bluuebunny/crossref_metadata_2025_split huggingface dataset:
PROTEIN SIDE-CHAIN PACKING PROBLEM: A MAXIMUM EDGE-WEIGHT CLIQUE ALGORITHMIC APPROACH
Authors: DUKKA BAHADUR K. C. , TOMITA ETSUJI , SUZUKI JUN'ICHI , AKUTSU TATSUYA 
Published: February 2005

"Protein Side-chain Packing" has an ever-increasing application in the field of bio-informatics, dating from the early methods of homology modeling to protein design and to the protein docking. However, this problem is computationally known to be NP-hard. In this regard, we have developed a novel approach to solve this problem using the notion of a maximum edge-weight clique. Our approach is based on efficient reduction of protein side-chain packing problem to a graph and then solving the reduced graph to find the maximum clique by applying an efficient clique finding algorithm developed by our co-authors. Since our approach is based on deterministic algorithms in contrast to the various existing algorithms based on heuristic approaches, our algorithm guarantees of finding an optimal solution. We have tested this approach to predict the side-chain conformations of a set of proteins and have compared the results with other existing methods. We have found that our results are favorably comparable or better than the results produced by the existing methods. As our test set contains a protein of 494 residues, we have obtained considerable improvement in terms of size of the proteins and in terms of the efficiency and the accuracy of prediction.
Can Zipf's law be adapted to normalize microarrays?
Authors: Lu Tim , Costello Christine M , Croucher Peter JP , Häsler Robert , Deuschl Günther , Schreiber Stefan 
Published: February 2005

Abstract
Background
Normalization is the process of removing non-biological sources of variation between array experiments. Recent investigations of data in gene expression databases for varying organisms and tissues have shown that the majority of expressed genes exhibit a power-law distribution with an exponent close to -1 (i.e. obey Zipf's law). Based on the observation that our single channel and two channel microarray data sets also followed a power-law distribution, we were motivated to develop a normalization method based on this law, and examine how it compares with existing published techniques. A computationally simple and intuitively appealing technique based on this observation is presented.

Results
Using pairwise comparisons using MA plots (log ratio vs. log intensity), we compared this novel method to previously published normalization techniques, namely global normalization to the mean, the quantile method, and a variation on the loess normalization method designed specifically for boutique microarrays. Results indicated that, for single channel microarrays, the quantile method was superior with regard to eliminating intensity-dependent effects (banana curves), but Zipf's law normalization does minimize this effect by rotating the data distribution such that the maximal number of data points lie on the zero of the log ratio axis. For two channel boutique microarrays, the Zipf's law normalizations performed as well as, or better than existing techniques.

Conclusion
Zipf's law normalization is a useful tool where the Quantile method cannot be applied, as is the case with microarrays containing functionally specific gene sets (boutique arrays).
Individual patient data meta-analysis : Cervical stitch (cerclage) for preventing pregnancy loss in women
Authors: Tudur-Smith Catrin , Jorgensen Andrea L , Alfirevic Zarko , Williamson Paula R 
Published: February 2005

Abstract

Background
Cervical cerclage is a surgical procedure involving suturing the cervix with a purse type stitch to keep it closed during pregnancy. This procedure has been used widely in the management of pregnancies considered at high risk of preterm delivery. Several observational studies into the efficacy of cervical cerclage have claimed high rates of successful pregnancy outcome in women with a poor obstetric history attributed to cervical incompetence. However, a recent aggregate data Cochrane review found no such conclusive evidence from seven included randomised studies. Current data suggests that cervical cerclage is likely to benefit women considered to be 'at very high risk' of a second trimester miscarriage due to a cervical factor, however identifying such women remains elusive and many women may be treated unnecessarily. Undertaking an individual patient data (IPD) meta-analysis of the studies will allow us to investigate whether treatment is more effective in particular subgroups. Such an analysis will also provide a more powerful analysis of the predictors of preterm delivery and pregnancy loss, including ultrasound measurement of cervical length, and will allow a more complete analysis of 'time to event' outcomes.

