bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunpathogenese der Psoriasis
Authors: Ghoreschi Kamran , Röcken Martin 
Published: August 2003

ZusammenfassungDie Psoriasis ist eine chronisch entzündliche Erkrankung der Haut und Gelenke. Die Entstehung einer Psoriasis unterliegt zahlreichen Einflüssen. Zu den am besten charakterisierten Faktoren gehören bestimmte genetische Merkmale wie Histokompatibilitätsantigene und sogenannte Psoriasis Suszeptibilitätsgene, sowie Triggerfaktoren, die eine Psoriasis auslösen oder ihren Verlauf verschlechtern können. Aus pathophysiologischer Sicht wird die Psoriasis heute überwiegend als eine durch T‐Lymphozyten vermittelte Autoimmunerkrankung angesehen, deren Autoantigen bis heute nicht bekannt ist. Diskutiert werden bakterielle Proteine mit Strukturähnlichkeit zu Keratinozytenproteinen. Ähnlich wie bei der Manifestation von Erkrankungsschüben anderer Autoimmunerkrankungen stehen Entzündungsmediatoren des angeborenen Immunsystems am Anfang einer Kaskade, die sowohl lokal in der Haut als auch generalisiert im Immunsystem eine Entzündungsreaktion hervorrufen. Eine zentrale Rolle nehmen IFN‐γ produzierende CD4+ T‐Lymphozyten, die Th1‐Lymphozyten ein, die durch direkte und indirekte Interaktionen mit Antigenpräsentierenden Zellen, Mastzellen, Neutrophilen Granulozyten und Endothelzellen für die Entstehung der Psoriasis verantwortlich sind. Diese Entzündungskaskade provoziert in der Haut gleichzeitig eine ausgeprägte Gefäßneubildung und die Keratinozytenproliferation. Eine Vielzahl von Rezeptoren und Mediatoren sind in dieses Netzwerk involviert. Neue Therapieansätze mit Zytokinen oder Zytokinantikörpern zielen entweder darauf ab, diese überschießende Immunantwort zu hemmen, oder darauf spezifisch die schädliche, gegen die Haut gerichtete Immunantwort, in einen schützenden Phänotyp mit anti‐entzündlichen Eigenschaften zu überführen.
Therapie der Akne mit Antiandrogenen – Eine evidenzbasierte Übersicht
Authors: Zouboulis Christos C. 
Published: August 2003

Zusammenfassung Hintergrund: Zu den wichtigsten Faktoren, die zur Pathogenese der Akne beitragen, gehört eine erhöhte Talgdrüsenaktivität mit Seborrhoe. Die antiandrogene Therapie zielt auf die androgenmetabolisierenden follikulären Keratinozyten und die Talgdrüse mit primärer sebostatischer Wirkung, wobei eine Minderung der Talgsyntheserate von 12,5 % bis zu 65 % erreicht werden kann. Nach ihrem Mechanismus teilt man die Antiandrogene ein in Androgenrezeptorblocker sowie Hemmer der zirkulierenden Androgene durch Wirkung auf das Ovar (orale Kontrazeptiva), Hemmer der zirkulierenden Androgene durch Wirkung auf die Hypophyse (Gonadotropin‐releasing‐Hormone‐Agonisten und Dopamin‐Agonisten bei Hyperprolaktinämie), Hemmer der Nebennierenrindenaktivität und Hemmer des peripheren Androgenmetabolismus (5α‐Reduktase‐Inhibitoren, Hemmer anderer Enzyme). Methoden: In dieser Studie wurden alle in MedLine publizierten Original‐ und Übersichtsarbeiten über die Therapie der Akne mit Antiandrogenen sowohl als Monotherapie als auch in Kombination mit Hilfe der Suchbegriffe „acne”, „seborrhea”, „polycystic ovary syndrome”, „hyperandrog*” und „treatment” ausgesucht und nach ihrer Evidenzebene eingeteilt. Ergebnisse: Von den zur Verfügung stehenden therapeutischen Möglichkeiten zeigen die Kombinationen Cyproteronacetat (2 mg)/Ethinylestradiol (35 µg), Drospirenon (3 mg)/Ethinylestradiol (30 µg) und das kombiphasische Präparat mit Desogestrel (25 µg)/Ethinylestradiol (40 µg) für 1 Woche gefolgt von Desogestrel (125 µg)/Ethinylestradiol (30 µg) für 2 Wochen die stärkste Antiakne‐Wirkung. Gestagene oder Östrogene jeweils als Monotherapie, Spironolacton, Flutamid, Gonadotropin‐Releasing‐Hormone‐Antagonisten und Hemmer des peripheren Androgenmetabolismus werden nach dem heutigen Kenntnisstand nicht empfohlen. Niedrig dosiertes Prednisolon wird nur bei late‐onset kongenitaler adrenaler Hyperplasie eingesetzt und Dopamin‐Agonisten nur bei Hyperprolaktinämie. Die Therapie mit Antiandrogenen setzt voraus, daß keine entsprechenden Kontraindikationen vorliegen. Schlußfolgerung: Die antiandrogene Therapie ist weiblichen Patienten vorbehalten, die weitere Zeichen eines peripheren Hyperandrogenismus oder einer Hyperandrogenämie aufweisen. Zudem können Frauen mit Acne tarda oder persistierender therapieresistenter Akne mit gleichzeitigem Kontrazeptionswunsch mit Antiandrogenen behandelt werden sowie im Rahmen der Durchführung einer systemischen Isotretinoin‐Therapie. Die antiandrogene Therapie ist keine primäre Monotherapie einer nicht entzündichen und milden entzündlichen Akne.
Die Anwendung des Excimerlasers 308 nm zur Psoriasis‐Behandlung
Authors: Fikrle Tomáš , Pizinger Karel 
Published: August 2003

