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PubMed2004

Tools for loading MEDLINE into a local relational database.

BACKGROUND: Researchers who use MEDLINE for text mining, information extraction, or natural language processing may benefit from having a copy of MEDLINE that they can manage locally. The National Library of Medicine (NLM) distributes MEDLINE in eXtensible Markup Language (XML)-formatted text files, but it is difficult to query MEDLINE in that format. We have developed software tools to parse the MEDLINE data files and load their contents into a relational database. Although the task is conceptually straightforward, the size and scope of MEDLINE make the task nontrivial. Given the increasing importance of text analysis in biology and medicine, we believe a local installation of MEDLINE will provide helpful computing infrastructure for researchers. RESULTS: We developed three software packages that parse and load MEDLINE, and ran each package to install separate instances of the MEDLINE database. For each installation, we collected data on loading time and disk-space utilization to provide examples of the process in different settings. Settings differed in terms of commercial database-management system (IBM DB2 or Oracle 9i), processor (Intel or Sun), programming language of installation software (Java or Perl), and methods employed in different versions of the software. The loading times for the three installations were 76 hours, 196 hours, and 132 hours, and disk-space utilization was 46.3 GB, 37.7 GB, and 31.6 GB, respectively. Loading times varied due to a variety of differences among the systems. Loading time also depended on whether data were written to intermediate files or not, and on whether input files were processed in sequence or in parallel. Disk-space utilization depended on the number of MEDLINE files processed, amount of indexing, and whether abstracts were stored as character large objects or truncated. CONCLUSIONS: Relational database (RDBMS) technology supports indexing and querying of very large datasets, and can accommodate a locally stored version of MEDLINE. RDBMS systems support a wide range of queries and facilitate certain tasks that are not directly supported by the application programming interface to PubMed. Because there is variation in hardware, software, and network infrastructures across sites, we cannot predict the exact time required for a user to load MEDLINE, but our results suggest that performance of the software is reasonable. Our database schemas and conversion software are publicly available at http://biotext.berkeley.edu.

Database Management Systems↗
PubMed2005

Vitamin A for non-measles pneumonia in children.

BACKGROUND: Acute respiratory infections, mostly in the form of pneumonia, are the leading causes of death in children under five years of age in developing countries. Some clinical trials have demonstrated that vitamin A supplementation reduces the severity of respiratory infection and mortality in children with measles. OBJECTIVES: To determine whether adjunctive vitamin A is effective in infants and children diagnosed with non-measles pneumonia. SEARCH STRATEGY: We searched the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library Issue 4, 2004); MEDLINE (1996 to November Week 3, 2004); EMBASE (1990 to September 2004); LILACS (9 January 2004); CINAHL (1990 to November 2004); Biological Abstracts (1990 to November 2004) and Current Contents (1990 to September 2004); and the Chinese Biomedicine Database (CBM) (1994 to November 2004). SELECTION CRITERIA: Only parallel-arm, randomised and quasi-randomised controlled trials in which children (younger than 15 years old) with non-measles pneumonia were treated with adjunctive vitamin A were included. DATA COLLECTION AND ANALYSIS: Two authors independently extracted data and assessed trial quality. Study authors were contacted for additional information. MAIN RESULTS: Five trials involving 1453 infants and children were included. There was no significant reduction in the mortality associated with pneumonia in children treated with vitamin A compared to those who were not (pooled odds ratio (OR) 1.49; 95% confidence interval (CI) 0.66 to 3.35). In addition, there was a lack of a statistically significant effect on duration of stay in hospital (weighted mean difference (WMD) 0.08; 95% CI -0.43 to 0.59). Vitamin A was associated with a 39% reduction in antibiotic firstline failure (OR 0.65; 95% CI 0.42 to 1.01). Children receiving vitamin A were no more likely to experience vomiting (OR 0.77; 95% CI 0.45 to 1.33), diarrhoea (OR 0.57; 95% CI 0.31 to 1.05), bulging of the fontanelles (OR 8.25; 95% CI 0.44 to 155.37) or irritability (OR 0.93, 95% CI 0.56 to 1.57) than those not receiving vitamin A. There was no statistical significance between vitamin A and placebo groups (OR 0.90; 95% CI -1.10 to 2.90) in chest x-ray results. Disease severity after supplementary high-dose vitamin A was significantly worse in children who received vitamin A compared with placebo. Low-dose vitamin A was associated with a significant reduction in the recurrent rate of bronchopneumonia (OR 0.12; 95% CI 0.03 to 0.46). AUTHORS' CONCLUSIONS: The evidence did not suggest a significant reduction with vitamin A adjunctive treatment in mortality, measures of morbidity, nor an effect on the clinical course of pneumonia in children with non-measles pneumonia. However, not all studies measured all outcomes, limiting the number of studies that could be incorporated into the meta-analyses, so that there may have been a lack of statistical power to detect statistically significant differences.

