bluuebunny/crossref_metadata_2025_split huggingface dataset:
A segment alignment approach to protein comparison
Authors: Ye Yuzhen , Jaroszewski Lukasz , Li Weizhong , Godzik Adam 
Published: April 2003

Abstract
Motivation: Local structure segments (LSSs) are small structural units shared by unrelated proteins. They are extensively used in protein structure comparison, and predicted LSSs (PLSSs) are used very successfully in ab initio folding simulations. However, predicted or real LSSs are rarely exploited by protein sequence comparison programs that are based on position-by-position alignments.
Results: We developed a SEgment Alignment algorithm (SEA) to compare proteins described as a collection of predicted local structure segments (PLSSs), which is equivalent to an unweighted graph (network). Any specific structure, real or predicted corresponds to a specific path in this network. SEA then uses a network matching approach to find two most similar paths in networks representing two proteins. SEA explores the uncertainty and diversity of predicted local structure information to search for a globally optimal solution. It simultaneously solves two related problems: the alignment of two proteins and the local structure prediction for each of them. On a benchmark of protein pairs with low sequence similarity, we show that application of the SEA algorithm improves alignment quality as compared to FFAS profile-profile alignment, and in some cases SEA alignments can match the structural alignments, a feat previously impossible for any sequence based alignment methods.
Availability: SEA is freely available for academic users on a web server http://ffas.ljcrf.edu/sea.
Supplementary information: http://ffas.ljcrf.edu/sea
Contact: adam@burnham.org
* To whom correspondence should be addressed. Program in Bioinformatics and Biological Complexity, The Burnham Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA.
Client–Server environment for high-performance gene expression data analysis
Authors: Sturn Alexander , Mlecnik Bernhard , Pieler Roland , Rainer Johannes , Truskaller Thomas , Trajanoski Zlatko 
Published: April 2003

Abstract
Summary: We have developed a platform independent, flexible and scalable Java environment for high-performance large-scale gene expression data analysis, which integrates various computational intensive hierarchical and non-hierarchical clustering algorithms. The environment includes a powerful client for data preparation and results visualization, an application server for computation and an additional administration tool. The package is available free of charge for academic and non-profit institutions.
Availability: http://genome.tugraz.at/Software
Contact: zlatko.trajanoski@tugraz.at
* To whom correspondence should be addressed.
Evaluation of annotation strategies using an entire genome sequence
Authors: Iliopoulos Ioannis , Tsoka Sophia , Andrade Miguel A. , Enright Anton J. , Carroll Mark , Poullet Patrick , Promponas Vassilis , Liakopoulos Theodore , Palaios Giorgos , Pasquier Claude , Hamodrakas Stavros , Tamames Javier , Yagnik Asutosh T. , Tramontano Anna , Devos Damien , Blaschke Christian , Valencia Alfonso , Brett David , Martin David , Leroy Christophe , Rigoutsos Isidore , Sander Chris , Ouzounis Christos A. 
Published: April 2003

Abstract
Motivation: Genome-wide functional annotation either by manual or automatic means has raised considerable concerns regarding the accuracy of assignments and the reproducibility of methodologies. In addition, a performance evaluation of automated systems that attempt to tackle sequence analyses rapidly and reproducibly is generally missing. In order to quantify the accuracy and reproducibility of function assignments on a genome-wide scale, we have re-annotated the entire genome sequence of Chlamydia trachomatis (serovar D), in a collaborative manner.
Results: We have encoded all annotations in a structured format to allow further comparison and data exchange and have used a scale that records the different levels of potential annotation errors according to their propensity to propagate in the database due to transitive function assignments. We conclude that genome annotation may entail a considerable amount of errors, ranging from simple typographical errors to complex sequence analysis problems. The most surprising result of this comparative study is that automatic systems might perform as well as the teams of experts annotating genome sequences.
Availability and supplementary information: http://www.ebi.ac.uk/research/cgg/annotation/cteval/
Contact: ouzounis@ebi.ac.uk
* To whom correspondence should be addressed.
† INA-EKETA, GR-57001 Thessaloniki, Greece
‡ Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
§ Aetion Technologies LLC, Worthington, OH 43085, USA
¶ Institut Curie, F-75248 Paris, France
∥ CNRS, UMR6543, F-06108 Nice, France
** Alma Bioinformatics, E-28760 Madrid, Spain
†† Cap Gemini Ernst & Young, London SW1X 7LX, UK
‡‡ Univ. of Rome ‘La Sapienza’, I-00185 Rome, Italy
§§ MWG-Biotech AG, Ebersberg, D-85560 Berlin, Germany
¶¶ Wellcome Trust Biocentre, Univ. of Dundee, Dundee DD1 5HN, UK
Perfect phylogeny haplotyper: haplotype inferral using a tree model
Authors: Chung Ren Hua , Gusfield Dan 
Published: April 2003

