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PubMed1997

Residues on both faces of the first immunoglobulin fold contribute to homophilic binding sites of PECAM-1/CD31.

CD31 (PECAM-1) is a member of the immunoglobulin superfamily whose extracellular domain is comprised of six immunoglobulin-like domains. It is widely expressed on endothelium, platelets, around 50% of lymphocytes, and cells of myeloid lineage. CD31 has been shown to be involved in interendothelial adhesion and leukocyte-endothelial interactions, particularly during transmigration. CD31-mediated adhesion is complex, because CD31 is capable of mediating both homophilic and multiple heterophilic adhesive interactions. Here we show that the NH2-terminal (membrane-distal) immunoglobulin domain of CD31 is necessary but not sufficient to support stable homophilic adhesion. Key residues forming the binding site within this domain have been identified by analysis of 26 single point mutations, representing the most systematic analysis of a fully homophilic interaction between immunoglobulin superfamily family members to date. This revealed five mutations that affect homophilic binding. Uniquely, the residues involved are exposed on both faces of the immunoglobulin fold, leading us to propose a novel mechanism for CD31 homophilic adhesion.

Amino Acid Sequence↗

PubMed2002

Serial analysis of gene expression in murine fetal thymocyte cell lines.

FTL-1, -3 and -10 are three murine day 14 fetal thymocyte cell lines produced in order to model developmental stages within early (CD3-CD4-CD8-) thymocyte differentiation. In this study, we used the serial analysis of gene expression (SAGE) method to perform a systematic analysis of transcripts present in these three cell lines. A total of 77,313 SAGE tags were sequence identified from the three cell lines, representing 24,645 unique transcripts. Differentially expressed mRNA transcripts representing different gene classes were identified, including T cell functional genes, cytokine receptors, adhesion molecules and transcription factors. These results may serve as a model of the transcriptome of early thymocyte differentiation. A large number of unknown expressed sequence tags were also found to be differentially expressed. In order to validate the SAGE data, selected differentially expressed transcripts identified by SAGE were analyzed by quantitative RT-PCR in normal murine double-negative stage DN1-4 thymocytes. Expression of the transcription factors RUNX2 and PHD finger protein 2 and of the IGF type 1 receptor was shown to have differentially regulated expression patterns in sorted DN1-4 cells. These genes, and others identified by this analysis, are likely to play important roles in the development of T cells.

Animals↗

PubMed2004

Prediction of lymph node metastasis with use of artificial neural networks based on gene expression profiles in esophageal squamous cell carcinoma.

BACKGROUND: The aim of the study was (1) to detect candidate genes involved in lymph node metastasis in esophageal cancers and (2) to investigate whether we can estimate and predict occurrence of lymph node metastasis by analyzing artificial neural networks (ANNs) using these gene subsets. METHODS: Twenty-eight primary esophageal squamous cell carcinomas were used. Gene expression profiles of all primary tumors were obtained by cDNA microarray. Lymph node metastasis-related genes were extracted with use of Significance Analysis of Microarrays (SAM). Predictive accuracy for lymph node metastasis was calculated by evaluation of 28 cases by ANNs with leave-one-out cross-n. The results were compared with those of other analyses such as clustering or predictive scoring (LMS). RESULTS: Our ANN model could predict lymph node metastasis most accurately with 60 clones. The highest predictive accuracy for lymph node metastasis by ANN was 10 of 13 (77%) in newly added cases that were not used for gene selection by SAM and 24 of 28 (86%) in all cases (sensitivity: 15/17, 88%; specificity: 9/11, 82%). Predictive accuracy of LMS was 9 of 13 (69%) in newly added cases and 24 of 28 (86%) in all cases (sensitivity: 17/17, 100%; specificity: 7/11, 67%). It was difficult to extract useful information for the prediction of lymph node metastasis by clustering analysis. CONCLUSIONS: ANN had superior potential in comparison with other methods of analysis for the prediction of lymph node metastasis. This systematic analysis combining SAM with ANN was very useful for the prediction of lymph node metastasis in esophageal cancers and could be applied clinically in the near future.

