bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methods for combining peptide intensities to estimate relative protein abundance
Authors: Carrillo Brian , Yanofsky Corey , Laboissiere Sylvie , Nadon Robert , Kearney Robert E. 
Published: November 2009

Abstract
Motivation: Labeling techniques are being used increasingly to estimate relative protein abundances in quantitative proteomic studies. These techniques require the accurate measurement of correspondingly labeled peptide peak intensities to produce high-quality estimates of differential expression ratios. In mass spectrometers with counting detectors, the measurement noise varies with intensity and consequently accuracy increases with the number of ions detected. Consequently, the relative variability of peptide intensity measurements varies with intensity. This effect must be accounted for when combining information from multiple peptides to estimate relative protein abundance.
Results: We examined a variety of algorithms that estimate protein differential expression ratios from multiple peptide intensity measurements. Algorithms that account for the variation of measurement error with intensity were found to provide the most accurate estimates of differential abundance. A simple Sum-of-Intensities algorithm provided the best estimates of true protein ratios of all algorithms tested.
Contact: robert.kearney@mcgill.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
GATE: software for the analysis and visualization of high-dimensional time series expression data
Authors: MacArthur Ben D. , Lachmann Alexander , Lemischka Ihor R. , Ma'ayan Avi 
Published: November 2009

Abstract
Summary: We present Grid Analysis of Time series Expression (GATE), an integrated computational software platform for the analysis and visualization of high-dimensional biomolecular time series. GATE uses a correlation-based clustering algorithm to arrange molecular time series on a two-dimensional hexagonal array and dynamically colors individual hexagons according to the expression level of the molecular component to which they are assigned, to create animated movies of systems-level molecular regulatory dynamics. In order to infer potential regulatory control mechanisms from patterns of correlation, GATE also allows interactive interroga-tion of movies against a wide variety of prior knowledge datasets. GATE movies can be paused and are interactive, allowing users to reconstruct networks and perform functional enrichment analyses. Movies created with GATE can be saved in Flash format and can be inserted directly into PDF manuscript files as interactive figures.
Availability: GATE is available for download and is free for academic use from http://amp.pharm.mssm.edu/maayan-lab/gate.htm
Contact: avi.maayan@mssm.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Rationale and design of a randomized, double‐blind, placebo‐controlled outcome trial of ivabradine in chronic heart failure: the Systolic Heart Failure Treatment with the If Inhibitor Ivabradine Trial (SHIFT)
Authors: Swedberg Karl , Komajda Michel , Böhm Michael , Borer Jeffrey S. , Ford Ian , Tavazzi Luigi 
Published: November 2009

AimsElevated heart rate is a significant marker for mortality and morbidity in cardiovascular disease including heart failure. Despite background treatment with a beta‐blocker, many patients with heart failure and low ejection fraction maintain a heart rate above 70 b.p.m. Ivabradine reduces heart rate directly through inhibition of the If ionic current.MethodsSHIFT is a randomized, double‐blind study designed to compare ivabradine with placebo on outcomes in patients with symptomatic chronic heart failure (NYHA class II–IV), left‐ventricular ejection fraction ≤35%, and a prior hospitalization for worsening heart failure within the previous 12 months. Randomized treatment is given on top of guidelines‐based therapy for chronic heart failure, including a beta‐blocker at optimized dose. Resting heart rate at baseline must be ≥70 b.p.m. The primary endpoint is the composite of the time to first event of cardiovascular death or hospitalization for worsening heart failure. Secondary endpoints include all‐cause, cardiovascular and heart failure mortality, and hospitalization. The randomized treatment period lasts approximately 12–48 months. The study will include approximately 6500 patients and will continue until ≥1600 primary endpoints have occurred. The first patient was randomized in October 2006, and the study is expected to end in 2010.ConclusionThe SHIFT study will assess if a heart rate reduction by direct sinus node inhibition can reduce cardiovascular outcomes in patients with chronic heart failure and left‐ventricular systolic dysfunction.
Comparing methods for building trophic spectra of ecological data
Authors: Libralato Simone , Solidoro Cosimo 
Published: November 2009

