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Database Search (database + search)
Kinds of Database Search Selected AbstractsEvaluation of DNA Mixtures from Database SearchBIOMETRICS, Issue 1 2010Yuk-Ka Chung Summary With the aim of bridging the gap between DNA mixture analysis and DNA database search, a novel approach is proposed to evaluate the forensic evidence of DNA mixtures when the suspect is identified by the search of a database of DNA profiles. General formulae are developed for the calculation of the likelihood ratio for a two-person mixture under general situations including multiple matches and imperfect evidence. The influence of the prior probabilities on the weight of evidence under the scenario of multiple matches is demonstrated by a numerical example based on Hong Kong data. Our approach is shown to be capable of presenting the forensic evidence of DNA mixtures in a comprehensive way when the suspect is identified through database search. [source] Nursing diagnoses, interventions and outcomes , application and impact on nursing practice: systematic reviewJOURNAL OF ADVANCED NURSING, Issue 5 2006Maria Müller-Staub Head of Pflege PBS EdN MNS RN Aim., This paper reports a systematic review on the outcomes of nursing diagnostics. Specifically, it examines effects on documentation of assessment quality; frequency, accuracy and completeness of nursing diagnoses; and on coherence between nursing diagnoses, interventions and outcomes. Background., Escalating healthcare costs demand the measurement of nursing's contribution to care. Use of standardized terminologies facilitates this measurement. Although several studies have evaluated nursing diagnosis documentation and their relationship with interventions and outcomes, a systematic review has not been carried out. Method., A Medline, CINAHL, and Cochrane Database search (1982,2004) was conducted and enhanced by the addition of primary source and conference proceeding articles. Inclusion criteria were established and applied. Thirty-six articles were selected and subjected to thematic content analysis; each study was then assessed, and a level of evidence and grades of recommendations assigned. Findings., Nursing diagnosis use improved the quality of documented patient assessments (n = 14 studies), identification of commonly occurring diagnoses within similar settings (n = 10), and coherence among nursing diagnoses, interventions, and outcomes (n = 8). Four studies employed a continuing education intervention and found statistically significant improvements in the documentation of diagnoses, interventions and outcomes. However, limitations in diagnostic accuracy, reporting of signs/symptoms, and aetiology were also reported (14 studies). One meta-analysis of eight trials including 1497 patients showed no evidence that standardized electronic documentation of nursing diagnosis and related interventions led to better nursing outcomes. Conclusion., Despite variable results, the trend indicated that nursing diagnostics improved assessment documentation, the quality of interventions reported, and outcomes attained. The study reveals deficits in reporting of signs/symptoms and aetiology. Consequently, staff educational measures to enhance diagnostic accuracy are recommended. The relationships among diagnoses, interventions and outcomes require further evaluation. Studies are needed to determine the relationship between the quality of documentation and practice. [source] Experiences and concerns about ,returning to work' for women breast cancer survivors: a literature reviewPSYCHO-ONCOLOGY, Issue 7 2010Corine Tiedtke Abstract Objective: To explore how female breast cancer patients experience work incapacity during the treatment and return-to-work phases and how interactions between patients and stakeholders affect this experience. Method: Database search for full text articles published between January 1995 and January 2008 that focused on employed female breast cancer patients, factors related to work incapacity, and returning to work. Only results based on self-report data were included. Studies focusing on treatment, financial factors, rate of return, or absence were excluded. Results: Six articles met the inclusion criteria. Women with breast cancer receive varied reactions but little advice about returning to work. Women were primarily concerned with disclosing the diagnosis to their employer and to relatives. Uncertainties about physical appearance, ability to work, and possible job loss affected the women's decisions about working during the treatment phase. After treatment, most women wanted to regain their ,normal life', but concentration and arm or fatigue problems potentially interfered. Although supportive work environments were helpful, the individual needs of women differed. Employers and employees need to find a balance in defining accommodating work. Many women received favourable support, but some reported feeling discriminated against. Many women re-evaluated the role of work in their lives after being confronted with breast cancer. Conclusion: Work adjustments could help women to keep their jobs during illness and recovery. To resolve women's concerns about returning to work, employers, physicians, and insurance institutions should consider increasing and improving communication with breast cancer patients and playing a more active and supportive role. Copyright © 2009 John Wiley & Sons, Ltd. [source] A novel gene, MDS2, is fused to ETV6/TEL in a t(1;12)(p36.1;p13) in a patient with myelodysplastic syndromeGENES, CHROMOSOMES AND CANCER, Issue 1 2002María D. Odero ETV6/TEL is the first transcription factor identified that is specifically required for hematopoiesis within the bone marrow. This gene has been found to have multiple fusion partners of which 16 have been cloned. Fluorescence in situ hybridization (FISH) analysis in a patient with myelodysplastic syndrome (MDS) revealed a t(1;12)(p36;p13) involving ETV6, with the breakpoint in this gene between exon 2 and exon 3. We report here the cloning of a novel ETV6 partner located on 1p36.1, involved in the t(1;12). 3, RACE-PCR from RNA identified a novel sequence fused to exon 2 of ETV6. Database searches localized this sequence in a bacterial artificial chromosome (BAC) mapped to 1p36 by fingerprint analysis. This result was confirmed by FISH using this BAC as probe. 