bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finding motifs in the twilight zone
Authors: Keich U. , Pevzner P.A. 
Published: October 2002

Abstract
Motivation: Gene activity is often affected by binding transcription factors to short fragments in DNA sequences called motifs. Identification of subtle regulatory motifs in a DNA sequence is a difficult pattern recognition problem. In this paper we design a new motif finding algorithm that can detect very subtle motifs.
Results: We introduce the notion of a multiprofile and use it for finding subtle motifs in DNA sequences. Multiprofiles generalize the notion of a profile and allow one to detect subtle patterns that escape detection by the standard profiles. Our MULTIPROFILER algorithm outperforms other leading motif finding algorithms in a number of synthetic models. Moreover, it can be shown that in some previously studied motif models, MULTIPROFILER is capable of pushing the performance envelope to its theoretical limits.
Availability: http://www-cse.ucsd.edu/groups/bioinformatics/software.html
Contact: keich@cs.ucsd.edu
* To whom correspondence should be addressed.
GENOTRACE: cDNA-based local GENOme assembly from TRACE archives
Authors: Berezikov Eugene , Plasterk Ronald H.A. , Cuppen Edwin 
Published: October 2002

Abstract
Summary: GENOTRACE identifies the genomic organization for a cDNA using raw data from genome sequencing projects in progress (trace archives). Local genomic contigs are generated, allowing for example the design of PCR primers in intronic sequences to amplify coding regions of a gene, needed for example for mutation or SNP detection.
Availability: The package and examples of output files can be downloaded from http://rat.niob.knaw.nl/GENOTRACE
Contact: ecuppen@niob.knaw.nl
* To whom correspondence should be addressed.
CINEMA-MX: a modular multiple alignment editor
Authors: Lord P.W. , Selley J.N. , Attwood T.K. 
Published: October 2002

Abstract
Summary: Analyzing and visualizing multiple sequence alignments is a common task in many areas of molecular biology and bioinformatics. Many tools exist for this purpose, but are not easily customizable for specific in-house uses. Here we report the development of an editor, CINEMA-MX, that addresses these issues. CINEMA-MX is highly modular and configurable, and we present examples to illustrate its extensibility.
Availability: The program and full source code, which are available from http://www.bioinf.man.ac.uk/dbbrowser/cinema-mx, are being released under a combination of the LGPL and GPL, for Unix or Windows platforms.
Contact: p.lord@russet.org.uk
* To whom correspondence should be addressed at Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK
CURRENT-DRIVEN MAGNONS IN MAGNETIC MULTILAYERS
Authors: TSOI M. 
Published: October 2002

Spin waves, or magnons, are intrinsic excitations in magnetic materials and have attracted considerable attention since introduced by Bloch in 1930.1 Recently ideas of spintronics have impacted this field dramatically. Berger2 and Sloczewski3 introduced completely new aspects of the physics of metallic ferromagnets in the presence of an electric current of high density. Excitation of magnons by an electric current has been predicted and seen in magnetic multilayers,4-6 where the driving force for the excitations is the spin-momentum transfer associated with an electric current flow. We have developed a microcontact technique (magnetic microcontact spectroscopy) to investigate the current-driven magnon generation.4,5 In our experiments we inject current densities as high as 109 A/cm2 into a Co/Cu multi-layer through a point contact made using a sharpened Ag wire carefully brought into contact with a multi-layer file. We observe current-driven magnons in multi-layers with both ferromagnetic4,5 and antiferromagnetic7 configuration of the adjacent layer magnetizations. Some further interesting applications of the technique, particularly, for studying fluctuation phenomena, resonant magnon generation, acoustic wave generation, etc., will be presented.
MAGNETIC FIELD AND IMPURITY EFFECTS IN PSEUDOGAP STATE OF CUPRATES
Authors: BALATSKY A. V. 
Published: October 2002