Methods/Design
The analysis will include data from randomised trials comparing the intervention of elective cerclage versus no cerclage or bedrest to prevent miscarriage or pre-term labour. A specific list of data will be requested for each trial, including demographic and obstetric history data. The primary outcomes of interest will be neonatal mortality/morbidity. Attention will also be given to secondary outcomes such as time from randomisation to delivery, preterm delivery before 32 weeks and maternal morbidity. An intention to treat analysis will be performed, with attention paid to assessing clinical and statistical heterogeneity. Multilevel models with patients and trials as the two levels will be explored to investigate treatment effect on various outcomes. Patient-level covariates will be incorporated into the models in an attempt to account for statistical heterogeneity as well as to investigate interactions with treatment effect.

Discussion
Predictive models generated from our analysis should lead to more effective counselling of women at risk and a more cost effective use of cerclage.
A comparative study on the degradation of cotton linters induced by carbonate and hydroxyl radicals generated from peroxynitrite
Authors: Carlsson Magnus , Stenman David , Merényi Gábor , Reitberger Torbjörn 
Published: February 2005

Abstract
Carbonate (CO3
•−) and hydroxyl (HO•) radicals were chemically produced in cotton linter suspensions using peroxynitrite as a radical precursor. Both radicals could degrade cotton linters, as shown by viscosity and GPC-SEC measurements. As evidenced by the viscosity measurements, the presence of oxygen during the cotton linter treatments slightly increased cellulose degradation by both radicals. For the carbonate radical, more than 90% of the viscosity losses could be recovered by reductive NaBH4 treatment before measuring the viscosity, whereas only approximately 40% of the viscosity was recovered after hydroxyl radical degradation and subsequent NaBH4 treatment. This indicates that carbonate radicals mainly abstract H-atoms adjacent to hydroxyl groups, i.e., at C2, C3 and C6. This intramolecular selectivity may reflect a polar effect, whereby hydrogen atom abstractions from these positions are favoured. In addition, abstraction at C6 would be sterically and statistically favoured.
Biomechanical pulping of spruce wood chips with Streptomyces cyaneus CECT 3335 and handsheet characterization
Authors: Hernández Manuel , Hernández-Coronado M. Jesus , Pérez M. Isabel , Revilla Esteban , Villar Juan C. , Ball Andrew S. , Viikari Liisa , Arias M. Enriqueta 
Published: February 2005

AbstractThe actinobacteriumStreptomyces cyaneusCECT 3335 was evaluated for its ability to delignify spruce wood chips (Picea abies) after 2 weeks of incubation prior to refiner mechanical pulping. Weight loss of the chips during the treatment ranged from 2% to 3%. Chemicalanalysis of the treated wood showed an increase in acid-soluble lignin content concomitant with a notable increase in the acid/aldehyde+ketone [AC/(AL+KE)] ratio of the lignin compared with the control. Structural alterations in wood cell walls were observed by optical and scanning microscopy using astra blue-safranin staining and cryosections stained with gold/palladium, respectively. A gradual loss of lignin from the lumen towards the middle lamella and incipient defiberization could be observed. The estimation of specific energy for the defibration and refining stages of treated pulp showed a 24% reduction in the energy required, largely due to a 30% saving in the defibration of chips. The analysis of handsheets obtained from treated pulp showed a notable improvement in some strength properties, such as breaking length, tear index and stretch. In addition, the high Gurley air resistance value indicates more packing of the voids of the fiber network. These results demonstrate for the first time the suitability ofStreptomyces cyaneusfor biomechanical pulping purposes.
Mass loss and moisture dynamics of Scots pine (Pinus sylvestris L.) exposed outdoors above ground in Sweden
Authors: Rydell Åsa , Bergström Mikael , Elowson Torbjörn 
Published: February 2005