5, and 3, RACE experiments with primers from this novel sequence were carried out on RNA from a healthy donor and identified a novel full-length mRNA, which we named MDS2 (myelodysplastic syndrome 2). RT-PCR experiments were performed on a panel of human cDNAs to analyze the expression pattern of this gene and they revealed four splicing variants. RT-PCR analysis showed that ETV6-MDS2, but not the reciprocal MDS2-ETV6 fusion transcript, was expressed in the bone marrow of the patient. The product of the ETV6-MDS2 fusion transcript predicts a short ETV6 protein containing the first 54 amino acids of ETV6 plus four novel amino acids, lacking both the PTN and the DNA-binding domains. Possible mechanisms to account for the development of MDS in this patient are discussed. © 2002 Wiley-Liss, Inc. [source] Induced and repressed genes after irradiation sensitizing by pentoxyphylline,INTERNATIONAL JOURNAL OF CANCER, Issue 6 2007Waldemar Waldeck Abstract Aim in cancer therapy is to increase the therapeutic ratio eliminating the disease while minimizing toxicity to normal tissues. Radiation therapy is a main component in targeting cancer. Radiosensitizing agents like pentoxyphylline (PTX) have been evaluated to improve radiotherapy. Commonly, cells respond to radiation by the activation of specific early and late response genes as well as by inhibition of genes, which are expressed under normal conditions. A display of the genetic distinctions at the level of transcription is given here to characterize the molecular events underlying the radiosensitizing mechanisms. The method of suppression subtractive hybridization allows the visualization of both induced and repressed genes in irradiated cells compared with cells sensitized immediately after irradiation. The genes were isolated by cDNA-cloning, differential analysis and sequence similarity search. Genes involved in protein synthesis, metabolism, proteolysis and transcriptional regulation were detected. It is important that genes like KIAA280, which were only known as unidentified EST sequences before without function, but inaccessible by array technology were recovered as functional genes. Database searches for PTX-induced genes detected a human mRNA completely unknown. In case of suppressed genes, we detected several mRNAs; one thereof shows homology to a hypothetical protein possibly involved in signal transduction. A further mRNA encodes the protein BM036 supposed to associate with the E2F transcription factor. A hypothetical protein H41 was detected, which may repress the Her-2/neu receptor influencing breast cancer, gliomas and prostate tumors. Radiation combined with PTX may lead to a better prognosis by down regulation of the Her-2/neu, which will be proven by clinical studies in the near future. © 2006 Wiley-Liss, Inc. [source] Two inducible, functional cyclooxygenase-2 genes are present in the rainbow trout genomeJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 6 2007Tomo-o Ishikawa Abstract The cyclooxygenases (Cox) catalyze the initial reactions in prostanoid biosynthesis, and produce the common prostanoids precursor, PGH2. Mammalian species have two Cox isoforms; constitutively expressed cyclooxygenase-1 (Cox-1) and inducible cyclooxygenase-2 (Cox-2). Database searches suggest three Cox genes are present in many fish species. In this study, we cloned and characterized a second Cox-2 cDNA, Cox-2b, from the rainbow trout. Rainbow trout Cox-2b protein contains all the functionally important conserved amino acids for Cox enzyme activity. Moreover, the Cox-2b message contains AU-rich elements (AREs) in the 3, untranslated region (3,UTR) characteristic of inducible Cox-2 mRNAs. We took advantage of the existence of a rainbow trout cell line to demonstrate that expression from both the originally reported Cox-2 (Cox-2a) and Cox-2b genes is inducible. However, differential induction responses to alternative inducers are observed for rainbow trout Cox-2a and Cox-2b. Both Cox-2a and Cox-2b proteins expressed in COS cells are enzymatically active. Thus the rainbow trout has two functional, inducible Cox-2 genes. The zebrafish also contains two Cox-2 genes. However, genome structure analysis suggests diversion of the Cox-2a gene between zebrafish and rainbow trout. J. Cell. Biochem. 102: 1486,1492, 2007. © 2007 Wiley-Liss, Inc. [source] Disease stress-inducible genes of tobacco: expression profile of elicitor-responsive genes isolated by subtractive hybridizationPHYSIOLOGIA PLANTARUM, Issue 4 2003Daigo Takemoto In order to investigate the change in mRNA profile during tobacco disease response, a subtractive hybridization procedure was used to generate a cDNA library for genes induced in tobacco (Nicotiana tabacum cv. Samsun NN) treated with oomycete elicitor. Database searches with the randomly isolated genes revealed that this cDNA library was enriched for reported disease stress-responsive genes such as pathogenesis-related proteins and cell wall protein genes. The expressions of eight newly isolated genes were induced by inoculation with the non-pathogenic bacteria, Pseudomonas syringae pv. glycinea. The NtEIGs (N.tabacumelicitor- inducible genes) showed similarity to genes for stellacyanin-like protein (NtEIG-A1), glutathione peroxidase (NtEIG-C08), extensin-like protein (NtEIG-C29), WRKY transcription factor (NtEIG-D48), glycine rich protein (NtEIG-E17), , -1, 3-glucanase-like protein (NtEIG-E76), photoassimilate-responsive protein-1 (NtEIG-E80) and wound-induced protein (NtEIG-D10). The expression patterns of NtEIGs in tobacco leaf in response to P. syringae pv. glycinea, salicylic acid (SA), methyl jasmonate (MeJA) and wound stress were analysed. The individual expression patterns of NtEIGs indicate that the transcriptional activation of NtEIGs is regulated by various signals and the products of NtEIGs are involved in different processes at different stages of the plant defence responses. [source] Phage display selection of efficient glutamine-donor substrate peptides for transglutaminase 2PROTEIN SCIENCE, Issue 11 2006Zsolt Keresztessy Abstract Understanding substrate specificity and identification of natural targets of transglutaminase 2 (TG2), the ubiquitous multifunctional cross-linking enzyme, which forms isopeptide bonds between protein-linked glutamine and lysine residues, is crucial in the elucidation of its physiological role. As a novel means of specificity analysis, we adapted the phage display technique to select glutamine-donor substrates from a random heptapeptide library via binding to recombinant TG2 and elution with a synthetic amine-donor substrate. Twenty-six Gln-containing sequences from the second and third biopanning rounds were susceptible for TG2-mediated incorporation of 5-(biotinamido)penthylamine, and the peptides GQQQTPY, GLQQASV, and WQTPMNS were modified most efficiently. A consensus around glutamines was established as pQX(P,T,S)l, which is consistent with identified substrates listed in the TRANSDAB database. Database searches showed that several proteins contain peptides similar to the phage-selected sequences, and the N-terminal glutamine-rich domain of SWI1/SNF1-related chromatin remodeling proteins was chosen for detailed analysis. MALDI/TOF and tandem mass spectrometry-based studies of a representative part of the domain, SGYGQQGQTPYYNQQSPHPQQQQPPYS (SnQ1), revealed that Q6, Q8, and Q22 are modified by TG2. Kinetic parameters of SnQ1 transamidation (KMapp = 250 ,M, kcat = 18.3 sec,1, and kcat/KMapp = 73,200) classify it as an efficient TG2 substrate. Circular