bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes.
Authors: Wagner A 
Published: July 2002

Abstract
MOTIVATION: The question addressed here is how cooperative interactions among transcription factors (TFs), a very frequent phenomenon in eukaryotic transcriptional regulation, can be used to identify genes that are regulated by one or more TFs with known DNA binding specificities. Cooperativity may be homotypic, involving binding of only one transcription factor to multiple sites in a gene's regulatory region. It may also be heterotypic, involving binding of more than one TF. Both types of cooperativity have in common that the binding sites for the respective TFs form tightly linked 'clusters', groups of binding sites often more closely associated than expected by chance alone. RESULTS: A statistical technique suitable for the identification of statistically significant homotypic or heterotypic TF binding site clusters in whole eukaryotic genomes is presented. It can be used to identify genes likely to be regulated by the TFs. Application of the technique is illustrated with two transcription factors involved in the cell cycle and mating control of the yeast Saccharomyces cerevisiae, indicating that the results obtained are biologically meaningful. This rapid and inexpensive computational method of generating hypotheses about gene regulation thus generates information that may be used to guide subsequent costly and laborious experimental approaches, and that may aid in the assignment of biological functions to putative open reading frames.
Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity.
Authors: Klingenhoff A , Frech K , Quandt K , Werner T 
Published: July 2002

Abstract
MOTIVATION: Gene regulation often depends on functional modules which feature a detectable internal organization. Overall sequence similarity of these modules is often insufficient for detection by general search methods like FASTA or even Gapped BLAST. However, it is of interest to evaluate whether modules, often known from experimental analysis of single sequences, are present in other regulatory sequences. RESULTS: We developed a new method (FastM) which combines a search algorithm for individual transcription factor binding sites (MatInspector) with a distance correlation function. FastM allows fast definition of a model of correlated binding sites derived from as little as a single promoter or enhancer. ModelInspector results are suitable for evaluation of the significance of the model. We used FastM to define a model for the experimentally verified NFkappaB/IRF1 regulatory module from the major histocompatibility complex (MHC) class I HLA-B gene promoter. Analysis of a test set of sequences as well as database searches with this model showed excellent correlation of the model with the biological function of the module. These results could not be obtained by searches using FASTA or Gapped BLAST, which are based on sequence similarity. We were also able to demonstrate association of a hypothetical GRE-GRE module with viral sequences based on analysis of several GenBank sections with this module. AVAILABILITY: The WWW version of FastM is accessible at: http://www.gsf.de/cgi-bin/fastm. pl and http://genomatix.gsf.de/cgi-bin/fastm2/fastm.pl
The Biopolymer Markup Language.
Authors: Feny√∂ D 
Published: July 2002

Abstract
SUMMARY: An XML derived from a data model designed to be a hierarchical representation of an organism has been specified and a browser to use this language has been developed. AVAILABILITY: The language definition is available in HTML form at http://www.proteometrics.com/BIOML/. The BioML browser is available on request from the author.
Sequence analysis by additive scales: DNA structure for
sequences and repeats of all lengths
Authors: Baldi Pierre , Baisnée Pierre-François 
Published: July 2002