Adult↗

PubMed1999

Synovial tissue analysis in rheumatoid arthritis.

In rheumatoid arthritis, synovial tissue is easily accessible for systematic analysis. Blind needle biopsy is a simple and safe procedure, but is restricted to smaller tissue samples. Arthroscopic biopsy is also safe but is more complicated as it allows access to most sites in the joint and provides adequate tissue for extensive laboratory investigations. Synovial tissue analysis has been successfully applied to studies of disease mechanisms, response to treatment and prognosis. The immuno-histological features in synovial tissue have consistently reflected disease status. Synovial tissue analysis has been particularly informative in the study of novel therapeutic agents.

Arthritis, Rheumatoid↗

PubMed2006

Mechanical thromboprophylaxis in critically ill patients: a systematic review and meta-analysis.

OBJECTIVE: To systematically review the randomized trials, observational studies, and survey evidence on compression and pneumatic devices for thromboprophylaxis in intensive care patients. METHODS: Published studies on the use of compression and pneumatic devices in intensive care patients were assessed. A meta-analysis was conducted by using the randomized controlled trials. RESULTS: A total of 21 relevant studies (5 randomized controlled trials, 13 observational studies, and 3 surveys) were found. A total of 811 patients were randomized in the 5 randomized controlled trials; 3421 patients participated in the observational studies. Trauma patients only were enrolled in 4 randomized controlled trials and 4 observational studies. Meta-analysis of 2 randomized controlled trials with similar populations and outcomes revealed that use of compression and pneumatic devices did not reduce the incidence of venous thromboembolism. The pooled risk ratio was 2.37, indicative of favoring the control over the intervention in reducing the deep venous thrombosis; however, the 95% CI of 0.57 to 9.90 indicated no significant differences between the intervention and the control. A range of methodological issues, including bias and confounding variables, make meaningful interpretation of the observational studies difficult. CONCLUSIONS: The limited evidence suggests that use of compressive and pneumatic devices yields results not significantly different from results obtained with no treatment or use of low-molecular-weight heparin. Until large randomized controlled trials are conducted, the role of mechanical approaches to thromboprophylaxis for intensive care patients remains uncertain.

Adolescent↗

PubMed2006

Prenatal exposure to misoprostol and congenital anomalies: systematic review and meta-analysis.

The present systematic review was proposed with the objective of estimating the risk of congenital anomalies and other adverse events in children exposed to misoprostol during fetal life. The data source consisted of case-control studies that analyzed the effect of prenatal exposure to misoprostol on the pregnancy outcome, which were located in electronic databases and published up to June 2005. The outcomes of interest included congenital anomalies, fetal death, low birth weight and prematurity. The odds ratios (OR) for the individual studies were pooled by meta-analysis. Sensitivity tests and heterogeneity analysis were performed. Four studies involving 4899 cases of congenital anomalies and 5742 controls were included in accordance with the selection criteria. None of the studies analyzed other adverse effects from misoprostol on the outcome from gestation. Increased risks of congenital anomalies related to misoprostol use were found for any congenital defect (OR=3.56; 95% CI: 0.98-12.98), Möbius sequence (OR=25.31; 95% CI: 11.11-57.66) and terminal transverse limb defects (OR=11.86; 95% CI: 4.86-28.90). In conclusion, prenatal exposure to misoprostol is associated with an increased risk of Möbius sequence and terminal transverse limb defects.

Anti-Ulcer Agents↗

PubMed2005

A comparison of pain, strength, range of motion, and functional outcomes after hemiarthroplasty and total shoulder arthroplasty in patients with osteoarthritis of the shoulder. A systematic review and meta-analysis.

