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PubMed2004

In silico estimation of DMSO solubility of organic compounds for bioscreening.

Solubility of organic compounds in DMSO is an important issue for commercial and academic organizations handling large compound collections or performing biological screening. In particular, solubility data are critical for the optimization of storage conditions and for the selection of compounds for bioscreening compatible with the assay protocol. Solubility is largely determined by the solvation energy and the crystal disruption energy, and these molecular phenomena should be assessed in structure-solubility correlation studies. The authors summarize our long-term experimental observations and theoretical studies of physicochemical determinants of DMSO solubility of organic substances. They compiled a comprehensive reference database of proprietary data on compound solubility (55,277 compounds with good DMSO solubility and 10,223 compounds with poor DMSO solubility), calculated specific molecular descriptors (topological, electromagnetic, charge, and lipophilicity parameters), and applied an advanced machine-learning approach for training neural networks to address the solubility. Both supervised (feed-forward, back-propagated neural networks) and unsupervised (Kohonen neural networks) learning methods were used. The resulting neural network models were validated by successfully predicting DMSO solubility of compounds in independent test selections.

Dimethyl Sulfoxide↗

PubMed2002

The potential role of Fourier transform infrared spectroscopy and imaging in cancer diagnosis incorporating complex mathematical methods.

Infrared spectroscopy and imaging technology can provide new diagnostic capabilities for cancer research applications and to physicians directly involved in patient treatment. A methodology that permits the phenotypical description of cells and tissues is introduced, as well as a variety of new evaluation techniques that allow researchers and physicians to evaluate the infrared data at different levels of sophistication. The detection of cell alterations in the case of Chronic Lymphocytic Leukemia (CLL) demonstrates the capability of infrared spectroscopy to identify and stage this type of cancer, providing new prospects for diagnosis and treatment. The pathological study of oral tissue affected by Squamous Cell Carcinoma (SCC) illustrates the potential of Infrared Spectroscopy and Imaging for tissue diagnosis and cancer staging based in altered cell biochemistry, without using stains or any other marker technology. An example of combined fluid, cell and tissue analysis of thyroid cancers based on infrared technology is introduced to demonstrate the possibility of earlier detection of gland abnormalities and biochemical alterations in cell extracts using fine needle aspirates. Simple statistical techniques such as bivariate histogram analysis can distinguish between normal and altered cells and tissues when applied to infrared spectra and images. More complex mathematical techniques such as Principal Component Analysis (PCA) or Artificial Neural Networks (ANN) provide additional evaluation capabilities that can relate spectra of an unknown sample to an infrared reference database of known cell states. It is documented how this new infrared technology could enhance the diagnoses, treatment decisions and prognoses of patients in the field of cancer medicine.

Apoptosis↗

PubMed2004

RNA profiling of cell-free saliva using microarray technology.

Saliva, like other bodily fluids, has been used to monitor human health and disease. This study tests the hypothesis that informative human mRNA exists in cell-free saliva. If present, salivary mRNA may provide potential biomarkers to identify populations and patients at high risk for oral and systemic diseases. Unstimulated saliva was collected from ten normal subjects. RNA was isolated from the cell-free saliva supernatant and linearly amplified. High-density oligonucleotide microarrays were used to profile salivary mRNA. The results demonstrated that there are thousands of human mRNAs in cell-free saliva. Quantitative PCR (Q-PCR) analysis confirmed the present of mRNA identified by our microarray study. A reference database was generated based on the mRNA profiles in normal saliva. Our finding proposes a novel clinical approach to salivary diagnostics, Salivary Transcriptome Diagnostics (STD), for potential applications in disease diagnostics as well as normal health surveillance.

Databases, Genetic↗

PubMed2026

Using Mapping-Profiles to Refine Strain-Level Metagenomic Classification.