Abstract
Motivation: DNA structure plays an important role in a variety of biological processes. Different di- and tri-nucleotide scales have been proposed to capture various aspects of DNA structure including base stacking energy, propeller twist angle, protein deformability, bendability, and position preference. Yet, a general framework for the computational analysis and prediction of DNA structure is still lacking. Such a framework should in particular address the following issues: (1) construction of sequences with extremal properties; (2) quantitative evaluation of sequences with respect to a given genomic background; (3) automatic extraction of extremal sequences and profiles from genomic databases; (4) distribution and asymptotic behavior as the length Nof the sequences increases; and (5) complete analysis of correlations between scales.
Results: We develop a general framework for sequence analysis based on additive scales, structural or other, that addresses all these issues. We show how to construct extremal sequences and calibrate scores for automatic genomic and database extraction. We show that distributions rapidly converge to normality as Nincreases. Pairwise correlations between scales depend both on background distribution and sequence length and rapidly converge to an analytically predictable asymptotic value. For di- and tri-nucleotide scales, normal behavior and asymptotic correlation values are attained over a characteristic window length of about 10–15 bp. With a uniform background distribution, pairwise correlations between empirically-derived scales remain relatively small and roughly constant at all lengths, except for propeller twist and protein deformability which are positively correlated. There is a positive (resp. negative) correlation between dinucleotide base stacking (resp. propeller twist and protein deformability) and AT-content that increases in magnitude with length. The framework is applied to the analysis of various DNA tandem repeats. We derive exact expressions for counting the number of repeat unit classes at all lengths. Tandem repeats are likely to result from a variety of different mechanisms, a fraction of which is likely to depend on profiles characterized by extreme structural features.
Contact: pfbaldi@ics.uci.edu; baisnee@ics.uci.edu
To whom all correspondence should be addressed.
Processing and quality control of DNA array hybridization data
Authors: Beißbarth T. , Fellenberg K. , Brors B. , Arribas-Prat R. , Boer J. M. , Hauser N. C. , Scheideler M. , Hoheisel J. D. , Schütz G. , Poustka A. , Vingron M. 
Published: July 2002

Abstract
Motivation: The technology of hybridization to DNA arrays is used to obtain the expression levels of many different genes simultaneously. It enables searching for genes that are expressed specifically under certain conditions. However, the technology produces large amounts of data demanding computational methods for their analysis. It is necessary to find ways to compare data from different experiments and to consider the quality and reproducibility of the data.
Results: Data analyzed in this paper have been generated by hybridization of radioactively labeled targets to DNA arrays spotted on nylon membranes. We introduce methods to compare the intensity values of several hybridization experiments. This is essential to find differentially expressed genes or to do pattern analysis. We also discuss possibilities for quality control of the acquired data.
Availability: http://www.dkfz.de/tbi
Contact: M.Vingron@dkfz-heidelberg.de
To whom correspondence should be addressed.
PHAT: a transmembrane-specific substitution matrix
Authors: Ng Pauline C. , Henikoff Jorja G. , Henikoff Steven 
Published: July 2002

Abstract
Motivation: Database searching algorithms for proteins use scoring matrices based on average protein properties, and thus are dominated by globular proteins. However, since transmembrane regions of a protein are in a distinctly different environment than globular proteins, one would expect generalized substitution matrices to be inappropriate for transmembrane regions.
Results: We present the PHAT (predicted hydrophobic and transmembrane) matrix, which significantly outperforms generalized matrices and a previously published transmembrane matrix in searches with transmembrane queries. We conclude that a better matrix can be constructed by using background frequencies characteristic of the twilight zone, where low-scoring true positives have scores indistinguishable from high-scoring false positives, rather than the amino acid frequencies of the database. The PHAT matrix may help improve the accuracy of sequence alignments and evolutionary trees of membrane proteins.
Availability: http://www.blocks.fhcrc.org/~pauline
Contact: steveh@muller.fhcrc.org
To whom correspondence should be addressed.
XML, bioinformatics and data integration
Authors: Achard Frédéric , Vaysseix Guy , Barillot Emmanuel 
Published: July 2002

Abstract
Motivation: The eXtensible Markup Language (XML) is an emerging standard for structuring documents, notably for the World Wide Web. In this paper, the authors present XML and examine its use as a data language for bioinformatics. In particular, XML is compared to other languages, and some of the potential uses of XML in bioinformatics applications are presented. The authors propose to adopt XML for data interchange between databases and other sources of data. Finally the discussion is illustrated by a test case of a pedigree data model in XML.
Contact: Emmanuel.Barillot@infobiogen.fr
* To whom correspondence should be addressed.
3 Present address: Cereon Genomics, 45 Sidney St, Cambridge, MA 02139, USA.
Distribution of genes for lysine biosynthesis through the

aminoadipate pathway among prokaryotic genomes
Authors: Nishida Hiromi 
Published: July 2002

