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Data inventories provide a concise reference base for researchers. The authors created a set of reference volumes listing databases used for studying cancer in New Jersey minorities. The process followed can be adapted for other disease outcomes or other regions.
This paper presents a QRS-detector error logger and the implementation of a fully automated system for evaluation of QRS-detector performance. The error logger requires a known reference, such as an electrocardiogram (ECG) database, that provides ECG data and reference pulses wherever QRS complexes occur. These reference pulses are used to validate detection pulses generated by a QRS detector in real time. Using an eight-bit microcontroller chip, the error logger was constructed at a very low materials cost. Applications include automated analysis of QRS-detector performance and optimization of parameters in QRS-detection algorithms.
OBJECTIVE: To compare the effectiveness of alternative partner notification strategies for gonorrhea, chlamydia, syphilis, HIV and hepatitis B. DATA SOURCES: Studies were identified using MEDLINE, EMBASE, SCISEARCH and other databases, review of reference lists and personal contact with over 80 international experts. STUDY SELECTION: Studies with at least two comparison groups exposed to different partner notification strategies were included. DATA EXTRACTION: Methodological rigor was assessed, and information regarding study populations, interventions and outcomes was extracted independently by two reviewers. MAIN RESULTS: Twelve studies met our inclusion criteria; five were methodologically strong; seven provided data on the referral process; four provided data on trained interviewers compared with routine care providers; and three provided data on the interview process. CONCLUSIONS: Only limited, broad conclusions regarding the effectiveness of various partner notification approaches could be drawn from these comparative studies. Until newer data become available, practice guidelines must be based to a large extent on other grounds.
The objective of the study was to review the clinical literature on the acute, somatic treatment of the depressed phase of bipolar disorder. We reviewed all available published studies of "standard" somatic treatments (lithium, antidepressant and anticonvulsant agents, and electroconvulsive therapy [ECT]) reporting three or more depressed bipolar patients who were not psychotic, rapid cycling, or previously treatment refractory. We also reviewed all studies of "nonstandard" pharmacologic treatments involving even a single case of a depressed bipolar patient. Data sources included the MEDLINE database and relevant references from articles obtained in this search and in major reviews. Five of seven studies comparing ECT with antidepressant agents find ECT more efficacious. Eight of nine controlled comparisons find lithium superior to placebo in depressed bipolar patients. Three controlled comparisons of lithium to tricyclic antidepressants suggest that lithium is equivalent to tricyclic drugs in such patients. Three double-blind, controlled studies indicate that carbamazepine is more effective than placebo. Limited data on other antidepressant classes suggest that monoamine oxidase inhibitors, bupropion, and serotonergic agents may offer some advantages over tricyclic antidepressants in this population. Some "nonstandard" treatments also show some potential in bipolar patients. The possibility of switching into a manic episode is an important consideration with many of the agents studied, although little remains known about spontaneous versus treatment-associated mood shifts. In contrast to the extensive literature on the acute treatment of the manic phase of bipolar disorder and on the prophylaxis of manic and depressive episodes, there are few studies of treatment of the depressed phase of bipolar disorder, and their results generally are limited or inconclusive. Lithium generated a revolution in psychiatric treatment, but the treatment of the depressed phase of bipolar disorder remains a relatively neglected corner of the field. Several study designs may help to augment knowledge in the treatment of bipolar depression.
BACKGROUND: We determined the relative efficacy of various agents or combinations of agents in the prophylaxis of deep venous thrombosis after elective hip arthroplasty. METHODS: Peer-reviewed, English-language, human studies articles from 1975 through 1991 were obtained through a MEDLINE database search. Additional references were obtained from bibliographies. Articles that compared the effect of two or more prophylactic agents or placebo in preventing deep venous thrombosis as assessed by venography were selected for further review. Only studies of elective hip surgery in which all patients had venographic screening for thrombosis were included. Twenty-three of 101 studies met these criteria. Data were abstracted by one of us. Methodologic criteria and outcome data from each study were recorded and analyzed. RESULTS: There was significant heterogeneity in the deep venous thrombosis rate among studies. Although the rates were lowest for low-molecular-weight heparin with or without the use of stockings, adjusted-dose heparin, and warfarin, many agents had similar low rates. There was less heterogeneity when the relative risk was used as a summary statistic for studies in which two agents were compared. With pairwise comparisons, low-molecular-weight heparin performed better than every agent with which it was compared. Other agents performed well but were not consistently better. CONCLUSIONS: Multiple agents or combinations are effective prophylaxis for deep venous thrombosis, but none decreases the rate to zero. There was overlap in the 95% confidence intervals for the probability of deep venous thrombosis for various agents and especially for the probabilities for proximal thrombi. Many agents have not been compared directly with each other, but low-molecular-weight heparin consistently performed well.