BACKGROUND: A systematic review of the literature was performed to estimate the impact of hemiarthroplasty compared with total shoulder arthroplasty on function and range of motion in patients suffering from osteoarthritis of the shoulder. METHODS: We conducted an electronic search for relevant studies published in any language from 1966 to 2004, a manual search of the proceedings from five major orthopaedic meetings from 1995 to 2003, and a review of the reference lists from potentially relevant studies. Four randomized clinical trials, with similar eligibility criteria and surgical techniques, that compared hemiarthroplasty and total shoulder arthroplasty for the treatment of primary osteoarthritis of the shoulder were found to be eligible. Authors from three of the four studies provided original patient data. Analysis of covariance focused on the two-year outcome and included a comparison of the aggregate University of California at Los Angeles shoulder score, four University of California at Los Angeles domain scores, and range of motion. RESULTS: A total of 112 patients (fifty managed with hemiarthroplasty and sixty-two managed with total shoulder arthroplasty), who had a mean age of sixty-eight years, were included in this analysis. A significant moderate effect was detected in the function domain of the University of California at Los Angeles shoulder score (p < 0.001) in favor of total shoulder arthroplasty (mean [and standard deviation], 8.1 +/- 0.3) compared with hemiarthroplasty (mean, 6.6 +/- 0.3). A significant difference in the pain score was found in favor of the total shoulder arthroplasty group (p < 0.0001). However, the large degree of heterogeneity (p = 0.006, I(2) = 80.2%) among the studies decreased our confidence that total shoulder arthroplasty provides a true, consistent benefit with regard to pain. There was a significant difference in the overall change in forward elevation of 13 degrees (95% confidence interval, 0.5 degrees to 26 degrees ) in favor of the total shoulder arthroplasty group (p = 0.008). CONCLUSIONS: At a minimum of two years of follow-up, total shoulder arthroplasty provided better functional outcome than hemiarthroplasty for patients with osteoarthritis of the shoulder. Since continuous degeneration of the glenoid after hemiarthroplasty or glenoid loosening after total shoulder arthroplasty may affect the eventual outcome, longer-term (five to ten-year) results are necessary to determine whether these findings remain consistent over time.

Activities of Daily Living↗

PubMed2005

Efficacy of rapid-rate repetitive transcranial magnetic stimulation in the treatment of depression: a systematic review and meta-analysis.

OBJECTIVE: To systematically review the literature pertaining to rapid-rate repetitive transcranial magnetic stimulation (rTMS) compared with sham therapy for the treatment of a major depressive episode in order to arrive at qualitative and quantitative conclusions about the efficacy of rapid-rate rTMS. METHODS: MEDLINE, the Cochrane Library, the metaRegister of Controlled Trials and abstracts from scientific meetings were searched for the years 1966 until July 2003. The search terms "transcranial magnetic stimulation" and "transcranial magnetic stimulation AND depression" were used. Eighty-seven randomized controlled trials investigating the efficacy of rTMS were referenced on MEDLINE. Nineteen of these involved treatment of a major depressive episode, and these were reviewed. Six met more specific inclusion criteria including the use of rapid-rate stimulation, application to the left dorsolateral prefrontal cortex, evaluation with the 21-item Hamilton Rating Scale for Depression (HAM-D) and use of an intent-to-treat analysis. Scores on the 21-item HAM-D after treatment and standard deviations were extracted from each article for treatment and control subjects. A random-effects model was chosen for the meta-analysis, and the weighted mean difference was used as a summary measure. RESULTS: Six studies that met the inclusion criteria were identified and included in the meta-analysis. Two of these reported a significantly greater improvement in mood symptoms in the treatment versus the sham group. When combined in the meta-analysis, the overall weighted mean difference was -1.1 (95% confidence interval -4.5 to 2.3), and the results of a test for heterogeneity were not significant (chi2(5) = 5.81, p = 0.33). CONCLUSIONS: This meta-analysis suggests that rapid-rate rTMS is no different from sham treatment in major depression; however, the power within these studies to detect a difference was generally low. Randomized controlled trials with sufficient power to detect a clinically meaningful difference are required.

Major Depressive Disorder↗

PubMed2025

The Impact of Nutritional Status on Oral Health Outcomes and Management in Older Adults: A Systematic Review and Meta-Analysis.

