The Phyre2 web portal for protein modeling, prediction and analysis

Phyre2 is a suite of tools available on the web to predict and analyze protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a paper in Nature Protocols. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) for a user's protein sequence. Users are guided through results by a simple interface at a level of detail they determine. This protocol will guide users from submitting a protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for proteins that are difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2. A typical structure prediction will be returned between 30 min and 2 h after submission

Case-control study on analgesics and nephropathy (SAN): protocol

BACKGROUND: The association between intake of non-phenacetin-containing analgesics and the occurrence of chronic renal failure is still controversially discussed. A new epidemiologic study was planned and conducted in Germany and Austria. METHODS/DESIGN: The objective of the international, multicenter case-control study was to evaluate the association between end-stage renal disease (ESRD) and use of non-phenacetin-containing analgesics with particular emphasis on combined formulations. A targeted sample of 1000 new (incident) dialysis patients, aged less than 50 years, was planned to recruit between January 1, 2001 and December 31, 2004. The age limit was chosen to avoid contamination of the study population with phenacetin-containing analgesics to the extent possible. Four control subjects per ESRD case, matched by age, sex, and region were selected from the population living in the region the case came from. Lifetime exposure to analgesics and potential renal risk factors were recorded in a single face-to-face interview. A set of aids was introduced to reinforce the memory of study participants. A standardized, pre-tested interview questionnaire (participants), a medical documentation sheet (physicians in dialysis centres), a logbook for all activities (dialysis centres) were used to collect the necessary data. Quality management consisted of the standardized procedures, (re-) training and supervision of interviewers, regular checks of all incoming data for completeness and plausibility. The study is scientifically independent and governed by a international Scientific Advisory Committee that bridged the gap between the sponsoring companies and the investigators. Also other advisory groups assisted the managing committee of the study. All relevant German and Austrian nephrological associations supported the study, and the study design was carefully reviewed and approved by the Kidney Foundation of Germany. DISCUSSION: The study is expected to answer the main research question by end 2005. There is however a high potential for various biases that we tried to address with adequate measure. One limitation however cannot be overcome: The methodologically needed age-limitation of the study will make it not easy to generalize the results to age groups over 50 years. It might be suggested to repeat the study for persons over 50 years in 10 years when contamination with phenacetin use early in life is likely to be outgrown

Distinctiveness and encoding effects in online sentence comprehension

In explicit memory recall and recognition tasks, elaboration and contextual isolation both facilitate memory performance. Here, we investigate these effects in the context of sentence processing: targets for retrieval during online sentence processing of English object relative clause constructions differ in the amount of elaboration associated with the target noun phrase, or the homogeneity of superficial features (text color). Experiment 1 shows that greater elaboration for targets during the encoding phase reduces reading times at retrieval sites, but elaboration of non-targets has considerably weaker effects. Experiment 2 illustrates that processing isolated superficial features of target noun phrases --- here, a green word in a sentence with words colored white --- does not lead to enhanced memory performance, despite triggering longer encoding times. These results are interpreted in the light of the memory models of Nairne 1990, 2001, 2006, which state that encoding remnants contribute to the set of retrieval cues that provide the basis for similarity-based interference effects

Primary health care services for the aged in the United Arab Emirates: a comparison of two models of care

Aim: To compare the quality of aged care provided by two different models of primary health care services in the United Arab Emirates. Methods: Cross sectional survey by chart review of 200 consecutive people aged 65 years and over attending two primary health care centers located in adjacent suburbs and serving populations with similar characteristics; a resource intensive center (RIC) and the other a resource thrifty center (RTC). Quality indicators were blood pressure levels in hypertensives and glycosylated hemoglobin (HbA1c) levels in diabetics. Results: There was no variation in age, sex or number of visits per year between the clinics. Osteoarthritis, hypertension, and diabetes were the most common diagnoses at both. The people attending the RIC had a substantially higher level of comorbidity (RIC=1.19±1.18, RTC=0.63 ± 0.68, p < 0.001), the average systolic and diastolic blood pressure for those diagnosed with hypertension was in the normal range at the RIC (138.5 ± 19.8/77.1 ± 9.9), whereas it was significantly higher and in the elevated range at the RTC (149.5 ± 17.7/85.2 ± 9.1, p < 0.001) and the HbA1c was significantly lower at the RIC (7.7 ± 1.4) than at the RTC (9.5 ± 2.0, p < 0.001). Conclusions:The quality of health outcomes for the two chronic diseases, hypertension and diabetes, appeared significantly higher at the RIC, when compared with the RTC. However, there may have been significant selection bias. Further studies are needed to determine if the RIC improves quality measures in other aspects of chronic disease care and provides a more cost effective health care service

Systematic Characterizations of Text Similarity in Full Text Biomedical Publications