Child↗
PubMed1991

Analog-to-digital clinical data collection on networked workstations with graphic user interface.

An innovative respiratory examination system has been developed that combines physiological response measurement, real-time graphic displays, user-driven operating sequences, and networked file archiving and review into a scientific research and clinical diagnosis tool. This newly constructed computer network is being used to enhance the research center's ability to perform patient pulmonary function examinations. Respiratory data are simultaneously acquired and graphically presented during patient breathing maneuvers and rapidly transformed into graphic and numeric reports, suitable for statistical analysis or database access. The environment consists of the hardware (Macintosh computer, MacADIOS converters, analog amplifiers), the software (HyperCard v2.0, HyperTalk, XCMDs), and the network (AppleTalk, fileservers, printers) as building blocks for data acquisition, analysis, editing, and storage. System operation modules include: Calibration, Examination, Reports, On-line Help Library, Graphic/Data Editing, and Network Storage.

Analog-Digital Conversion↗
PubMed2006

Antibiotics for community acquired pneumonia in children.

BACKGROUND: Pneumonia is the leading cause of mortality in children. In developing countries, pneumonia is usually caused by bacterial pathogens. The early administration of empirical antibiotics improves the patients' clinical outcomes. There are currently no systematic reviews of clinical trials on this subject. OBJECTIVES: To identify effective antibiotic drug therapy for community acquired pneumonia (CAP) in children by comparing various antibiotics. SEARCH STRATEGY: We searched the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library, Issue 4, 2005), MEDLINE (OVID) (1966 to January 2006) and EMBASE (WebSPIRS) (1990 to September 2005). There were no language restrictions. SELECTION CRITERIA: Randomized controlled trials (RCTs) in children of either sex, which compared at least two antibiotics for CAP in hospital or ambulatory settings. DATA COLLECTION AND ANALYSIS: Data from full articles of selected studies were independently extracted by two authors. MAIN RESULTS: The review of these studies suggests that for treatment of pneumonia, co-trimoxazole is inferior in efficacy to both amoxycillin (failure rates odds ratio (OR) 1.33; 95% CI 1.05 to 1.67) and procaine penicillin (cure rates OR 2.64; 95% CI 1.57 to 4.45). Penicillin in conjunction with gentamycin was better than chloramphenicol alone (re-hospitalization rates OR 1.61; 95% CI 1.02 to 2.55). Co-amoxyclavulanic acid was better than amoxycillin alone (cure rates OR 10.44; 95% CI 2.85 to 38.21). There was no differences between injectable penicillin and oral amoxycillin (failure rates OR 1.03; 95% CI 0.81 to 1.31); azithromycin and erythromycin (cure rates OR 1.17; 95% CI 0.70 to 1.95); cefpodoxime and amoxycillin (cure rates OR 0.69; 95% CI 0.18 to 2.60); or azithromycin and co-amoxyclavulanic acid (cure rates OR 1.02; 95% CI 0.54 to 1.95, failure rates OR 1.42; 95% CI 0.43 to 4.66). AUTHORS' CONCLUSIONS: There were many studies each investigating multiple antibiotics with different methodologies. For treatment of ambulatory patients with CAP, amoxycillin was better than co-trimoxazole; there was no difference between azithromycin and erythromycin, or between cefpodoxime and co-amoxyclavulanic acid. For hospitalized patients, procaine penicillin was better than co-trimoxazole; and the combination of penicillin and gentamycin was better than chloramphenicol alone. Injectable penicillin and oral amoxycillin had similar failure rates. For the rest of the antibiotics there were only single studies available. There is a need for more studies with large patient populations and similar methodologies in order to compare newer antibiotics.