Both impurities and magnetic field can be used as a tool to investigate the properties of superconducting state of cuprates. Recent STM tunneling experiments on impurity states in superconducting state provide a new set of results that can be compared with the expectations for d-wave pairing in cuprates. We will argue that impurities and magnetic field could be used to test the nature of the pseudogap state (PG). i) We will present the extension of the theory of impurity on the pseudogap regime. The impurity such as Zn or Ni, will generate resonance state in PG state on very general grounds. Single vs double impurity peak will appear depending on the superconducting vs non-superconducting origin of the PG. ii) For the particular proposal of the d- density wave PG (DDW) we found that out of plane magnetic field will induce complex, proportional to the field, id xy -wave density wave component. Physical properties of this, previously not considered, state will be discussed.
DYNAMICAL STRUCTURE FACTORS OF THE S = 1/2 SPIN LADDER SYSTEMS WITH A DIAGONAL INTERACTION IN THE MAGNETIZATION-PLATEAU STATE
Authors: HAGA N. , SUGA S. 
Published: October 2002

We investigate the dynamical structure factors of the S = 1/2 spin ladder systems with a diagonal interaction in the magnetization-plateau state. The results show characteristic behaviors depending on the chain interaction α, the ladder interaction 1 + δ and the diagonal interaction 1 - δ. The large weights are located at q = π, when δ is small. With increasing δ, the wavenumber of the large weights shifts towards q = π/2 taking the incommensurate value. The almost dispersionless behavior comes out at several combinations of α and δ, indicating that the elementary excitation is localized spatially. We discuss our results in comparison with the exact excitation spectrums of the S = 1/2 XXZ model which is an effective Hamiltonian of the present system in α ~ 0 and δ ~ 1. Dynamical structure factors of some S = 1/2 one-dimensional quantum spin systems in the magnetic fields were measured by inelastic neutron-scattering experiments1,2 and it has been shown the theoretical results from the numerical diagonalization of finite systems can explain them.3–5
Ternary single‐source precursors for polycrystalline thin‐film solar cells
Authors: Banger Kulbinder K. , Hollingsworth Jennifer A. , Harris Jerry D. , Cowen Jonathan , Buhro William E. , Hepp Aloysius F. 
Published: October 2002

AbstractThe development of thin‐film solar cells on flexible, lightweight, space‐qualified substrates provides an attractive cost solution for fabricating solar arrays with high specific power (W kg−1). The use of a polycrystalline chalcopyrite absorber layer for thin‐film solar cells is considered as the next generation in photovoltaic devices. At NASA GRC we have focused on the development of new single‐source precursors (SSPs) and their utility to deposit the chalcopyrite semiconducting layer (CIS) onto flexible substrates for solar‐cell fabrication. The syntheses and thermal modulation of SSPs via molecular engineering are described. Thin‐film fabrication studies demonstrate that the SSPs can be used in a spray chemical vapor deposition process for depositing CIS at reduced temperatures, and result in electrical properties that are suitable for photovoltaic devices. Copyright © 2002 John Wiley & Sons, Ltd.
In situ syntheses of a suspension agent based on a styrene–acrylic acid copolymer for the suspension polymerization of styrene
Authors: Vilchis Leopoldo , Ríos Leonardo , Villalobos Marco A. , Guyot Alain 
Published: October 2002

AbstractWe carried out the suspension polymerization of styrene, initiated with benzoyl peroxide at 80°C, in the presence of the simultaneous polymerization of acrylic acid in the water phase, initiated by potassium peroxidisulfate (KPS) at the same temperature. The polymerization in the water phase was started at certain times after the beginning of the polymerization of styrene. Then, a continuous addition of KPS was carried out at a given landing rate and during variable feeding times. The water‐phase polymerization actually produced a copolymer of styrene and acrylic acid, which displayed surface‐active properties. The particle size distribution depended on the variables mentioned earlier (starting time, KPS feeding rate, and addition time), being controlled by the molecular weight, and on the composition of the copolymer produced and its availability at the increasing conversion of styrene. A second distribution of submicronic particles was produced. Both families of particles had about the same molecular weight. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 3271–3285, 2002
Surface modification with waterborne fluorinated anionic polyurethane dispersions
Authors: Lim Chul Hwan , Choi Hee Sung , Noh Si Tae 
Published: October 2002