Metagenomic classification at the strain level remains challenging due to high sequence similarity among closely related genomes, which leads to ambiguous read mappings and frequent false-positive strain detections. Reducing such errors improves the reliability of strain-level analyses, which is critical for applications such as pathogen detection. We introduce StrainRefine, a post-mapping refinement method that analyzes read-reference mapping profiles to resolve ambiguous assignments among highly similar genomes. The method represents candidate reference genomes using binary profiles that capture read-support patterns and measures similarity between references based on profile overlap. The method clusters references based on similar mapping profiles, filters weakly supported genomes, and reassigns reads to representative references, reducing redundant reporting of near-identical strains. StrainRefine substantially reduces false-positive strain detections while preserving recall and improving agreement between predicted and true abundance profiles. On large-scale metagenomic datasets, it achieves a substantially improved precision-recall balance compared with existing mapping-based approaches, with the standalone method obtaining the highest read-level classification accuracy on the most complex evaluated dataset. Unlike many strain-level tools designed for individual species, StrainRefine operates without prior assumptions about sample composition or curated species-specific reference collections, while still achieving comparable performance in single-species settings on species-specific reference databases. These results highlight mapping-profile similarity as an effective signal for improving strain-level metagenomic classification.

false-positive reduction↗

PubMed2006

Natural history of cerebral vein thrombosis: a systematic review.

UNLABELLED: Cerebral vein thrombosis (CVT) has been considered, until a few years ago, an uncommon disease with significant long-term morbidity and high mortality rate. New noninvasive diagnostic techniques have increased the frequency with which this disease is diagnosed; despite this, there continues to be little data on its natural history. The objectives of this study were to evaluate the mortality rate, the rate of disability at long-term follow-up, and the incidence of recurrence after a first episode of CVT; to determine clinical and radiologic predictors of death and dependence; and to identify possible risk factors for recurrence. ( DATA SOURCE: MEDLINE and EMBASE databases, reference lists of selected articles and authors' libraries.) Nineteen studies were identified. Mortality rate during peri-hospitalization period is 5.6% (range, 0%-15.2%) and 9.4% (range, 0%-39%) at the end of follow-up period. Eighty-eight percent of surviving patients recover completely or have only a mild functional or cognitive deficit. Two thirds of patients with CVT recanalized within the first few months after presentation, and 2.8% (range, 0%-11.7%) had objectively confirmed recurrence. We conclude that patients with CVT have a low risk of death and that most patients have a good long-term prognosis.

Diagnosis, Differential↗

PubMed2004

Risk factors for osteoporosis in postmenopausal African-American women.

BACKGROUND: Although postmenopausal African-American women are at lower risk for osteoporosis-related fractures compared with white women, fractures in African-American women are associated with significantly higher morbidity and mortality. Therefore, early diagnosis and treatment of osteoporosis in this population is just as important as it is for other ethnic groups and worthy of the attention of physicians and healthcare organizations. OBJECTIVE: The purpose of this study was to evaluate risk factors for osteoporosis in postmenopausal African-American women. DESIGN: This was a retrospective, case-control study in 201 postmenopausal African-American women at a community-based osteoporosis center. Spine and hip bone mineral density measurements were obtained by dual-energy x-ray absorptiometry. Patient and family medical history, past and present pharmaceutical use, and dietary and exercise habits were collected using a patient self-administered questionnaire. RESULTS: Using the manufacturer's African-American referent database, 56 women had osteoporosis, 99 had osteopenia, and 46 had normal bone mineral density. Risk factors more common in the osteoporotic group compared with the normal group included sedentary lifestyle (P < 0.03), family history of osteoporosis (P < 0.03), low body mass index (P < 0.05), and history of bilateral oophorectomy (P < 0.03). Polyarthritis was more prevalent in the normal versus the osteoporotic group (P < 0.001). In addition, premenopausal use of oral contraceptives (P < 0.005) and postmenopausal use of estrogen therapy (P < 0.05) were more common in the normal compared with the osteoporotic group. CONCLUSIONS: Many risk factors for osteoporosis in African-American women are similar to those in white women and can aid in the selection of patients in need of bone density testing.

