bluuebunny/crossref_metadata_2025_split huggingface dataset:
Paircoil2: improved prediction of coiled coils from sequence
Authors: McDonnell A. V. , Jiang T. , Keating A. E. , Berger B. 
Published: November 2005

Abstract
Summary: We introduce Paircoil2, a new version of the Paircoil program, which uses pairwise residue probabilities to detect coiled–coil motifs in protein sequence data. Paircoil2 achieves 98% sensitivity and 97% specificity on known coiled coils in leave-family-out cross-validation. It also shows superior performance compared with published methods in tests on proteins of known structure.
Availability: Paircoil2 is freely available as a web application and for download at
Contact: keating@mit.edu; bab@mit.edu
Supplementary information: Available at Bioinformatics online and at the Paircoil website.
Comparison of Bayesian and maximum-likelihood inference of population genetic parameters
Authors: Beerli Peter 
Published: November 2005

Abstract
Comparison of the performance and accuracy of different inference methods, such as maximum likelihood (ML) and Bayesian inference, is difficult because the inference methods are implemented in different programs, often written by different authors. Both methods were implemented in the program MIGRATE, that estimates population genetic parameters, such as population sizes and migration rates, using coalescence theory. Both inference methods use the same Markov chain Monte Carlo algorithm and differ from each other in only two aspects: parameter proposal distribution and maximization of the likelihood function. Using simulated datasets, the Bayesian method generally fares better than the ML approach in accuracy and coverage, although for some values the two approaches are equal in performance.
Motivation: The Markov chain Monte Carlo-based ML framework can fail on sparse data and can deliver non-conservative support intervals. A Bayesian framework with appropriate prior distribution is able to remedy some of these problems.
Results: The program MIGRATE was extended to allow not only for ML(-) maximum likelihood estimation of population genetics parameters but also for using a Bayesian framework. Comparisons between the Bayesian approach and the ML approach are facilitated because both modes estimate the same parameters under the same population model and assumptions.
Availability: The program is available from
Contact: beerli@csit.fsu.edu
SimShift: Identifying structural similarities from NMR chemical shifts
Authors: Ginzinger Simon W. , Fischer Johannes 
Published: November 2005

Abstract
Motivation: An important quantity that arises in NMR spectroscopy experiments is the chemical shift. The interpretation of these data is mostly done by human experts; to our knowledge there are no algorithms that predict protein structure from chemical shift sequences alone. One approach to facilitate this process could be to compare two such sequences, where the structure of one protein has already been resolved. Our claim is that similarity of chemical shifts thereby found implies structural similarity of the respective proteins.
Results: We present an algorithm to identify structural similarities of proteins by aligning their associated chemical shift sequences. To evaluate the correctness of our predictions, we propose a benchmark set of protein pairs that have high structural similarity, but low sequence similarity (because with high sequence similarity the structural similarities could easily be detected by a sequence alignment algorithm). We compare our results with those of HHsearch and SSEA and show that our method outperforms both in &gt;50% of all cases.
Contact: Simon.Ginzinger@bio.ifi.lmu.de
Application of compression-based distance measures to protein sequence classification: a methodological study
Authors: Kocsor András , Kertész-Farkas Attila , Kaján László , Pongor Sándor 
Published: November 2005

Abstract
Motivation: Distance measures built on the notion of text compression have been used for the comparison and classification of entire genomes and mitochondrial genomes. The present study was undertaken in order to explore their utility in the classification of protein sequences.
Results: We constructed compression-based distance measures (CBMs) using the Lempel-Zlv and the PPMZ compression algorithms and compared their performance with that of the Smith–Waterman algorithm and BLAST, using nearest neighbour or support vector machine classification schemes. The datasets included a subset of the SCOP protein structure database to test distant protein similarities, a 3-phosphoglycerate-kinase sequences selected from archaean, bacterial and eukaryotic species as well as low and high-complexity sequence segments of the human proteome, CBMs values show a dependence on the length and the complexity of the sequences compared. In classification tasks CBMs performed especially well on distantly related proteins where the performance of a combined measure, constructed from a CBM and a BLAST score, approached or even slightly exceeded that of the Smith–Waterman algorithm and two hidden Markov model-based algorithms.
Contact: kocsor@inf.u-szeged.hu
Supplementary information:
Sclerotinia sclerotiorum (Lib.) de Bary: biology and molecular traits of a cosmopolitan pathogen
Authors: BOLTON MELVIN D. , THOMMA BART P. H. J. , NELSON BERLIN D. 
Published: November 2005