dichroism spectra indicated that SnQ1 has a random coil conformation, supporting its accessibility in the full-length parental protein. Added together, here we report a novel use of the phage display technology with great potential in transglutaminase research. [source] Strategy for comprehensive identification of human N -myristoylated proteins using an insect cell-free protein synthesis systemPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 9 2010Takashi Suzuki Abstract To establish a strategy for the comprehensive identification of human N -myristoylated proteins, the susceptibility of human cDNA clones to protein N -myristoylation was evaluated by metabolic labeling and MS analyses of proteins expressed in an insect cell-free protein synthesis system. One-hundred-and-forty-one cDNA clones with N -terminal Met-Gly motifs were selected as potential candidates from ,2000 Kazusa ORFeome project human cDNA clones, and their susceptibility to protein N -myristoylation was evaluated using fusion proteins, in which the N -terminal ten amino acid residues were fused to an epitope-tagged model protein. As a result, the products of 29 out of 141 cDNA clones were found to be effectively N -myristoylated. The metabolic labeling experiments both in an insect cell-free protein synthesis system and in the transfected COS-1 cells using full-length cDNA revealed that 27 out of 29 proteins were in fact N -myristoylated. Database searches with these 27 cDNA clones revealed that 18 out of 27 proteins are novel N -myristoylated proteins that have not been reported previously to be N -myristoylated, indicating that this strategy is useful for the comprehensive identification of human N -myristoylated proteins from human cDNA resources. [source] BNR , a LINE family from Beta vulgaris, contains a RRM domain in open reading frame 1 and defines a L1 sub-clade present in diverse plant genomesTHE PLANT JOURNAL, Issue 6 2009Tony Heitkam Summary We characterized a novel type of plant non-LTR retrotransposons, identified as the BNR family, in sugar beet (Beta vulgaris) genomes. Although their ORF2 sequences were similar to those of previously analysed LINEs (long interspersed nuclear elements) of the L1 clade, their ORF1 sequences differ strongly from those of most plant LINEs. Two novel domains were identified, containing a conserved secondary motif, known as the RNA recognition motif (RRM). ORF1 lacks the zinc finger motif that is typical of plant LINEs, but has an RRM that is likely to have a RNA-binding function. BNR LINEs are highly diverse, and were characterized by gel-blot and fluorescent in situ hybridization, showing a widespread occurrence and clustering along chromosome arms. Insertion of BNR1 into a well-described satellite repeat was detected in two cultivars only, indicating recent activity. Database searches revealed the existence of LINE families possessing an ORF1 sequence similar to that of BNR in the genomes of higher plants such as poplar, lotus and soybean. Comparing their reverse transcriptase regions with those of other retrotransposons, these LINEs were assigned to the L1 clade, but form a distinct group, providing evidence of a major separation of L1 elements in plants. This indicates a common origin of BNR-like LINEs, suggesting that these elements form a sub-clade designated as the BNR sub-clade. [source] Characterization of a new xyloglucan endotransglucosylase/hydrolase (XTH) from ripening tomato fruit and implications for the diverse modes of enzymic actionTHE PLANT JOURNAL, Issue 2 2006Montserrat Saladié Summary Xyloglucan endotransglucosylase/hydrolases (XTHs) are cell wall-modifying enzymes that align within three or four distinct phylogenetic subgroups. One explanation for this grouping is association with different enzymic modes of action, as XTHs can have xyloglucan endotransglucosylase (XET) or endohydrolase (XEH) activities. While Group 1 and 2 XTHs predominantly exhibit XET activity, to date the activity of only one member of Group 3 has been reported: nasturtium TmXH1, which has a highly specialized function and hydrolyses seed-storage xyloglucan rather than modifying cell wall structure. Tomato fruit ripening was selected as a model to test the hypothesis that preferential XEH activity might be a defining characteristic of Group 3 XTHs, which would be expressed during processes where net xyloglucan depolymerization occurs. Database searches identified 25 tomato XTHs, and one gene (SlXTH5) was of particular interest as it aligned within Group 3 and was expressed abundantly during ripening. Recombinant SlXTH5 protein acted primarily as a transglucosylase in vitro and depolymerized xyloglucan more rapidly in the presence than in the absence of xyloglucan oligosaccharides (XGOs), indicative of XET activity. Thus, there is no correlation between the XTH phylogenetic grouping and the preferential enzymic activities (XET or XEH) of the proteins in those groups. Similar analyses of SlXTH2, a Group 2 tomato XTH, and nasturtium seed TmXTH1 revealed a spectrum of modes of action, suggesting that all XTHs have the capacity to function in both modes. The biomechanical properties of plant walls were unaffected by incubation with SlXTH5, with or without XGOs, suggesting that XTHs do not represent primary cell wall-loosening agents. The possible roles of SlXTH5 in vivo are discussed. [source] Cloning and Characterization of the cDNA Encoding the Masquerade-like Serine Proteinase Homologue Gene of the Silkworm, Bombyx moriENTOMOLOGICAL RESEARCH, Issue 3 2002Doo-Sang PARK ABSTRACT From Bombyx mori larvae, RT-PCR and cDNA library screening isolated masquerade-like serine proteinase homologue cDNA gene, proposed to be related to insect immunity and its characteristics were examined. The isolated gene is composed of 1.3 kb of nucleotide and 420 amino acid residues were encoded. According to the results of database search, the isolated gene showed high sequence homology with Holotrichia and Tenebrio's 45 kDa protein, Drosophila CG5390 gene. Moreover, it is composed of regulatory domain and catalytic domain, which is characteristic of serine proteinase that can be found in the insect immune reaction and embryonic development processes. Enzyme activation site by proteolytic cleavage and the sequence of three amino acids participate in the catalytic triad of enzyme and 14 cystein residues used in disulfide bridges are well conserved with the compared genes. The mRNA expression was increased following E. coli injection and constitutive expression was also observed before injection by Northern blot analysis. [source] Evolution of astacin-like metalloproteases in animals and their function in developmentEVOLUTION AND DEVELOPMENT, Issue 2 2006Frank Möhrlen SUMMARY Astacin-like metalloproteases are ubiquitous in the animal kingdom but their phylogenetic relationships and ancient functions within the Metazoa are unclear. We have cloned and characterized four astacin-like cDNAs from the