Abstract
The durability of 566 Scots pine (Pinus sylvestris) samples was tested during a period of 9 years of exposure to weather in Sweden. The parameters investigated were heartwood/sapwood, origin, surface treatment, end-seal, storage and drying method, annual ring width and density. The weight was measured on 67 occasions during 9 years in order to assess the moisture content of the samples. The mass loss was determined for each sample at the end of the trial. Sapwood had a higher moisture uptake and a higher mass loss compared with heartwood. Even if sapwood was painted with an impermeable paint and then end-sealed, it still had higher average moisture content than heartwood. The results also demonstrated that sapwood was more sensitive to different handling conditions than heartwood. Sapwood was sensitive to air-drying and water storage, which was evident in the higher moisture uptake. In terms of mass loss, some differences were evident but they were not statistically significant due to the large standard deviation of the sapwood samples from water-stored logs. The only positive influence of water storage was on samples end-dipped in oil. One explanation could be that water storage led to increased permeability due to bacterial attack, which in turn enhanced the penetration of the oil. Heartwood had low and stable moisture dynamics during the test period, almost independent of treatment or handling conditions. No correlation with moisture uptake or mass loss was evident among annual ring width, origin or density.
The influence of cation and anion structure of new quaternary ammonium salts on adsorption and leaching
Authors: Zabielska-Matejuk Jadwiga 
Published: February 2005

Abstract
This study examined the effect of cation and anion chemical structure of new quaternary ammonium and imidazolium compounds (QAC, bis-QAC, IC, bis-IC) on the adsorption onto Scots pine wood (Pinus sylvestris L.) and resistance to water leaching. The group of copper (II) modified QACs, containing copper-chloro-acetate complexes in the anion structure, was also examined. The length of alkyl hydrophobic substituents in the cation structure significantly influences adsorption. The adsorption characteristics were statistically related to the alkyl chain length of new quaternary ammonium salts (quantitative correlations between CMC and adsorption values). Bis-ICs adsorb onto Scots pine wood with the greatest difficulty and the slowest and are also leached to the greatest degree. A varied adsorption of chloride ion cations and a several times higher leaching of chlorides than cations of the examined salts from the saturated wood were observed. The anion modification of bis-QAC and bis-IC of copper-chloro-acetate complexes causes decreased adsorption and resistance to the leaching of these salts. As a result of the performed regression analysis of Langmuir and Freundlich adsorption isotherms, it was found that the adsorption of the examined compounds onto wood was governed by both chemical and physical processes. New quaternary ammonium and imidazolium compounds represent potential wood preservatives.
Comparison of Pinus taeda L. wood property calibrations based on NIR spectra from the radial-longitudinal and radial-transverse faces of wooden strips
Authors: Schimleck Laurence R. , Stürzenbecher Reinhard , Mora Christian , David Jones P. , Daniels Richard F. 
Published: February 2005

Abstract
When a radial strip is cut from an increment core it can potentially be cut with two orientations: parallel to longitudinal tracheids, i.e., a radial-longitudinal (RL) strip (the orientation of SilviScan samples), or at an orientation of 90° to the tracheids, i.e., a radial-transverse (RT) strip. Both strips could be used for near-infrared (NIR) analysis, but it is unknown how calibrations based on RT-face NIR spectra compare with those based on RL-face NIR spectra. A total of 20 Pinus taeda L. (loblolly pine) RL strips were characterized in terms of air-dry density, microfibril angle (MFA), stiffness and several tracheid morphological characteristics. NIR spectra were collected in 10-mm increments from the RL and RT faces of matching strips and used to develop calibrations for each property. In general, RL-face NIR spectra gave calibrations that provided stronger relationships. Differences between the two sets of calibrations were small, indicating that either face could be used for NIR analysis.
Properties of chemically and mechanically isolated fibres of spruce (Picea abies[L.] Karst.). Part 2: Twisting phenomena
Authors: Burgert Ingo , Frühmann Klaus , Keckes Jozef , Fratzl Peter , Stanzl-Tschegg Stefanie 
Published: February 2005

Abstract
The twisting behaviour of chemically and mechanically isolated fibres of spruce (Picea abies[L.] Karst.) was examined. Mechanical isolation was carried out using very fine tweezers to obtain fibres with an unmodified cell wall assembly. Chemical isolation was achieved using hydrogen peroxide and glacial acetic acid, leading to partial degradation of lignin and hemicelluloses. Besides normal adult wood, compression wood and opposite wood fibres were investigated. Fibre twisting while drying increased with higher microfibril angles in the S2 layer, and was significantly less pronounced for mechanically isolated compared to chemically macerated fibres. A simple model is introduced that takes into account the interdependency between lateral cell-wall shrinkage and the microfibril angle in the S2 cell wall.
Radiometric method for the study of the corrosion reactions of steel samples in strongly acidic media
Authors: Cecal Alexandru , Popa Karin , Draghici Camelia L. 
Published: February 2005

