bluuebunny/crossref_metadata_2025_split huggingface dataset:
GeneComber: combining outputs of gene prediction programs for
improved results
Authors: Shah Sohrab P. , McVicker Graham P. , Mackworth Alan K. , Rogic Sanja , Ouellette B. F. Francis 
Published: June 2003

Abstract
Summary: We recently demonstrated that combining the output from Genscan and HMMgene can provide increased accuracy of gene predictions. We have created a robust software system that runs algorithms previously described on DNA sequences and provides a public web interface to the system for use by the biological community worldwide. The GeneComber system performs ab initio gene prediction by first taking a user inputted DNA sequence and running Genscan and HMMgene. The outputs of Genscan and HMMgene are then integrated using the EUI, GI and EUI_frame algorithms. All results are then stored into a relational database management system (RDBMS) and can then be retrieved through a web interface. The web interface provides a unified view of the GeneComber predictions by graphically overlaying outputs from Genscan, HMMgene, EUI, GI and EUI_frame. Outputs can also be retrieved in general feature format (GFF) or FASTA format. The software is written in the Perl programming language and is both dependent on and interoperable with the Bioperl toolkit. It includes high-level application programming interfaces (APIs) to run Genscan, HMMgene and a database API to insert prediction results into an RDBMS. The APIs are assembled into the genecomber script which is executed by the web interface or can be run directly from the Unix command line. The web interface is written in PHP and is structured so as to be easily modified for viewing data from any database that stores gene structures.
Availability: The GeneComber public web interface and supplementary information is located at http://bioinformatics.ubc.ca/genecomber The source code is released under the GNU General Public License and is available at ftp://ftp.bioinformatics.ubc.ca/pub/genecomber/software
Contact: francis@bioinformatics.ubc.ca
* To whom correspondence should be addressed.
† Present address: EMBL - European Bioinformatics Institute, Cambridge CB10 1SD, UK.
Chaos in the Galactic Dynamics
Authors: Tomaschitz Roman 
Published: June 2003

An elementary survey of cosmic chaos, its origins, and its physical impact in an open and multiply connected universe is given. A new type of cosmic evolution by global metrical deformations, unpredicted by Einstein's equations, is pointed out. The uniformity and the inhomogeneities of the galactic background are discussed in this context. There is a finite region in the open 3-space in which the galactic world-lines are chaotic, and the mixing taking place in this chaotic nucleus of the universe provides a mechanism to create the galactic equidistribution. We review in a completely untechnical way how global metrical deformations of space-time cause particle creation in quantum fields, and induce angular fluctuations in the temperature of the cosmic microwave background radiation. They can generate topology changes without distorting the constant curvature of the 3-space. The micro-topology causes parity violation (i.e., a violation of the space-reflection symmetry) by self-interference.
Liaison psychiatry or psychological medicine?
Authors: Lloyd Geoffrey G. , Mayou Richard A. 
Published: June 2003

Liaison psychiatry has been recognised in many countries as a special interest or sub-speciality of psychiatry concerned with the management of general hospital patients with psychological problems. However, despite increasing awareness of the emotional and behavioural aspects of illness, it has yet to achieve substantial influence within psychiatry and, more importantly, has had only modest effects on the delivery of medical care by physicians and other specialists. Recognition of its potential by planners and commissioners has been disappointing. Regrettably, in the UK and elsewhere, recent changes in the organisation of health care could hinder its development. This paper argues that in order to make substantial progress there is a compelling need to solve a fundamental obstacle – the separation between psychiatric and general medical care. This requires:(a) convincing the psychiatric profession that consultation-liaison is a distinct sub-speciality;(b) continuing efforts by liaison psychiatrists to define their special expertise and to demonstrate that their services are effective and acceptable to medical colleagues and to patients;(c) persuading those who organise health care that liaison psychiatry services need to be provided and administered as an integral component of comprehensive medical care.
Randomized, Placebo-Controlled Trial of Combined Pentoxifylline and Tocopherol for Regression of Superficial Radiation-Induced Fibrosis
Authors: Delanian Sylvie , Porcher Raphael , Balla-Mekias Saida , Lefaix Jean-Louis 
Published: June 2003