Anti-Bacterial Agents↗
PubMed2006

Gene expression changes during step-wise differentiation of embryonic stem cells along the inner ear hair cell pathway.

CONCLUSION: Our study outlines an alternative approach for the selection and investigation of genes involved in inner ear function. OBJECTIVE: To gain understanding of the gene pathways involved in the development of the normal cochlea. MATERIALS AND METHODS: Microarray technology currently offers the most efficient approach to investigate gene expression and identify pathways involved in cell differentiation. Epidermal growth factor (EGF) induces cultures derived from the organ of Corti to proliferate and produce new hair cells. Since pluripotent embryonic stem (ES) cells have the capacity to generate all tissues, we induced murine ES cells to differentiate towards ectodermal and neuroectodermal cell types and from there investigated their commitment towards the hair cell lineage in the presence of EGF. Cells were collected at three points along the differentiation pathway and their expression profiles were determined using the Soares NMIE mouse inner ear cDNA library printed in microarray format. RESULTS: Three genes up-regulated after addition of EGF (serine (or cysteine) proteinase inhibitor, clade H, member 1 (Serpinh1), solute carrier family 2 (facilitated glucose transporter), member 10 (Slc2a10) and secreted acidic cysteine-rich glycoprotein (Sparc)) were selected for further analysis and characterization. Of the three genes, Serpinh1 and Slc2a10 have never been implicated in the hearing process.

Animals↗
PubMed1999

Androgen receptor, estrogen receptor alpha, and estrogen receptor beta show distinct patterns of expression in forebrain song control nuclei of European starlings.

In songbirds, singing behavior is controlled by a discrete network of interconnected brain nuclei known collectively as the song control system. Both the development of this system and the expression of singing behavior in adulthood are strongly influenced by sex steroid hormones. Although both androgenic and estrogenic steroids have effects, androgen receptors (AR) are more abundantly and widely expressed in song nuclei than are estrogen receptors (ER alpha). The recent cloning of a second form of the estrogen receptor in mammals, ER beta, raises the possibility that a second receptor subtype is present in songbirds and that estrogenic effects in the song system may be mediated via ER beta. We therefore cloned the ER beta complementary DNA (cDNA) from a European starling preoptic area-hypothalamic cDNA library and used in situ hybridization histochemistry to examine its expression in forebrain song nuclei, relative to the expression of AR and ER alpha messenger RNA (mRNA), in the adjacent brain sections. The starling ER beta cDNA has an open reading frame of 1662-bp, predicted to encode a protein of 554 amino acids. This protein shares greater than 70% sequence identity with ER beta in other species. We report that starling ER beta is expressed in a variety of tissues, including brain, pituitary, skeletal muscle, liver, adrenal, kidney, intestine, and ovary. Similar to reports in other songbird species, we detected AR mRNA-containing cells in several song control nuclei, including the high vocal center (HVc), the medial and lateral portions of the magnocellular nucleus of the anterior neostriatum, and the robust nucleus of the archistriatum. We detected ER alpha expression in the medial portion of HVc (also called paraHVc) and along the medial border of the caudal neostriatum. ER beta was not expressed in HVc, in the medial and lateral portions of the magnocellular nucleus of the anterior neostriatum, in the robust nucleus of the archistriatum, or in area X. In contrast, ER beta mRNA-containing cells were detected in the caudomedial neostriatum and medial preoptic area in a pattern reminiscent of P450 aromatase expression in the same brain regions in other songbirds. These data suggest that estrogenic effects on the song system are not mediated via ER beta-producing cells within song nuclei. Nonetheless, the overlapping expression of ER beta- and aromatase-producing cells in the caudomedial neostriatum suggests that locally synthesized estrogens may act via ER beta, in addition to ER alpha, to mediate seasonal or developmental effects on nearby song nuclei (e.g. HVc).

