bluuebunny/crossref_metadata_2025_split huggingface dataset:
Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling
Authors: Sweredoski Michael J. , Donovan Kevin J. , Nguyen Bao D. , Shaka A.J. , Baldi Pierre 
Published: September 2007

AbstractMotivation: Recent advances in cell-free protein expression systems allow specific labeling of proteins with amino acids containing stable isotopes (15N, 13 C and 2H), an important feature for protein structure determination by nuclear magnetic resonance (NMR) spectroscopy. Given this labeling ability, we present a mathematical optimization framework for designing a set of protein isotopomers, or labeling schedules, to reduce the congestion in the NMR spectra. The labeling schedules, which are derived by the optimization of a cost function, are tailored to a specific protein and NMR experiment.Results: For 2D 15N-1H HSQC experiments, we can produce an exact solution using a dynamic programming algorithm in under 2 h on a standard desktop machine. Applying the method to a standard benchmark protein, calmodulin, we are able to reduce the number of overlaps in the 500 MHz HSQC spectrum from 10 to 1 using four samples with a true cost function, and 10 to 4 if the cost function is derived from statistical estimates. On a set of 448 curated proteins from the BMRB database, we are able to reduce the relative percent congestion by 84.9% in their HSQC spectra using only four samples. Our method can be applied in a high-throughput manner on a proteomic scale using the server we developed. On a 100-node cluster, optimal schedules can be computed for every protein coded for in the human genome in less than a month.Availability: A server for creating labeling schedules for 15N-1H HSQC experiments as well as results for each of the individual 448 proteins used in the test set is available at http://nmr.proteomics.ics.uci.edu.Contact: pfbaldi@ics.uci.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Clustering by soft-constraint affinity propagation: applications to gene-expression data
Authors: Leone Michele , Sumedha  , Weigt Martin 
Published: September 2007

AbstractMotivation: Similarity-measure-based clustering is a crucial problem appearing throughout scientific data analysis. Recently, a powerful new algorithm called Affinity Propagation (AP) based on message-passing techniques was proposed by Frey and Dueck (2007a). In AP, each cluster is identified by a common exemplar all other data points of the same cluster refer to, and exemplars have to refer to themselves. Albeit its proved power, AP in its present form suffers from a number of drawbacks. The hard constraint of having exactly one exemplar per cluster restricts AP to classes of regularly shaped clusters, and leads to suboptimal performance, e.g. in analyzing gene expression data.Results: This limitation can be overcome by relaxing the AP hard constraints. A new parameter controls the importance of the constraints compared to the aim of maximizing the overall similarity, and allows to interpolate between the simple case where each data point selects its closest neighbor as an exemplar and the original AP. The resulting soft-constraint affinity propagation (SCAP) becomes more informative, accurate and leads to more stable clustering. Even though a new a priori free parameter is introduced, the overall dependence of the algorithm on external tuning is reduced, as robustness is increased and an optimal strategy for parameter selection emerges more naturally. SCAP is tested on biological benchmark data, including in particular microarray data related to various cancer types. We show that the algorithm efficiently unveils the hierarchical cluster structure present in the data sets. Further on, it allows to extract sparse gene expression signatures for each cluster.Contact: leone@isi.it, sumedha@isi.it and weigt@isi.it
SnoReport: computational identification of snoRNAs with unknown targets
Authors: Hertel Jana , Hofacker Ivo L. , Stadler Peter F. 
Published: September 2007