Abstract
Summary: Deinococcus radioduranshas homologous genes to the genes which from the Thermus thermophilus gene cluster for lysine biosynthesis. Interestingly, those genes are clustered in Thermus, nevertheless they are scattered in Deinococcus. A similar gene cluster has only been found in Pyrococcus. However, the phylogenetic analyses indicated that the deduced gene products from Deinococcus were the most closely related to the proteins encoded in the Thermus gene cluster for lysine biosynthesis. Therefore, those genes had not been transferred horizontally between Pyrococcus and Thermus. It is strongly suggested that a common ancestor of Deinococcus and Thermus possessed the genes for lysine biosynthesis through the aminoadipate pathway. These had been clustered through the evolution of Thermus or had been scattered from the gene cluster through the evolution of Deinococcus. In addition, I showed that LysW and its homologues were specialized proteins for the prokaryotic lysine biosynthesis through the aminoadipate pathway.
Contact: hnishida@iam.u-tokyo.ac.jp
Retrieval and on-the-fly alignment of sequence fragments from

the HIV database
Authors: Gaschen Brian , Kuiken Carla , Korber Bette , Foley Brian 
Published: July 2002

Abstract
Motivation: The amount of HIV-1 sequence data generated (presently around 42000 sequences, of which more than 22000 are from the V3 region of the viral envelope) presents a challenge for anyone working on the analysis of these data. A major problem is obtaining the region of interest from the stored sequences, which often contain but are not limited to that region. In addition, multiple alignment programs generally cannot deal with the large numbers of sequences that are available for many HIV-1 regions. We set out to provide our users with a tool that will retrieve and create an initial alignment of the HIV sequences that are available for a given genomic region.
Results: The MPAlign (Multiple Pairwise Alignment) web interface is a collection of Perl scripts that retrieves sequences from the Los Alamos HIV sequence database based on a number of search parameters. All sequences were pairwise-aligned to a model sequence using the Hidden Markov Model-based program HMMER. The HMMER model is general enough to accommodate virtually all HIV-1 sequences stored in the database. To create a multiple sequence alignment, gaps were inserted into the sequences during retrieval, so that they are aligned to one another. Retrieving and aligning the almost 560 gp120 sequences (\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \({\sim}\) \end{document}1500 nt) stored in the database is at least 1500 times faster than a similar Clustal alignment.
Availability: At http://www.hiv.lanl.gov/
Contact: Brian Gaschen at bkg@lanl.gov
* To whom correspondence should be addressed.
Avoiding cross hybridization by choosing nonredundant targets
on cDNA arrays
Authors: Nielsen H. B. , Knudsen S. 
Published: July 2002

Abstract
Summary: PROBEWIZ designs PCR primers for amplifying probes for cDNA arrays. The probes are designed to have minimal homology to other expressed sequences from a given organism. The primer selection is based on user-defined penalties for homology, primer quality, and proximity to the 3′end.
Availability: PROBEWIZ is accessible from http://www.cbs.dtu.dk/services/DNAarray/probewiz.html
Contact: hbjorn@cbs.dtu.dk; steen@cbs.dtu.dk
DRAGON View: information visualization for annotated microarray
data
Authors: Bouton Christopher M. L. S. , Pevsner Jonathan 
Published: July 2002

Abstract
Summary: The DRAGON View information visualization tools aid in the comprehensive analysis of large-scale gene expression data that has been annotated with biologically relevant information through the generation of three types of complementary graphical outputs.
Availability: The DRAGON View tools are freely available on the DRAGON web site at http://pevsnerlab.kennedykrieger.org/dragonview.htm.
Contact: pevsner@kennedykrieger.org; cbouton@jhmi.edu
* To whom correspondence should be addressed.
3 Present address: LION Bioscience Research Inc.
Analysis of matched mRNA measurements from two different
microarray technologies
Authors: Kuo Winston Patrick , Jenssen Tor-Kristian , Butte Atul J. , Ohno-Machado Lucila , Kohane Isaac S. 
Published: July 2002

