the Adolescent Medicine HIV/AIDS Research Network was designed as a study of an adolescent cohort composed of HIV-1-infected and -uninfected subjects. The goal of the analysis presented was to examine the relationship of CD4+ T cell counts and HIV-1 plasma viral loads in adolescents. The CD4+ T cell counts of 84 HIV+ subjects who were 13 to 19 years of age were measured at the clinical sites, using ACTG standardized techniques. HIV-1 viral loads in frozen plasma were determined by the NASBA/NucliSens assay at a central laboratory. Past and current treatment with antiretroviral drugs was determined by medical record abstraction and interview data. The slope of the line generated by regressing log10 HIV-1 RNA (copies/ml) versus CD4+ T cell counts of REACH subjects who are antiretroviral drug naive was negative and significantly different than zero. A negative association has also been reported for antiretroviral drug-naive, adult males in the Pittsburgh Men's Study, a component of MACS (Pitt-MACS) (Mellors J, et al.: Science 1996;272:1167). These data show that in adolescents, as in adults, HIV-1 RNA concentrations are correlated with corresponding absolute CD4+ T cell count. The slopes of the lines generated with data from each cohort were different (p = 0.003). In addition to age, there are sex and racial differences in the makeup of the two cohorts. Any or all of these differences may affect the slopes of the lines.

Adolescent↗

PubMedDate not supplied

Genealogical data and the biodemography of human longevity.

Biodemography of human longevity is an emerging interdisciplinary field of sociobiological research with deep historical roots. Two research questions are examined in this article: (1) What evidence is there for the familial transmission of human longevity?, and (2) what are the effects of parental age at reproduction on offspring longevity, and in particular, are there long-term adverse health consequences associated with the trend toward delayed reproduction? The ability of scientists to conduct biodemographic studies depends not only on merging theoretical and methodological elements from the biological and demographic/actuarial sciences, but unique sources of data and statistical methods must also be developed. In this article we describe how gencalogical data have been used for over a century to explore basic questions about human longevity, and how similar kinds of data now being developed are driving the formation of new testable research hypotheses in the field of biodemography.

Demography↗

PubMed2002

Did Weir Mitchell anticipate important concepts in ambulatory care and clinical epidemiology?

During the decade from 1977 to 1986, four models of care pertaining to ambulatory medicine and certain aspects of clinical epidemiology were proposed. All were concerned with the frequently heard accusation that medicine was becoming dehumanized by being overly dependent on powerful new technologies. Some of the authors went so far as to suggest that the view, according to which medical science must restrict itself to "hard" data of the kind provided by the serum multichannel analyzer, should be considered outdated and, in fact, unscientific. Their plea was to develop a science of the clinical encounter that would shift the emphasis from explication to prediction and management, the latter term being virtually synonymous with decision making. For this change to come about, they wrote, it would be necessary to collect "soft" data on such subjects as family relationships, psychic traits and states, perceptions of life quality, patient expectations and many others. We believe that some of these subjects as well as the models themselves were anticipated in the writings, both medical and fictional, of Weir Mitchell, nearly a century earlier. This paper, after presenting a brief overview of the career of a colorful and commanding figure from the annals of American medicine, will seek to illustrate his extraordinary farsightedness as a practitioner of primary care and his relevance for some aspects of clinical epidemiology. Because the attempts to link his ideas to modern concepts are ours, we accept the possibility that, here and there, we may have read things into his writings that he did not intend.

Ambulatory Care↗

PubMed2006

Integrating social science and design inquiry through interdisciplinary design charrettes: an approach to participatory community problem solving.

Interdisciplinary collaborations that aim to facilitate meaningful community outcomes require both the right mix of disciplinary knowledge and effective community participation, which together can deepen collective knowledge and the capacity to take action. This article explores three interdisciplinary design charrettes, intensive participatory workshops that addressed specific community problems and provided a context for integrating design and social science inquiry with local community knowledge. Evaluation data from the charrettes shed light on how students from the design and social science disciplines experienced the charrettes, and on their interactions with community members. Key advantages to this interdisciplinary, community-based collaboration included expanded knowledge derived from the use of multiple modes of inquiry, particularly the resulting visualization tools that helped community members understand local issues and envision novel solutions. Key drawbacks included difficulties in balancing the two disciplines, the tendency for social scientists to feel out of place on designers' turf, and the increased disciplinary and interpersonal conflicts arising from a more diverse pool of participants.

Community Health Planning↗

PubMed2005

Application of fast Fourier transform cross-correlation for the alignment of large chromatographic and spectral datasets.