Amino Acid Sequence↗
PubMedDate not supplied

Identification of neural crest derived cells within the cellular microenvironment of the human thymus employing a library of monoclonal antibodies raised against neuronal tissues.

The organization of optimal microenvironmental conditions within the developing thymus for lymphatic stem cell migration and their further maturation requires cellular and humoral participation of the neural crest. Recently, the immunophenotypical (IP) heterogeneity of lymphatic cells has become a scientific fact. Monoclonal antibodies (MoABs) produced against the various subpopulations of the reticulo-epithelial cells (RE) demonstrated their heterogeneity. We suggest that with a library of MoABs, raised against normal neuronal tissues, neural tumors, and a medulloblastoma cell line, including UJ13/A, UJ127.11, UJ167.11, UJ223.8, UJ308, J1153, A2B5, 215.D11, 275.G7, 282.1, antineurofilament (NF - med. m.w.), and anti-Thy-1 it is possible to recognize cells of neural crest origin within the postnatal thymic cellular microenvironment. Evidence has been collected concerning such connections between the nervous system and the thymus, such as the production of neuropeptides, oxytocin, and neurophysin by the thymus. Our immunohistochemical study was carried out on quick-frozen sections of human postnatal thymuses removed during open heart surgery, employing an indirect, alkaline phosphatase conjugated streptavidin-biotin technique. The employed MoABs reacted with the subcapsular (outer cortex) thymic nurse cells (TNCs) and with medullary RE cells, in close contact with already mature, immunocompetent T lymphocytes ready to leave the thymic microenvironment and enter the peripheral blood. The thymic medulla's strong immunoreactivity with A2B5, which binds to the GQ ganglioside, is typical for peptide secreting cells often migrated from the neural crest. A2B5+, Thy-1+ IP was demonstrated on the large TNCs. Cortical RE cells showed reactivity with UJ127.11, UJ223.8, and UJ308. Dense expression of neural crest antigens was detected in the Hassall's bodies (HBs) employing MoABs UJ223.8, UJ308, 215.D11, and 275.G7. These results suggest a neural crest origin for TNCs and for 20% to 30% of the cells of thymic microenvironment. The outer (peripheral) part of the HBs contained functionally very active RE cells. These RE cells also expressed antigens characteristic of the neural crest, detectable with MoABs UJ127.11, UJ223.8, UJ308, J1153, 215.D11, 275.G7 and A2B5.

Animals↗
PubMed2005

An oligonucleotide barcode for species identification in Trichoderma and Hypocrea.