marine hydroid Hydractinia echinata and performed a database search for related genes in the draft genome sequence of the sea anemone Nematostella vectensis. These sequences and those of higher animals' astacins were subjected to phylogenetic analysis revealing five clusters within the Eumetazoa. The bone morphogenetic protein-1/tolloid-like astacins were represented in all eumetazoan phyla studied. The meprins were only found in vertebrates and cnidarians. Two clusters were taxon-specific, and one cluster represented astacins, which probably evolved after the split of the Cnidaria. Interestingly, grouping of astacins according to the protease catalytic domain alone resulted in clusters of proteins with similar overall domain architecture. The Hydractinia astacins were expressed in distinct cells during metamorphosis and some also during wound healing. Previously characterized cnidarian astacins also act during development. Based on our phylogeny, however, we propose that the developmental function of most of them is not homologous to the developmental function assigned to higher animals' astacins. [source] Marine range shifts and species introductions: comparative spread rates and community impactsGLOBAL ECOLOGY, Issue 3 2010Cascade J. B. Sorte ABSTRACT Aim, Shifts in species ranges are a predicted and realized effect of global climate change; however, few studies have addressed the rates and consequence of such shifts, particularly in marine systems. Given ecological similarities between shifting and introduced species, we examined how our understanding of range shifts may be informed by the more established study of non-native species introductions. Location, Marine systems world-wide. Methods, Database and citation searches were used to identify 129 marine species experiencing range shifts and to determine spread rates and impacts on recipient communities. Analyses of spread rates were based on studies for which post-establishment spread was reported in linear distance. The sizes of the effects of community impacts of shifting species were compared with those of functionally similar introduced species having ecologically similar impacts. Results, Our review and meta-analyses revealed that: (1) 75% of the range shifts found through the database search were in the poleward direction, consistent with climate change scenarios, (2) spread rates of range shifts were lower than those of introductions, (3) shifting species spread over an order of magnitude faster in marine than in terrestrial systems, and (4) directions of community effects were largely negative and magnitudes were often similar for shifters and introduced species; however, this comparison was limited by few data for range-shifting species. Main conclusions, Although marine range shifts are likely to proceed more slowly than marine introductions, the community-level effects could be as great, and in the same direction, as those of introduced species. Because it is well-established that introduced species are a primary threat to global biodiversity, it follows that, just like introductions, range shifts have the potential to seriously affect biological systems. In addition, given that ranges shift faster in marine than terrestrial environments, marine communities might be affected faster than terrestrial ones as species shift with climate change. Regardless of habitat, consideration of range shifts in the context of invasion biology can improve our understanding of what to expect from climate change-driven shifts as well as provide tools for formal assessment of risks to community structure and function. [source] Systematic review of cholecystostomy as a treatment option in acute cholecystitisHPB, Issue 3 2009Anders Winbladh Abstract Objectives:, Percutaneous cholecystostomy (PC) is an established low-mortality treatment option for elderly and critically ill patients with acute cholecystitis. The primary aim of this review is to find out if there is any evidence in the literature to recommend PC rather than cholecystectomy for acute cholecystitis in the elderly population. Methods:, In April 2007, a systematic electronic database search was performed on the subject of PC and cholecystectomy in the elderly population. After exclusions, 53 studies remained, comprising 1918 patients. Three papers described randomized controlled trials (RCTs), but none compared the outcomes of PC and cholecystectomy. A total of 19 papers on mortality after cholecystectomy in patients aged >65 years were identified. Results:, Successful intervention was seen in 85.6% of patients with acute cholecystitis. A total of 40% of patients treated with PC were later cholecystectomized, with a mortality rate of 1.96%. Procedure mortality was 0.36%, but 30-day mortality rates were 15.4 % in patients treated with PC and 4.5% in those treated with acute cholecystectomy (P < 0.001). Conclusions:, There are no controlled studies evaluating the outcome of PC vs. cholecystectomy and the papers reviewed are of evidence grade C. It is not possible to make definitive recommendations regarding treatment by PC or cholecystectomy in elderly or critically ill patients with acute cholecystitis. Low mortality rates after cholecystectomy in elderly patients with acute cholecystitis have been reported in recent years and therefore we believe it is time to launch an RCT to address this issue. [source] Familial desmoplastic trichoepithelioma: limitation of electronic database search and solutionsINTERNATIONAL JOURNAL OF DERMATOLOGY, Issue 11 2008Ching-Chi Chi MD No abstract is available for this article. [source] Association between pacifier use and breast-feeding, sudden infant death syndrome, infection and dental malocclusionINTERNATIONAL JOURNAL OF EVIDENCE BASED HEALTHCARE, Issue 6 2005Ann Callaghan RN RM BNurs(Hons) Executive summary Objective, To critically review all literature related to pacifier use for full-term healthy infants and young children. The specific review questions addressed are: What is the evidence of adverse and/or positive outcomes of pacifier use in infancy and childhood in relation to each of the following subtopics: ,breast-feeding; ,sudden infant death syndrome; ,infection; ,dental malocclusion. Inclusion criteria, Specific criteria were used to determine which studies would be included in the review: (i) the types of participants; (ii) the types of research design; and (iii) the types of outcome measures. To be included a study has to meet all criteria. Types of participants,The participants included in the review were healthy term infants and healthy children up to the age of 16 years. Studies that focused on preterm infants, and infants and young children with serious illness or congenital malformations were excluded. However, some total population studies did include these children. Types of research design, It became evident early in the review process that very few randomised controlled trials had been conducted. A decision was