Abstract
This study investigates the corrosion of OL–37, OL–60 and 316L type steel samples immersed in acidic media (HCl, HClO4, H2SO4 and HNO3), based on a new radioactive tracer method. This procedure, used for the determination of the global rate constant of metal corrosion reaction, is based on the screening of β
--rays emitted by 204Tl+ radionuclides, present in the aggressive medium of the iron ions which are formed during the process. The global rate constants of corrosion reaction decrease, for a certain metallic sample, in the series HCl > HClO4 > H2SO4 > HNO3, and increase with the concentration of the used acid. For a given aggressive solution, the corrosion process decreased with the decreasing of the carbon amount in each steel sample.
Eu(III), Sm(III), Np(V), Pu(V), and Pu(IV) sorption to calcite
Authors: Zavarin Mavrik , Roberts S. K. , Hakem N. , Sawvel A. M. , Kersting A. B. 
Published: February 2005

Abstract
The sorption behavior of Eu(III), Sm(III), Np(V), Pu(V), and Pu(IV) in the presence of calcite and as a function of pH and carbonate alkalinity was measured by batch sorption experiments. Eu(III) and Sm(III) sorption is similar, consistent with their observed aqueous speciation and precipitation behavior. For both rare earth elements, sorption decreases at the highest and lowest measured pHs. This is likely the result of speciation changes both of the calcite surface and the sorber. An increase in the equilibrium CO2(g) fugacity results in a shift in the sorption behavior to lower pH, consistent with a predicted aqueous speciation shift. Np(V) and Pu(V) sorption exhibited a strong pH dependence. For Np(V), K
ds range from 0 to 217 mL/g suggesting that carbonate aqueous speciation as well as changes in the calcite surface speciation greatly affect Np(V) sorption to the calcite surface. Similar behavior was found for Pu(V). Pu(IV) sorption is also strongly pH dependent. Sorption decreases significantly at high pH as a result of Pu-carbonate complexation in solution. A surface complexation model of Sm(III), Eu(III), Np(V), Pu(V), and Pu(IV) sorption to the calcite surface was developed based on the calcite surface speciation model of Pokrovsky and Schott [1]. Sorption data were fit using one or two surface species for each sorber and could account for the effect of pH and CO2(g) fugacity on sorption. A relatively poor model fit to Pu(IV) sorption data at high pH may result from our poor understanding of Pu(IV)-carbonate aqueous speciation. While our surface complexation model may not represent a unique solution to the sorption data, it illustrates that a surface complexation modeling approach may adequately describe the sorption behavior of a number of radionuclides at the calcite surface over a range of solution conditions.
Identification of a Novel Point Mutation of Mouse Proto-Oncogene c-kit Through N-Ethyl-N-nitrosourea MutagenesisSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY536430 and AY536431.
Authors: Ruan Hai-Bin , Zhang Nian , Gao Xiang 
Published: February 2005

Abstract
Manipulation of the mouse genome has emerged as an important approach for studying gene function and establishing human disease models. In this study, the mouse mutants were generated through N-ethyl-N-nitrosourea (ENU)-induced mutagenesis in C57BL/6J mice. The screening for dominant mutations yielded several mice with fur color abnormalities. One of them causes a phenotype similar to that shown by dominant-white spotting (W) allele mutants. This strain was named Wads because the homozygous mutant mice are white color, anemic, deaf, and sterile. The new mutation was mapped to 42 cM on chromosome five, where proto-oncogene c-kit resides. Sequence analysis of c-kit cDNA from Wadsm/m revealed a unique T-to-C transition mutation that resulted in Phe-to-Ser substitution at amino acid 856 within a highly conserved tyrosine kinase domain. Compared with other c-kit mutants, Wads may present a novel loss-of-function or hypomorphic mutation. In addition to the examination of adult phenotypes in hearing loss, anemia, and mast cell deficiency, we also detected some early developmental defects during germ cell differentiation in the testis and ovary of neonatal Wadsm/m mice. Therefore, the Wads mutant may serve as a new disease model of human piebaldism, anemia, deafness, sterility, and mast cell diseases.
The First Steps of Transposable Elements Invasion
Authors: Le Rouzic Arnaud , Capy Pierre 
Published: February 2005