AbstractSummary: Unlike tRNAs and microRNAs, both classes of snoRNAs, which direct two distinct types of chemical modifications of uracil residues, have proved to be surprisingly difficult to find in genomic sequences. Most computational approaches so far have explicitly used the fact that snoRNAs predominantly target ribosomal RNAs and spliceosomal RNAs. The target is specified by a short stretch of sequence complementarity between the snoRNA and its target. This sequence complementarity to known targets crucially contributes to sensitivity and specificity of snoRNA gene finding algorithms.The discovery of ‘orphan’ snoRNAs, which either have no known target, or which target ordinary protein-coding mRNAs, however, begs the question whether this class of ‘housekeeping’ non-coding RNAs is much more widespread and might have a diverse set of regulatory functions. In order to approach this question, we present here a combination of RNA secondary structure prediction and machine learning that is designed to recognize the two major classes of snoRNAs, box C/D and box H/ACA snoRNAs, among ncRNA candidate sequences. The snoReport approach deliberately avoids any usage of target information. We find that the combination of the conserved sequence boxes and secondary structure constraints as a pre-filter with SVM classifiers based on a small set of structural descriptors are sufficient for a reliable identification of snoRNAs.Tests of snoReport on data from several recent experimental surveys show that the approach is feasible; the application to a dataset from a large-scale comparative genomics survey for ncRNAs suggests that there are likely hundreds of previously undescribed ‘orphan’ snoRNAs still hidden in the human genome.Availability: The snoReport software is implemented in ANSI C. The source code is available under the GNU Public License at http://www.bioinf.uni-leipzig.de/Software/snoReport.Supplementary Material is available at http://www.bioinf.uni-leipzig.de/Publications/SUPPLEMENTS/07-015Contact: jana@bioinf.uni-leipzig.deSupplementary information: Supplementary data are available at Bioinformatics online.
Reducing Beta‐Glucan Solubility in Oat Bran Muffins by Freeze‐Thaw Treatment Attenuates Its Hypoglycemic Effect
Authors: Lan‐Pidhainy Xiaomiao , Brummer Yolanda , Tosh Susan M. , Wolever Thomas M. , Wood Peter J. 
Published: October 2007

ABSTRACTThe viscosity of soluble fibers such as β‐glucan depends on their concentration in solution and molecular weight (MW) distribution. We investigated whether freezing treatment of oat bran muffins affected the physicochemical properties of β‐glucan, and its physiological effectiveness in lowering postprandial blood glucose response. A controlled range of β‐glucan solubility was achieved by subjecting oat bran muffins containing two levels of β‐glucan to repeated freeze‐thaw temperature cycling. β‐Glucan solubilized by in vitro digestion extraction was measured by flow‐injection analysis. MW distributions of β‐glucan were analyzed using size‐exclusion chromatography. β‐Glucan solubility decreased as the number of freeze‐thaw cycles increased, while MW distribution of β‐glucan decreased slightly. Peak blood glucose rise (PBGR) after fresh muffins (8 and 12 g of β‐glucan/serving) was significantly lower than that after muffins (8 and 12 g of β‐glucan/serving) treated with four freeze‐thaw (FT) cycles (1.84 ± 0.2 vs. 2.31 ± 0.1 mmol/L, P = 0.007). Compared with the control whole wheat muffins, the reduction in incremental area under the glucose response curve (AUC) after fresh muffins (8 and 12 g of β‐glucan/serving) was nearly twice that after 4 FT cycles (43.3 ± 4.4% vs. 27.0 ± 5.4%, P = 0.016). A significant inverse linear relationship was found between the log [concentration] of extractable β‐glucan and PBGR (r2 = 0.85, P = 0.01), and AUC (r2 = 0.71, P = 0.03). The results show that reduction of β‐glucan solubility in foods attenuates its physiological effectiveness in lowering postprandial glycemia.
Imaging Exocytosis with Total Internal Reflection Microscopy (TIRFM)
Authors: Zenisek David , Perrais David 
Published: October 2007

INTRODUCTIONAlthough electrophysiological techniques such as membrane capacitance measurements, electrochemical detection, and post-synaptic recordings are powerful ways of studying exocytosis, information concerning any steps prior to vesicle fusion must be inferred indirectly. Total internal reflection fluorescence microscopy (TIRFM) is a powerful technique for studying events that, like exocytosis, occur near a cell surface. The technique allows selective imaging of fluorescent molecules that are closest to a high refractive index substance such as glass. In this protocol, TIRFM is used to investigate the steps leading up to vesicle fusion in both retinal bipolar neurons and chromaffin cells by directly imaging synaptic vesicles and dense core granules prior to and including exocytosis.
Transposon-Mediated Transgenesis in Rats
Authors: Jang Chuan-Wei , Behringer Richard R. 
Published: October 2007