made to include observational epidemiological designs, specifically prospective cohort studies and, in the case of sudden infant death syndrome research, case,control studies. Purely descriptive and cross-sectional studies were excluded, as were qualitative studies and all other forms of evidence. A number of criteria have been proposed to establish causation in the scientific and medical literature. These key criteria were applied in the review process and are described as follows: (i) consistency and unbiasedness of findings; (ii) strength of association; (iii) temporal sequence; (iv) dose,response relationship; (v) specificity; (vi) coherence with biological background and previous knowledge; (vii) biological plausibility; and (viii) experimental evidence. Studies that did not meet the requirement of appropriate temporal sequencing of events and studies that did not present an estimate of the strength of association were not included in the final review. Types of outcome measures,Our specific interest was pacifier use related to: ,breast-feeding; ,sudden infant death syndrome; ,infection; ,dental malocclusion. Studies that examined pacifier use related to procedural pain relief were excluded. Studies that examined the relationship between pacifier use and gastro-oesophageal reflux were also excluded as this information has been recently presented as a systematic review. Search strategy, The review comprised published and unpublished research literature. The search was restricted to reports published in English, Spanish and German. The time period covered research published from January 1960 to October 2003. A protocol developed by New Zealand Health Technology Assessment was used to guide the search process. The search comprised bibliographic databases, citation searching, other evidence-based and guidelines sites, government documents, books and reports, professional websites, national associations, hand search, contacting national/international experts and general internet searching. Assessment of quality, All studies identified during the database search were assessed for relevance to the review based on the information provided in the title, abstract and descriptor/MeSH terms, and a full report was retrieved for all studies that met the inclusion criteria. Studies identified from reference list searches were assessed for relevance based on the study title. Keywords included: dummy, dummies, pacifier(s), soother(s), comforter(s), non-nutritive sucking, infant, child, infant care. Initially, studies were reviewed for inclusion by pairs of principal investigators. Authorship of articles was not concealed from the reviewers. Next, the methodological quality of included articles was assessed independently by groups of three or more principal investigators and clinicians using a checklist. All 20 studies that were accepted met minimum set criteria, but few passed without some methodological concern. Data extraction, To meet the requirements of the Joanna Briggs Institute, reasons for acceptance and non-acceptance at each phase were clearly documented. An assessment protocol and report form was developed for each of the three phases of review. The first form was created to record investigators' evaluations of studies included in the initial review. Those studies that failed to meet strict inclusion criteria were excluded at this point. A second form was designed to facilitate an in-depth critique of epidemiological study methodology. The checklist was pilot tested and adjustments were made before reviewers were trained in its use. When reviewers could not agree on an assessment, it was passed to additional reviewers and discussed until a consensus was reached. At this stage, studies other than cohort, case,control and randomised controlled trials were excluded. Issues of clarification were also addressed at this point. The final phase was that of integration. This phase, undertaken by the principal investigators, was assisted by the production of data extraction tables. Through a process of trial and error, a framework was formulated that adequately summarised the key elements of the studies. This information was tabulated under the following headings: authors/setting, design, exposure/outcome, confounders controlled, analysis and main findings. Results, With regard to the breast-feeding outcome, 10 studies met the inclusion criteria, comprising two randomised controlled trials and eight cohort studies. The research was conducted between 1995 and 2003 in a wide variety of settings involving research participants from diverse socioeconomic and cultural backgrounds. Information regarding exposure and outcome status, and potential confounding factors was obtained from: antenatal and postnatal records; interviews before discharge from obstetric/midwifery care; post-discharge interviews; and post-discharge postal and telephone surveys. Both the level of contact and the frequency of contact with the informant, the child's mother, differed widely. Pacifier use was defined and measured inconsistently, possibly because few studies were initiated expressly to investigate its relationship with breast-feeding. Completeness of follow-up was addressed, but missing data were not uniformly identified and explained. When comparisons were made between participants and non-participants there was some evidence of differential loss and a bias towards families in higher socioeconomic groups. Multivariate analysis was undertaken in the majority of studies, with some including a large number of sociodemographic, obstetric and infant covariates and others including just maternal age and education. As might be expected given the inconsistency of definition and measurement, the relationship between pacifier use and breast-feeding was expressed in many different ways and a meta-analysis was not appropriate. In summary, only one study did not report a negative association between pacifier use and breast-feeding duration or exclusivity. Results indicate an increase in risk for a reduced overall duration of breast-feeding from 20% to almost threefold. The data suggest that very infrequent use may not have any overall negative impact on breast-feeding outcomes. Six sudden infant death syndrome case,control studies met the criteria for inclusion. The research was conducted with information gathered between 1984 and 1999 in Norway, UK, New Zealand, the Netherlands and USA. Exposure information was obtained from a variety of sources including: hospital and antenatal records, death scene investigation, and interview and questionnaire. Information for cases was sought within 2 days after death, within 2,4 weeks after death and in one study between 3 and 11 years after death. Information for controls was sought from as early as 4 days of a nominated sudden infant death syndrome case, to between 1 and 7 weeks from the case date, and again in one study some 3,11 years later. In the majority of the studies case