AbstractWaterborne fluorinated anionic polyurethane dispersions (FAPUDs) were synthesized from tris(6‐isocyanatohexyl) isocyanurate, N‐ethyl‐N‐2‐hydroxyethyl‐perfluorooctanesulfonamide, poly(oxytetramethylene glycol) (PTMG), dimethylolpropionic acid (DMPA), hexamethylene diisocyanate, 1,4‐butanediol, and two different neutralizing agents (triethylamine and sodium carbonate). Waterborne polyurethane dispersions (PUDs) were synthesized from isophorone diisocyanate, PTMG, DMPA, and ethylenediamine as chain extenders. The particle size of the FAPUDs, based on the fluorine content and degree of neutralization (DN), was measured with dynamic light scattering. So that the surface modification and morphology variations of the PUDs through the addition of the FAPUDs could be observed, the surface energy and thermal properties of the blending films [fluorine PUD mixtures (FPMs)] were measured with contact‐angle analysis and differential scanning calorimetry. The particle size of the FAPUDs increased as the fluorine content in the FAPUDs increased and decreased as the DN increased. The surface energy of the FPM films made from the blending of the FAPUD T series (neutralization with triethylamine) gradually decreased above the critical fluorine concentration (0.02797 wt %). However, for the blending of the FAPUD 25Na series (neutralization with sodium carbonate), the surface energy increased above the critical fluorine concentration (0.02797 wt %) because of the increase in Na salts. The FAPUDs showed the native thermal behavior of the fluorine. However, the thermal properties of the blending films were like those of pure PUDs. This showed that the morphology of the PUDs was rarely unchanged when the FAPUDs were added. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 3322–3330, 2002
Effect of poly(vinyl chloride) resin type in the preparation process of slush powder
Authors: Luo Yuxiang , Dai Gance 
Published: October 2002

AbstractDuring the preparation of the poly(vinyl chloride) (PVC) slush powder, we found that PVC resins obtained by different polymerization methods affected many properties of slush powder and its products. Two types of commercial PVC resins were used for slush powder preparation: mass poly(vinyl chloride) (M‐PVC) and suspension poly(vinyl chloride) (S‐PVC). We used the Haake rheomix test to characterize the absorption of plasticizers into PVC resins, and the results showed that M‐PVC absorbed the plasticizers more quickly than S‐PVC. The fusion behavior of the two slush powders was studied by the thermal plate test and Haake rheomix test, and the results showed that the slush powder of M‐PVC was easier to fuse than that of S‐PVC. The different properties of the two resins and slush powder could be explained by the morphology, average size, and size distribution. Due to the “skin” of the particles' surfaces, the wider size distribution, and the large size of particles, S‐PVC absorbed the plasticizers more slowly and was more difficult to fuse. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 3331–3335, 2002
Human serum albumin (HSA) adsorption with chitosan microspheres
Authors: Denkbas Emir Baki , Odabasi Mehmet , Kiliçay Ebru , Özdemir Nalan 
Published: October 2002

AbstractIn this study, chitosan microspheres were prepared and characterized for adsorption of human serum albumin (HSA) as affinity sorbent. The chitosan microspheres were obtained with a “suspension crosslinking technique” in the size range of 30–700 μm by using a crosslinker, i.e., glutaraldehyde. The chitosan microspheres used in HSA adsorption studies were having the average size of 170 ± 81 μm. Adsorption medium pH and the initial HSA concentration in the adsorption medium were changed as 4.0–7.0 and 0.5–2.0 mg HSA/mL, respectively, to investigate the HSA adsorption capacity of chitosan microspheres. Maximum HSA adsorption (i.e., 11.35 mg HSA/g chitosan microspheres) was obtained at pH 5.0 and 1.5 mg HSA/mL of the initial HSA concentration in the adsorption medium was obtained as the saturation value for HSA adsorption. A very common dye ligand, i.e., Cibacron Blue F3GA was attached to the chitosan microspheres to increase the HSA adsorption capacity. Actually, the HSA adsorption capacity was increased up to 15.35 mg HSA/g chitosan microspheres in the case of Cibacron Blue F3GA attached to chitosan microspheres used. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 3035–3039, 2002
Monitoring of nylon 6,6/carbon fiber composites processing by X‐ray diffraction and thermal analysis
Authors: Botelho Edson Cocchieri , Nogueira Clara Leal , Rezende Mirabel Cerqueira 
Published: October 2002