Abstract
Libralato, S., and Solidoro, C. 2010. Comparing methods for building trophic spectra of ecological data. – ICES Journal of Marine Science, 67: 426–434. The distribution of biomass, production, and catches over trophic levels (TLs) of the foodweb has been shown theoretically and empirically to provide powerful insights into ecosystem functioning and the effects of fishing. One approach for building trophic spectra of ecological data is based on smoothing original data and assuming zeroes when no values are available for a TL (smoothing-based method). An alternative method is proposed, based on the distribution of ecological data according to density functions (dispersion-based method), and a systematic review of the different alternatives is presented. Six different methods for building trophic spectra, i.e. the smoothing-based and five alternative forms for dispersion-based (using normal, lognormal, and Weibull distributions, also including shifted lognormal and Weibull with zero at TL 2), were applied to ecological properties (i.e. production, biomass, and catches) derived for 24 foodweb models to test their relative performance. The smoothing-based method suffers from the lack of consistency with original data and from unrealistic emergent properties, such as transfer efficiency. The analysis demonstrates the advantages of the dispersion-based method for overcoming these issues and shows, using transfer efficiencies estimated from the models (flow-based estimates) as a reference, that the normal density distribution function performs better.
The MORPHEUS protein crystallization screen
Authors: Gorrec Fabrice 
Published: November 2009

A 96-condition initial screen for protein crystallization, called MORPHEUS, has been developed at the MRC Laboratory of Molecular Biology, Cambridge, England (MRC-LMB). The concept integrates several innovative approaches, such as chemically compatible mixes of potential ligands, new buffer systems and precipitant mixes that also act as cryoprotectants. Instead of gathering a set of crystallization conditions that have already been successful, a selection of molecules frequently observed in the Protein Data Bank (PDB) to co-crystallize with proteins has been made. These have been put together in mixes of similar chemical behaviour and structure, and combined with buffers and precipitant mixes that were also derived from PDB searches, to build the screende novo. Observations made at the MRC-LMB and many practical aspects were also taken into account when formulating the screen. The resulting screen is easy to use, comprehensive yet small, and has already yielded a list of crystallization hits using both known and novel samples. As an indicator of success, the screen has now become one of the standard screens used routinely at the MRC-LMB when searching initial crystallization conditions for biological macromolecules.
An increased frequency of 13q deletions detected by fluorescence in situ hybridization and its impact on survival in children and adolescents with Burkitt lymphoma: results from the Children’s Oncology Group study CCG‐5961
Authors: Nelson Marilu , Perkins Sherrie L. , Dave Bhavana J. , Coccia Peter F. , Bridge Julia A. , Lyden Elizabeth R. , Heerema Nyla A. , Lones Mark A. , Harrison Lauren , Cairo Mitchell S. , Sanger Warren G. 
Published: November 2009

SummaryBurkitt lymphoma (BL), an aggressive B‐cell malignancy, is often curable with short intensive treatment regiments. Nearly all BLs contain rearrangements of the MYC/8q24 region; however, recent cytogenetic studies suggest that certain secondary chromosomal aberrations in BL correlate with an adverse prognosis. In this multi‐centre study, the frequency and impact on clinical outcome of del(13q) and +7 in addition to MYC rearrangements as detected by fluorescence in situ hybridization (FISH) in children and adolescents with intermediate and high‐risk BL registered on Children’s Cancer Group study CCG‐5961 were investigated. Analysis with 13q14.3 and 13q34 loci specific probes demonstrated deletions of 13q in 38/90 (42%) cases. The loss of either 13q14.3 or 13q34 alone occurred in 14% and 8% respectively, while 20% exhibited loss of both regions. Gain of chromosome 7 was observed in 7/68 (10%) cases and MYC rearrangements were detected in 84/90 (93%). Prognostic analysis controlling for known risk factors demonstrated that patients exhibiting loss of 13q, particularly 13q14.3, had a significant decrease in 5‐year overall survival (77% vs. 95%, P = 0·012). These observations indicate that del(13q) occurs in childhood BL at frequencies higher than previously detected by classical cytogenetics and underscores the importance of molecular cytogenetics in risk stratification.
A comprehensive evaluation of the prognostic significance of 13q deletions in patients with B‐chronic lymphocytic leukaemia
Authors: Van Dyke Daniel L. , Shanafelt Tait D. , Call Timothy G. , Zent Clive S. , Smoley Stephanie A. , Rabe Kari G. , Schwager Susan M. , Sonbert Jessica C. , Slager Susan L. , Kay Neil E. 
Published: November 2009