Abstract
Transposable elements are often considered as selfish DNA sequences able to invade the genome of their host species. Their evolutive dynamics are complex, due to the interaction between their intrinsic amplification capacity, selection at the host level, transposition regulation, and genetic drift. Here, we propose modeling the first steps of TE invasion, i.e., just after a horizontal transfer, when a single copy is present in the genome of one individual. If the element has a constant transposition rate, it will disappear in most cases: the elements with low-transposition rate are frequently lost through genetic drift, while those with high-transposition rate may amplify, leading to the sterility of their host. Elements whose transposition rate is regulated are able to successfully invade the populations, thanks to an initial transposition burst followed by a strong limitation of their activity. Self-regulation or hybrid dysgenesis may thus represent some genome-invasion parasitic strategies.
Agenesis of tibia with bifid femur, congenital heart disease, and cleft lip with cleft palate or tracheoesophageal fistula: Possible variants of Gollop‐Wolfgang complex
Authors: Erickson Robert P. 
Published: February 2005

AbstractTwo patients with bifurcation of one femur, ipsilateral absence of tibia and one partially formed tibia, or bilateral absent tibiae, club feet with normal or nearly normal digits, congenital heart disease and, in one case, tracheoesophageal fistula; in the second, cleft lip and cleft palate and enlarged head with increased fluid and lissencephaly, are described. These appear to be unique combinations of defects but overlap with the Gollop‐Wolfgang complex is present, particularly with the case of possible Gollop‐Wolfgang described by Raas‐Rothschild et al. (1999); Am J Med Genet 84:361–364. © 2005 Wiley‐Liss, Inc.
Radiation‐induced grafting of glycidyl methacrylate onto high‐density polyethylene (HDPE) and radiation lamination of HDPE
Authors: Li Zhirong , Wang Huiliang 
Published: February 2005

AbstractRadiation‐induced grafting of glycidyl meth‐acrylate (GMA) onto high‐density polyethylene (HDPE) and the radiation lamination of HDPE by bulk grafting of GMA were reported. The effects of irradiation dose, monomer concentration, and atmosphere on grafting were investigated. The extent of grafting initially increased with irradiation dose and then remained almost constant. The extent of grafting was higher in 2M GMA than in 1M GMA at the same irradiation dose. The extent of grafting in nitrogen was higher than that in air. The grafted samples were characterized with FTIR spectrometry and thermogravimetric (TG) analysis. A carbonyl group was found on grafted HDPE samples, and the carbonyl index increased with the extent of grafting. TG analyses proved the existence of grafted materials on HDPE and the grafted GMA thermally decomposes at a temperature lower than that of HDPE. Strong adhesion could be obtained with radiation lamination of HDPE by bulk grafting of GMA. Benzophenone facilitates the grafting in a proper concentration range. The adhesion mechanism of the laminated samples was the entanglement of the grafted chains. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 96: 772–779, 2005
Effect of “glutaraldehyde” functionality on network formation in poly(vinyl alcohol) membranes
Authors: Purss Helen K. , Qiao Greg G. , Solomon David H. 
Published: February 2005

AbstractThe use of higher‐functionality oligomers of glutaraldehyde on network formation was investigated and compared with glutaraldehyde monomer in step‐growth reactions. The effect of using such oligomers in network formation depends on the stoichiometry, which alters either the branching or both the branching and crosslinking of the network. This was demonstrated in the properties of poly(vinyl alcohol) (PVA) networks crosslinked with glutaraldehyde using cryogenic scanning electron microscopy, water swelling studies, and protein transfer across membranes. General guidelines were given for the proper use of glutaraldehyde solutions. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 96: 780–792, 2005