Abstract
Motivation: The existence of several technologies for measuring gene expression makes the question of cross-technology agreement of measurements an important issue. Cross-platform utilization of data from different technologies has the potential to reduce the need to duplicate experiments but requires corresponding measurements to be comparable.
Methods: A comparison of mRNA measurements of 2895 sequence-matched genes in 56 cell lines from the standard panel of 60 cancer cell lines from the National Cancer Institute (NCI 60) was carried out by calculating correlation between matched measurements and calculating concordance between cluster from two high-throughput DNA microarray technologies, Stanford type cDNA microarrays and Affymetrix oligonucleotide microarrays.
Results: In general, corresponding measurements from the two platforms showed poor correlation. Clusters of genes and cell lines were discordant between the two technologies, suggesting that relative intra-technology relationships were not preserved. GC-content, sequence length, average signal intensity, and an estimator of cross-hybridization were found to be associated with the degree of correlation. This suggests gene-specific, or more correctly probe-specific, factors influencing measurements differently in the two platforms, implying a poor prognosis for a broad utilization of gene expression measurements across platforms.
Contact: wpkuo@mit.edu
* To whom correspondence should be addressed.
1 These authors contributed equally to this work.
A comparative review of statistical methods for discovering
differentially expressed genes in replicated microarray experiments
Authors: Pan Wei 
Published: July 2002

Abstract
Motivation: A common task in analyzing microarray data is to determine which genes are differentially expressed across two kinds of tissue samples or samples obtained under two experimental conditions. Recently several statistical methods have been proposed to accomplish this goal when there are replicated samples under each condition. However, it may not be clear how these methods compare with each other. Our main goal here is to compare three methods, the t-test, a regression modeling approach (Thomas et al. , Genome Res. , 11, 1227–1236, 2001) and a mixture model approach (Pan et al. , http://www.biostat.umn.edu/cgi-bin/rrs?print+2001,2001a,b) with particular attention to their different modeling assumptions.
Results: It is pointed out that all the three methods are based on using the two-sample t-statistic or its minor variation, but they differ in how to associate a statistical significance level to the corresponding statistic, leading to possibly large difference in the resulting significance levels and the numbers of genes detected. In particular, we give an explicit formula for the test statistic used in the regression approach. Using the leukemia data of Golub et al. (Science , 285, 531–537, 1999), we illustrate these points. We also briefly compare the results with those of several other methods, including the empirical Bayesian method of Efron et al. (J. Am. Stat. Assoc. , to appear, 2001) and the Significance Analysis of Microarray (SAM) method of Tusher et al. (Proc. Natl Acad. Sci. USA , 98, 5116–5121, 2001).
Contact: weip@biostat.umn.edu
Xdigitise: visualization of hybridization experiments
Authors: Wruck Wasco , Griffiths Huw , Steinfath Matthias , Lehrach Hans , Radelof Uwe , O'Brien John 
Published: July 2002

Abstract
Xdigitise is a software system for visualization of hybridization experiments giving the user facilities to analyze the corresponding images manually or automatically. Images of the high-density DNA arrays are displayed as well as the results of an external image analysis bundled with Xdigitise, e.g. the spot locations are marked and the duplicate correlations are shown by a color scale.
Availability: Xdigitise can be downloaded from http://www.molgen.mpg.de/~xdigitise.
Contact: wruck_w@molgen.mpg.de
* To whom correspondence should be addressed.
Cognitive reserve protects ALS‐typical cognitive domains: A longitudinal study.
Authors: Temp Anna G. M. , Kasper Elisabeth , Machts Judith , Vielhaber Stefan , Teipel Stefan , Hermann Andreas , Prudlo Johannes 
Published: July 2022