OBJECTIVE: This systematic review and meta-analysis evaluated the relationship between nutritional status and the oral health of older adults (aged 75 years or older). The PECO focus question was, 'What is the occurrence, association and impact of nutritional state on the oral health outcomes and its management in older adults?' METHODS: A comprehensive literature search was performed across MEDLINE (PubMed), Embase and the Cochrane Library. Publications up to April 2025 were considered, yielding 3324 records for initial screening. Quality assessment of the included studies predominantly revealed a low to moderate risk of bias. RESULTS: Eighty-three studies were included for data analysis. Meta-analyses demonstrated that older adults at risk of malnutrition had fewer teeth (SMD = -0.29; 95% CI: -0.46, -0.11; p = 0.002). Those with < 20 teeth and who were not rehabilitated with dentures were more likely to be malnourished (OR = 4.00; 95% CI: 1.21, 13.18; p = 0.02). Malnutrition was associated with self-reported chewing problems (OR = 2.38; 95% CI: 1.74, 3.26; p < 0.0001), swallowing problems (OR = 3.18; 95% CI: 2.20, 4.61; p < 0.0001) or dry mouth (OR = 2.35; 95% CI: 1.91, 2.88; p < 0.0001). Conversely, those with oral pain showed lower odds of malnutrition risk (OR = 0.68; 95% CI: 0.52, 0.89; p = 0.005). CONCLUSIONS: Fewer teeth, existing chewing or swallowing problems, dry mouth and the absence of removable dentures where needed, were associated with malnutrition in care-dependent older adults. The current lack of longitudinal studies and proof of causality for malnutrition affecting oral health outcomes underscores the need for further research to better clarify the complex relationship between oral health and nutrition in older populations. TRIAL REGISTRATION: PROSPERO Registration: CRD420251003549.

Humans↗

PubMed1999

Whole genome protein domain analysis using a new method for domain clustering.

We present the outcome of a systematic analysis of protein domain shuffling in 17 completed microbial genomes. This analysis has been performed using MKDOM Version 2, a completely new version of the domain clustering program MKDOM based on PSI-BLAST recursive homology searches. It allows to delineate the most frequent protein domain building blocks, which domains are found specifically in Bacteria, Archaea or yeast, and which domains are shared between two or all three domains of life. The latter are good candidates as the basic protein building blocks underlying all forms of cellular life. Statistics of multi-domain proteins indicate that some organisms such as Bacillus subtilis or Mycobacterium tuberculosis contain an abnormally high number of large multi-domain proteins. We also provide examples of highly shuffled or circularly permutated domains. A WWW graphical interface has been made available to interactively browse domain arrangements of proteins in all 17 genomes, at http:@www.toulouse.inra.fr/prodomCG.html.

Archaea↗

PubMed2003

Relationships between families and registered nurses in long-term-care facilities: a critical analysis.

Although much has been written about the relationship between families and nurses, little systematic analysis has been undertaken of this dyadic relationship in long-term care (LTC). Using a critical ethnographic approach, the researchers conducted separate in-depth interviews with 17 family-nurse dyads caring for residents with Alzheimer disease or a related disorder in one LTC setting. Analysis of interview transcripts and fieldnotes revealed 4 types of family-nurse relationships--conventional, competitive, collaborative, and "carative"--each reflecting the roles of nurse and family, negotiating strategies, and consequences. In addition, it became apparent that intrinsic and extrinsic factors influence the development of certain types of relationships. The findings have implications for nursing practice, policy development, and further research within LTC settings.

Adult↗

PubMed2026

Effects of short-bout accumulated exercise on postprandial metabolism in adults: A systematic review and meta-analysis.

