SEARCH · Search PubMed
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Bibliographic control of audiovisuals or nonprint materials, generated at the point of publication, is almost nonexistent. The authors address this problem and present an outline of bibliographic elements that nonprint producers need to include on each individual production.
Lignite biosolubilization offers a mild route for valorizing low-rank coal, although the microbial processes that accompany solubilization remain incompletely defined. Here, an endogenous isolate designated Lysinibacillus sphaericus strain SH19 was evaluated using nitric-acid-pretreated Shengli lignite. Under the selected working conditions (4 M nitric-acid pretreatment, initial pH 8, 40°C, and 16 days), the apparent solubilization rate reached 66.81%. Changes in A450, residual solid mass, culture pH, and extracellular protein concentration showed that chemical pretreatment and bacterial culture were both associated with the release of soluble lignite-derived material. SDS-PAGE and two-dimensional electrophoresis revealed treatment-associated differences in extracellular and intracellular protein patterns. LC-MS/MS analysis of excised protein spots yielded 85 candidate protein assignments; the revised supplementary table reports PEAKS scores, sequence coverage, peak area, and unique-peptide counts and highlights the limited support for several entries. GC-MS analysis produced 33 tentative library assignments in the solubilized fraction, but siloxane- and silyl-related signals were treated as possible analytical background, and no pathway was inferred from these assignments alone. Together, the data identify strain SH19 as a promising lignite-biosolubilizing isolate and provide candidate proteins and product signals for future validation. The proposed process model remains exploratory because direct enzyme assays, inhibitor experiments, carbon-balance measurements, transcriptomic or genetic validation, complete GC-MS blank subtraction, and authentic-standard confirmation were not available.
RNA-binding proteins (RBPs) are critical regulators of gene expression and RNA processing. Identification of their binding sites has important implications for their physiological and disease-related functions. Crosslinking and immunoprecipitation, followed by sequencing (CLIP-seq) and its derivatives, are the most commonly used methods to identify RBP binding sites, but are laborious and require a large amount of starting material. Recent advancements harnessing RNA deaminases in fusion to any RBP of interest, allow for the profiling of RBP binding sites from low-input samples in simpler procedures. Among these efforts, we developed STAMP (Surveying Targets by APOBEC-Mediated Profiling), which efficiently detects RBP-RNA interactions. This chapter describes the detailed protocol for the STAMP method, including plasmid construction, delivery and sorting, library preparation and bioinformatic data analysis.
OBJECTIVES: Surfactant proteins A (SP-A) and D are collectins that play key roles in innate immune defense of the lung. Recent studies suggest that these proteins have a direct effect on the growth and viability of Gram-negative bacteria, Mycoplasma pneumoniae and Histoplasma capsulatum. METHODOLOGY: The researchers examined membrane permeabilization by BAL fluid of mice that were sufficient or deficient in surfactant proteins, of rough and smooth LPS-containing membranes, and of genetically altered bacteria. The permeability assay is based on the ability of agents to promote access of impermeable dyes propidium iodide and ELF97 to intracellular targets. RESULTS: The permeabilizing activity of concentrated BAL material from SP-A+/+ mice was substantially greater than that from SP-A-/- animals, and was sensitive to hyperoxic exposure. Oxidation of the collectins in vitro also blocked their antimicrobial effects. Rough but not smooth LPS conferred susceptibility of model bacterial membranes to permeabilization by the collectins. The screening of genetically engineered SP-A mice with a Pseudomonas aeruginosa signature tagged mutagenesis library has revealed several pathways which are required for resistance to the permeabilizing effects of SP-A, including those required for salicylate biosynthesis and flagellar function. CONCLUSION: The researchers conclude that the pulmonary collectins directly permeabilize bacteria in an LPS-dependent and rough LPS-specific manner. Oxidative damage blocks the permeabilizing activity of alveolar lining fluid and purified proteins. The mechanism(s) of permeabilization is not known, but the crystal structure of SP-A reveals a hydrophobic cleft lined by charged residues which may play a role in membrane perturbation.
A rapid method for the extraction and purification of DNA from environmental samples for molecular cloning applications was developed. The indigenous cells from plant debris, organic materials, sediments, and soils were lysed directly by using DAS-IZ solution and the nucleic acids were precipitated with isopropanol. A simple purification step using DAS-IIZ solution without binding matrix produced highly pure, colorless and undegraded DNA with molecular weight of more than 20 kb. The superiority of this method was tested for wide applications in molecular cloning, i.e., construction of genomic library by using Lambda DASHII Vector and GigapackIII XL, plasmid library, cloning of gene encoding protease, and molecular microbial diversity analysis. An additional advantage of this method is that only 0.1 g of sample is required, if analysis of many samples in short time should be done. To extract large amounts of environmental DNA for molecular cloning lasts only 30 min and to purify it less than 1 h.