One of the biggest obstructions to studies on Trichoderma has been the incorrect and confused application of species names to isolates used in industry, biocontrol of plant pathogens and ecological surveys, thereby making the comparison of results questionable. Here we provide a convenient, on-line method for the quick molecular identification of Hypocrea/Trichoderma at the genus and species levels based on an oligonucleotide barcode: a diagnostic combination of several oligonucleotides (hallmarks) specifically allocated within the internal transcribed spacer 1 and 2 (ITS1 and 2) sequences of the rDNA repeat. The barcode was developed on the basis of 979 sequences of 88 vouchered species which displayed in total 135 ITS1 and 2 haplotypes. Oligonucleotide sequences which are constant in all known ITS1 and 2 of Hypocrea/Trichoderma but different in closely related fungal genera, were used to define genus-specific hallmarks. The library of species-, clade- and genus-specific hallmarks is stored in the MySQL database and integrated in the TrichOKey v. 1.0 - barcode sequence identification program with the web interface located on . TrichOKey v. 1.0 identifies 75 single species, 5 species pairs and 1 species triplet. Verification of the DNA-barcode was done by a blind test on 53 unknown isolates of Trichoderma, collected in Central and South America. The obtained results were in a total agreement with phylogenetic identification based on tef1 (large intron), NCBI BLAST of vouchered records and postum morphological analysis. We conclude that oligonucleotide barcode is a powerful tool for the routine identification of Hypocrea/Trichoderma species and should be useful as a complement to traditional methods.

Base Sequence↗
PubMed2002

Automated high throughput screening for serine kinase inhibitors using a LEADseeker scintillation proximity assay in the 1536-well format.

High-throughput screening in the 1536-well format has been largely restricted to solution-based and cell-based screens. In this article, we show the feasibility of a completely automated, robust scintillation proximity assay in the 1536-well format that is suitable to identify inhibitors for a serine/threonine kinase from a compound library. The introduction of [(33)P]phosphate into a biotinylated peptide substrate mirrors the activity of the kinase. The peptide is immobilized on streptavidin-coated LEADseeker imaging beads and [(33)P]phosphate incorporation is detected with the LEADseeker imaging system of Amersham Pharmacia Biotech. To improve the liquid handling procedures for imaging bead suspensions in the low microliter range, we developed a novel trough with an integrated stirring function. A comparison of the 1536-well assay to a 384-well assay revealed a comparable assay quality with Z' factors of about 0.7 for the 384-well format and 0.6 for the 1536-well format. In an automated screen of a random compound collection, 94.4% of the inhibitory compounds could be identified with both assay formats. Dose-response curves were performed for a selection of identified kinase inhibitors and revealed similar IC(50) values for both assay formats.

Automation↗
PubMed2004

An online learning course in Ergonomics.

For the past two years, the Department of Occupational Therapy at the University of Haifa has offered an online course to third year occupational therapists on the topic of Ergonomics for Health Care Professionals. The development and implementation of this course was funded by the Israeli Ministry of Education. Unique teaching materials, developed and uploaded to the University's server via "High Learn", included interactive and self-directed documents containing graphics, animations, and video clips. Extensive use was made of the discussion forum and survey tools, and students submitted all assignments online. For the final topic, an expert in ergonomics from Boston University delivered a lecture via two-way videoconferencing. The course site included comprehensive library listings in which all bibliographic materials were made available online. Students accessed course materials at the University in a computer classroom and at home via modem. In an accompanying research study, the frequency of student usage of the various online tools was tracked and extensive data were collected via questionnaires documenting students' demographic background, preferred learning style, prior usage of technology, satisfaction with the course and academic achievement. This paper focuses on the results of the research study that examined how the students responded to and coped with teaching material presented and accessed in this format.

Adult↗
PubMed1996

An object-oriented class library for medical software development.

The objective of this research is the development of a Medical Object Library (MOL) consisting of reusable, inheritable, portable, extendable C++ classes that facilitate rapid development of medical software at reduced cost and increased functionality. The result of this research is a library of class objects that range in function from string and hierarchical file handling entities to high level, procedural agents that perform increasingly complex, integrated tasks. A system built upon these classes is compatible with any other system similarly constructed with respect to data definitions, semantics, data organization and storage. As new objects are built, they can be added to the class library for subsequent use. The MOL is a toolkit of software objects intended to support a common file access methodology, a unified medical record structure, consistent message processing, standard graphical display facilities and uniform data collection procedures. This work emphasizes the relationship that potentially exists between the structure of a hierarchical medical record and procedural language components by means of a hierarchical class library and tree structured file access facility. In doing so, it attempts to establish interest in and demonstrate the practicality of the hierarchical medical record model in the modern context of object oriented programming.