Zusammenfassung Hintergrund: Mit den gängigen Methoden der Phototherapie bei Psoriasis, UVB bei 311 nm und Photochemotherapie, wird auch die gesunde Haut einer potentiell schädigenden Strahlenbelastung ausgesetzt. Bei Verwendung eines 308 nm XeCl Excimerlasers können die psoriatischen Läsionen hingegen gezielt behandelt werden. In der vorliegenden Studie wird die Wirksamkeit einer solchen Laserbehandlung untersucht. Patienten/Methodik: Die Studie wurde an 28 Patienten mit Plaquepsoriasis begonnen, 26 waren zu Studienende auswertbar. Bei jedem Patienten wurde eine einzige Plaque zur Behandlung ausgewählt und dreimal wöchentlich mit dichtgesetzten Laserpulsen behandelt. Die Initialdosis entsprach der doppelten MED (minimale Erythemdosis), Steigerungen um je eine MED erfolgten in der Regel bei jeder zweiten Behandlung. Die verabreichten Dosen lagen zwischen 2 – 5 MED, die kumulative UVB‐Gesamtdosis zwischen 3,6 – 15,2 J/cm2. 17 Patienten wurden insgesamt 6‐mal, weitere 11 Patienten 10‐mal behandelt. Die Bewertung der klinischen Wirksamkeit erfolgte durch die Berechnung des Psoriasis Severity Indexes (PSI) für das jeweils behandelte Hautareal. Die Patienten wurden regelmäßig bis drei Monate nach der letzten Laserbehandlung beobachtet, eine Nachuntersuchung erfolgte nach einem Jahr. Ergebnisse: Bei den meisten Patienten trat eine deutliche Besserung des klinischen Befundes ein: bei 90 % war bei Behandlungsende der PSI auf wenigstens 50 %, in 72 % auf wenigstens 33 % des urprünglichen Wertes abgesunken. Das Ansprechen der Patientengruppen mit 6‐maliger bzw. 10‐maliger Behandlung war weitgehend gleich. Bei 6 Patienten der gesamten Gruppe war die Laser‐behandelte psoriatische Läsion auch nach einem Jahr noch abgeheilt, bei weiteren 7 war eine langfristige Besserung eingetreten. Die häufigsten Nebenwirkungen waren Rötung und Juckreiz (100 %), Blasenbildung (35 %) sowie Hyperpigmentationen im Behandlungsareal (80 %). Schlußfolgerung: Die Anwendung des Excimerlasers mit 308 nm ist bei chronischer, lokalisierter Psoriasis wirksam und kann zu langanhaltender Remission führen.
Differential expression in SAGE: accounting for normal between-library variation
Authors: Baggerly Keith A. , Deng Li , Morris Jeffrey S. , Aldaz C. Marcelo 
Published: August 2003

Abstract
Motivation: In contrasting levels of gene expression between groups of SAGE libraries, the libraries within each group are often combined and the counts for the tag of interest summed, and inference is made on the basis of these larger ‘pseudolibraries’. While this captures the sampling variability inherent in the procedure, it fails to allow for normal variation in levels of the gene between individuals within the same group, and can consequently overstate the significance of the results. The effect is not slight: between-library variation can be hundreds of times the within-library variation.
Results: We introduce a beta-binomial sampling model that correctly incorporates both sources of variation. We show how to fit the parameters of this model, and introduce a test statistic for differential expression similar to a two-sample t-test.
Contact: kabagg@mdanderson.org
Supplementary information http://bioinformatics.mdanderson.org/ Includes Matlab and R code for fitting the model.
* To whom correspondence should be addressed.
RankGene: identification of diagnostic genes
based on expression data
Authors: Su Yang , Murali T.M. , Pavlovic Vladimir , Schaffer Michael , Kasif Simon 
Published: August 2003