PURPOSE/OBJECTIVES: To review the literature on confusion at the end of life, provide accurate definitional and defining characteristics of confusion, and outline nursing strategies for its resolution. DATA SOURCES: Published articles, computerized databases, book chapters, reference lists from chapters and journal articles. DATA SYNTHESIS: As a major component of symptom distress in terminal care, confusion has not been defined clearly and therefore has not benefited from rigorous assessment and study as have other end-of-life symptoms. CONCLUSIONS: Increased knowledge about confusion that occurs in patients with widely metastatic cancer will assist in accurate symptom identification, early recognition, and timely management to reduce cognitive symptom distress at the end of life. Improved symptom resolution also can benefit family coping during terminal care. IMPLICATIONS FOR NURSING PRACTICE: Oncology nurses can devise management protocols for confused patients that include screening criteria, pharmacologic interventions, environmental support, and prophylactic safety measures.
Protein databases serve as general reference resources providing an orientation on two-dimensional electrophoresis (2-DE) patterns of interest. The intention behind constructing a 2-DE database of the water soluble proteins from wild-type mouse mammary gland tissue was to create a reference before going on to investigate cancer-associated protein variations. This database shall be deemed to be a model system for mouse tissue, which is open for transgenic or knockout experiments. Proteins were separated and characterized in terms of their molecular weight (M(r)) and isoelectric point (pI) by high resolution 2-DE. The proteins were identified using prevalent proteomics methods. One method was peptide mass fingerprinting by matrix-assisted laser desorption/ionization-mass spectrometry. Another method was N-terminal sequencing by Edman degradation. By N-terminal sequencing M(r) and pI values were specified more accurately and so the calibration of the master gel was obtained more systematically and exactly. This permits the prediction of possible post-translational modifications of some proteins. The mouse mammary gland 2-DE protein database created presently contains 66 identified protein spots, which are clickable on the gel pattern. This relational database is accessible on the WWW under the URL: http://www.mpiib-berlin.mpg.de/2D-PAGE.
Reference data on pathologies, their management, risk factors and the use of drugs in real life is necessary. In France, there are no existing databases of a set of systematically recorded data which associate information on drugs and morbidity/mortality. In contrast, there are a great number of studies focused on pathologies, their management or on drugs. A directory that could identify these databases and a means of accessing them would be desirable. Pharmaco-epidemiology studies must answer epidemiologically specific quality criteria, which must be planned at study conception. The protocol must be developed with a scientific committee on which there are epidemiologically experienced people. It is a prerequisite that a committee of experts with epidemiological competence should give advice on the 'acceptability' of the protocol, that is on the aim and the methodology. Data collection must be the subject of specific quality control of both the study and its aims. Cross-checking with other sources of data is recommended when possible. The coordinator of each study must send a final report to investigators and publish the results.
Calcium is a common component of an atherosclerotic plaque; therefore, the presence of coronary artery calcium (CAC) indicates atherosclerosis. This study investigated the difference in total CAC scores between HIV-infected patients treated with highly active antiretroviral therapy (HAART) and HIV-negative age-matched controls. HIV patients were 27 men treated with a protease inhibitor-containing HAART regimen for more than 1 year (M = 4.92 years, SD = 2.02), aged 30 to 60 years (M = 43.52 years, SD = 6.65), and not receiving lipid-lowering or hypoglycemic drugs. Controls were age-matched men randomly selected (three controls to one case, for a total of 81 controls) from our existing database of 25,250 men who self-referred for CAC screening (control database). Electron beam tomography was used to obtain CAC scores. The CAC scores were coded as above or below the age-specific (stratified in 5-year increments) 10th, 25th, 50th, 75th, or 90th percentile of our control database. Chi-square analyses for two independent samples indicated (1) a larger frequency of controls with CAC scores above the 10th (chi1= 8.32, P = .004) and 25th (chi1= 5.45, P = .02) percentiles than that of HIV patients, (2) no differences in CAC scores between groups above the 50th (chi = 0.85, P = .357) or 75th (chi = 0.46, P = .497) percentile, and (3) a larger frequency of HIV patients who were above the 90th percentile (chi = 4.5, P = .034). The strength of the relationship between group membership and scoring above the 90th percentile was significant (phi = 0.20, P = .034). These results tentatively suggest that there is an elevated level of subclinical atherosclerosis in HIV patients treated with HAART.
This paper describes a system of generally applicable index files provided on the EMBL sequence databases CD-ROM to facilitate the development of front-end software to the sequence databases available on this CD-ROM. The index files are used by a new versatile and user-friendly database retrieval program for the Apple Macintosh, EMBL-Search, which allows the easy construction of complex database queries. EMBL-Search utilizes cross-reference information contained in the databases to support navigation between different information resources. The ability to run EMBL-Search on a local computer network accessing a shared database CD-ROM makes its use particularly cost effective.
SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc), a minimal level of redundancy and a high level of integration with other databases. Recent developments of the database include: an increase in the number and scope of model organisms; cross-references to seven additional databases; a variety of new documentation files; the creation of TREMBL, and unannotated supplement to SWISS-PROT. This supplement consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except CDS already included in SWISS-PROT.
SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, structure of its domains, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. Recent developments of the database include: an increase in the number and scope of model organisms; cross-references to two additional databases; a variety of new documentation files and the creation of TrEMBL, a computer annotated supplement to SWISS-PROT. This supplement consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except the CDS already included in SWISS-PROT.
SWISS-PROT (http://www.expasy.ch/) is a curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. Recent developments of the database include: an increase in the number and scope of model organisms; cross-references to two additional databases; a variety of new documentation files and improvements to TrEMBL, a computer annotated supplement to SWISS-PROT. TrEMBL consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except the CDS already included in SWISS-PROT.
BACKGROUND: Anxiety disorders are characterised by long term worry, tension, nervousness, fidgeting and symptoms of autonomic system hyperactivity. Meditation is an age-old self regulatory strategy which is gaining more interest in mental health and psychiatry. Meditation can reduce arousal state and may ameliorate anxiety symptoms in various anxiety conditions. OBJECTIVES: To investigate the effectiveness of meditation therapy in treating anxiety disorders SEARCH STRATEGY: Electronic databases searched include CCDANCTR-Studies and CCDANCTR-References, complementary and alternative medicine specific databases, Science Citation Index, Health Services/Technology Assessment Text database, and grey literature databases. Conference proceedings, book chapters and references were checked. Study authors and experts from religious/spiritual organisations were contacted. SELECTION CRITERIA: Types of studies: Randomised controlled trials. TYPES OF PARTICIPANTS: patients with a diagnosis of anxiety disorders, with or without another comorbid psychiatric condition. Types of interventions: concentrative meditation or mindfulness meditation. Comparison conditions: one or combination of 1) pharmacological therapy 2) other psychological treatment 3) other methods of meditation 4) no intervention or waiting list. Types of outcome: 1) improvement in clinical anxiety scale 2) improvement in anxiety level specified by triallists, or global improvement 3) acceptability of treatment, adverse effects 4) dropout. DATA COLLECTION AND ANALYSIS: Data were independently extracted by two reviewers using a pre-designed data collection form. Any disagreements were discussed with a third reviewer, and the authors of the studies were contacted for further information. MAIN RESULTS: Two randomised controlled studies were eligible for inclusion in the review. Both studies were of moderate quality and used active control comparisons (another type of meditation, relaxation, biofeedback). Anti-anxiety drugs were used as standard treatment. The duration of trials ranged from 3 months (12 weeks) to 18 weeks. In one study transcendental meditation showed a reduction in anxiety symptoms and electromyography score comparable with electromyography-biofeedback and relaxation therapy. Another study compared Kundalini Yoga (KY), with Relaxation/Mindfulness Meditation. The Yale-Brown Obsessive Compulsive Scale showed no statistically significant difference between groups. The overall dropout rate in both studies was high (33-44%). Neither study reported on adverse effects of meditation. AUTHORS' CONCLUSIONS: The small number of studies included in this review do not permit any conclusions to be drawn on the effectiveness of meditation therapy for anxiety disorders. Transcendental meditation is comparable with other kinds of relaxation therapies in reducing anxiety, and Kundalini Yoga did not show significant effectiveness in treating obsessive-compulsive disorders compared with Relaxation/Meditation. Drop out rates appear to be high, and adverse effects of meditation have not been reported. More trials are needed.
Alternative splicing plays a crucial role in expanding proteomic diversity but can also generate identical isoforms under certain conditions. While mutually exclusive splicing of tandem exons has occasionally been reported to produce identical isoforms, the extent to which other splicing events contribute to this phenomenon remains unclear. In this study, we demonstrate that alternative 5' and 3' splice site selection can also lead to the formation of identical isoforms, providing an additional type of splicing event for functional redundancy in transcriptomes. To address this, we analyzed reference genome annotations from 15 plant species, including Arabidopsis thaliana and wheat (Triticum aestivum), obtained from the RefSeq database. Identical isoforms were computationally defined as transcripts with distinct exon-intron structures but identical coding sequences. Our analysis reveals that the majority of alternative 5' and 3' fragments originate from small segmental duplications, suggesting that sequence repetition within gene regions facilitates the emergence of such splicing patterns. We also observed differences in the annotated 5' UTRs of some identical isoforms. However, since the alternative splicing sites themselves were not located within UTRs, these differences may reflect annotation uncertainty rather than genuine AS-derived variation. Given that UTR predictions in reference databases are not always precise, such observations should be interpreted cautiously. Expression analysis using an isoform-specific k-mer approach confirmed that identical isoforms can be differentially regulated. These findings suggest that, beyond expanding protein diversity, alternative splicing can also generate redundant isoforms that are differentially expressed at the RNA level, indicating potential regulatory roles. By elucidating the structural and regulatory factors contributing to the formation and retention of identical isoforms, our study provides new insights into the evolutionary and functional significance of alternative splicing in plants.