Preprocessing of chromatographic and spectral data is an important aspect of analytical sciences. In particular, recent advances in proteomics have resulted in the generation of large data sets that require analysis. To assist accurate comparison of chemical signals, we propose two methods for the alignment of multiple spectral data sets. Based on methods previously described, each chromatograph or spectrum to be aligned is divided and aligned as individual segments to a reference. However, our methods make use of fast Fourier transform for the rapid computation of a cross-correlation function that enables alignments between samples to be optimized. The proposed methods are demonstrated in comparison with an existing method on a chromatographic and a mass spectral data set. It is shown that our methods provide an advantage of speed and a reduction of the number of input parameters required. The software implementations for the proposed alignment methods are available under the downloads section at http://ptcl.chem.ox.ac.uk/~jwong/specalign.

Algorithms↗

PubMed2001

Statistical issues in the analysis of low-dose endocrine disruptor data.

UNLABELLED: The National Institute of Environmental Health Sciences (NIEHS) and the U.S. Environmental Protection Agency (U.S. EPA) recently cosponsored the Endocrine Disruptors Low-Dose Peer REVIEW: The purpose of this meeting was to examine data supporting the presence or absence of low-dose effects of endocrine disruptors in specific studies and then to evaluate the likelihood and significance of these and/or other potential low-dose effects for humans. All invited speakers agreed to provide their raw data in advance of the meeting to a Statistics Subpanel, which was asked to reevaluate the authors' experimental design, data analysis, and interpretation of experimental results. The purpose of this statistical reevaluation was to provide an independent assessment of the experimental design and data analysis used in each of the studies and to identify key statistical issues relevant to the evaluation and interpretation of the data. This paper presents a summary of the Statistics Subpanel's evaluation. Specific examples are presented to illustrate problems that arose in the experimental design and data analysis of certain studies. The statistical principles and issues that are discussed in this paper are not unique to endocrine disruptor studies and should provide important guidelines regarding appropriate experimental design and statistical analysis for other types of laboratory investigations.

Analysis of Variance↗

PubMed1980

Implications of a biopsychosocial model for research in psychiatry.

Developments in general and living systems theory, in computer science, and in research instrumentation and technology have led to new perspectives on the patient as a person. The biopsychosocial model forces realization that states of health and illness can be understood fully only in terms of their biological, psychological, and social parameters. Research implications of this model, particularly the appreciation it engenders for the brain's role in mediating and regulating transactions along the society-mind-brain-body continuum, are discussed. Objective data generated by skilled clinical psychiatric methods will be needed in addition to data generated in the basic science area for the full range of research challenges in psychiatry to be met.

Adult↗

PubMed2006

Dementia with lewy bodies: therapeutic opportunities and pitfalls.

OBJECTIVE: To review diagnoses and challenges of treating patients with dementia with Lewy bodies (DLB), commonly considered the second most common form of dementia. DATA SOURCES: MEDLINE, Web of Science, and International Pharmaceutical Abstracts databases were searched in January 2006 for clinical studies, case series, case studies, letters, and review articles on the treatment of DLB. Search terms included: aripiprazole, cholinesterase inhibitors, clozapine, dementia with Lewy bodies, donepezil, galantamine, Lewy body dementia, neuroleptics, olanzapine, quetiapine, risperidone, rivastigmine, tacrine, ziprasidone. Applicable articles in the English language were reviewed. The bibliographies of these articles provided additional references. STUDY SELECTION: Articles describing studies, case series, and case studies are included in this review. DATA SYNTHESIS: DLB is commonly considered the second most common form of dementia, although some experts believe vascular dementia to be the second most common form. DLB is often under-diagnosed and misdiagnosed as Alzheimer's disease or Parkinson's related dementia. The core features of dementia with Lewy bodies are cognitive decline plus at least one of the following: fluctuations in cognition, visual hallucinations, and parkinsonism. Other supportive features include: neuroleptic sensitivity, repeated falls, syncope, transient loss of consciousness, REM sleep disturbances, depression, delusions, and nonvisual hallucinations. CONCLUSION: Increased prudence with the use of neuroleptic agents is essential in DLBs because the use of these agents is associated with physical and cognitive decline and increased mortality. While neuroleptic sensitivity has been reported with the use of both typical and atypical antipsychotic medications, these medications are often necessary for the treatment of psychotic symptoms. Decreases in neuroleptic sensitivity can often be achieved by dose reductions, although neuroleptic discontinuation is sometimes necessary. Cholinesterase inhibitors may be especially useful in the treatment of DLB. Cholinergic deficits are associated with visual hallucinations, and cholinesterase inhibitors often result in resolution of hallucinations, improved cognition, and decreased behavioral disturbances.