Abstract
Summary: RankGene is a program for analyzing gene expression data and computing diagnostic genes based on their predictive power in distinguishing between different types of samples. The program integrates into one system a variety of popular ranking criteria, ranging from the traditional t-statistic to one-dimensional support vector machines. This flexibility makes RankGene a useful tool in gene expression analysis and feature selection.
Availability: http://genomics10.bu.edu/yangsu/rankgene
Contact: murali@bu.edu
* To whom correspondence should be addressed.
MrBayes 3: Bayesian phylogenetic inference under mixed models
Authors: Ronquist Fredrik , Huelsenbeck John P. 
Published: August 2003

Abstract
Summary: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g. morphological, nucleotide, and protein—and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
Availability: http://morphbank.ebc.uu.se/mrbayes
Contact: fredrik.ronquist@ebc.uu.se
* To whom correspondence should be addressed.
AGenDA: homology-based gene prediction
Authors: Taher Leila , Rinner Oliver , Garg Saurabh , Sczyrba Alexander , Brudno Michael , Batzoglou Serafim , Morgenstern Burkhard 
Published: August 2003

Abstract
Summary: We present a www server for homology-based gene prediction. The user enters a pair of evolutionary related genomic sequences, for example from human and mouse. Our software system uses CHAOS and DIALIGN to calculate an alignment of the input sequences and then searches for conserved splicing signals and start/stop codons around regions of local sequence similarity. This way, candidate exons are identified that are used, in turn, to calculate optimal gene models. The server returns the constructed gene model by email, together with a graphical representation of the underlying genomic alignment.
Availability: http://bibiserv.TechFak.Uni-Bielefeld.DE/agenda/
Contact: ltaher@TechFak.Uni-Bielefeld.DE
* To whom correspondence should be addressed.
PseuRECA: genome annotation and gene context analysis for
Pseudomonas aeruginosa PAO1
Authors: Weinel Christian , Ermolaeva Maria D. , Ouzounis Christos 
Published: August 2003

Abstract
Availability:The PseuRECA database is accesible at http://maine.ebi.ac.uk:8000/services/pseureca/
Contact: weinel.christian@mh-hannover.de
* To whom correspondence should be addressed.
Identification of functional links between genes using phylogenetic
profiles
Authors: Wu Jie , Kasif Simon , DeLisi Charles 
Published: August 2003

Abstract
Motivation: Genes with identical patterns of occurrence across the phyla tend to function together in the same protein complexes or participate in the same biochemical pathway. However, the requirement that the profiles be identical (i) severely restricts the number of functional links that can be established by such phylogenetic profiling; (ii) limits detection to very strong functional links, failing to capture relations between genes that are not in the same pathway, but nevertheless subserve a common function and (iii) misses relations between analogous genes. Here we present and apply a method for relaxing the restriction, based on the probability that a given arbitrary degree of similarity between two profiles would occur by chance, with no biological pressure. Function is then inferred at any desired level of confidence.
Results: We derive an expression for the probability distribution of a given number of chance co-occurrences of a pair of non-homologous orthologs across a set of genomes. The method is applied to 2905 clusters of orthologous genes (COGs) from 44 fully sequenced microbial genomes representing all three domains of life. Among the results are the following. (1) Of the 51 000 annotated intrapathway gene pairs, 8935 are linked at a level of significance of 0.01. This is over 30-fold greater than the 271 intrapathway pairs obtained at the same confidence level when identical profiles are used. (2) Of the 540 000 interpathway genes pairs, some 65 000 are linked at the 0.01 level of significance, some 12 standard deviations beyond the number expected by chance at this confidence level. We speculate that many of these links involve nearest-neighbor path, and discuss some examples. (3) The difference in the percentage of linked interpathway and intrapathway genes is highly significant, consistent with the intuitive expectation that genes in the same pathway are generally under greater selective pressure than those that are not. (4) The method appears to recover well metabolic networks. This is illustrated by the TCA cycle which is recovered as a highly connected, weighted edge network of 30 of its 31 COGs. (5) The fraction of pairs having a common pathway is a symmetric function of the Hamming distance between their profiles. This finding, that the functional correlation between profiles with near maximum Hamming distance is as large as between profiles with near zero Hamming distance, and as statistically significant, is plausibly explained if the former group represents analogous genes.
Contact: delisi@bu.edu
Pandit: a database of protein and associated nucleotide domains with
inferred trees
Authors: Whelan Simon , de Bakker Paul I. W. , Goldman Nick 
Published: August 2003