SummaryDeletion 13q14 on fluorescence in situ hybridization (FISH) analysis is the most common cytogenetic abnormality in chronic lymphocytic leukaemia (CLL), and is a favourable prognostic biomarker when detected as a sole abnormality. We intensively interrogated clinical outcome in 323 consecutive, untreated CLL patients with isolated 13q‐ identified within 2 years of diagnosis. We also analyzed outcome in 217 additional patients with deletion 11q22.3 or 17p13.1, or trisomy 12, based on whether these occurred in isolation or in conjunction with 13q‐. Patients with a heterozygous 13q‐ and those with a homozygous deletion had similar time to first treatment (TFT) and overall survival (OS). In contrast, a higher percentage of 13q‐ nuclei was associated with significantly shorter TFT (P < 0·001). The 5‐year untreated rate was 79% for patients with isolated 13q‐ in ≤65·5% of nuclei compared to 38% among those with 13q‐ in >65·5% of nuclei (P < 0·001). The percentage of nuclei exhibiting 13q‐ remained an independent predictor of TFT after controlling for ZAP‐70, IGHV, or CD38 (all P < 0·001). Among patients with 13q‐ plus one other FISH abnormality, concomitant 13q‐ appeared to attenuate the shorter survival associated with 17p‐ (P = 0·019). The clinical implications of 13q‐ in CLL appear more complex than originally appreciated.
Molecular variability of group 1 and 5 grass pollen allergens between Pooideae species: implications for immunotherapy
Authors: Chabre H. , Gouyon B. , Huet A. , Boran‐Bodo V. , Nony E. , Hrabina M. , Fenaille F. , Lautrette A. , Bonvalet M. , Maillère B. , Bordas‐Le Floch V. , Van Overtvelt L. , Jain K. , Ezan E. , Batard T. , Moingeon P. 
Published: November 2009

SummaryBackground
Differences between major allergens from distinct grass species remain to be investigated, both in terms of structure and antigenicity.Methods
Group 1 and 5 allergens purified from five common Pooideae species were analysed by mass spectrometry (MS). Major histocompatibility complex (MHC) class II‐restricted T cell epitopes were identified using predictive algorithms and human leucocyte antigen (HLA)‐binding assays. CD4+ T cell reactivity and IgE binding were assessed based on the induction of CD154 expression in peripheral blood mononuclear cells and using competitive ELISA assays, respectively.Results
MS analysis of group 5 pollen allergens reveals considerable intra‐ and inter‐species variability in amino acid sequence, with 30–50 predominant isoforms found for each species. Differences in the amino acid sequence as well as N‐ and O‐glycosylation contribute to the variability of group 1 allergens, yielding 5–10 main isoforms, depending on the species. Out of 14 MHC class II‐restricted T cell epitopes identified within group 1, only one is conserved among the five grass species. Significant differences in binding affinities for HLA‐DR molecules result in variable CD4+ T cell recognition of group 1 and 5 allergens purified from the various species. Up to 38% and 85% of patients exhibit seric IgE responses to species‐restricted (or semi‐restricted) epitopes associated with group 1 or 5 allergens, respectively.Conclusion
Major pollen allergens from distinct grass species bear both shared and species‐restricted T and B cell immune epitopes. When compared with single extracts, a five grass pollen extract is thus more suitable for specific immunotherapy, as it contains a broader repertoire of the IgE epitopes to which patients are sensitized. Cite this as: H. Chabre, B. Gouyon, A. Huet, V. Baron‐Bodo, E. Nony, M. Hrabina, F. Fenaille, A. Lautrette, M. Bonvalet, B. Maillère, V. Bordas‐Le Floch, L. Van Overtvelt, K. Jain, E. Ezan, T. Batard and P. Moingeon, Clinical & Experimental Allergy, 2010 (40) 505–519.
Outcomes of cervical liquid‐based cytology suggesting a glandular abnormality
Authors: Finall A. I. , Olafsdottir R. 
Published: November 2009