OBJECTIVE: Maintaining high standards in a large CT imaging department with multiple scanners, a large technical and clerical staff, and a rotating staff of radiologists is an ongoing challenge. We undertook a project to design and implement a simple, rapidly performed computer-assisted system of quality assurance (QA) for use in abdominal CT. In our project, we also analyzed the results of that QA system. MATERIALS AND METHODS: We graded 1810 abdominal CT studies done in a 50-week period, using a three-point scale to indicate the quality of the following five parameters of technical quality: IV contrast enhancement, oral contrast opacification, window settings and artifacts, conformity to radiologists' protocol, and completeness and accuracy of header and scout data. In addition, a parameter reflecting performance of the film library and clerical staff was similarly graded. To provide a measure of peer review for radiologists, any disagreements with prior CT study reports were recorded when comparison studies were reviewed in the process of CT interpretation. A commercially available spreadsheet and database software program was tailored to allow rapid, easily performed data entry and analysis. Tables and graphs showing performance of technologists and film library and clerical staff were generated. This customized program was made available on the radiology department computer network. Results generated by the program were further analyzed with linear regression models. RESULTS: Our QA system was successfully integrated into the routine operation of the abdominal CT division. During the first 11.5 months of operation, the system reflected improvement in each of the technical parameters with a statistically significant improvement in the combined average technical score (from 1.15 to 1.68 on a scale of 0-2; p < .0001). The "Throughout Speed/Old Exams" parameter for performance of the film library and clerical staff, which was analyzed separately from the technical parameters, also improved significantly (from 1.3 to 1.8; p < .02). Improvements were statistically significant, even when we controlled for potential variations in quality among different CT scanners and variations among the radiologists who rated the quality of the examination. Thirty-eight disagreements with previous scan interpretations (5% of all scan comparisons) were recorded for evaluation at peer review conferences. CONCLUSION: The ability to monitor performance continuously using a rapid, computer-assisted system has effected measurable improvement in our CT service. Technologist and film library and clerical staff performance improved for all parameters studied. Deficiencies were revealed and trends demonstrated. The QA system allowed us to identify disagreements in interpretation of CT examinations for subsequent peer review by radiologists. Our QA software program has been made available on the Internet as freeware to licensed Excel users via anonymous file transfer protocol at Internet Protocol 134.192.6.110.
Fraud is a dramatic offense in scientific publishing but other offenses are more frequent and probably far more damaging. The most frequent lesser offenses are irresponsible authorship and wasteful publication. The authorship problems include listing of "authors" who made little or no contribution to the work reported and omitting of persons who made major contributions. Wasteful publication includes dividing the results in a single study into two or more papers ("salami science"); republishing the same material in successive papers (which need not have identical format and content); and blending data from one study with additional data to extract yet another paper that could not make its way on the second set of data alone ("meat extenders"). Wasteful publication may be the most frequent of these offenses and is probably the most damaging because of its economic implications for publishers, readers, libraries, and indexes.
BACKGROUND: Fracture of the distal radius is a common clinical problem particularly in elderly white women with osteoporosis, in whom the lifetime risk of this injury has been estimated as 15 per cent. OBJECTIVES: To determine the most appropriate conservative treatment for fractures (such as Colles') of the distal radius in adults. SEARCH STRATEGY: We searched the Cochrane Musculoskeletal Injuries Group trials register, Medline and reference lists of trials. Date of the most recent search: April 1998. SELECTION CRITERIA: Randomised or quasi-randomised clinical trials involving skeletally mature patients with a fracture of the distal radius, which compared commonly applied conservative interventions for fracture fixation. These included the application of an external support (plaster cast or brace) and fracture manipulation. DATA COLLECTION AND ANALYSIS: All trials, judged as fitting the selection criteria by both reviewers, were independently assessed by both reviewers for methodological quality. Data were extracted for anatomical, functional and clinical, including complications, outcomes. The trials were grouped into categories relating to cast position, extent and duration of immobilisation, use of braces, cast material and fracture manipulation. Although quantitative data from some trials are presented, the lack of good quality trials and trial heterogeneity inhibited pooling of results. MAIN RESULTS: Over 50 randomised trials comparing treatment options for distal radial fractures were identified. Twenty nine trials of these, involving a total of 3199 mainly female and older patients, met the inclusion criteria for this review. Comprehensive details of the individual trials are provided in tabular form, and their results, grouped as indicated above, have been presented in text and analyses tables. The poor quality and heterogeneity in terms of patient characteristics, interventions compared and outcome measurement, of the included trials meant that no meta-analyses were undertaken. REVIEWER'S CONCLUSIONS: There is insufficient evidence from randomised trials to determine which methods of conservative treatment are the most appropriate for the more common types of distal radial fractures in adults. Therefore, at present, practitioners applying conservative management should use an accepted technique with which they are familiar, and which is cost-effective from the perspective of their provider unit. Whilst tempting, any call for further research to clarify the most appropriate conservative treatment for this common fracture must be resisted for now. Instead it is important to reflect on the issues raised in this review, to ascertain patient preferences, prioritise researchable questions and undertake a systematic programme of research after agreeing a core data set for classification of fractures and outcomes.