Abstract
Motivation: A large, high-quality database of homologous sequence alignments with good estimates of their corresponding phylogenetic trees will be a valuable resource to those studying phylogenetics. It will allow researchers to compare current and new models of sequence evolution across a large variety of sequences. The large quantity of data may provide inspiration for new models and methodology to study sequence evolution and may allow general statements about the relative effect of different molecular processes on evolution.
Results: The Pandit 7.6 database contains 4341 families of sequences derived from the seed alignments of the Pfam database of amino acid alignments of families of homologous protein domains (Bateman et al., 2002). Each family in Pandit includes an alignment of amino acid sequences that matches the corresponding Pfam family seed alignment, an alignment of DNA sequences that contain the coding sequence of the Pfam alignment when they can be recovered (overall, 82.9% of sequences taken from Pfam) and the alignment of amino acid sequences restricted to only those sequences for which a DNA sequence could be recovered. Each of the alignments has an estimate of the phylogenetic tree associated with it. The tree topologies were obtained using the neighbor joining method based on maximum likelihood estimates of the evolutionary distances, with branch lengths then calculated using a standard maximum likelihood approach.
Availability: The Pandit database is available for browsing and download via its home page at http://www.ebi.ac.uk/goldman-srv/pandit/
Contact: simon@ebi.ac.uk
* To whom correspondence should be addressed.
Greedy method for inferring tandem duplication history
Authors: Zhang Louxin , Ma Bin , Wang Lusheng , Xu Ying 
Published: August 2003

Abstract
Motivation: Genome analysis suggests that tandem duplication is an important mode of evolutionary novelty by permitting one copy of each gene to drift and potentially to acquire a new function. With more and more genomic sequences available, reconstructing duplication history has received extensive attention recently.
Results: An efficient method is presented for inferring the duplication history of tandemly repeated sequences based on the model proposed by Fitch (1977). We validate the method by using simulation results and real data sets of mucin genes, ZNF genes, and olfactory receptors genes. The agreement with conclusions drawn by other biological researchers strongly indicates that our method is efficient and robust.
Availability:The program is available by request.
Contact: matzlx@nus.edu.sg
* To whom correspondence should be addressed.
A hidden Markov model for progressive multiple alignment
Authors: Löytynoja Ari , Milinkovitch Michel C. 
Published: August 2003

Abstract
Motivation: Progressive algorithms are widely used heuristics for the production of alignments among multiple nucleic-acid or protein sequences. Probabilistic approaches providing measures of global and/or local reliability of individual solutions would constitute valuable developments.
Results: We present here a new method for multiple sequence alignment that combines an HMM approach, a progressive alignment algorithm, and a probabilistic evolution model describing the character substitution process. Our method works by iterating pairwise alignments according to a guide tree and defining each ancestral sequence from the pairwise alignment of its child nodes, thus, progressively constructing a multiple alignment. Our method allows for the computation of each column minimum posterior probability and we show that this value correlates with the correctness of the result, hence, providing an efficient mean by which unreliably aligned columns can be filtered out from a multiple alignment.
Availability: The software is freely available http://www.ulb.ac.be/sciences/ueg/
Contact: aloytyno@ulb.ac.be; mcmilink@ulb.ac.be.
* To whom correspondence should be addressed.
GenoMap, a circular genome data viewer
Authors: Sato Naoki , Ehira Shigeki 
Published: August 2003

Abstract
Summary: A Tcl/Tk-based application called GenoMap is described, a viewer for genome-wide map of microarray expression data within a circular bacterial genome. An interactive interface facilitates easy identification of the expressed region. This software is also used for drawing genome-wide quantitative data.
Availability: The program is freely available to academic users as a Tcl/Tk source code at http://www.molbiol.saitama-u.ac.jp/~naoki/GenoMap/
Contact: naokisat@molbiol.saitama-u.ac.jp
ESTWeb: bioinformatics services for EST sequencing projects
Authors: Paquola Apuã C. M. , Nishyiama Milton Y. , Reis Eduardo M. , da Silva Aline M. , Verjovski-Almeida Sergio 
Published: August 2003