AbstractBackground and ObjectivesTo determine whether cognitive reserve (CR) as measured by verbal intelligence quotient, educational length, and achievement protects amyotrophic lateral sclerosis (ALS) patients' verbal fluency, executive functioning, and memory against brain volume loss over a period of 12 months.MethodsThis cohort study was completed between 2013 and 2016 with a follow‐up duration of 12 months. ALS patients were recruited from two specialist out‐patient clinics in Rostock and Magdeburg in Germany. Participants underwent cognitive testing and magnetic resonance imaging both at baseline and again after 12 months. The cognitive domains assessed included verbal memory in addition to executive functions such as verbal fluency, working memory, shifting and selective attention.ResultsThirty‐eight ALS patients took part; 25 patients had no cognitive impairment (ALSni), and 13 were cognitively impaired (ALSci). On average, patients lost 294 mm3 in their superior frontal gyri, 225 mm3 in their orbitofrontal gyri, and 15.97 mm3 in their hippocampi over 12 months. There was strong evidence that CR protected letter fluency from further decline (Bayes factor [BF] >10) and moderate evidence that it supported learning effects in letter flexibility (BF >3). However, there is a lack of evidence supporting the notion that working memory, shifting, selective attention or verbal memory (BF = 1) are protected.DiscussionAs CR is easily determined and protects ALS‐specific cognitive domains over time, it should be regarded as a valuable predictive marker.
How Do Nonsurgical Interventions Improve Pain and Physical Function in People With Osteoarthritis? A Scoping Review of Mediation Analysis Studies
Authors: Lima Yuri Lopes , Lee Hopin , Klyne David M. , Dobson Fiona L. , Hinman Rana S. , Bennell Kim L. , Hall Michelle 
Published: July 2022

ObjectiveNonsurgical interventions are recommended for osteoarthritis (OA). However, how interventions change pain and physical function is unclear. Therefore, the objectives of this scoping review were to 1) identify what potential mediators of nonsurgical interventions on pain and physical function have been evaluated and 2) summarize the findings according to intervention, joint, and outcome.MethodsWe searched Medline, Embase, CINAHL, Cochrane Central Register of Controlled Trials, and Scopus databases. Studies were included if they conducted a mediation analysis on a randomized controlled trial evaluating a nonsurgical intervention on OA of any joint. Outcomes were pain and physical function.ResultsNine knee OA studies, evaluating diet plus exercise, exercise, unloading shoes, high‐expectation communication during acupuncture, and telephone‐based weight loss plus exercise were identified. Except for weight loss and self‐efficacy, putative mediators (knee muscle perfusion/extensor strength/adduction moment, systemic inflammatory biomarkers, physical activity, dietary intake, and pain beliefs) were evaluated by single studies. Ten mediators partially mediated intervention (diet plus exercise, exercise, high‐expectation communication) effects on pain and physical function. Eight mediators were common to pain and function (reduced weight, increased knee extensor strength, and increased self‐efficacy). Constant knee flexor muscle perfusion partially mediated exercise effects on pain, and knee pain relief partially mediated exercise effects on function.ConclusionIn knee OA, some evidence suggests that the benefits of 1) diet and exercise are mediated through changes in body weight, systemic inflammation, and self‐efficacy; 2) exercise is mediated through changes in knee muscle strength and self‐efficacy; and 3) high‐expectation communication style is mediated through changes in self‐efficacy.
A Highly Stable All‐Solid‐State Na–O2/H2O Battery with Low Overpotential Based on Sodium Hydroxide
Authors: Jiang Chenggong , Zhang Hui , Li Peng , Zhan Xiaoyi , Liu Zhenjie , Wang Liang , Mao Baohua , Li Qingtian , Wen Zhaoyin , Peng Zhangquan , Chen Shengli , Liu Zhi 
Published: July 2022

AbstractThe rechargeable all‐solid‐state Na–O2 battery is one of the most promising candidates for next‐generation energy storage devices owing to its high theoretical specific energy, safety, electrochemical stability, and abundant Na resources. However, the practical implementation of current all‐solid‐state Na–O2 batteries is still limited by low‐resistance interfaces, low energy efficiency, and poor cycle life. Herein, an all‐solid‐state Na–O2/H2O battery that can sustain highly reversible cycling with a low overpotential is reported. Using a customized silver–polymer composite cathode, this battery can be operated under ≈7% relative humidity (RH) at 80 °C and cycled for more than 100 times with a low overpotential (≈75 mV at 100th cycle) and high round trip efficiency >97% at 100th cycle) at an energy density of 20 mA g−1. Furthermore, mechanistic insight that the RH intimately controls the type and hydration state of the discharge product is also provided, and thereby the charge kinetics and battery performance are modulated. It is also revealed that silver catalyst can efficiently reduce the reaction barrier of NaOH decomposition. With the further optimization, this battery potentially can be implemented in real‐world applications and confer practical applicability that can extend to other energy‐storage systems, such as other metal–air batteries.