SUMMARY Sclerotinia sclerotiorum (Lib.) de Bary is a necrotrophic fungal pathogen causing disease in a wide range of plants. This review summarizes current knowledge of mechanisms employed by the fungus to parasitize its host with emphasis on biology, physiology and molecular aspects of pathogenicity. In addition, current tools for research and strategies to combat S. sclerotiorum are discussed.Taxonomy: Sclerotinia sclerotiorum (Lib.) de Bary: kingdom Fungi, phylum Ascomycota, class Discomycetes, order Helotiales, family Sclerotiniaceae, genus Sclerotinia.Identification: Hyphae are hyaline, septate, branched and multinucleate. Mycelium may appear white to tan in culture and in planta. No asexual conidia are produced. Long‐term survival is mediated through the sclerotium; a pigmented, multi‐hyphal structure that can remain viable over long periods of time under unfavourable conditions for growth. Sclerotia can germinate to produce mycelia or apothecia depending on environmental conditions. Apothecia produce ascospores, which are the primary means of infection in most host plants.Host range: S. sclerotiorum is capable of colonizing over 400 plant species found worldwide. The majority of these species are dicotyledonous, although a number of agriculturally significant monocotyledonous plants are also hosts.Disease symptoms: Leaves usually have water‐soaked lesions that expand rapidly and move down the petiole into the stem. Infected stems of some species will first develop dark lesions whereas the initial indication in other hosts is the appearance of water‐soaked stem lesions. Lesions usually develop into necrotic tissues that subsequently develop patches of fluffy white mycelium, often with sclerotia, which is the most obvious sign of plants infected with S. sclerotiorum.Useful websites: http://www.whitemoldresearch.com; http://www.broad.mit.edu/annotation/fungi/sclerotinia_sclerotiorum
The presence of IFNG 3/3 genotype in the recipient associates with increased risk for Epstein–Barr virus reactivation after allogeneic haematopoietic stem cell transplantation
Authors: Bogunia‐Kubik Katarzyna , Mlynarczewska Anna , Jaskula Emilia , Lange Andrzej 
Published: November 2005

SummaryRecent studies have shown that interferon‐γ gene (IFNG) polymorphism constitutes a risk factor for acute and chronic graft‐versus‐host disease (GvHD) after allogeneic haematopoietic stem cell transplantation (HSCT). Patients with IFNG 3/3 have been found to be more prone to GvHD. This rather puzzling result, as 3/3 genotype is associated with a decreased IFN‐γ production, was investigated in the present study in the context of Epstein–Barr virus (EBV) reactivation. Microsatellite polymorphism (CA)n within the first intron of IFNG gene was assessed in 83 HSCT recipients and related to EBV load. Quantification of EBV copies was performed by a real‐time polymerase chain reaction in peripheral blood cells taken from the patients 2–3 months after HSCT. It was found, that patients having IFNG 3/3 genotype presented with a high number of EBV copies (over 10/105 blood cells) when compared with the recipients with other IFNG genotypes (10/14 vs. 17/69, P < 0·001). This association was independent of recipient's age, underlying disease, conditioning regimen, type of donor, source of stem cells or pretransplant donor and recipient EBV serological status. Thus IFNG 3/3 genotype, known to be associated with a decreased IFN‐γ production, appeared as a factor significantly contributing to the risk of EBV reactivation after allogeneic HSCT.
Deeply divergent lineages of the widespread New Zealand amphipod Paracalliope fluviatilis revealed using allozyme and mitochondrial DNA analyses
Authors: HOGG IAN D. , STEVENS MARK I. , SCHNABEL KAREEN E. , ANN CHAPMAN M. 
Published: November 2005