Antiparkinson Agents↗

PubMed2000

Interlibrary loan in primary access libraries: challenging the traditional view.

INTRODUCTION: Primary access libraries serve as the foundation of the National Network of Libraries of Medicine (NN/LM) interlibrary loan (ILL) hierarchy, yet few published reports directly address the important role these libraries play in the ILL system. This may reflect the traditional view that small, primary access libraries are largely users of ILL, rather than important contributors to the effectiveness and efficiency of the national ILL system. OBJECTIVE: This study was undertaken to test several commonly held beliefs regarding ILL system use by primary access libraries. HYPOTHESES: Three hypotheses were developed. HI: Colorado and Wyoming primary access libraries comply with the recommended ILL guideline of adhering to a hierarchical structure, emphasizing local borrowing. H2: The closures of two Colorado Council of Medical Librarians (CCML) primary access libraries in 1996 resulted in twenty-three Colorado primary access libraries' borrowing more from their state resource library in 1997. H3: The number of subscriptions held by Colorado and Wyoming primary access libraries is positively correlated with the number of items they loan and negatively correlated with the number of items they borrow. METHODS: The hypotheses were tested using the 1992 and 1997 DOCLINE and OCLC data of fifty-four health sciences libraries, including fifty primary access libraries, two state resource libraries, and two general academic libraries in Colorado and Wyoming. The ILL data were obtained electronically and analyzed using Microsoft Word 98, Microsoft Excel 98, and JMP 3.2.2. RESULTS: CCML primary access libraries comply with the recommended guideline to emphasize local borrowing by supplying each other with the majority of their ILLs, instead of overburdening libraries located at higher levels in the ILL hierarchy (H1). The closures of two CCML primary access libraries appear to have affected the entire ILL system, resulting in a greater volume of ILL activity for the state resource library and other DOCLINE libraries higher up in the ILL hierarchy and highlighting the contribution made by CCML primary access libraries (H2). CCML primary access libraries borrow and lend in amounts that are proportional to their collection size, rather than overtaxing libraries at higher levels in the ILL hierarchy with large numbers of requests (H3). LIMITATIONS: The main limitations of this study were the small sample size and the use of data collected for another purpose, the CCML ILL survey. CONCLUSIONS: The findings suggest that there is little evidence to support several commonly held beliefs regarding ILL system use by primary access libraries. In addition to validating the important contributions made by primary access libraries to the national ILL system, baseline data that can be used to benchmark current practice performance are provided.

Benchmarking↗

PubMed2001

International scientific production in digestive laparoscopic surgery.

OBJECTIVE: To obtain data on research in laparoscopic digestive surgery over the period of 1991 to 1996. MATERIAL AND METHODS: We used Medline and the Science Citation Index to obtain general data on production. For more specific data (contents, etc.) we used random samples with a confidence level of 99%. RESULTS: There were 4825 publications on laparoscopic digestive surgery and 4.085 on other specialties; of these, articles represented 85% and editorials and letters 15%. University hospitals published 40% of this production. The producing countries were USA (45%), France (8.2%), United Kingdom (7.9%) and Germany (7.5%). The publishing countries were USA (41%), Germany (15.3%), United Kingdom (9.7%) and France (6.7%). The publication with the largest influence was the New England Journal of Medicine with a total Impact Factor of 589; the British Journal of Surgery with a factor of 436, Archives of Surgery with 343, American Journal of Surgery with 336 and Annals of Surgery with 302; the mean relative Impact Factor was 1.886. Method was involved in 756 retrospective studies, 275 prospective studies and 43 random clinical trials; the rest were not series. The majority of contents are on techniques and instruments, indications and general reflections. The most researched anatomical region was the gall bladder, followed by the bile ducts and the colon. The differences had a "z" > 1.645, that is to say, p < 0.05, and so considered statistically significant. CONCLUSIONS: The largest production and publication takes place in the USA and the journal with the greatest influence is the New England. Important studies on method are extremely scarce, random clinical trials representing only 1%.

Bibliometrics↗

PubMed2002

Application of hidden Markov models on residuals: an example using Canadian traffic accident data.

Laverty, Kelly, Rotton, and Flynn conducted a regression analysis in 1992 on 9 years of automobile accidents in Saskatchewan (a total of 200,545 accidents) to find a small linear trend, season effects, holiday, and day of the week effects. The application of a hidden Markov model to the residuals of this analysis uncovered two states which are likely to be related to the weather. These states can be described as low volatility' and 'high volatility'. The 'low volatility' state involves low variability compared to the 'high volatility' state (occurring during the colder months) during which the largest numbers of accidents occur. It is suggested that hidden Markov models are a useful method for uncovering hidden, underlying states in social science and health-related data.