ascertainment was determined by post-mortem. Pacifier use was again defined and measured somewhat inconsistently. All studies controlled for confounding factors by matching and/or using multivariate analysis. Generally, antenatal and postnatal factors, as well as infant care practices, and maternal, family and socioeconomic issues were considered. All five studies reporting multivariate results found significantly fewer sudden infant death syndrome cases used a pacifier compared with controls. That is, pacifier use was associated with a reduced incidence of sudden infant death syndrome. These results indicate that the risk of sudden infant death syndrome for infants who did not use a pacifier in the last or reference sleep was at least twice, and possibly five times, that of infants who did use a pacifier. Three studies reported a moderately sized positive association between pacifier use and a variety of infections. Conversely, one study found no positive association between pacifier use at 15 months of age and a range of infections experienced between the ages of 6 and 18 months. Given the limited number of studies available and the variability of results, no meaningful conclusions could be drawn. Five cohort studies and one case,control study focused on the relationship between pacifier use and dental malocclusion. Not one of these studies reported a measure of association, such as an estimate of relative risk. It was therefore not possible to include these studies in the final review. Implications for practice, It is intended that this review be used as the basis of a ,best practice guideline', to make health professionals aware of the research evidence concerning these health and developmental consequences of pacifier use, because parents need clear information on which they can base child care decisions. With regard to the association between pacifier use and infection and dental malocclusion it was found that, due to the paucity of epidemiological studies, no meaningful conclusion can be drawn. There is clearly a need for more epidemiological research with regard to these two outcomes. The evidence for a relationship between pacifier use and sudden infant death syndrome is consistent, while the exact mechanism of the effect is not well understood. As to breast-feeding, research evidence shows that pacifier use in infancy is associated with a shorter duration and non-exclusivity. It is plausible that pacifier use causes babies to breast-feed less, but a causal relationship has not been irrefutably proven. Because breast-feeding confers an important advantage on all children and the incidence of sudden infant death syndrome is very low, it is recommended that health professionals generally advise parents against pacifier use, while taking into account individual circumstances. [source] Aetiology of molar,incisor hypomineralization: a critical reviewINTERNATIONAL JOURNAL OF PAEDIATRIC DENTISTRY, Issue 2 2009FELICITY CROMBIE Objective., The objective of this study was to assess the strength of evidence for the aetiology of molar,incisor hypomineralization (MIH), often as approximated by demarcated defects. Method., A systematic search of online medical databases was conducted with assessment of titles, abstracts, and finally full articles for selection purposes. The level and quality of evidence were then assessed for each article according to Australian national guidelines. Results., Of 1123 articles identified by the database search, 53 were selected for review. These covered a variety of potential aetiological factors, some of which were grouped together for convenience. The level of evidence provided by the majority of papers was low and most did not specifically investigate MIH. There was moderate evidence that polychlorinated biphenyl/dioxin exposure is involved in the aetiology of MIH; weak evidence for the role of nutrition, birth and neonatal factors, and acute or chronic childhood illness/treatment; and very weak evidence to implicate fluoride or breastfeeding. Conclusion., There is currently insufficient evidence in the literature to establish aetiological factor/s relevant for MIH. Improvements in study design, as well as standardization of diagnostic and examination protocols, would improve the level and strength of evidence. [source] Oral hygiene care for residents with dementia: a literature reviewJOURNAL OF ADVANCED NURSING, Issue 4 2005Jane Chalmers MS PhD Aim., This paper presents a literature review of oral hygiene care for adults with dementia in residential aged care facilities, including evidence for: (1) prevalence, incidence, experiences and increments of oral diseases; (2) use of assessment tools to evaluate residents' oral health; (3) preventive oral hygiene care strategies; and (4) provision of dental treatment. Background., The impact of dementia on residential care is ever-increasing and regular oral hygiene care provision is challenging for cognitively impaired residents. Although an abundance of oral hygiene care recommendations for older people have been published, the supporting evidence has not been clearly delineated. Methods., A review was conducted of English language publications (1980,2002), using a two-step approach (keyword electronic database search, supplemented with secondary search of cited references). All 306 selected articles were critically reviewed and systematically categorized. Results., Evidence confirmed clinicians' observations of poor oral health in older residents with dementia. Possible risk factors identified were: salivary dysfunction, polypharmacy, medical conditions, swallowing and dietary problems, functional dependence, oral hygiene care assistance and poor use of dental care. One comprehensive, reliable and validated oral assessment screening tool for residents with dementia had been published. Expert opinion indicated that oral assessment screening by staff and a dentist would be ideal at admission and regularly thereafter. Clinicians and researchers suggested that oral hygiene care strategies were effective in preventing oral diseases and appropriate for residents with dementia. Conclusion., These literature review findings supported the use of oral assessment screening tools by staff and efficacious preventive oral hygiene care strategies/products for adults with dementia in residential care facilities. Further research with this population is needed to develop and validate oral assessment tools and staff education programmes, trial preventive oral hygiene care strategies/products and trial dementia-focused behaviour management and communication strategies. [source] Diversification in MHC class II invariant chain-like proteins among fishesJOURNAL OF APPLIED ICHTHYOLOGY, Issue 4 2004M. Sakai Summary The major histocompatibility complex (MHC) class II invariant chains are important for an efficient and complete presentation of antigens by MHC class II molecules. Invariant chain-like proteins (Iclp) 1 and 2 were