Summary1. We evaluated the population genetic structure of the common New Zealand amphipod Paracalliope fluviatilis using eight allozyme loci, and the mitochondrial cytochrome oxidase c subunit I (COI) gene locus. Morphological analyses were also conducted to evaluate any phenotypic differences. Individuals belonging to P. fluviatilis were collected from a total of 14 freshwater fluvial habitats on the North and South Islands, New Zealand.2. We found evidence for strong genetic differentiation among locations (Wright's FST > 0.25), and fixed differences (non‐shared alleles) at two of the eight allozyme loci indicating the possibility of previously unknown species. Analysis of a 545‐bp fragment of the COI locus was mostly congruent with the allozyme data and revealed the same deeply divergent lineages (sequence divergences up to 26%).3. Clear genetic breaks were identified between North Island and South Island populations. North Island populations separated by <100 km also showed genetic differences between east and west draining watersheds (sequence divergence >12%). Accordingly, present‐day dispersal among hydrologically isolated habitats appears minimal for this taxon.4. Although population differences were clearly shown by allozyme and mtDNA analyses, individuals were morphologically indistinguishable. This suggests that, as in North American and European taxa (e.g. Hyalella and Gammarus), morphological conservatism may be prevalent among New Zealand's freshwater amphipods. We conclude that molecular techniques, particularly the COI gene locus, may be powerful tools for resolving species that show no distinctive morphological differences.
National audit of continence care: laying the foundation
Authors: Mian Sarah , Wagg Adrian , Irwin Penny , Lowe Derek , Potter Jonathan , Pearson Michael 
Published: November 2005

AbstractIntroduction  National audit provides a basis for establishing performance against national standards, benchmarking against other service providers and improving standards of care. For effective audit, clinical indicators are required that are valid, feasible to apply and reliable. This study describes the methods used to develop clinical indicators of continence care in preparation for a national audit.Aim  To describe the methods used to develop and test clinical indicators of continence care with regard to validity, feasibility and reliability. Method  A multidisciplinary working group developed clinical indicators that measured the structure, process and outcome of care as well as case‐mix variables. Literature searching, consensus workshops and a Delphi process were used to develop the indicators. The indicators were tested in 15 secondary care sites, 15 primary care sites and 15 long‐term care settings.  Results  The process of development produced indicators that received a high degree of consensus within the Delphi process. Testing of the indicators demonstrated an internal reliability of 0.7 and an external reliability of 0.6. Data collection required significant investment in terms of staff time and training.Conclusion  The method used produced indicators that achieved a high degree of acceptance from health care professionals. The reliability of data collection was high for this audit and was similar to the level seen in other successful national audits. Data collection for the indicators was feasible to collect, however, issues of time and staffing were identified as limitations to such data collection. The study has described a systematic method for developing clinical indicators for national audit. The indicators proved robust and reliable in primary and secondary care as well as long‐term care settings.
Appraising the quality of randomized controlled trials: inter‐rater reliability for the OTseeker evidence database
Authors: Tooth Leigh , Sally Bennett BOccThy(Hons)  , McCluskey Annie , Hoffmann Tammy , McKenna Kryss , Lovarini Meryl 
Published: November 2005

AbstractRationale and aims  ‘OTseeker’ is an online database of randomized controlled trials (RCTs) and systematic reviews relevant to occupational therapy. RCTs are critically appraised and rated for quality using the ‘PEDro’ scale. We aimed to investigate the inter‐rater reliability of the PEDro scale before and after revising rating guidelines.Methods  In study 1, five raters scored 100 RCTs using the original PEDro scale guidelines. In study 2, two raters scored 40 different RCTs using revised guidelines. All RCTs were randomly selected from the OTseeker database. Reliability was calculated using Kappa and intraclass correlation coefficients [ICC (model 2,1)].Results  Inter‐rater reliability was ‘good to excellent’ in the first study (Kappas ≥  0.53; ICCs ≥  0.71). After revising the rating guidelines, the reliability levels were equivalent or higher to those previously obtained (Kappas ≥  0.53; ICCs ≥  0.89), except for the item, ‘groups similar at baseline’, which still had moderate reliability (Kappa = 0.53). In study 2, two PEDro scale items, which had their definitions revised, ‘less than 15% dropout’ and ‘point measures and variability’, showed higher reliability. In both studies,  the  PEDro  items  with  the  lowest  reliability  were  ‘groups similar at baseline’ (Kappas = 0.53), ‘less than 15% dropout’ (Kappas ≤  0.68) and ‘point measures and variability data’ (Kappas ≤  0.68). Conclusion  The PEDro scale is a reliable instrument for rating the quality of RCTs. Revised rating guidelines are provided for scale items that are difficult to rate, and helped to improve inter‐rater reliability.
Diabetic patients with prior specialist care have better glycaemic control than those with prior primary care
Authors: Shah Baiju R. , Hux Janet E. , Laupacis Andreas , Mdcm Bernard Zinman , Austin Peter C. , Van Walraven Carl 
Published: November 2005