BACKGROUND: Sickle cell disease comprises of a group of genetic blood disorders, and occurs when the sickle cell haemoglobin gene is inherited from both parents. The effects of the condition are: varying degrees of anaemia which if severe reduce the capacity for mobility; predisposition to obstruction of small blood capillaries causing pain in muscle and bone known as "crises"; damage to major organs such as the spleen, liver, kidneys, and lungs; and increased vulnerability to severe infections. There are both medical and non-medical complications, and treatment is usually symptomatic and palliative in nature. Psychological intervention for individuals with sickle cell disease seems viable in complementing current medical treatment, and studies examining their efficacy appear to have also yielded encouraging results. OBJECTIVES: To examine the evidence that in patients with sickle cell disease, psychological treatment improves the ability to cope with the condition. SEARCH STRATEGY: The Cochrane Cystic Fibrosis and Genetic Disorders Group specialist trials register which comprises references from comprehensive electronic database searches, handsearching relevant journals and handsearching abstract books of conference proceedings. Also, searches on the Internet were performed. SELECTION CRITERIA: All randomised or quasi-randomised controlled trials comparing the use of psychological intervention to no (psychological) intervention in patients with sickle cell disease. DATA COLLECTION AND ANALYSIS: The following outcomes were assessed: pain, mood, coping, health service utilisation, general health, quality of life, and life satisfaction. MAIN RESULTS: Four trials which reported results were all found to be unsuitable for inclusion at the present time, owing to incomplete data in the published papers. REVIEWER'S CONCLUSIONS: Psychological approaches are commonly used in an attempt to improve coping ability in patients with sickle cell disease. No conclusions can be made about the use of specific psychological therapies in sickle cell disease from the information currently available. This systematic review has clearly identified the need for well designed, adequately-powered, multicentre, RCTs assessing the effectiveness of specific interventions in sickle cell disease.
BACKGROUND: The MEDLINE database contains over 12 million references to scientific literature, with about 3/4 of recent articles including an abstract of the publication. Retrieval of entries using queries with keywords is useful for human users that need to obtain small selections. However, particular analyses of the literature or database developments may need the complete ranking of all the references in the MEDLINE database as to their relevance to a topic of interest. This report describes a method that does this ranking using the differences in word content between MEDLINE entries related to a topic and the whole of MEDLINE, in a computational time appropriate for an article search query engine. RESULTS: We tested the capabilities of our system to retrieve MEDLINE references which are relevant to the subject of stem cells. We took advantage of the existing annotation of references with terms from the MeSH hierarchical vocabulary (Medical Subject Headings, developed at the National Library of Medicine). A training set of 81,416 references was constructed by selecting entries annotated with the MeSH term stem cells or some child in its sub tree. Frequencies of all nouns, verbs, and adjectives in the training set were computed and the ratios of word frequencies in the training set to those in the entire MEDLINE were used to score references. Self-consistency of the algorithm, benchmarked with a test set containing the training set and an equal number of references randomly selected from MEDLINE was better using nouns (79%) than adjectives (73%) or verbs (70%). The evaluation of the system with 6,923 references not used for training, containing 204 articles relevant to stem cells according to a human expert, indicated a recall of 65% for a precision of 65%. CONCLUSION: This strategy appears to be useful for predicting the relevance of MEDLINE references to a given concept. The method is simple and can be used with any user-defined training set. Choice of the part of speech of the words used for classification has important effects on performance. Lists of words, scripts, and additional information are available from the web address http://www.ogic.ca/projects/ks2004/.
A proteomic approach was used for the identification of larval hemolymph proteins of Drosophila melanogaster. We report the initial establishment of a two-dimensional gel electrophoresis reference map for hemolymph proteins of third instar larvae of D. melanogaster. We used immobilized pH gradients of pH 4-7 (linear) and a 12-14% linear gradient polyacrylamide gel. The protein spots were silver-stained and analyzed by nanoLC-Q-Tof MS/MS (on-line nanoscale liquid chromatography quadrupole time of flight tandem mass spectrometry) or by Matrix assisted laser desorption time of flight MS (MALDI-TOF MS). Querying the SWISSPROT database with the mass spectrometric data yielded the identity of the proteins in the spots. The presented proteome map lists those protein spots identified to date. This map will be updated continuously and will serve as a reference database for investigators, studying changes at the protein level in different physiological conditions.