Humans↗
PubMed2005

Drosophila genome-scale screen for PAN GU kinase substrates identifies Mat89Bb as a cell cycle regulator.

Although traditional organism-based mutational analysis is powerful in identifying genes involved in specific biological processes, limitations include incomplete coverage and time required for gene identification. Biochemical screens using cell transfection or yeast two-hybrid methods are rapid, but they are limited by cDNA library quality. The recent establishment of "uni-gene sets" has made it feasible to biochemically screen an organism's entire genome. Radiolabeled protein pools prepared from the Drosophila Gene Collection were used in a Drosophila in vitro expression cloning ("DIVEC") screen for substrates of PAN GU kinase, which is crucial for S-M embryonic cell cycles. Ablation of one identified substrate, Mat89Bb, by RNAi produces a polyploid phenotype similar to that of pan gu mutants. Xenopus embryos injected with Mat89Bb morpholinos arrest with polyploid nuclei, and Mat89Bb RNAi in HeLa cells gives rise to multinucleated cells. Thus, Mat89Bb plays an evolutionarily conserved role as a crucial regulator of both cell cycle and development.

Animals↗
PubMed2006

Establishment of the platform for reverse chemical genetics targeting novel protein-protein interactions.

In the "drug discovery" era, protein-protein interaction modules are becoming the most exciting group of targets for study. Although combinatorial libraries and active natural products are rapidly and systemically being equipped by both for-profit and not-for-profit organizations, complete drug-screening systems have not been achieved. There is a growing need for the establishment of drug discovery assays for highly effective utilization of the collected small molecules on a large scale. To generate drug-screening systems, we plan to identify novel protein-protein interactions that may participate in human diseases. The interactions have been identified by MS/MS analysis following immunoprecipitation using antibodies prepared from our cDNA projects. The intracellular pathway involving the identified interaction is computationally constructed, which then clarifies its relationship to the candidate disease. The development of reverse chemical genetics based on such information should help us to realize a significant increment in the number of drug discovery assays available for use. In this article, I describe our strategy for drug discovery and then introduce the applicability of fluorescence intensity distribution analysis (FIDA) and the expression-ready constructs called "ORF trap clones" to reverse chemical genetics.

Antibodies↗
PubMed2005

Novel microbial diversity adherent to plant biomass in the herbivore gastrointestinal tract, as revealed by ribosomal intergenic spacer analysis and rrs gene sequencing.

It is well recognized that a dynamic biofilm develops upon plant biomass in the herbivore gastrointestinal tract, but this component of the microbiome has not previously been specifically sampled, or directly compared with the biodiversity present in the planktonic fraction of digesta. In this study, the digesta collected from four sheep fed two different diets was separated into three fractions: the planktonic phase, and the microbial populations either weakly or tightly adherent to plant biomass. The community DNA prepared from each fraction was then subjected to both ribosomal intergenic spacer analysis (RISA) and denaturing gradient gel electrophoresis (DGGE). Both types of analysis showed that dietary factors influence community structure, and that the adherent fractions produced more complex profiles. The RIS-clone libraries prepared from the planktonic and adherent populations were then subjected to restriction fragment length polymorphism (RFLP) and DNA sequence analyses, which resulted in a far greater degree of discrimination among the fractions. Although many of the sequenced clones from the adherent populations were assigned to various clusters within the low G+C Gram-positive bacteria, the clone libraries from animals consuming an all-grass diet were largely comprised of novel lineages of Clostridium, while in animals consuming the starch-containing diet, Selenomonas and Ruminococcus spp. were the dominant low G+C Gram-positive bacteria. Additionally, the libraries from hay-fed animals also contained clones most similar to asaccharolytic Clostridia, and other Gram-positive bacteria that specialize in the transformation of plant phenolic compounds and the formation of cinnamic, phenylacetic and phenylpropionic acids. These results reveal, for the first time, the phylogeny of adherent subpopulations that specialize in the transformation of plant lignins and other secondary compounds, which potentiate polysaccharide hydrolysis by other members of the biofilm.