Abstract
Summary: ESTWeb is an internet based software package designed for uniform data processing and storage for large-scale EST sequencing projects. The package provides for: (a) reception of sequencing chromatograms; (b) sequence processing such as base-calling, vector screening, comparison with public databases; (c) storage of data and analysis in a relational database, (d) generation of a graphical report of individual sequence quality; and (e) issuing of reports with statistics of productivity and redundancy. The software facilitates real-time monitoring and evaluation of EST sequence acquisition progress along an EST sequencing project.
Availability: http://bioinfo.iq.usp.br/estweb
Contact: verjo@iq.usp.br
Supplementary information: http://bioinfo.iq.usp.br/estweb
* To whom correspondence should be addressed.
QAlign: quality-based multiple alignments with dynamic
phylogenetic analysis
Authors: Sammeth M. , Rothgänger J. , Esser W. , Albert J. , Stoye J. , Harmsen D. 
Published: August 2003

Abstract
Summary: Integrating different alignment strategies, a layout editor and tools deriving phylogenetic trees in a ‘multiple alignment environment’ helps to investigate and enhance results of multiple sequence alignment by hand. QAlign combines algorithms for fast progressive and accurate simultaneous multiple alignment with a versatile editor and a dynamic phylogenetic analysis in a convenient graphical user interface.
Availability: QAlign is freely available over the internet at http://www.ridom.de/qalign/. The platform-independent JAVA technology used provides distributions for various operating systems and hardware architectures.
Contact: qalign@ridom.de
* To whom correspondence should be addressed.
† Present address: Genome Informatics, Department of Technology, Bielefeld University, 33594 Bielefeld, Germany.
Serial BLAST searching
Authors: Korf Ian 
Published: August 2003

Abstract
Motivation: The translating BLAST algorithms are powerful tools for finding protein-coding genes because they identify amino acid similarities in nucleotide sequences. Unfortunately, these kinds of searches are computationally intensive and often represent bottlenecks in sequence analysis pipelines. Tuning parameters for speed can make the searches much faster, but one risks losing low-scoring alignments. However, high scoring alignments are relatively resistant to such changes in parameters, and this fact makes it possible to use a serial strategy where a fast, insensitive search is used to pre-screen a database for similar sequences, and a slow, sensitive search is used to produce the sequence alignments.
Results: Serial BLAST searches improve both the speed and sensitivity.
Contact: ik1@sanger.ac.uk
A comparison of statistical methods for analysis of
high density oligonucleotide array data
Authors: Rajagopalan Dilip 
Published: August 2003

Abstract
Motivation: Gene expression profiling has become an invaluable tool in functional genomics. A wide variety of statistical methods have been employed to analyze the data generated in experiments using Affymetrix GeneChip® microarrays. It is important to understand the relative performance of these methods in terms of accuracy in detecting and quantifying relative gene expression levels and changes in gene expression.
Results: Three different analysis approaches have been compared in this work: non-parametric statistical methods implemented in Affymetrix Microarray Analysis Suite v5.0 (MAS5); an error-modeling based approach implemented in Rosetta Resolver® v3.1; and an intensity-modeling approach implemented in dChip v1.1. A Latin Square data set generated and made available by Affymetrix was used in the comparison. All three methods—Resolver, MAS5 and the version of dChip based on the difference between perfect match and mismatch intensities—perform well in quantifying gene expression. Presence calls made by MAS5 and Resolver perform well at high concentrations, but they cannot be relied upon at low concentrations. The performance of Resolver and MAS5 in detecting 2-fold changes in transcript concentration is superior to that of dChip. At a comparable false positive rate, Resolver and MAS5 are able to detect many more true changes in transcript concentration. Estimated fold changes calculated by all the methods are biased below the true values.
Contact: dilip.2.rajagopalan@gsk.com
Political Ethics and Public Policy: Homosexuals between Moral Dilemmas and Political Considerations in Danish Parliamentary Debates
Authors: Albæk Erik 
Published: August 2003

Political science has abundantly proved that politics involves power, conflict, and self‐serving interests. Much less frequently does political science deal with ethics in public policymaking. This article analyses the appeal to moral principles in the political process of drafting three bills, all concerning homosexuals, in which the Danish parliamentary parties, in contrast to normal practice, allowed their members to deviate from the party line and vote in accordance with their ‘conscience’. Analysis of the cases indicates that moral considerations are capable of structuring and constraining arguments and that they are decisive for some politicians’ positions in some situations. The cases also raise doubts concerning the widely held view that decisions based on votes of conscience, because they are informed by ‘ethical’ rather than ‘political’ considerations, are qualitatively superior to ordinary political decisions.
MANKINDMen, said the Devil,Are good to their brothers:They don’t want to mendTheir own ways, but each other’s.– grook by Piet Hein