AbstractObjective  To compare glycaemic control, as reflected in the A1c level, of diabetic  patients  with  primary  care  vs.  with  specialist  care.Methods  The study used administrative data from eastern Ontario, Canada, and a database containing the results of all A1c tests from this region between 1 September 1999 and 1 September 2000. To avoid referral bias, diabetic patients with an index specialist visit were selected and separated into those with exclusively primary care previously (n = 974) and those with prior specialist care (n = 3533). We compared A1c levels measured within 30 days of the index visit and hence attributable to the prior care. To control for confounding between the groups, both multiple linear regression and propensity score‐based matching were used.Results  After controlling for confounders, patients with prior specialist care had significantly lower A1c levels (P < 0.0001). Other predictors of lower A1c included older age, shorter diabetes duration, rural residence and higher neighbourhood income. In propensity score‐matched cohorts, the A1c level was 8.3 ± 2.0% with prior primary care vs. 7.9 ± 1.6% with prior specialist care (P < 0.0001).Conclusions  Specialist care prior to the index visit was associated with a lower A1c level than prior primary care. This difference would result in reductions in diabetes complications for patients with ongoing specialist care.
Benefit assessment of preventive medical check‐ups in patients suffering from chronic granulomatous disease (CGD)
Authors: Roesler Joachim , Koch Anne , Pörksen Gönke , Von Bernuth Horst , Brenner Sebastian , Hahn Gabriele , Fischer Rainer , Lorenz Norbert , Gahr Manfred , Rösen‐Wolff Angela 
Published: November 2005

AbstractBackground  Chronic granulomatous disease (CGD) patients are susceptible to recurrent opportunistic infections and to recurrent or chronic inflammations of presumably non‐infectious origin. Both types of manifestations are often accompanied by granuloma formation. Both can remain unnoticed until they deteriorate considerably and can become life‐threatening if not treated in time.Objective  To evaluate the effectiveness of regular follow‐up  visits  in  CGD  patients. Methods  Findings of imaging (ultrasound, radiographs, computer‐tomography, magnetic resonance imaging), lung function tests, histopathological and microbiological assessments of biopsies  have  been  reviewed. Results  A total of 32 CGD patients have been evaluated within 15 years. Of these eight patients have been checked regularly for more than 5 years. Early detection prior to specific clinical signs and consecutive treatment of six lung manifestations and one liver manifestation such as interstitial pneumonia with formation of small granulomas, formation of large granulomas, fibrosis, Aspergillus infections, and abscesses could presumably prevent considerable aggravation in seemingly healthy or mildly symptomatic patients. In contrast, patients without surveillance who presented with severe symptoms (seven manifestations)  often  had  irreversible  organ  damage  or  even  died.Conclusions  Regular follow‐up visits can help prevent or mitigate clinical manifestations, improve life quality and expectancy and weigh indication for bone marrow transplantation in CGD patients.
Assessing the impact of clinical information‐retrieval technology in a family practice residency
Authors: Grad Roland M. , Pluye Pierre , Meng Yuejing , Segal Bernard , Tamblyn Robyn 
Published: November 2005