Purpose: Radiation-induced fibrosis (RIF) is a rare morbid complication of radiotherapy, without an established method of management. RIF treatment with a combination of pentoxifylline (PTX) and alpha-tocopherol (vitamin E; Vit E) was recently prompted by the good results of a clinical trial and an animal study. The present double-blind, placebo-controlled, monocentric study was designed to assess the efficacy of this combination in treating RIF sequelae. Patients and Methods: Twenty-four eligible women with 29 RIF areas involving the skin and underlying tissues were enrolled from December 1998 to April 2000. These patients, previously irradiated for breast cancer, were randomly assigned to four balanced treatment groups: (A) 800 mg/d of PTX and 1,000 U/d of Vit E; (B) PTX plus placebo; (C) placebo plus Vit E; and (D) placebo-placebo. The main end point measure was the relative regression of measurable RIF surface after 6 months of treatment. Assessment was completed by depth (with ultrasonography) and associated symptom measures. Results: Twenty-two patients with 27 RIF areas were analyzed at 6 months. Mean RIF surface regression was significant with combined PTX/Vit E versus double placebo (60% ± 10% v 43% ± 17%; P = .038). The median slope for the speed of RIF surface area and volume regression was significantly higher for group A than groups B, C, and D. All treatments were well tolerated. Conclusion: Six months’ treatment of combined PTX/Vit E can significantly reduce superficial RIF. Synergism between PTX and Vit E is likely, as treatment with each drug alone is ineffective, but these results require confirmation in larger series.
Survival and Neurologic Outcomes in a Randomized Trial of Motexafin Gadolinium and Whole-Brain Radiation Therapy in Brain Metastases
Authors: Mehta Minesh P. , Rodrigus Patrick , Terhaard C.H.J. , Rao Aroor , Suh John , Roa Wilson , Souhami Luis , Bezjak Andrea , Leibenhaut Mark , Komaki Ritsuko , Schultz Christopher , Timmerman Robert , Curran Walter , Smith Jennifer , Phan See-Chun , Miller Richard A. , Renschler Markus F. 
Published: June 2003

Purpose: This phase III randomized trial evaluated survival as well as neurologic and neurocognitive function in patients with brain metastases from solid tumors receiving whole-brain radiation therapy (WBRT) with or without motexafin gadolinium (MGd). Patients and Methods: Patients were randomly assigned to 30 Gy of WBRT ± 5 mg/kg/d MGd. Survival and time to neurologic progression determined by a blinded events review committee (ERC) were coprimary end points. Standardized investigator neurologic assessment and neurocognitive testing were evaluated. Results: Four hundred one (251 non–small-cell lung cancer) patients were enrolled. There was no significant difference by treatment arm in survival (median, 5.2 months for MGd v 4.9 months for WBRT; P = .48) or time to neurologic progression (median, 9.5 months for MGd v 8.3 months for WBRT; P = .95). Treatment with MGd improved time to neurologic progression in patients with lung cancer (median, not reached for MGd v 7.4 months for WBRT; P = .048, unadjusted). By investigator, MGd improved time to neurologic progression in all patients (median, 4.3 months for MGd v 3.8 months for WBRT; P = .018) and in lung cancer patients (median, 5.5 months for MGd v 3.7 months for WBRT; P = .025). MGd improved neurocognitive function in lung cancer patients. Conclusion: The overall results did not demonstrate significant differences by treatment arm for survival and ERC time to neurologic progression. Investigator neurologic assessments demonstrated an MGd treatment benefit in all patients. In lung cancer patients, ERC- and investigator-determined time to neurologic progression demonstrated an MGd treatment benefit. MGd may improve time to neurologic and neurocognitive progression in lung cancer.
TheCaenorhabditis elegans spalt-like genesem-4restricts touch cell fate by repressing the selector Hox geneegl-5and the effector genemec-3
Authors: Toker Anne S. , Teng Yingqi , Ferreira Henrique B. , Emmons Scott W. , Chalfie Martin 
Published: June 2003