Animals↗
PubMed2002

Heuristic haptic texture for surgical simulations.

Generation of credible force feedback renderings adds the sense of touch crucial for the development of a realistic virtual surgical environment. However, a number of difficulties must be overcome before this can be achieved. One of the problems is the paucity of data on the in-vivo tissue compliance properties needed to generate acceptable output forces. Without this "haptic texture," the sense of touch component remains relatively primitive and unrealistic. Current research in the quantitative analysis of biomechanics of living tissue, including collection of in-vivo tissue compliance data using specialized sensors, has made tremendous progress. However, integration of all facets of biomechanical data in order to transfer them into haptic texture remains a very difficult problem. For this reason, we are attempting to create a library of heuristic haptic textures of anatomical structures. The library of heuristic haptic textures will capture the expert's sense of feel for selected anatomical structures and will be used to convey the sense of touch for surgical training simulations. Once the techniques for converting biomechanical data into haptic texture become more robust, this library can be used as a benchmark to verify theoretical computational models used for generating output forces in haptic devices.

Biomechanical Phenomena↗
PubMed2006

Broad issues to consider for library involvement in bioinformatics.

BACKGROUND: The information landscape in biological and medical research has grown far beyond literature to include a wide variety of databases generated by research fields such as molecular biology and genomics. The traditional role of libraries to collect, organize, and provide access to information can expand naturally to encompass these new data domains. METHODS: This paper discusses the current and potential role of libraries in bioinformatics using empirical evidence and experience from eleven years of work in user services at the National Center for Biotechnology Information. FINDINGS: Medical and science libraries over the last decade have begun to establish educational and support programs to address the challenges users face in the effective and efficient use of a plethora of molecular biology databases and retrieval and analysis tools. As more libraries begin to establish a role in this area, the issues they face include assessment of user needs and skills, identification of existing services, development of plans for new services, recruitment and training of specialized staff, and establishment of collaborations with bioinformatics centers at their institutions. CONCLUSIONS: Increasing library involvement in bioinformatics can help address information needs of a broad range of students, researchers, and clinicians and ultimately help realize the power of bioinformatics resources in making new biological discoveries.

Computational Biology↗
PubMed2000

Nasal continuous positive airways pressure immediately after extubation for preventing morbidity in preterm infants.

BACKGROUND: Preterm infants being extubated following a period of intermittent positive pressure ventilation via an endotracheal tube are at risk of developing respiratory failure as a result of apnea, respiratory acidosis and hypoxia. Nasal continuous positive airway pressure appears to stabilise the upper airway, improve lung function and reduce apnea and may therefore have a role in facilitating extubation in this population. OBJECTIVES: In preterm infants having their endotracheal tube removed following a period of intermittent positive pressure ventilation (IPPV), does management with nasal continuous positive airways pressure (NCPAP) lead to an increased proportion remaining free of additional ventilatory support, compared to extubation directly to headbox oxygen? SEARCH STRATEGY: Searches were made of the Oxford Database of Perinatal Trials, Medline, previous reviews including cross references, abstracts of conferences and symposia proceedings, expert informants, journal handsearching mainly in the English language and expert informant searches in the Japanese language by Prof. Ogawa. SELECTION CRITERIA: All trials utilising random or quasi-random patient allocation, in which NCPAP (delivered by any method) was compared with headbox oxygen for post-extubation care were included. Methodological quality was assessed independently by the two authors. DATA COLLECTION AND ANALYSIS: Data were extracted independently by the two authors. Prespecified subgroup analysis to determine the impact of different levels of NCPAP, differences in duration of IPPV and use of aminophylline were also performed using the same package. MAIN RESULTS: Nasal CPAP, when applied to preterm infants being extubated following IPPV, reduces the incidence of adverse clinical events (apnea, respiratory acidosis and increased oxygen requirements) indicating the need for additional ventilatory support. A reduction in the incidence of chronic lung disease at 28 days of age is also seen in the group extubated to NCPAP. REVIEWER'S CONCLUSIONS IMPLICATIONS FOR PRACTICE: nasal CPAP is effective in preventing failure of extubation and reducing oxygen use at 28 days of life in preterm infants following a period of endotracheal intubation and IPPV. Implication for research: further definition of the patient gestational age and weight groups in whom these results apply is required. Optimal levels of NCPAP as well as methods of administration remain to be determined.