INTRODUCTIONThis protocol describes a method for the production of transgenic rats by coinjecting circular PiggyBac transposon-containing plasmid DNA with transposase-encoding mRNA. After fertilized eggs are collected from females, pronuclei are microinjected with the DNA and mRNA and then transferred immediately into the oviducts of pseudopregnant foster females. Using this procedure, we have obtained transformation frequencies of 33%-100% (average of ~80%). Traditional methods for generating transgenic rats (i.e., microinjection of linear DNA) yield 3%-41% transgenic founders. Thus, transposon-mediated transformation of fertilized rat eggs is an efficient alternative method to generate transgenic rats.
Principles of Multiphoton-Excitation Fluorescence Microscopy
Authors: Denk Winfried 
Published: October 2007

INTRODUCTIONFluorescence microscopy has been gaining importance in quantitative biological research due to dramatic improvements in fluorophores, optical systems, light sources, and detectors. In particular, confocal fluorescence microscopy, usually by laser scanning, has for the first time allowed the observation of biological processes with high spatial resolution inside intact living tissue. Often called “optical sectioning,” this method allows spatial reconstruction of 3D specimens without the use of a microtome. This article presents the physical mechanisms upon which the properties of multiphoton microscopy are based and discusses some practical aspects of its implementation.
Lack of association between CpG island methylator phenotype in human gastric cancers and methylation in their background non‐cancerous gastric mucosae
Authors: Enomoto Shotaro , Maekita Takao , Tsukamoto Tetsuya , Nakajima Takeshi , Nakazawa Kazuyuki , Tatematsu Masae , Ichinose Masao , Ushijima Toshikazu 
Published: September 2007

The presence of high levels of aberrant DNA methylation in gastric mucosae correlates with risk of gastric cancer. Some gastric cancers are known to have methylation of multiple CpG islands (CGI), which is referred to as the CGI methylator phenotype (CIMP). In the present study, we aimed to clarify the possible association between the CIMP in cancers and high methylation levels in their background mucosae by accurate quantitative methylation analysis of 14 carefully selected promoter CGI. Methylation levels were measured in 66 cancers and their background mucosae, along with 19 normal mucosae of healthy volunteers. Methylation in cancers was classified as absent (methylation level = 0%) or positive. The number of methylated CGI in a cancer showed a continuous distribution, and cancers were classified as CIMP high (21 cases), CIMP low (30 cases), or CIMP negative (15 cases). CIMP‐high gastric cancer patients had significantly better survival rates than CIMP‐negative patients. Of the Epstein–Barr virus‐positive gastric cancers studied, eight out of nine presented as CIMP high. Methylation in background mucosae showed a unimodal distribution, and was assessed by their degree. The gastric mucosae of cancer patients showed higher levels than normal gastric mucosae of healthy volunteers. Finally, the CIMP‐high, CIMP‐low, and CIMP‐negative statuses in cancers were not associated with methylation levels of individual genes and their means in the background mucosae. These showed that the CIMP statuses in gastric cancers had no association with methylation levels in the background gastric mucosae. (Cancer Sci 2007; 98: 1853–1861)
Reference range of thyroid hormones in normal Indian school‐age children
Authors: Marwaha R. K. , Tandon Nikhil , Desai Ankush , Kanwar Ratnesh , Grewal Khushi , Aggarwal Rashmi , Sastry Aparna , Singh Satveer , Ganguly S. K. , Mani Kalaivani 
Published: September 2007

SummaryObjective  There is an ongoing debate on narrowing the TSH reference range in adults. In view of the scarce data on normal values of thyroid function tests in children from India, we planned to establish a reference range for thyroid hormones in school‐age children.Design and subjects  All children (N = 9527; 6–19 years) from six schools representing various zones of Delhi were evaluated for clinical evidence of goitre, thyroid ultrasound, serum free T3 (FT3), free T4 (FT4) and TSH and anti‐thyroid peroxidase (anti‐TPO) antibodies. From this sample, a reference population (N = 5122) was obtained by excluding those with a personal or family history of thyroid disease, use of thyroid medications, goitre, hypoechogenicity/nodularity on ultrasound or serum anti‐TPO antibodies.Measurements  Thyroid hormone (FT3, FT4 and TSH) reference ranges were established for each year of life for the total and reference populations.Results  In the reference population, mean serum FT3 was in the range 4·19–4·84 pm/l for boys and 4·03–4·47 pm/l for girls, mean serum FT4 14·69–17·36 pm/l for boys and 14·32–15·88 pm/l for girls, and mean serum TSH 2·57–3·6 mIU/l for boys and 1·83–3·58 mIU/l for girls. For TSH, the 97th percentile was in the range 6·01–8·4 mIU/l for boys and 5·28–8·04 mIU/l for girls, suggesting that at least in children there may not be a need to reduce the upper limit of normal for serum TSH.Conclusions  This study provides mean reference intervals for FT3, FT4 and TSH for each year of life for both the sexes separately using strict exclusion criteria.
Ontogenetic changes in the drifting of four species of elmid beetles elucidate the complexity of drift‐benthos relationships in a small stream in Northwest England
Authors: ELLIOTT J. M. 
Published: September 2007