OBJECTIVE: To systematically evaluate the acute effects of short-bout accumulated exercise (SBAE) interrupting prolonged sedentary behaviour on postprandial glucose, insulin, and triglycerides in adults. METHODS: Systematic searches in PubMed, Web of Science, Embase, Cochrane Library, CINAHL, SPORTDiscus, and CNKI (inception to 10 December 2025) identified randomised crossover trials comparing SBAE (≤10 min/bout, inter-bout interval ≥30 min or adequate recovery) with continuous sedentary behaviour. Outcomes included postprandial glucose, insulin, and triglyceride AUCs. Standardised mean differences (SMD) were pooled using random-effects models. RESULTS: Thirty-one publications reporting data from 29 independent cohorts involving 573 unique participants (mean age 47.8 ± 20.3 years; 47.5% female; mean BMI 29.0 ± 5.1 kg/m²) were included. Compared with continuous sedentary behaviour, SBAE significantly reduced glucose AUC (SMD = -0.53, 95% CI: -0.71 to -0.34, P < 0.001) and insulin AUC (SMD = -0.58, 95% CI: -0.85 to -0.31, P < 0.001), but not triglyceride AUC (SMD = -0.17, 95% CI: -0.48 to 0.15, P = 0.306).Exploratory subgroup analyses showed statistically significant reductions in glucose and insulin for walking and for inter-bout intervals < 60 min, but not for standing alone or intervals ≥ 60 min. A statistically significant insulin-lowering effect was observed in obese individuals. CONCLUSION: SBAE acutely improves postprandial glucose and insulin control. Exploratory subgroup analyses showed statistically significant effects for walking and for inter-bout intervals < 60 min, but these comparisons are observational and no formal interaction test was conducted. These findings provide preliminary evidence for acute SBAE in sedentary populations, though long-term health effects and real-world generalisability require further investigation.

Adult↗

PubMed2002

"In-gel" purified ditags direct synthesis of highly efficient SAGE Libraries.

BACKGROUND: SAGE (serial analysis of gene expression) is a recently developed technique for systematic analysis of eukaryotic transcriptomes. The most critical step in the SAGE method is large scale amplification of ditags which are then are concatemerized for the construction of representative SAGE libraries. Here, we report a protocol for purifying these ditags via an 'in situ' PAGE purification method. This generates ditags free of linker contaminations, making library construction simpler and more efficient. RESULTS: Ditags used to generate SAGE libraries were demarcated 'in situ' on preparative polyacrylamide gels using XC and BPB dyes, which precisely straddle the ditag band when a 16% PAGE gel (19:1 acrylamide:bis, 5% cross linker) is used to resolve the DNA bands. Here, the ditag DNA was directly excised from gel without visualization via EtBr or fluorescent dye staining, resulting in highly purified ditag DNA free of contaminating linkers. These ditags could be rapidly self ligated even at 4 degrees C to generate concatemers in a controlled manner, which in turn enabled us to generate highly efficient SAGE libraries. This reduced the labor and time necessary, as well as the cost. CONCLUSIONS: This approach greatly simplified the ditag purification procedure for constructing SAGE libraries. Since the traditional post-run staining with EtBr or fluorescent dyes routinely results in cross contamination of a DNA band of interest by other DNA in the gel, the dry gel DNA excision method described here may also be amenable to other molecular biology techniques in which DNA purity is critically important.

Journal Article↗

PubMed2005

Genetically encoded sensors for metabolites.

BACKGROUND: Metabolomics, i.e., the multiparallel analysis of metabolite changes occurring in a cell or an organism, has become feasible with the development of highly efficient mass spectroscopic technologies. Functional genomics as a standard tool helped to identify the function of many of the genes that encode important transporters and metabolic enzymes over the past few years. Advanced expression systems and analysis technologies made it possible to study the biochemical properties of the corresponding proteins in great detail. We begin to understand the biological functions of the gene products by systematic analysis of mutants using systematic PTGS/RNAi, knockout and TILLING approaches. However, one crucial set of data especially relevant in the case of multicellular organisms is lacking: the knowledge of the spatial and temporal profiles of metabolite levels at cellular and subcellular levels. METHODS: We therefore developed genetically encoded nanosensors for several metabolites to provide a basic set of tools for the determination of cytosolic and subcellular metabolite levels in real time by using fluorescence microscopy. RESULTS: Prototypes of these sensors were successfully used in vitro and also in vivo, i.e., to measure sugar levels in fungal and animal cells. CONCLUSIONS: One of the future goals will be to expand the set of sensors to a wider spectrum of substrates by using the natural spectrum of periplasmic binding proteins from bacteria and by computational design of proteins with altered binding pockets in conjunction with mutagenesis. This toolbox can then be applied for four-dimensional imaging of cells and tissues to elucidate the spatial and temporal distribution of metabolites as a discovery tool in functional genomics, as a tool for high-throughput, high-content screening for drugs, to test metabolic models, and to analyze the interplay of cells in a tissue or organ.