identified by expressed sequence tag analysis from cDNA library of common carp head kidney (HK) stimulated with concanavalin A and lipopolysaccharide. The sequences were 1043 and 1016 bp in length encoding 234 and 198 amino acid proteins, respectively. Based on their predicted structure, the genes harboured transmembrane domain (TMD) and Tg (thyroglobulin) type 1 domains. Expression analysis revealed that both genes were expressed in normal tissues of HK, intestine, brain and gill. By database search, similar homologues were found in Atlantic salmon, fugu and catfish. Phylogenetic and alignment analysis indicate diversity among fish Iclps. [source] Therapeutic effect of statin on aortic stenosis: a review with meta-analysisJOURNAL OF CLINICAL PHARMACY & THERAPEUTICS, Issue 4 2010H. Ge MD Background:, Aortic stenosis (AS) is a common progressive disease. Statins have been hypothesized to delay its progression via pleiotropic mechanisms. However, results of clinical trials focusing on statin therapy in AS patients have been controversial. Objective:, To analyse and summarize the findings in recent statin trials and to discuss the rationale of statin usage in AS populations. Methods:, A comprehensive database search was conducted by two independent reviewers. Controlled trials that compared progression of AS between statin and non-statin therapy published before 31 December 2008 were included. Data were extracted for meta-analysis, to estimate overall effects, if available. Factors that contributed to heterogeneities among the trials were analysed. Results:, The meta-analysis included nine trials with a total of 2947 patients. Statin therapy displayed an overall statistically significant effect on delaying AS progression. The weighted mean difference (statin vs. control) of annual increase of peak aortic-jet velocity was ,0·12 m/s (95% confidence interval ,0·22 to ,0·03); the increase of mean transaortic pressure gradient was ,1·64 mmHg per year (,3·27 to ,0·01); Heterogeneity-analysis suggested that the baseline risk factors and characteristics of the patients, the use of different statins, and the time point to initiate statin therapy, may be important considerations when interpreting the result of individual studies. Conclusion:, Although the Simvastatin and Ezetimibe in Aortic Stenosis (SEAS) trial reported negative results in delaying AS progression in low-risk patients, the potential benefits of statins in those with multiple risk factors and their value in preventing future coronary events call for further investigation of different categories of AS patients. [source] Histologic features of melanocytic nevi seen in association with mycosis fungoidesJOURNAL OF CUTANEOUS PATHOLOGY, Issue 10 2003Jennifer M. McNiff Background:, Many different tumors have been reported to occur simultaneously as collision lesions. To date, no such events have been reported between mycosis fungoides (MFs) and melanocytic neoplasms. Methods:, Two cases are presented in which patches of MF were superimposed on melanocytic nevi. In addition, 967 biopsies of MF from 411 patients were identified in an 8-year retrospective database search. Patient pathology history summaries were reviewed to identify inflamed nevi, atypical nevi, and melanoma submitted for histologic evaluation from this population. Results:, The occurrence of MF in a congenital nevus was associated with a halo phenomenon restricted to the affected region of the nevus in one patient. In the other patient, nests of two morphologies (lymphocytic and melanocytic) in the same biopsy presented a potentially confusing histologic picture. No other cases of MF superimposed on a nevus were identified in 967 biopsies from 411 patients with a histological diagnosis of MF seen over the past 8 years. In this population, 57 biopsies of melanocytic lesions were identified from 28 patients, including three atypical nevi and three melanomas. Conclusions:, The presence of MF superimposed on a nevus is rare and may lead to confounding histologic features or the development of a halo nevus phenomenon. [source] Forensic psychiatric nursing: a literature review and thematic analysis of role tensionsJOURNAL OF PSYCHIATRIC & MENTAL HEALTH NURSING, Issue 5 2002T. Mason phd bsc (hons) rmn pnmh rgn This literature review was undertaken to explore the emergent issues relating to the difficulties encountered in forensic psychiatric nursing. The rationale for the study revolved around the paucity of research undertaken to identify the constituent parts of this professional practice. The aims included both a thematic analysis of the literature and the construction of a theoretical framework to guide further research. The method was a snowballing collection of literature and a computerized database search. The results were the identification of a series of major issues, which were broadly categorized as negative and positive views, security vs. therapy, management of violence, therapeutic efficacy, training and cultural formation. From this the six binary oppositions, or domains of practice, emerged as a theoretical framework to develop further research. These were medical vs. lay knowledge, transference vs. counter-transference, win vs. lose, success vs. failure, use vs. abuse, and confidence vs. fear. Further research is currently underway. [source] Protein microarray analysis identifies cyclic nucleotide phosphodiesterase as an interactor of Nogo-ANEUROPATHOLOGY, Issue 1 2010Kenta Sumiyoshi Nogo-A, a neurite outgrowth inhibitor, is expressed exclusively on oligodendrocytes and neurons in the CNS. The central domain of Amino-Nogo spanning amino acids 567,748 in the human Nogo-A designated NIG, mediates persistent inhibition of axonal outgrowth and induces growth cone collapse by signaling through an as yet unidentified NIG receptor. We identified 82 NIG-interacting proteins by screening a high-density human protein microarray composed of 5000 proteins with a recombinant NIG protein as a probe. Following an intensive database search, we selected 12 neuron/oligodendrocyte-associated NIG interactors. Among them, we verified the molecular interaction of NIG with 2,, 3,-cyclic nucleotide 3,-phosphodiesterase (CNP), a cell type-specific marker of oligodendrocytes, by immunoprecipitation and cell imaging analysis. Although CNP located chiefly in the cytoplasm of oligodendrocytes might not serve as a cell-surface NIG receptor, it could act as a conformational stabilizer for the intrinsically unstructured large segment of Amino-Nogo. [source] Therapeutic touch and postmodernism in nursing,NURSING PHILOSOPHY, Issue 3 2001Sarah Glazer Abstract Therapeutic touch, a healing technique based upon the laying-on of hands, has found wide acceptance in the nursing profession despite its lack of scientific plausibility. Its acceptance is indicative of a broad antiscientific trend in nursing. Adherents of this movement use the jargon of postmodern philosophy to justify their enthusiasm