AbstractThis work reports a study made to obtain carbon fiber/nylon 6,6 prepreg composites by hot‐compression molding. Thermogravimetric analysis (TG) and crystallinity degree determination were carried out to monitor the nylon 6,6 behavior during the different steps of the composite processing. The homogeneity of the carbon fiber/polymer matrix distribution was verified using microscopic analyses and the fiber content was determined by the acid‐digestion method. The results show that the processing parameters employed were adequate, allowing the manufacture of laminates with good texture and an adequate reinforcement/matrix relation (60/40). However, improvements need be done to minimize the pullout effect observed in the tensile specimens. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 3114–3119, 2002
Suppression of necking in polyethylene
Authors: Unwin A. P. , Duckett R. A. , Ward I. M. , Collins T. L. D. , Sweeney J. , Coates P. D. 
Published: October 2002

AbstractThe deformation behavior of a particular grade of high‐density polyethylene prepared in a number of different ways has been examined. The samples all have an initially isotropic crystalline texture but differ in the levels of network preorientation surviving as a legacy of the melt processing history. Measurements of shrinkage and shrinkage force have been used to characterize this network, and the results suggest that the density of active chains is much lower than found in the main molecular network operating during solid‐state drawing. The subnetwork properties vary depending on the level of extrusion and rate of cooling experienced during processing, with those entanglements surviving in the oriented melt at the point of crystallization having a long relaxation time. The presence of this subnetwork can lead to the suppression of necking during subsequent solid‐state deformation. The implication is that simple processing procedures can be devised to remove or control the instability associated with necking. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 3135–3147, 2002
Atomic force microscopy of cellulose membranes prepared from the N‐methylmorpholine‐N‐oxide/water solvent system
Authors: Zhang Yaopeng , Shao Huili , Hu Xuechao 
Published: October 2002

AbstractCellulose membranes were obtained by solutions of cellulose being cast into a mixture of N‐methylmorpholine‐N‐oxide (NMMO) and water under different processing conditions. Atomic force microscopy (AFM) was used to investigate the surface structures of the membranes. The AFM method provided information on both the size and shape of the pores on the surface, as well as the roughness of the skin, through a computerized analysis of AFM micrographs. The results obtained showed that the surface morphologies were intrinsically associated with the permeation properties. For the cellulose membranes, increasing the NMMO concentration and the temperature of the coagulation bath led to higher fluxes and lower bovine serum albumin rejection. These were always correlated with higher values of the roughness parameters and larger pore sizes of the membrane surfaces. When the cellulose concentration of the casting solution was 11 wt %, the membrane showed a nodular structure with interconnected cavity channels between the agglomerated nodules. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 3389–3395, 2002
Sulfonated polybutadiene ionomer‐templated nanocopper composites
Authors: Nandi Arun , Dutta Gupta Maya , Banthia A. K. 
Published: October 2002

AbstractNew composites based on nanosize particles provide a promising route to the fabrication of novel materials for advanced technology applications in the 21st century. To prepare desired materials, it is important to control the composition and distribution of nanoclusters within the bulk or surface coating of nanostructured materials. To achieve this aim, we developed a novel method of preparing nanocopper–ionomer thermoplastic composite material with sulfonated cis‐1,4‐polybutadiene random ionomer as a matrix and a capping polymer in organic solvent. The effect of sonication on stabilized nanocopper colloid was studied. The self‐assembled composite film was characterized by ultraviolet–visible spectroscopy, transmission electron microscopy, 1H‐NMR, and thermogravimetric analysis. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 3180–3184, 2002
Radiation effects on poly(propylene) (PP)/ethylene–vinyl acetate copolymer (EVA) blends
Authors: Dalai Siqin , Wenxiu Chen 
Published: October 2002

AbstractRadiation effects on poly(propylene)/ethylene–vinyl acetate copolymer (PP/EVA) blends are discussed. Increasing the EVA content enhanced the crosslinking effect of radiation in PP/EVA blends. This effect was significant when the EVA content was ≥50% in PP/EVA blends that were exposed to γ‐ray irradiation in air. This phenomenon is discussed in relation to the compatibility, morphology, and thermal properties of PP/EVA blends. The results indicate that the effect is dependent on the compatibility, the increase in the amorphous region content, and the EVA content in PP/EVA blends. The possible mechanism of radiation crosslinking or degradation in irradiated PP/EVA blends was studied quantitatively by a novel method, a “step analysis” process, and thermal gravimetric analysis. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 3420–3424, 2002
Mechanical properties of silk fibroin–microcrystalline cellulose composite films
Authors: Noishiki Yasutomo , Nishiyama Yoshiharu , Wada Masahisa , Kuga Shigenori , Magoshi Jun 
Published: October 2002