Summary1. This study aimed to quantify ontogenetic changes in the drifting of Elmis aenea, Oulimnius tuberculatus, Esolus parallelepipedus and Limnius volkmari (Coleoptera: Elmidae), and to relate their drift to benthic density. Monthly samples were taken over 39 months, using three surface nets at each of two contrasting sites in a small stream: one in a deep section with abundant macrophytes, and the other in a shallow stony section.2. Most larvae and adults were taken in the drift at night with little variation between catches in the three nets at each site. Day catches were very low, often zero. No significant relationships could be established between mean numbers in the drift catches and benthic densities.3. When night catches were converted to drift densities (number caught per 100 m3 of water sampled), the latter were positively related to monthly losses in the benthos, but not to benthic densities. A linear regression described the relationship, and equations for the different life‐stages within each species were not significantly different from the equation for all life‐stages combined. However, drift losses were only about 0.07% of total losses in the benthos. A severe spate in October 1967 increased the number of larvae and adults in the drift, but not drift densities, except for immature adults of E. aenea, O. tuberculatus and E. parallelepipedus.4. Key life‐stages with the highest drift density were the earliest life‐stage soon after egg hatching for E. aenea, the start of the larval overwintering period for O. tuberculatus and L. volkmari, and mature adults during the mating season for all three species. Drift density for E. parallelepipedus was too low to identify a key life‐stage. These key life‐stages corresponded with critical periods for survival in the life cycle, as identified in an earlier study in the same stream. Mortality was high during these critical periods, hence the strong relationship between drift density and benthic losses. The latter relationship was very consistent for different life‐stages within each species, and partially supported the rarely‐tested hypothesis that drift represents surplus production in the benthos.
Anisotropic reverse‐time migration for tilted TI media
Authors: Du Xiang , Bancroft John C. , Lines Larry R. 
Published: September 2007

ABSTRACTSeismic anisotropy in dipping shales results in imaging and positioning problems for underlying structures. We develop an anisotropic reverse‐time depth migration approach for P‐wave and SV‐wave seismic data in transversely isotropic (TI) media with a tilted axis of symmetry normal to bedding. Based on an accurate phase velocity formula and dispersion relationships for weak anisotropy, we derive the wave equation for P‐wave and SV‐wave propagation in tilted transversely isotropic (TTI) media. The accuracy of the P‐wave equation and the SV‐wave equation is analyzed and compared with other acoustic wave equations for TTI media. Using this analysis and the pseudo‐spectral method, we apply reverse‐time migration to numerical and physical‐model data. According to the comparison between the isotropic and anisotropic migration results, the anisotropic reverse‐time depth migration offers significant improvements in positioning and reflector continuity over those obtained using isotropic algorithms.
Global evidence that deforestation amplifies flood risk and severity in the developing world
Authors: BRADSHAW COREY J. A. , SODHI NAVJOT S. , PEH KELVIN S.‐H. , BROOK BARRY W. 
Published: September 2007