Objective:  To ascertain the positive predictive value of both ?glandular neoplasia (national standard code 6) and borderline change (national standard code 8) in glandular cells in liquid‐based cervical cytology specimens in Cardiff and Vale NHS Trust and to outline the histological outcomes of these cases.Method:  Eighty‐nine liquid‐based (Surepath™) cervical cytology cases were retrospectively identified from a 2‐year period (January 2005 to December 2006) and correlated with histopathological diagnoses.Results:  Initial punch biopsy histology revealed 18 cases (21%) of cervical glandular intraepithelial neoplasia (CGIN). A further nine cases (10%) of CGIN were identified following local excision or hysterectomy. Ten cases of invasive malignancy were identified: four endocervical adenocarcinomas (all node negative, TNM stage T1b1), five endometrial adenocarcinomas and one squamous cell carcinoma. There were 10 with high‐grade cervical intraepithelial neoplasia (CIN) alone. Women diagnosed with endometrial malignancy presented later with an average age of 64.6 years compared with 34.9 years for endocervical lesions. Taking high‐grade CIN or worse as a positive outcome, the overall positive predictive value (PPV) of glandular abnormalities on cytology (both code 6 and 8) was 58.1% [95% confidence interval (CI) 47.8, 68.4]. PPV for borderline change in glandular cells alone was 24.1% (95% CI 8.5, 39.6) and for ?glandular neoplasia alone 75.4% (95% CI 64.3, 86.5).Conclusion:  With our interpretation of the classification, women with cytological diagnoses of glandular neoplasia of the cervix should initially be investigated by local resection rather than punch biopsy, and those with borderline change in glandular cells with repeat cytology.
Acquisition and processing of simultaneous vibroseis data
Authors: Bagaini Claudio 
Published: November 2009

ABSTRACTNumerous methods have been developed in the past three decades to speed up vibroseis acquisition. This paper gives an overview of the most promising ones and proposes a classification of them into three categories: simultaneous shooting, cascaded sweeps and slip‐sweep. The principles upon which these methods are based, the processing techniques developed to separate the simultaneously acquired data and their main features are also discussed. Finally, some criteria for the selection of the most suitable methods for the acquisition and the separation stages are proposed.
Validity, reliability and acceptability of the Imperial Nutritional Screening System (INSYST): a tool that does not require the body mass index
Authors: Tammam J. D. , Gardner L. , Hickson M. 
Published: November 2009

AbstractBackground: Nutritional screening tools are central to identifying malnourished patients, but their efficacy is often reduced as a result of difficulties in obtaining height for body mass index (BMI) calculations. The present study aimed to evaluate the validity, reliability and acceptability of the Imperial Nutritional Screening System (INSYST); a tool that does not require the BMI.Methods: Patients were screened by the researcher within 72 h of admission using INSYST I & II, Malnutrition Universal Screening Tool (MUST) and Mini Nutritional Assessment (MNA), including taking height and weight. Routine INSYST data, completed by nursing staff, were subsequently collected. At risk and malnourished patients were combined for statistical analysis. Inter‐tool and inter‐rater agreement (kappa, κ) was evaluated. Sensitivity and specificity were calculated. Nurses were timed using INSYST. Acceptability, including ease and speed of use, was evaluated.Results: Kappa (agreement) scores (allP < 0.001) were substantial for INSYST I versus MUST and MNA (κ = 0.73 and κ = 0.76, respectively) and moderate for INSYST II (both κ = 0.53). The sensitivity of INSYST I and II was high (95–100%), whereas specificity was lower (65–83%). The agreement between dietitian and nurse for INSYST I was substantial κ = 0.77 and that for INSYST II was fair κ = 0.39 (bothP ≤ 0.001). There was little disagreement for INSYST I, although nurses tended to underestimate malnutrition risk when using INSYST II. INSYST I took a median of 60 s to complete, INSYST II took 102 s and weighing took 100 s, giving a total time of approximately 5 min. Likert scales showed that the majority of nurses scored INSYST as being fast and easy to use.Conclusions: INSYST has shown promising levels of concurrent validity (versus MUST and MNA), inter‐rater reliability and acceptability, suggesting that BMI (and therefore height) is unnecessary for identifying malnourished patients.
The Malnutrition Screening Tool is a useful tool for identifying malnutrition risk in residential aged care
Authors: Isenring E. A. , Bauer J. D. , Banks M. , Gaskill D. 
Published: November 2009