Members of the spalt (sal) gene family encode zinc-finger proteins that are putative tumor suppressors and regulate anteroposterior (AP) patterning,cellular identity, and, possibly, cell cycle progression. The mechanism through which sal genes carry out these functions is unclear. The Caenorhabditis elegans sal gene sem-4 controls the fate of several different cell types, including neurons, muscle and hypodermis. Mutation of sem-4 transforms particular tail neurons into touch-neuron-like cells. In wild-type C. elegans, six touch receptor neurons mediate the response of the worm to gentle touch. All six touch neurons normally express the LIM homeobox gene mec-3. A subset, the two PLM cells, also express the Hox gene egl-5, an Abdominal-B homolog, which we find is required for correct mec-3 expression in these cells. The abnormal touch-neuron-like-cells in sem-4 animals express mec-3; we show that a subset also express egl-5.We report: (1) that ectopic expression of sem-4 in normal touch cells represses mec-3 expression and reduces touch cell function; (2)that egl-5 expression is required for both the fate of normal PLM touch neurons in wild-type animals and the fate of a subset of abnormal touch neurons in sem-4 animals, and (3) that SEM-4 specifically binds a shared motif in the mec-3 and egl-5 promoters that mediates repression of these genes in cells in the tail. We conclude that sem-4 represses egl-5 and mec-3 through direct interaction with regulatory sequences in the promoters of these genes, that sem-4 indirectly modulates mec-3 expression through its repression of egl-5 and that this negative regulation is required for proper determination of neuronal fates. We suggest that the mechanism and targets of regulation by sem-4 are conserved throughout the sal gene family: other sal genes might regulate patterning and cellular identity through direct repression of Hox selector genes and effector genes.
The Upper Temperature Limit in Cooperative Assembly of Ordered Mesoporous Materials
Authors: Yuan Minjia , Tang Jiawei , Yu Chengzhong , Chen Yinghua , Tu Bo , Zhao Dongyuan 
Published: June 2003

Abstract
Several examples for high temperature (95 °C, higher than the cloud point of pure surfactant) synthesis of highly ordered hexagonal mesoporous silica structures by employing triblock copolymers such as P65 (EO20PO30EO20) as structure-directing agents have been presented. Such understanding may increase the range of surfactants and the temperature regime under which ordered mesoporous materials can be cooperatively assembled.
Distributional issues in check‐off funded programs
Authors: Alston Julian M. , Freebairn John W. , James Jennifer S. 
Published: June 2003

AbstractAgricultural commodity taxes, called check‐offs, are used to finance promotion, research, and other activities that can be regarded as industry collective goods. The collection of the check‐offs and the programs they are used to fund have implications for the welfare of consumers, other producers, and taxpayers in addition to their effects on those producers who are allowed to vote in the procedures for authorizing the programs. As well as simple fairness or equity considerations, such shifting of the incidence of benefits and costs to others can lead to a divergence between producer and national optimal choices, and hence efficiency losses. From a public policy perspective, then, the implications for others ought to be considered in the design of the enabling legislation, in the evaluation of the specific programs, and in the rules governing the behavior of the agricultural producer groups engaged in commodity check‐off programs. [EconLit citations: Q180, Q130, H420]. © 2003 Wiley Periodicals, Inc. Agribusiness 19: 277–287, 2003.
Distributional effects of generic dairy advertising throughout the marketing channel
Authors: Kaiser Harry M. , Schmit Todd M. 
Published: June 2003