AbstractRationale and objective  Evidence‐based sources of information do not integrate self‐assessment tools to assess the impact of a users’ search for clinical information. We present a method to evaluate evidence‐based sources of information, by systematically assessing the impact of searches for  clinical  information  in  everyday  practice. Methods  We integrated an information management tool (InfoRetriever 2003) with an educational intervention in a cohort of 26 family medicine residents. An electronic impact assessment scale was used by these doctors to report the perceived impact of each item of information (each hit) retrieved on hand‐held computer. We compared the types of impact associated with hits in two distinct categories: clinical decision support systems (CDSS) vs. clinical information‐retrieval technology (CIRT). Information hits in CDSS were defined  as any hit in the following InfoRetriever databases: Clinical Prediction Rules, History and Physical Exam diagnostic calculator and Diagnostic Test calculator. CIRT information hits were defined as any hit in: Abstracts of Cochrane Reviews, InfoPOEMs, evidence‐based practice guideline summaries and  the  Griffith's  5  Minute  Clinical  Consult.Results  The impact assessment questionnaire was linked to 5160 information hits. 4946 impact assessment questionnaires were answered (95.9%), and 2495 contained reports of impact (48.4%). Reports of positive impact on doctors were most frequently in the areas of learning and practice improvement. In comparison to CDSS, CIRT hits were more frequently associated with learning and recall. CDSS hits were more frequently associated with reports of practice improvement.Conclusions  Our new method permits systematic and comparative assessment of impact associated with distinct categories of information.
Intracolony variation of bacterial gut microbiota among castes and ages in the fungus‐growing termite Macrotermes gilvus
Authors: HONGOH Y. , EKPORNPRASIT L. , INOUE T. , MORIYA S. , TRAKULNALEAMSAI S. , OHKUMA M. , NOPARATNARAPORN N. , KUDO T. 
Published: November 2005

AbstractThe fungus‐growing termites Macrotermes cultivate the obligate ectosymbiontic fungi, Termitomyces. While their relationship has been extesively studied, little is known about the gut bacterial symbionts, which also presumably play a crucial role for the nutrition of the termite host. In this study, we investigated the bacterial gut microbiota in two colonies of Macrotermes gilvus, and compared the diversity and community structure of bacteria among nine termite morphotypes, differing in caste and/or age, using terminal restriction fragment length polymorphism (T‐RFLP) and clonal analysis of 16S rRNA. The obtained molecular community profiles clustered by termite morphotype rather than by colony, and the clustering pattern was clearly more related to a difference in age than to caste. Thus, we suggest that the bacterial gut microbiota change in relation to the food of the termite, which comprises fallen leaves and the fungus nodules of Termitomyces in young workers, and leaves degraded by the fungi, in old workers. Despite these intracolony variations in bacterial gut microbiota, their T‐RFLP profiles formed a distinct cluster against those of the fungus garden, adjacent soil and guts of sympatric wood‐feeding termites, implying a consistency and uniqueness of gut microbiota in M. gilvus. Since many bacterial phylotypes from M. gilvus formed monophyletic clusters with those from distantly related termite species, we suggest that gut bacteria have co‐evolved with the termite host and form a microbiota specific to a termite taxonomic and/or feeding group, and furthermore, to caste and age within a termite species.
The Elongator subunit Elp3 contains a Fe4S4 cluster and binds S‐adenosylmethionine
Authors: Paraskevopoulou Christina , Fairhurst Shirley A. , Lowe David J. , Brick Peter , Onesti Silvia 
Published: November 2005

SummaryThe Elp3 subunit of the Elongator complex is highly conserved from archaea to humans and contains a well‐characterized C‐terminal histone acetyltransferase (HAT) domain. The central region of Elp3 shares significant sequence homology to the Radical SAM superfamily. Members of this large family of bacterial proteins contain a FeS cluster and use S‐adenosylmethionine (SAM) to catalyse a variety of radical reactions. To biochemically characterize this domain we have expressed and purified the corresponding fragment of the Methanocaldococcus jannaschii Elp3 protein. The presence of a Fe4S4 cluster has been confirmed by UV‐visible spectroscopy and electron paramagnetic resonance (EPR) spectroscopy and the Fe content determined by both a colorimetric assay and atomic absorption spectroscopy. The cysteine residues involved in cluster formation have been identified by site‐directed mutagenesis. The protein binds SAM and the binding alters the EPR spectrum of the FeS cluster. Our results provide biochemical support to the hypothesis that Elp3 does indeed contain the Fe4S4 cluster which characterizes the Radical SAM superfamily and binds SAM, suggesting that Elp3, in addition to its HAT activity, has a second as yet uncharacterized catalytic function. We also present preliminary data to show that the protein cleaves SAM.