AbstractBackground:  The Malnutrition Screening Tool (MST) is a valid nutrition screening tool in the acute hospital setting but has not been assessed in residential aged care facilities. The aim of this secondary analysis was to determine whether the MST could be a useful nutrition screening tool when compared with a full nutrition assessment by Subjective Global Assessment (SGA) in the residential aged care setting.Methods:  Two hundred and eighty‐five residents (29% male; mean age 84 ± 9 years) from eight residential aged care facilities in Australia participated in the study. A secondary analysis of data collected during a nutrition intervention study was conducted. The MST consists of two questions related to recent weight loss and appetite. Although the MST was not specifically applied, weight loss and appetite information was available and an estimated MST score (0–5) was calculated. Nutritional status was assessed by a research assistant trained in using the SGA.Results:  Malnutrition prevalence was 42.8% (122 malnourished out of 285 residents). Compared to the SGA, the MST was an effective predictor of nutritional risk (sensitivity = 83.6%, specificity = 65.6%, positive predictive value = 0.65, negative predictive value = 0.84).Conclusions:  The components of the MST have acceptable sensitivity and specificity, suggesting that it can play a valuable role in quickly identifying the risk of malnutrition in the residential aged care setting. Further prospective research using the MST tool against a broader array of objective and subjective nutritional parameters is required to confirm its validity as a screening tool in aged care settings.
Conventional protein kinase C plays a critical role in negative regulation of CD98‐induced homotypic aggregation
Authors: Cho J. Y. , Katz D. R. , Skubitz K. M. , Chain B. M. 
Published: November 2009

Abstract CD98, a heterodimeric type II transmembrane protein, is involved in many different cellular events, ranging from amino acid transport to cell–cell adhesion. Little is known about the positive and negative signalling pathways involved in these responses. Therefore, we examined the role of conventional protein kinase C (PKC) isoforms during CD98‐induced intracellular signalling and homotypic aggregation of U937 cells. The CD98‐induced aggregation was enhanced by the general protein kinase inhibitors GF109203X and staurosporin, and by specific PKC‐α/‐β peptide inhibitor 19–27, but inhibited by PKC activators such as phorbol 12‐myristate 13‐acetate (PMA). PMA‐inhibition was reversed by PKC inhibitors recognising the ATP‐binding site in PKC (e.g. staurosporin, GF109203X and Go6983). Inhibitors which bind to diacylglycerol (DAG) or Ca2+‐binding sites of PKC (calphostin C and Go6967) had no effect. PMA‐induced translocation of conventional PKC (cPKC) isozymes (α, β and γ), but decreased the expression of PKC‐δ, which plays an important role in CD98‐induced homotypic aggregation. PMA treatment also suppressed the surface level of CD98 but not CD29, CD18 and CD147, dose‐ and time‐dependently. These data provide evidence that PMA‐responsive cPKC isoforms (α, β and γ) play a key role in negative regulation of CD98 signalling and homotypic aggregation.
Morphological evolution in Tropidurinae squamates: an integrated view along a continuum of ecological settings
Authors: GRIZANTE M. B. , NAVAS C. A. , GARLAND Jr T. , KOHLSDORF T. 
Published: November 2009

AbstractVariation in squamate foot morphology is likely relevant during evolutionary processes of habitat colonization because distinct surfaces differ in energetic and functional demands for locomotion. We combined new foot morphological data with published information of limb and tail lengths to investigate evolutionary changes possibly associated with the differential usage of ecological settings by Tropidurinae species. Several traits exhibited significant phylogenetic signal, and we performed conventional and phylogenetic regressions of PC scores (retained from Principal Components Analyses of morphometric traits) on continuous ecological indices. Tropidurines from sandy habitats exhibit larger foot soles, opposite to the evolution of narrow feet in species that use branches and rocks. Also, species that usually move along trunks present longer femora. This study provides evidence for morphological adaptations associated with substrate usage in Tropidurinae, and suggests that opposite morphological profiles might evolve associated with the use of surfaces energetically and functionally contrasting, possibly leading to trade‐offs.