Humans↗
PubMed2000

Crisis intervention for people with severe mental illnesses.

BACKGROUND: A particularly difficult challenge for treatment of people with serious mental illnesses in the community is the delivery of an acceptable level of care during the acute phases of severe mental illness. Crisis intervention models of care were developed as a possible solution to this problem. OBJECTIVES: To review the effects of a crisis intervention model for anyone with serious mental illness experiencing an acute episode, compared to 'standard care'. SEARCH STRATEGY: Relevant randomised trials were identified by searching Biological Abstracts (1985-1998), CINAHL (1982-1998), The Cochrane Library, the Cochrane Schizophrenia Group's Register of trials, EMBASE (1980-1998), MEDLINE (1966-1998), PsycLIT (1974-1998), sociofile (1974-1998) and the ISI database (Science Citations and Social Science Citations). Further references were sought from published trials and their authors. SELECTION CRITERIA: All randomised controlled trials of crisis intervention models (however defined) versus standard care for people with severe mental illnesses (however diagnosed). DATA COLLECTION AND ANALYSIS: Reviewers evaluated data independently and analysed on an intention-to-treat basis. Reviewers assumed that people who left the study early or were lost to follow-up had no improvement. Where possible and appropriate odds ratios (OR) and their 95% confidence intervals (CI) were calculated. The number needed to treat (NNT) was estimated. For continuous data Weighted Mean Differences (WMD) were calculated. Data were inspected for heterogeneity. MAIN RESULTS: None of the five included studies investigated 'crisis intervention' in a pure form. They all used a form of home care for acutely ill people, which included elements of crisis intervention. Despite its ethos, 45% of the home care group were unable to avoid hospital admission during their treatment period. Home care, however, was slightly superior in avoiding repeat admissions (OR 0.63 CI 0.42 - 0. 94), although this result is not robust due to significant heterogeneity. Other results suggest home care reduces loss to follow-up at six and 12 months (OR 0.62, CI 0.42-0.91, NNT 12, CI 6-53; OR 0.65, CI 0.44-0.96, NNT 13, CI 7-130 respectively), reduces family burden (OR 0.20, CI 0.10-0.42, NNT 3, CI 1-5), and is a more satisfactory form of care for both patients and families. No differences in loss, death or mental state were found suggesting home care is as effective as hospital care for these outcomes. All studies found home care to be more cost effective than hospital care but all data were either skewed or unusable. No data on staff satisfaction, carer input, compliance with medication and number of relapses were available. REVIEWER'S CONCLUSIONS: It is difficult to draw any robust conclusions from the data presented in this review. It is also difficult to comment on the effectiveness of crisis intervention in its pure form (i.e. specific results for the acute phase of mental illness only). Overall the review suggests that home care crisis treatment, coupled with an ongoing home care package, is a viable and acceptable way of treating people with serious mental illnesses. Other reviews of more clinically effective home care packages have had similar but more robust results and this review can give tentative support to their findings ( approximately approximately Marshall 1999 approximately approximately ). However, if a pure form of crisis intervention policy is to be specifically practised or implemented it would be hard to justify this outside of a simple well-designed trial. The reviewers also suggest that issues such as staff satisfaction and burnout would be important outcomes to consider in future research.

Crisis Intervention↗