Computational methods have been used to find duplicate biomedical publications in MEDLINE. Full text articles are becoming increasingly available, yet the similarities among them have not been systematically studied. Here, we quantitatively investigated the full text similarity of biomedical publications in PubMed Central.72,011 full text articles from PubMed Central (PMC) were parsed to generate three different datasets: full texts, sections, and paragraphs. Text similarity comparisons were performed on these datasets using the text similarity algorithm eTBLAST. We measured the frequency of similar text pairs and compared it among different datasets. We found that high abstract similarity can be used to predict high full text similarity with a specificity of 20.1% (95% CI [17.3%, 23.1%]) and sensitivity of 99.999%. Abstract similarity and full text similarity have a moderate correlation (Pearson correlation coefficient: -0.423) when the similarity ratio is above 0.4. Among pairs of articles in PMC, method sections are found to be the most repetitive (frequency of similar pairs, methods: 0.029, introduction: 0.0076, results: 0.0043). In contrast, among a set of manually verified duplicate articles, results are the most repetitive sections (frequency of similar pairs, results: 0.94, methods: 0.89, introduction: 0.82). Repetition of introduction and methods sections is more likely to be committed by the same authors (odds of a highly similar pair having at least one shared author, introduction: 2.31, methods: 1.83, results: 1.03). There is also significantly more similarity in pairs of review articles than in pairs containing one review and one nonreview paper (frequency of similar pairs: 0.0167 and 0.0023, respectively).While quantifying abstract similarity is an effective approach for finding duplicate citations, a comprehensive full text analysis is necessary to uncover all potential duplicate citations in the scientific literature and is helpful when establishing ethical guidelines for scientific publications

AdS_3/LCFT_2 - Correlators in Cosmological Topologically Massive Gravity

For cosmological topologically massive gravity at the chiral point we calculate momentum space 2- and 3-point correlators of operators in the postulated dual CFT on the cylinder. These operators are sourced by the bulk and boundary gravitons. Our correlators are fully consistent with the proposal that cosmological topologically massive gravity at the chiral point is dual to a logarithmic CFT. In the process we give a complete classification of normalizable and non-normalizeable left, right and logarithmic solutions to the linearized equations of motion in global AdS_3.Comment: 39 pages + appendices, 1 eps figure, v2: minor changes in text in 4.1.2, corrected typo in (2.31

Financial considerations in the conduct of multi-centre randomised controlled trials: evidence from a qualitative study.

National Coordinating Centre for Research Methodology; Medical Research Council, UK Department of Health; Chief Scientist OfficeNot peer reviewedPublisher PD

Amniotic fluid embolism incidence, risk factors and outcomes: a review and recommendations

<p>Abstract</p> <p>Background</p> <p>Amniotic fluid embolism (AFE) is a rare but severe complication of pregnancy. A recent systematic review highlighted apparent differences in the incidence, with studies estimating the incidence of AFE to be more than three times higher in North America than Europe. The aim of this study was to examine population-based regional or national data from five high-resource countries in order to investigate incidence, risk factors and outcomes of AFE and to investigate whether any variation identified could be ascribed to methodological differences between the studies.</p> <p>Methods</p> <p>We reviewed available data sources on the incidence of AFE in Australia, Canada, the Netherlands, the United Kingdom and the USA. Where information was available, the risk factors and outcomes of AFE were examined.</p> <p>Results</p> <p>The reported incidence of AFE ranged from 1.9 cases per 100 000 maternities (UK) to 6.1 per 100 000 maternities (Australia). There was a clear distinction between rates estimated using different methodologies. The lowest estimated incidence rates were obtained through validated case identification (range 1.9-2.5 cases per 100 000 maternities); rates obtained from retrospective analysis of population discharge databases were significantly higher (range 5.5-6.1 per 100 000 admissions with delivery diagnosis). Older maternal age and induction of labour were consistently associated with AFE.</p> <p>Conclusions</p> <p>Recommendation 1: Comparisons of AFE incidence estimates should be restricted to studies using similar methodology. The recommended approaches would be either population-based database studies using additional criteria to exclude false positive cases, or tailored data collection using existing specific population-based systems.</p> <p>Recommendation 2: Comparisons of AFE incidence between and within countries would be facilitated by development of an agreed case definition and an agreed set of criteria to minimise inclusion of false positive cases for database studies.</p> <p>Recommendation 3: Groups conducting detailed population-based studies on AFE should develop an agreed strategy to allow combined analysis of data obtained using consistent methodologies in order to identify potentially modifiable risk factors.</p> <p>Recommendation 4: Future specific studies on AFE should aim to collect information on management and longer-term outcomes for both mothers and infants in order to guide best practice, counselling and service planning.</p