Black or African American↗

PubMed2005

Text detective: a rule-based system for gene annotation in biomedical texts.

BACKGROUND: The identification of mentions of gene or gene products in biomedical texts is a critical step in the development of text mining applications in biosciences. The complexity and ambiguity of gene nomenclature makes this a very difficult task. METHODS: Here we present a novel approach based on a combination of carefully designed rules and several lexicons of biological concepts, implemented in the Text Detective system. Text Detective is able to normalize the results of gene mentions found by offering the appropriate database reference. RESULTS: In BioCreAtIvE evaluation, Text Detective achieved results of 84% precision, 71% recall for task 1A, and 79% precision, 71% recall for mouse genes in task 1B.

Biomedical Research↗

PubMed2006

Bacterial genotyping by 16S rRNA mass cataloging.

BACKGROUND: It has recently been demonstrated that organism identifications can be recovered from mass spectra using various methods including base-specific fragmentation of nucleic acids. Because mass spectrometry is extremely rapid and widely available such techniques offer significant advantages in some applications. A key element in favor of mass spectrometric analysis of RNA fragmentation patterns is that a reference database for analysis of the results can be generated from sequence information. In contrast to hybridization approaches, the genetic affinity of any unknown isolate can in principle be determined within the context of all previously sequenced 16S rRNAs without prior knowledge of what the organism is. In contrast to the original RNase T1 cataloging method, when digestion products are analyzed by mass spectrometry, products with the same base composition cannot be distinguished. Hence, it is possible that organisms that are not closely related (having different underlying sequences) might be falsely identified by mass spectral coincidence. We present a convenient spectral coincidence function for expressing the degree of similarity (or distance) between any two mass-spectra. Trees constructed using this function are consistent with those produced by direct comparison of primary sequences, demonstrating that the inherent degeneracy in mass spectrometric analysis of RNA fragments does not preclude correct organism identification. RESULTS: Neighbor-joining trees for important bacterial pathogens were generated using distances based on mass spectrometric observables and the spectral coincidence function. These trees demonstrate that most pathogens will be readily distinguished using mass spectrometric analyses of RNA digestion products. A more detailed, genus-level analysis of pathogens and near relatives was also performed, and it was found that assignments of genetic affinity were consistent with those obtained by direct sequence comparisons. Finally, typical values of the coincidence between organisms were also examined with regard to phylogenetic level and sequence variability. CONCLUSION: Cluster analysis based on comparison of mass spectrometric observables using the spectral coincidence function is an extremely useful tool for determining the genetic affinity of an unknown bacterium. Additionally, fragmentation patterns can determine within hours if an unknown isolate is potentially a known pathogen among thousands of possible organisms, and if so, which one.

Bacteria↗

PubMed2006

Pain in veterans of the Gulf War of 1991: a systematic review.

BACKGROUND: Veterans of the Persian Gulf War of 1991 have reported a range of adverse health symptoms. This systematic review aims to identify all studies that have compared the prevalence of symptoms of pain in veterans of the Gulf War to that in a non-Gulf military comparison group, and to determine whether Gulf War veterans are at increased risk of reporting pain. METHODS: Studies published between January 1990 and May 2004 were identified by searching a large number of electronic databases. Reference lists and websites were also searched and key researchers were contacted. Studies were included if they reported the prevalence of any symptom or condition that included the word "pain" in Gulf War veterans and in a comparison group of non-Gulf veterans. 2401 abstracts were independently reviewed by two authors. RESULTS: Twenty studies fulfilled the inclusion criteria. Five main sites of pain were identified (muscle, joint, chest/heart, back and abdominal pain) and separate meta-analyses were performed to summarise the results related to each site. A greater proportion of Gulf veterans reported symptoms at each site of pain when compared to a non-Gulf military group. Gulf deployment was most strongly associated with abdominal pain, with Gulf veterans being more than three times more likely to report such pain than a comparison group (OR 3.23; 95% CI 2.31-4.51). Statistical heterogeneity between study estimates was significant, probably due to variation in measured periods of prevalence and symptom measurement methods. CONCLUSION: A higher proportion of veterans of the Persian Gulf War of 1991 reported symptoms of pain than military comparison groups. This is consistent with previously demonstrated increased reporting of more general symptoms (fatigue, multiple chemical sensitivity, post traumatic stress disorder) in these veterans compared with non-Gulf military groups. However, the primary studies were heterogeneous and varied greatly in quality.