Accidents, Traffic↗

PubMed2006

Sliding friction between polymer surfaces: a molecular interpretation.

For two contacting rigid bodies, the friction force F is proportional to the normal load and independent of the macroscopic contact area and relative velocity V (Amonton's law). With two mutually sliding polymer samples, the surface irregularities transmit deformation to the underlying material. Energy loss along the deformation cycles is responsible for the friction force, which now appears to depend strongly on V [see, e.g., N. Maeda et al., Science 297, 379 (2002)]. We base our theoretical interpretation on the assumption that polymer chains are mainly subjected to oscillatory "reptation" along their "tubes." At high deformation frequencies-i.e., with a large sliding velocity V-the internal viscosity due to the rotational energy barriers around chain bonds hinders intramolecular mobility. As a result, energy dissipation and the correlated friction force strongly diminish at large V. Derived from a linear differential equation for chain dynamics, our results are basically consistent with the experimental data by Maeda et al. [Science 297, 379 (2002)] on modified polystyrene. Although the bulk polymer is below T(g), we regard the first few chain layers below the surface to be in the liquid state. In particular, the observed maximum of F vs V is consistent with physically reasonable values of the molecular parameters. As a general result, the ratio FV is a steadily decreasing function of V, tending to V(-2) for large velocities. We evaluate a much smaller friction for a cross-linked polymer under the assumption that the junctions are effectively immobile, also in agreement with the experimental results of Maeda et al. [Science 297, 379 (2002)].

Journal Article↗

PubMed1984

Project community diagnosis: participatory research as a first step toward community involvement in primary health care.

'Community participation' and 'bottom up planning' have become fashionable themes in international health circles. However, in the absence of sociocultural perspective these themes remain largely rhetoric. In this paper, a deprofessionalization of social science is advocated in the service of participatory research as a first step towards community involvement in primary health care. Deprofessionalization is suggested as an adjunct to, not a replacement for in-depth professional social science research. An exploratory community diagnosis of health project conducted in rural south India is described. During the project, lay researchers received rudimentary social science field training and collected data on health behaviour deemed important to health planners as well as the health concerns of the community. Illustrative data, generated by the project is presented on the rural poors' utilization of government health facilities, their attitudes towards Primary Health Centre staff, and their ideas about how a proposed community health worker scheme could best serve them.

Community Health Workers↗

PubMed2004

Analysis of pharmacokinetics, pharmacodynamics, and pharmacogenomics data sets using VizStruct, a novel multidimensional visualization technique.

PURPOSE: Data visualization techniques for the pharmaceutical sciences have not been extensively investigated. The purpose of this study was to evaluate the usefulness of VizStruct, a multidimensional visualization tool, for applications in pharmacokinetics, pharmacodynamics, and pharmacogenomics. METHODS: The VizStruct tool uses the first harmonic of the discrete Fourier transform to map multidimensional data to two dimensions for visualization. The mapping was used to visualize several published pharmacokinetic, pharmacodynamic, and pharmacogenomic data sets. The VizStruct approach was evaluated using simulated population pharmacokinetics data sets, the data from Dalen and colleagues (Clin. PharmacoL Ther. 63:444-452, 1998) on the kinetics of nortriptyline and its 10-hydroxynortriptyline metabolite in subjects with differing number of copies of the CYP2D6, and the gene expression profiling data of Bohen and colleagues (Proc. Natl. Acad. Sci. USA 100:1926-1930, 2003) on follicular lymphoma patients responsive and nonresponsive to rituximab. RESULTS: The VizStruct mapping preserves the key characteristics of multidimensional data in two dimensions in a manner that facilitates visualization. The mapping is computationally efficient and can be used for cluster detection and class prediction in pharmaceutical data sets. The VizStruct visualization succinctly summarized the salient similarities and differences in the nortriptyline and 10-hydroxynortriptyline pharmacokinetic profiles in subjects with increasing number of CYP2D6 gene copies. In the simulated population pharmacokinetic data sets, it was capable of discriminating the subtle differences between pharmacokinetic profiles derived from 1- and 2-compartment models with the same area under the curve. The two-dimensional VizStruct mapping computed from a subset of 102 informative genes from the Bohen and colleagues data set effectively separated the rituximab responder, rituximab nonresponder, and control subject groups. CONCLUSIONS: The VizStruct approach is a computationally efficient and effective approach for visualizing complex, multidimensional data sets. It could have many useful applications in the pharmaceutical sciences.

Algorithms↗