AbstractWith the wide acceptance of forest‐protection policies in the developing world comes a requirement for clear demonstrations of how deforestation may erode human well‐being and economies. For centuries, it has been believed that forests provide protection against flooding. However, such claims have given rise to a heated polemic, and broad‐scale quantitative evidence of the possible role of forests in flood protection has not been forthcoming. Using data collected from 1990 to 2000 from 56 developing countries, we show using generalized linear and mixed‐effects models contrasted with information‐theoretic measures of parsimony that flood frequency is negatively correlated with the amount of remaining natural forest and positively correlated with natural forest area loss (after controlling for rainfall, slope and degraded landscape area). The most parsimonious models accounted for over 65% of the variation in flood frequency, of which nearly 14% was due to forest cover variables alone. During the decade investigated, nearly 100 000 people were killed and 320 million people were displaced by floods, with total reported economic damages exceeding US$1151 billion. Extracted measures of flood severity (flood duration, people killed and displaced, and total damage) showed some weaker, albeit detectable correlations to natural forest cover and loss. Based on an arbitrary decrease in natural forest area of 10%, the model‐averaged prediction of flood frequency increased between 4% and 28% among the countries modeled. Using the same hypothetical decline in natural forest area resulted in a 4–8% increase in total flood duration. These correlations suggest that global‐scale patterns in mean forest trends across countries are meaningful with respect to flood dynamics. Unabated loss of forests may increase or exacerbate the number of flood‐related disasters, negatively impact millions of poor people, and inflict trillions of dollars in damage in disadvantaged economies over the coming decades. This first global‐scale empirical demonstration that forests are correlated with flood risk and severity in developing countries reinforces the imperative for large‐scale forest protection to protect human welfare, and suggests that reforestation may help to reduce the frequency and severity of flood‐related catastrophes.
Assembly of pili on the surface of Bacillus cereus vegetative cells
Authors: Budzik Jonathan M. , Marraffini Luciano A. , Schneewind Olaf 
Published: September 2007

SummaryVegetative forms of Bacillus cereus are reported to form pili, thin protein filaments that protrude up to 1 μm from the bacterial surface. Pili are assembled from two precursor proteins, BcpA and BcpB, in a manner requiring a pilus‐associated sortase enzyme (SrtD). Pili are also formed on the surface of Bacillus anthracis expressing bcpA‐srtD‐bcpB. BcpA is distributed throughout the entire pilus, whereas BcpB appears positioned at its tip. In agreement with the hypothesis for pilus assembly in Gram‐positive bacteria, BcpA encompasses the YPK pilin motif and the LPXTG sorting signal, each of which is absolutely required for the incorporation of BcpA and BcpB into pili. In contrast to BcpB, which relies on the presence of BcpA for incorporation into pili, BcpA fibre assembly occurs even in the absence of BcpB. B. anthracis sortase A (srtA), but not sortase B (srtB) or C (srtC), is required for proper anchoring of pili to the bacterial envelope, suggesting that BcpA/BcpB pili are linked to peptidoglycan cross‐bridges.
AtKC1, a conditionally targeted Shaker‐type subunit, regulates the activity of plant K+ channels
Authors: Duby Geoffrey , Hosy Eric , Fizames Cécile , Alcon Carine , Costa Alex , Sentenac Hervé , Thibaud Jean‐Baptiste 
Published: September 2007

SummaryAmongst the nine voltage‐gated K+ channel (Kv) subunits expressed in Arabidopsis, AtKC1 does not seem to form functional Kv channels on its own, and is therefore said to be silent. It has been proposed to be a regulatory subunit, and to significantly influence the functional properties of heteromeric channels in which it participates, along with other Kv channel subunits. The mechanisms underlying these properties of AtKC1 remain unknown. Here, the transient (co‐)expression of AtKC1, AKT1 and/or KAT1 genes was obtained in tobacco mesophyll protoplasts, which lack endogenous inward Kv channel activity. Our experimental conditions allowed both localization of expressed polypeptides (GFP‐tagging) and recording of heterologously expressed Kv channel activity (untagged polypeptides). It is shown that AtKC1 remains in the endoplasmic reticulum unless it is co‐expressed with AKT1. In these conditions heteromeric AtKC1‐AKT1 channels are obtained, and display functional properties different from those of homomeric AKT1 channels in the same context. In particular, the activation threshold voltage of the former channels is more negative than that of the latter ones. Also, it is proposed that AtKC1‐AKT1 heterodimers are preferred to AKT1‐AKT1 homodimers during the process of tetramer assembly. Similar results are obtained upon co‐expression of AtKC1 with KAT1. The whole set of data provides evidence that AtKC1 is a conditionally‐targeted Kv subunit, which probably downregulates the physiological activity of other Kv channel subunits in Arabidopsis.