Gulf War↗

PubMed2005

Pretest probability assessment derived from attribute matching.

BACKGROUND: Pretest probability (PTP) assessment plays a central role in diagnosis. This report compares a novel attribute-matching method to generate a PTP for acute coronary syndrome (ACS). We compare the new method with a validated logistic regression equation (LRE). METHODS: Eight clinical variables (attributes) were chosen by classification and regression tree analysis of a prospectively collected reference database of 14,796 emergency department (ED) patients evaluated for possible ACS. For attribute matching, a computer program identifies patients within the database who have the exact profile defined by clinician input of the eight attributes. The novel method was compared with the LRE for ability to produce PTP estimation <2% in a validation set of 8,120 patients evaluated for possible ACS and did not have ST segment elevation on ECG. 1,061 patients were excluded prior to validation analysis because of ST-segment elevation (713), missing data (77) or being lost to follow-up (271). RESULTS: In the validation set, attribute matching produced 267 unique PTP estimates [median PTP value 6%, 1st-3rd quartile 1-10%] compared with the LRE, which produced 96 unique PTP estimates [median 24%, 1st-3rd quartile 10-30%]. The areas under the receiver operating characteristic curves were 0.74 (95% CI 0.65 to 0.82) for the attribute matching curve and 0.68 (95% CI 0.62 to 0.77) for LRE. The attribute matching system categorized 1,670 (24%, 95% CI = 23-25%) patients as having a PTP < 2.0%; 28 developed ACS (1.7% 95% CI = 1.1-2.4%). The LRE categorized 244 (4%, 95% CI = 3-4%) with PTP < 2.0%; four developed ACS (1.6%, 95% CI = 0.4-4.1%). CONCLUSION: Attribute matching estimated a very low PTP for ACS in a significantly larger proportion of ED patients compared with a validated LRE.

Acute Disease↗

PubMed2005

Differential gene expression in anatomical compartments of the human eye.

BACKGROUND: The human eye is composed of multiple compartments, diverse in form, function, and embryologic origin, that work in concert to provide us with our sense of sight. We set out to systematically characterize the global gene expression patterns that specify the distinctive characteristics of the various eye compartments. RESULTS: We used DNA microarrays representing approximately 30,000 human genes to analyze gene expression in the cornea, lens, iris, ciliary body, retina, and optic nerve. The distinctive patterns of expression in each compartment could be interpreted in relation to the physiology and cellular composition of each tissue. Notably, the sets of genes selectively expressed in the retina and in the lens were particularly large and diverse. Genes with roles in immune defense, particularly complement components, were expressed at especially high levels in the anterior segment tissues. We also found consistent differences between the gene expression patterns of the macula and peripheral retina, paralleling the differences in cell layer densities between these regions. Based on the hypothesis that genes responsible for diseases that affect a particular eye compartment are likely to be selectively expressed in that compartment, we compared our gene expression signatures with genetic mapping studies to identify candidate genes for diseases affecting the cornea, lens, and retina. CONCLUSION: Through genome-scale gene expression profiling, we were able to discover distinct gene expression 'signatures' for each eye compartment and identified candidate disease genes that can serve as a reference database for investigating the physiology and pathophysiology of the eye.

Adult↗

PubMed2004

Official positions of the international society for clinical densitometry.