AbstractIf generic advertising is effective at increasing the demand for the advertised product, then there will not only be direct effects on the sponsors of the advertising, but also indirect effects on other market participants. This article addresses two such distributional issues using the U.S. dairy industry as a case study. First, how are fluid milk and cheese processors impacted by cheese and milk advertising conducted by farmers? We find that the welfare of both processor classes is improved due to the dairy farmer advertising program for fluid milk and cheese products. Second, how are fluid milk (or cheese) processors impacted by the other product's farmer‐funded advertising? As expected, own‐product advertising increased equilibrium output levels, while cross‐advertising impacts slightly reduced supply levels. Generic advertising, regardless of product, positively affected fluid milk processor gross margins, while increases in cheese advertising reduced the price margin for cheese processors. In general, own‐product advertising had larger price margin impacts for fluid milk processors, while cheese processors benefited more from larger supply gains. These larger supply effects translated further into larger increases in raw milk costs tightening cheese price margins. Because changes in cheese supplies affect both Class I and Class III prices, input prices to processors are affected relatively more by increases in cheese advertising, as opposed to fluid milk advertising. The relatively larger gains in output prices, combined with lower relative increases in input class prices contributed to higher producer welfare impacts for fluid milk processors than cheese processors when confronted with equivalent increases in their own‐product advertising. [EconLit citations: Q130, Q180]. © 2003 Wiley Periodicals, Inc. Agribusiness 19: 289–300, 2003.
Distribution of gains from research and promotion in the presence of market power
Authors: Wohlgenant Michael K. , Piggott Nicholas E. 
Published: June 2003

AbstractThis article evaluates how marginal returns to producers from promotion and research are affected when market intermediaries have market power in the retail market. Using an equilibrium displacement model, the relative importance of market power is evaluated for a “typical” food‐processing industry, and the empirical analysis focuses on how much profits from advertising, off‐farm research, and farm research are affected by a one dollar increase in check‐off funds, assuming equal efficiency in funds spent at each level of the marketing channel. The empirical analysis systematically considers alternative values of the underlying structural parameters of the model using Monte Carlo simulations to generate confidence intervals of marginal returns from each alternative use of the funds. Important findings are that the results with market power are indistinguishable from those obtained under pure competition and the results are most affected by input substitutability. [EconLit citations: L660]. © 2003 Wiley Periodicals, Inc. Agribusiness 19: 301–314, 2003.
Distributional effects of commodity promotion programs by type of producer
Authors: Chung Chanjin , Kaiser Harry M. 
Published: June 2003

AbstractThis study provides a theoretical background for the firm‐level analysis on the distributional effects of commodity promotion programs. The conceptual basis of this approach is that firms differ due to differences in possessing endowments of fixed factors, and net returns to firms can be viewed as rents accruing to these factors. Therefore, the marginal return from an increase in demand due to a successful generic promotion programs may not be the same across firms because firms do not have the same level of fixed factors. The result of our analysis indicates that producers may not equally benefit from the collectively funded programs. Our marginal profit analysis indicates that a producer‐financed promotion program may have greater benefits for producers with more endowed fixed factors than those with less endowed fixed factors.[EconLit citations: M370 and Q130]. © 2003 Wiley Periodicals, Inc. Agribusiness 19: 325–332, 2003.
Study on surface modification by surface‐modifying macromolecules and its applications in membrane‐separation processes
Authors: Khayet M. , Suk D. E. , Narbaitz R. M. , Santerre J. P. , Matsuura T. 
Published: June 2003

AbstractSurface‐modifying macromolecules (SMMs) are oligomeric fluoropolymers synthesized by polyurethane chemistry and tailored with fluorinated end groups. In the literature, several formulations of SMMs have been developed and blended with base polymers of polyurethanes and polyethersulfone for surface modification. It has been shown that SMMs migrate to the surface and the fluorine end groups orient themselves toward the air–polymer interface, reducing the surface energy of the hydrophilic base polymer to values close to that of polytetrafluoroethylene (Teflon). Because only a small amount of SMMs was needed, the bulk properties of the base polymer remained relatively unchanged. The properties of the SMM polymers were characterized, including molecular weights, elemental analysis, and thermal transitions. The morphology and surface properties of the SMM‐modified and unmodified membranes were assessed. The use of SMMs has been tested for use in ultrafiltration, pervaporation, and biomedical applications. SMM‐modified membranes offer advantages over unmodified membranes and the use of SMMs will continue to be the focus of future studies. This study reviews the recent development of surface‐modifying macromolecules (SMMs) and SMM‐blended membranes. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 89: 2902–2916, 2003
Preparation and characterization of benzylated sisal fibers
Authors: Ferreira Fábio C. , Curvelo Antonio A. S. , Mattoso Luiz H. C. 
Published: June 2003