for a variety of mystically based techniques, citing such postmodern critics of science as Derrida and Michel Foucault as well as philosophical forerunners Heidegger and Husserl. Between 1997 and 1999, 94 articles in nursing journals referred to postmodernism, according to a database search. This paper criticizes the postmodern movement for abandoning the biological underpinnings of nursing and for misreading philosophy in the service of an antiscientific world-view. It is also suggested that nursing can retain its tradition of ,caring' without abandoning the scientific method. [source] Confidence assessment for protein identification by using peptide-mass fingerprinting dataPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 11 2009Zhao Song Abstract Protein identification using Peptide Mass Fingerprinting (PMF) data remains an important yet only partially solved problem. Current computational methods may lead to false positive identification since the top hit from a database search may not be the target protein. In addition, the identification scores assigned singly by a scoring function (raw scores) are not normalized. Therefore, the ranking based on raw scores may be biased. To address the above issue, we have developed a statistical model to evaluate the confidence of the raw score and to improve the ranking of proteins for identification. The results show that the statistical model better ranks the correct protein than the raw scores. Our study provides a new method to enhance the accuracy of protein identification by using PMF data. We incorporated the method into our software package "Protein-Decision" together with a user-friendly graphical interface. A standalone version of Protein-Decision is freely available at http://digbio.missouri.edu/ProteinDecision/. [source] The neuropeptidome of Rhodnius prolixus brainPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 3 2009Sheila Ons Abstract We show a sensitive and straightforward off-line nano-LC-MALDI-MS/MS workflow that allowed the first comprehensive neuropeptidomic analysis of an insect disease vector. This approach was applied to identify neuropeptides in the brain of Rhodnius prolixus, a vector of Chagas disease. This work will contribute to the annotation of genes in the ongoing R. prolixus genome sequence project. Peptides were identified by de novo sequencing and comparisons to known neuropeptides from different organisms by database search. By these means, we were able to identify 42 novel neuropeptides from R. prolixus. The peptides were classified as extended FMRF-amide-related peptides, sulfakinins, myosuppressins, short neuropeptide F, long neuropeptide F, SIF-amide-related peptides, tachykinins, orcokinins, allatostatins, allatotropins, calcitonin-like diuretic hormones, corazonin, and pyrokinin. Some of them were detected in multiple isoforms and/or truncated fragments. Interestingly, some of the R. prolixus peptides, as myosuppressin and sulfakinins, are unique in their characteristic C-terminal domain among insect neuropeptides identified so far. [source] A new strategy to filter out false positive identifications of peptides in SEQUEST database search resultsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 22 2007Jiyang Zhang Abstract Based on the randomized database method and a linear discriminant function (LDF) model, a new strategy to filter out false positive matches in SEQUEST database search results is proposed. Given an experiment MS/MS dataset and a protein sequence database, a randomized database is constructed and merged with the original database. Then, all MS/MS spectra are searched against the combined database. For each expected false positive rate (FPR), LDFs are constructed for different charge states and used to filter out the false positive matches from the normal database. In order to investigate the error of FPR estimation, the new strategy was applied to a reference dataset. As a result, the estimated FPR was very close to the actual FPR. While applied to a human K562 cell line dataset, which is a complicated dataset from real sample, more matches could be confirmed than the traditional cutoff-based methods at the same estimated FPR. Also, though most of the results confirmed by the LDF model were consistent with those of PeptideProphet, the LDF model could still provide complementary information. These results indicate that the new method can reliably control the FPR of peptide identifications and is more sensitive than traditional cutoff-based methods. [source] Fe3+ immobilized metal affinity chromatography with silica monolithic capillary column for phosphoproteome analysisPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 3 2007Shun Feng Abstract Immobilized metal affinity chromatography (IMAC) is a commonly used technique for phosphoproteome analysis due to its high affinity for adsorption of phosphopeptides. Miniaturization of IMAC column is essential for the analysis of a small amount of sample. Nanoscale IMAC column was prepared by chemical modification of silica monolith with iminodiacetic acid (IDA) followed by the immobilization of Fe3+ ion inside the capillary. It was demonstrated that Fe3+ -IDA silica monolithic IMAC capillary column could specifically capture the phosphopeptides from tryptic digest of ,-casein with analysis by MALDI-TOF MS. The silica monolithic IMAC capillary column was manually coupled with nanoflow RPLC/nanospray ESI mass spectrometer (,RPLC,nanoESI MS) for phosphoproteome analysis. The system was validated by analysis of standard phosphoproteins and then it was applied to the analysis of protein phosphorylation in mouse liver lysate. Besides MS/MS spectra, MS/MS/MS spectra were also collected for neutral loss peak. After database search and manual validation with conservative criteria, 29 singly phosphorylated peptides were identified by analyzing a tryptic digest of only 12,,g mouse liver lysate. The results demonstrated that the silica monolithic IMAC capillary column coupled with ,RPLC-nanoESI MS was very suitable for the phosphoproteome analysis of minute sample. [source] Carbon starvation survival of Listeria monocytogenes in planktonic state and in biofilm: A proteomic studyPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 10 2003Emmanuelle Helloin Abstract The proteomes of Listeria monocytogenes expressed in suspension and biofilm state, in the presence and absence of a caron source, were analysed by two-dimensional electrophoresis with the help of computer software. The up-regulated proteins in each case were identified by peptide sequencing using electrospray ionisation tandem mass spectrometry and a database search against the Listeria genome was performed. Relevant functions could be attributed to a number of the induced proteins which contibute to the understanding of the mechanisms of starvation survival of L. monocytogenes in planktonic state and in biofilm. 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