Neutron cross sections for nonelastic and elastic reactions on a range of elements have been evaluated for incident energies up to 150 MeV. These cross sections agree well with experimental cross section data for charged-particle production as well as neutron and photon production. Therefore they can be used to determine kerma coefficients for calculations of energy deposition by neutrons in matter. Methods used to evaluate the neutron cross sections above 20 MeV, using nuclear model calculations and experimental data, are described. Below 20 MeV, the evaluated cross sections from the ENDF/B-VI library are adopted. Comparisons are shown between the evaluated charged-particle production cross sections and measured data. Kerma coefficients are derived from the neutron cross sections, for major isotopes of H, C, N, O, Al, Si, P, Ca, Fe, Cu, W, Pb, and for ICRU-muscle, A-150 tissue-equivalent plastic, and other compounds important for treatment planning and dosimetry. Numerous comparisons are made between our kerma coefficients and experimental kerma coefficient data, to validate our results, and agreement is found to be good. An important quantity in neutron dosimetry is the kerma coefficient ratio of ICRU-muscle to A-150 plastic. When this ratio is calculated from our kerma coefficient data, and averaged over the neutron energy spectra for higher-energy clinical therapy beams [three p (68) + Be beams, and a d (48.5) + Be beam], a value of 0.94 +/- 0.03 is obtained. Kerma ratios for water to A-150 plastic, and carbon to oxygen, are also compared with measurements where available.
A comprehensive analysis of the differences between the genomes of two closely related bacterial strains should give insight into the molecular basis of their individual phenotypic and genotypic characteristics. Here we present an integrative approach including two different strategies for the thorough investigation of genomic divergence. We have combined two techniques including genomic subtractive hybridization and comparative genome mapping by pulsed field gel electrophoresis (PFGE) techniques. The subtractive method for which a protocol is given herein results in the production of a library of specific DNA sequence tags present only in one strain, while the construction of macrorestriction maps of the bacterial chromosomes yields data about the overall genome organization and the arrangement and distance of gene loci. Comparison of the physical and genetic maps and determination of the map positions of the strain-specific DNA sequences reveals gross chromosomal modifications, insertions or deletions of additional genetic material, and transpositional events. The further investigation of the strain-specific regions yields information about the nature and origin of the acquired DNA and their influence on the evolution of the individual bacterial genome. The two methods were applied to differential genome analysis of clonal divergence in Pseudomonas aeruginosa choosing two clone C isolates from diverse habitats.
The interaction of an external effector, ZnII ions, with a constitutional dynamic library of fluorescent polyiminofluorenes leads to component exchange, which generates an entity responding by a change in emission to the effector that has induced its formation. The overall coupled system displays a tuning of optical signal, resulting from two synergistic processes: adaptative constitutional reorganization and self-sensing. In broader terms, this work highlights the perspectives opened by constitutional dynamic chemistry toward the design of smart materials, capable of expressing different latent properties in response to environmental conditions.
We introduce a novel method of inorganic synthesis using the catalytic and structure-directing properties of the demosponge enzyme silicatein-alpha. Recombinant silicatein-alpha was displayed at the surface of Escherichia coli cells by fusion to outer membrane protein A and used to biocatalytically direct the formation of layered and amorphous titanium phosphates from a small water-soluble precursor at near-neutral pH at 16 degrees C. Synthesis of titanium phosphates, with potential applications in catalysis and separation technology, previously has required prolonged reactions with phosphoric acid at elevated temperatures. Additionally, we use library screening to isolate a 15-mer with affinity toward the silicatein active site (Kd ca. 50 nM) and introduce this new approach to demonstrate the success of our display strategy. Considering our previous findings with native silicatein filaments, we suggest that this scalable, efficient, cell-based system may have a broad utility for the synthesis of a range of structured metallophosphates and other inorganic materials.