AbstractSisal fibers were benzylated under different conditions and were characterized with infrared spectroscopy, X‐ray diffraction, thermal analysis, and scanning electron microscopy. The benzylation reaction was monitored by the mass gain as a function of the reaction time. In the first stage, there was a mass loss associated with the loss of lignin and polyoses from the raw fiber, which was accompanied by an increase in mass due to benzyl incorporation. When fiber delignification was carried out before benzylation, the mass gain curves of the benzylation reaction presented no initial mass loss and a much higher mass gain. Benzylation promoted several morphological changes: (1) the loss of the parenchyma cells, (2) the defibrillation of the technical fibers into ultimate fibers, (3) the microdefibrillation of the ultimate fibers, and (4) benzyl incorporation. The crystallinity of the fibers decreased with benzylation, as observed by X‐ray diffraction. The thermal stability of the fibers varied according to the treatment used. Other changes promoted in the fibers by chemical modification were examined. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 89: 2957–2965, 2003
Semibatch styrene suspension polymerization processes
Authors: Lenzi Marcelo Kaminski , Silva Fabricio Machado , Lima Enrique Luis , Pinto José Carlos 
Published: June 2003

AbstractEmulsion and suspension polymerization processes have widely been studied for more than 40 years. Although both polymerization processes are performed in heterogeneous media, each one presents its own typical characteristics, such as the particle size distribution, molecular weight distribution, polymer particle nucleation rate, and polymerization rate. In this study, semibatch styrene suspension polymerizations were carried out with feed compositions typical of emulsion processes. The initial reactor charge resembled the recipe of standard styrene suspension polymerizations, and the emulsion polymerization constituents were added during the batch. The influence of the moment at which the emulsion feed was started on the course of the polymerization and the effects of the feed on the polymer properties were analyzed. The polymer particle morphology and the average molecular weights changed very significantly with the emulsion feed time, and the changes could lead to the production of broad molecular weight distributions. Core–shell polymer particles could also be obtained, with the core being formed of polymer particles originating from the suspension polymerization process and the shell being formed of polymer particles originating from the emulsion polymerization. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 89: 3021–3038, 2003
Tautomerism of 4‐Hydroxy‐2,5‐dimethyl‐3(2H)‐furanone: Evidence for its enantioselective biosynthesis
Authors: Raab Thomas , Hauck Tobias , Knecht Anja , Schmitt Ulrich , Holzgrabe Ulrike , Schwab Wilfried 
Published: June 2003

AbstractChiral natural flavor compounds exhibit characteristic enantiomeric excesses due to stereoselective, enzymatically catalyzed reactions during biogenesis. Although the enzymatic formation of the strawberry key flavor compound 4‐hydroxy‐2,5‐dimethyl‐3(2H)‐furanone (HDMF; Furaneol®) is anticipated, the naturally occurring compound is racemic. As racemization due to keto‐enol‐tautomerism of HDMF could account for this observation, HDMF was investigated by 1H‐NMR spectroscopy tracing the exchange of the proton bound to the furanone‐ring at C2 with deuteron from the medium (D2O). In addition, the racemization rate of HDMF was directly determined by cyclodextrin‐modified capillary electrophoresis of enantiomerically enriched HDMF stored at different pH values. Tautomerism and the racemization rate of HDMF was lowest at pH values between 4 and 5. However, tautomerism and thus racemization was catalyzed under stronger acidic conditions (pH 2) and especially at pH values greater than 7, the value published for plant cell cytosol. Approximately 50% of the protons at C2 were exchanged with deuteron within 1 h at pH 7.2. Therefore, in order to demonstrate the enzymatic formation of HDMF, incubation experiments with Zygosaccharomyces rouxii as well as strawberry protein extract were carried out under slightly acidic conditions (pH 5), the most suitable pH value for studies on the enantiomeric ratio of HDMF. In both experiments the formation of enantiomerically enriched HDMF could be demonstrated for the first time, whereas incubation experiments under neutral conditions resulted in the detection of racemic HDMF. Chirality 15:573–578, 2003. © 2003 Wiley‐Liss, Inc.