The International Society for Clinical Densitometry (ISCD) periodically holds Position Development Conferences for the purpose of establishing standards and guidelines for indications, acquisition, and interpretation of bone density tests. Topics are selected for consideration by the ISCD Scientific Advisory Committee, reviewed by scientific working groups, and presented to an international panel of experts. Topic categories addressed to date include indications for bone density testing, selection of reference databases for T-scores and Z-scores, clinical applications for central and peripheral bone densitometry, serial bone density testing, instrument precision assessment, phantom scanning and calibration testing, requirements for a bone density report, nomenclature, and diagnosis of osteoporosis in postmenopausal women, premenopausal women, men, and children. After an open session for public comment and discussion, the panel convenes for consideration of each topic and makes recommendations for positions to the ISCD Board of Directors. Recommendations that are accepted become the Official Positions of the ISCD. This Special Report summarizes the methodology of the ISCD Position Development Conferences and presents selected Official Positions of general interest.

Absorptiometry, Photon↗

PubMed2004

[A systematic review of the clinical effectiveness of azathioprine in patients with ulcerative colitis].

To clarify the effectiveness and safety of azathioprine (AZA) and 6-mercaptopurine (6MP) in the induction and maintenance of remission in ulcerative colitis (UC) by using a systematic review of published studies. Studies were searched for from within the 1966 to March 2003 MEDLINE database, Cochrane Library 2003 issue 1, and the 1981 to March 2003 Japana Centra Revuo Medicina database. References from published studies and reviews were also obtained. Randomized, placebo-controlled trials of oral AZA or 6MP therapy in adult patients with active or quiescent UC were included. Ratios for the induction and maintenance of remission, the steroid-sparing effect, and the incidence of adverse drug reactions (ADRs) were compared and evaluated between the two study arms and expressed by the odds ratio (OR) specific for the individual studies and the meta-analytic summary for the OR. We could find no randomized controlled trial for 6MP therapy. However, four clinical trials for AZA therapy were included in this meta-analysis. For the induction of remission, the pooled OR of the response to AZA therapy compared with placebo in active UC was 1.45 (95% Confidence Interval (CI): 0.68 to 3.08). For the maintenance of remission, the pooled OR for AZA therapy was 2.26 (95% CI: 1.27 to 4.01). The number needed to treat (NNT) to prevent one recurrence was 6 patients. The pooled OR for AZA therapy's ADRs compared with placebo was 2.11 (95% CI: 0.92 to 4.84). From the viewpoint of effectiveness and safety, this meta-analysis suggests that AZA might be useful in the maintenance of remission in UC patients.

Adult↗

PubMed1998

Teleradiology: results of a questionnaire of German radiologists.

A questionnaire was sent by mail to 4400 radiologists (i.e. to at least 1000 radiological institutions). The response rate was about 5%. The results showed that 47% of respondents felt well informed about teleradiology, 49% not enough and 3% not at all. Image and report transfer as well as interfaces to reference databases, educational applications, technical quality surveillance and product support (maintenance) were considered to be increasingly important areas. Smaller institutions (1-3 doctors) judged expert consultation as more important than bigger institutions. Standardization, system stability and data security were demanded as well as guidelines, for example concerning the linking of report and image, correct documentation and required image quality. Technically most demands can be fulfilled today but this technology is not yet commonly included in teleradiology systems.

Attitude of Health Personnel↗

PubMed1999

MultiMed--remote interactive medical simulation.

MultiMed is a telemedicine and tele-education project to extend access to a sophisticated medical simulation facility in Bristol. It will allow remote users to undertake simulated medical scenarios and to access a reference database, for a comprehensive remote learning experience. The first phase will focus on the area of anaesthesia and all remote users will be based in the UK.

Anesthesiology↗

PubMed2025

Establishing the ELIXIR Microbiome Community.

Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples. In particular, experimental approaches such as metagenomics, metabarcoding, metatranscriptomics and metaproteomics have provided profound insights into the vast, hitherto unknown, microbial biodiversity. The ELIXIR Marine Metagenomics Community, initiated amongst researchers focusing on marine microbiomes, has concentrated on promoting standards around microbiome-derived sequence analysis, as well as understanding the gaps in methods and reference databases, and identifying solutions to the computational overheads of performing such analyses. Nevertheless, the methods used and the challenges faced are not confined to marine microbiome studies, but are broadly applicable to other biomes. Thus, expanding this Marine Metagenomics Community to a more inclusive ELIXIR Microbiome Community will enable it to encompass a broader range of biomes and link expertise across 'omics technologies. Furthermore, engaging with a large number of researchers will improve the efficiency and sustainability of bioinformatics infrastructure and resources for microbiome research (standards, data, tools, workflows, training), which will enable a deeper understanding of the function and taxonomic composition of the different microbial communities.

Computational Biology↗

PubMed2002

Pharmacy-based bone mass measurement to assess osteoporosis risk.

OBJECTIVE: To evaluate elderly women's knowledge of their skeletal status, assess adequacy of calcium intake, determine the prevalence of low bone density, and determine whether peripheral bone density testing led to medical interventions in a group of rural, elderly Wisconsin women recruited in community pharmacies. DESIGN: Recruiting notices were posted in each pharmacy, and eligible women were enrolled in the order in which they volunteered. Each completed a fracture-risk questionnaire. Calcaneal bone density was measured within the following 6 weeks, using peripheral dual-energy X-ray absorptiometry. Mail surveys were used to assess interventions subsequent to the womens' study participation. SETTING: The study was conducted at 5 community pharmacies in rural Wisconsin. RESULTS: Of 133 women, 20% had calcaneal osteoporosis, defined as a T score < or =2.5 (calcaneal bone density <2.5 SDs below the young reference database). Thirty percent of women met National Osteoporosis Foundation (NOF) treatment criteria based on heel bone density and NOF-designated risk factors. Of those meeting treatment criteria, 75% were unaware of their low bone mass. Half of the women received <1200 mg/d of calcium, the recommended dose for osteoporosis prevention. Those who were taking a calcium supplement were much more likely to receive the recommended amount. Women who had discussed bone density test results with their physicians were more likely to receive central dual energy X-ray absorptiometry (DXA) measurements and/or start antiresorptive therapy than women who did not. CONCLUSIONS: Rural, elderly Wisconsin women are at substantial risk for osteoporosis, based on calcaneal bone density, but most are unaware of their risk. Compounding this risk is low calcium intake. Community screening of rural, elderly women by peripheral bone density measurement can lead to medical interventions in such individuals.

Absorptiometry, Photon↗

PubMed2006

Genome-scale identification of membrane-associated human mRNAs.

The subcellular localization of proteins is critical to their biological roles. Moreover, whether a protein is membrane-bound, secreted, or intracellular affects the usefulness of, and the strategies for, using a protein as a diagnostic marker or a target for therapy. We employed a rapid and efficient experimental approach to classify thousands of human gene products as either "membrane-associated/secreted" (MS) or "cytosolic/nuclear" (CN). Using subcellular fractionation methods, we separated mRNAs associated with membranes from those associated with the soluble cytosolic fraction and analyzed these two pools by comparative hybridization to DNA microarrays. Analysis of 11 different human cell lines, representing lymphoid, myeloid, breast, ovarian, hepatic, colon, and prostate tissues, identified more than 5,000 previously uncharacterized MS and more than 6,400 putative CN genes at high confidence levels. The experimentally determined localizations correlated well with in silico predictions of signal peptides and transmembrane domains, but also significantly increased the number of human genes that could be cataloged as encoding either MS or CN proteins. Using gene expression data from a variety of primary human malignancies and normal tissues, we rationally identified hundreds of MS gene products that are significantly overexpressed in tumors compared to normal tissues and thus represent candidates for serum diagnostic tests or monoclonal antibody-based therapies. Finally, we used the catalog of CN gene products to generate sets of candidate markers of organ-specific tissue injury. The large-scale annotation of subcellular localization reported here will serve as a reference database and will aid in the rational design of diagnostic tests and molecular therapies for diverse diseases.

Biomarkers, Tumor↗