Animals↗

PubMed1998

Analysis of EST-driven gene annotation in human genomic sequence.

We have performed a systematic analysis of gene identification in genomic sequence by similarity search against expressed sequence tags (ESTs) to assess the suitability of this method for automated annotation of the human genome. A BLAST-based strategy was constructed to examine the potential of this approach, and was applied to test sets containing all human genomic sequences longer than 5 kb in public databases, plus 300 kb of exhaustively characterized benchmark sequence. At high stringency, 70%-90% of all annotated genes are detected by near-identity to EST sequence; >95% of ESTs aligning with well-annotated sequences overlap a gene. These ESTs provide immediate access to the corresponding cDNA clones for follow-up laboratory verification and subsequent biologic analysis. At lower stringency, up to 97% of annotated genes were identified by similarity to ESTs. The apparent false-positive rate rose to 55% of ESTs among all sequences and 20% among benchmark sequences at the lowest stringency, indicating that many genes in public database entries are unannotated. Approximately half of the alignments span multiple exons, and thus aid in the construction of gene predictions and elucidation of alternative splicing. In addition, ESTs from multiple cDNA libraries frequently cluster over genes, providing a starting point for crude expression profiles. Clone IDs may be used to form EST pairs, and particularly to extend models by associating alignments of lower stringency with high-quality alignments. These results demonstrate that EST similarity search is a practical general-purpose annotation technique that complements pattern recognition methods as a tool for gene characterization.

Base Sequence↗

PubMed2001

Forgiveness. A concept analysis.

This article provides an operational definition of forgiveness as a first step in the systematic analysis of the concept. Using the method described by Walker and Avant (1995), the authors identify the attributes and characteristics of forgiveness and its theoretical and practical implications for nursing. Sample cases from clinical practice help illustrate the concept further. Further nursing research needs to test the theoretical relationships between forgiveness and nursing practice outcomes.

Attitude↗

PubMed2000

A comparison of aorta and vena cava medial message expression by cDNA array analysis identifies a set of 68 consistently differentially expressed genes, all in aortic media.

We performed a systematic analysis of gene expression in arteries and veins by comparing message profiles of macaque aorta and vena cava media using a cDNA array containing 4048 known human genes, approximately 35% of currently named human genes (approximately 11,000). The data show extensive differences in RNA expression in artery versus vein media. Sixty-eight genes had consistent elevation in message expression by the aorta, but none were elevated in the vena cava. The most differentially expressed gene was regulator of G-protein signaling (RGS) 5, at an expression ratio of 46.5+/-12.6 (mean+/-SEM). The data set also contained 2 genes already known to be expressed in the aorta, elastin at 5.0+/-1.4, and the aortic preferentially expressed gene 1 (APEG-1) at 2.3+/-0.6. We chose to analyze RGS5 expression further because of its high level of differential expression in the aorta. Levels of RGS5 mRNA were confirmed by Northern analysis and in situ hybridization. A human tissue RNA dot blot showed that RGS5 message is highest in aorta, followed by small intestine, stomach, and then heart. Northern analysis confirmed that RGS5 expression in human aorta is higher than in any region of the heart. RGS5 is a G-protein signaling regulator of unknown specificity most homologous to RGS4, an inhibitory regulator of pressure-induced cardiac hypertrophy. The expression pattern of the 68 differential genes as a whole is a start toward identifying the molecular phenotypes of arteries and veins on a systematic basis.

Adult↗

PubMed2005

The evolution of noncoding DNA: how much junk, how much func?

Comparative sequence analysis on a genomic scale has opened the door for the systematic analysis of cis-acting regulatory DNA. It is now possible to begin to answer basic questions such as, how much meaningful noncoding sequence is in the genome? How strong is natural selection on functional noncoding sequences in different species? Two recent articles have capitalized on the comparative genomic approach in an attempt to answer these questions with surprising results.

DNA, Intergenic↗