In this brief essay we argue that the best efforts of archivists, scholars, and practitioners within the National Health Service have not prevented the wholesale destruction of the bulk of patient records created during the twentieth century. This is a matter of vital concern not merely for historians of modern medicine. Important clinical work has frequently been undertaken on materials which have survived, usually by chance or by the foresight of physicians, matrons, and administrators. Even the significant fragments of historical documents which remain in the hands of the health authorities have been threatened by the continuing drive to reduce storage and maintenance costs within hospitals. Archivists and academics have struggled to address the problems of sampling, storage, and access which the enormous bulk of modern records present. In this essay we suggest that the first step must be to raise awareness amongst professionals and the public of the extent to which any future history of the medical services and of patient care will depend on a reasonable rate of survival of these records. The second step must be to confront the problem of resources and the inevitable task of selection which must form the foundations of any long-term policy of preservation. An initial survey of archival materials in Devon indicates that the records of community health care form a substantial and potentially invaluable research source for future historians, though their relevance has rarely been recognized within the academic community.
BACKGROUND: The interaction of T cell receptors (TCRs) with peptide fragments bound to major histocompatibility complex (MHC) molecules is central to the initiation and propagation of most immune responses. In order to understand and control the molecular interactions underlying T cell recognition of MHC/peptide complexes, recent efforts have focused on the production of recombinant soluble forms of the TCR heterodimer. METHODS: TCRA variable (TCRAV) and TCRBV sequences used by human T cell clones were amplified by PCR, cloned and sequenced. The deduced amino acid sequences of the complementarity determining region (CDR) 3 loops of TCRs specific for the same allergenic epitope were compared. V region genes of a selected TCR were expressed as a single-chain (sc) molecule in the periplasm of Escherichia coli. RESULTS: Conserved amino acid motifs specific for allergenic peptides of Bet v 1 and Phl p 1 were identified in CDR3 sequences of TCRs. A recombinant scTCR was produced. The ratio of insoluble to soluble material was 1:1. The recombinant protein was of the correct size and showed no signs of degradation. CONCLUSIONS: Conservation of amino acid motifs in CDR3 loops of TCRs specific for the same allergen fragments indicated that the three-dimensional structure of the CDR3 was determined by the presented peptide. The recombinant scTCR will be used to identify ligands for the CDR3s from random peptide libraries to interfere with TCR binding to the MHC/peptide complex.
BACKGROUND: Serial analysis of gene expression using small amounts of starting material (microSAGE) has not yet been conclusively shown to be representative, reproducible or accurate. RESULTS: We show that microSAGE is highly representative, reproducible and accurate, but that pronounced differences in gene expression are seen between tissue samples taken from different individuals. CONCLUSIONS: MicroSAGE is a reliable method of comprehensively profiling differences in gene expression among samples, but care should be taken in generalizing results obtained from libraries constructed from tissue obtained from different individuals and/or processed or stored differently.
This article discusses how to transform material worthy of dissemination into a form that leads to successful publication. It focuses on publication of systematic and literature reviews, empirical studies and conceptual analyses undertaken as part of a course of academic study. An increasing number of nurses and midwives are undertaking healthcare-related courses at BSc, MSc, MPhil and PhD level. Many of their theses are ultimately left to gather dust on library shelves, and are only read by examiners. The authors have worked with many novice writers whose attempts to write up their theses have been unsuccessful for a number of reasons. These are explored in this article. Suggestions for avoiding the many pitfalls that can prevent publication are offered.
Growing consumer interest in health-related information has created a need for professionals to manage, provide, and interpret such material. In preparing for the new demands of the market, HIM professionals can learn from the example of medical librarians, who are already working to meet those needs.
'Tsuda' turnip (Brassica campestris L. ssp. rapa), in which roots anthocyanin pigmentation is light-sensitive, was used as the material. 'Tsuda' plants were held in darkness or irradiated with sun light and constant light for different time. Anthocyanins in root peel of 'Tsuda' turnip exposed to constant light were identified and quantified with a UV-visual spectrophotometer. The results demonstrated that the anthocyanins accumulation in 'Tsuda' was related with light-exposure time (Fig.1 and Table 1). Fragments of genes selected from the subtraction library of 'Tsuda' turnip involved in anthocyanin biosynthesis were used as probes. The Northern blotting results showed that the expression of PAL, CHS, F3H, DFR and ANS could be induced by irradiation with light and the expression of these genes was related with light exposure time. The expression of MYB was basically the same whether in darkness or in light (Figs.2,3).