AbstractSilk fibroin–microcrystalline cellulose (cellulose whisker) composite films with varied compositions were prepared by casting mixed aqueous solution/suspensions of the two components. Silk fibroin was dissolved in 10M LiSCN followed by dialysis; a cellulose whisker suspension was prepared by sulfuric acid hydrolysis of tunicate cellulose. Macroscopically homogeneous films were obtained at all mixing ratios. While the Young's modulus of the composite films showed a linear, additive dependence on the mixing ratio, the tensile strength and ultimate strain showed a maximum at a 70–80% cellulose content, reaching five times those of fibroin‐alone or cellulose‐alone films. At the same mixing ratio, infrared spectra of the composite films showed a shift of the amide I peak from 1654 to 1625 cm−1, indicating the conformational change of fibroin from a random coil to a β structure (silk II) at the whisker–matrix interface. This change seems to be induced by contact of fibroin molecules with a highly ordered surface of cellulose whisker. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 3425–3429, 2002
Systemic therapy with lesbian and gay clients: a truly social approach to psychological practice
Authors: Malley Maeve 
Published: October 2002

AbstractSystemic therapy is considered as a modality which may be well‐suited to therapeutic work with lesbian and gay male populations, whether as individuals, couples or families of choice. Issues within systemic therapy and practice are discussed with reference to working with these populations. Copyright © 2002 John Wiley & Sons, Ltd.
Systematic review and meta‐analysis of monotherapy compared with combined androgen blockade for patients with advanced prostate carcinoma
Authors: Samson David J. , Seidenfeld Jerome , Schmitt Brian , Hasselblad Vic , Albertsen Peter C. , Bennett Charles L. , Wilt Timothy J. , Aronson Naomi 
Published: October 2002

AbstractBACKGROUNDThe current systematic review and meta‐analysis compared monotherapy and combined androgen blockade in the treatment of men with advanced prostate carcinoma. Outcomes of interest included overall, cancer specific, and progression‐free survival; time to treatment failure; adverse events; and quality of life.METHODSThe literature search identified randomized trials comparing monotherapy (orchiectomy and luteinizing hormone‐releasing hormone [LHRH] agonists) with combination therapy using orchiectomy or a LHRH agonist plus a nonsteroidal or steroidal antiandrogen. Dual independent review occurred. The meta‐analysis used a random effects model.RESULTSTwenty‐one trials compared survival after monotherapy with survival after combined androgen blockade (n = 6871 patients). The meta‐analysis found no statistically significant difference in survival at 2 years between patients treated with combined androgen blockade and those treated with monotherapy (20 trials; hazard ratio [HR] = 0.970; 95% confidence interval [95% CI], 0.866–1.087). The authors determined a statistically significant difference in survival at 5 years that favored combined androgen blockade (10 trials; HR = 0.871; 95% CI, 0.805–0.942). For the subgroup of patients with a good prognosis, there was no statistically significant difference in survival. Adverse effects leading to withdrawal from therapy occurred more often with combined androgen blockade. To the authors' knowledge there is little evidence published to date comparing the effects of combined androgen blockade and monotherapy on quality of life, but the single randomized trial that adequately addressed this outcome reported an advantage for monotherapy over combined androgen blockade.CONCLUSIONSA thorough examination of the usefulness of combined androgen blockade must balance the modest increase in expected survival observed at 5 years against the increased risk of adverse effects and the potential for adversely affecting the patient's overall quality of life. [See editorial on pages 209–10, this issue.] Cancer 2002;95:361–76. © 2002 American Cancer Society.DOI 10.1002/cncr.10647
Monotherapy versus combined androgen blockade in patients with advanced prostate cancer
Authors: Errejon Abelardo , Crawford E. David 
Published: October 2002

Despite a number of large randomized clinical trials, there still is uncertainty regarding the value of maximal androgen blockade in the treatment of patients with advanced prostate carcinoma. In the referenced article, the authors provide a very comprehensive review of the literature concerning one of the most controversial issues in contemporary urology. See also pages 361–76.