Abstract
Summary: We have developed an efficient program, the Perfect Phylogeny Haplotyper (PPH) that takes in unphased population genotype data, and determines if that data can be explained by haplotype pairs that could have evolved on a perfect phylogeny.
Availability: Executable code for four common platforms is available at: http://wwwcsif.cs.ucdavis.edu/~gusfield
Contact: gusfield@cs.ucdavis.edu
* To whom correspondence should be addressed.
Directed indices for exploring gene expression data
Authors: LeBlanc Michael , Kooperberg Charles , Grogan Thomas M. , Miller Thomas P. 
Published: April 2003

Abstract
Motivation: Large expression studies with clinical outcome data are becoming available for analysis. An important goal is to identify genes or clusters of genes where expression is related to patient outcome. While clustering methods are useful data exploration tools, they do not directly allow one to relate the expression data to clinical outcome. Alternatively, methods which rank genes based on their univariate significance do not incorporate gene function or relationships to genes that have been previously identified. In addition, after sifting through potentially thousands of genes, summary estimates (e.g. regression coefficients or error rates) algorithms should address the potentially large bias introduced by gene selection.
Results: We developed a gene index technique that generalizes methods that rank genes by their univariate associations to patient outcome. Genes are ordered based on simultaneously linking their expression both to patient outcome and to a specific gene of interest. The technique can also be used to suggest profiles of gene expression related to patient outcome. A cross-validation method is shown to be important for reducing bias due to adaptive gene selection. The methods are illustrated on a recently collected gene expression data set based on 160 patients with diffuse large cell lymphoma (DLCL).
Availability: A program written in the R language implementing the gene index can be obtained at http://www.crab.org/papers/
Contact: mikel@crab.org
* To whom correspondence should be addressed.
The First Oral Rotavirus Vaccine, 1998–1999: Estimates of Uptake from the National Immunization Survey
Authors: Smith Philip J. , Schwartz Ben , Mokdad Ali , Bloch Alan B. , McCauley Mary , Murphy Trudy V. 
Published: April 2003

Objective. On August 31, 1998, the rhesus-human reassortant rotavirus vaccine (RRV-TV) was licensed for use in the U.S. During the next nine months, 15 cases of intussusception were reported among infants who received the vaccine. Case-control and cohort studies showed a significantly increased risk of developing intussusception within one week of receiving the vaccine; subsequent ecologic studies did not. In this study, the authors used data on RRV-TV vaccination rates from the National Immunization Survey (NIS) to estimate state and national RRV-TV uptake rates and factors associated with receiving RRV-TV. These estimates are a key component in evaluating published ecologic studies designed to investigate the relationship between receipt of the vaccine and intussusception. Methods. The authors analyzed NIS data for children ages 19 to 35 months who were eligible to receive RRV-TV between September 1998 and July 1999. The authors estimated vaccine coverage and the number of doses administered by state, NIS sampling quarter, and birth cohort, and analyzed demographic and socioeconomic variables to evaluate their relationship with receiving RRV-TV. Results. It was estimated that approximately 1 million doses of RRV-TV were administered to 504,585 (±61,854) children, 13.4% (±1.6%) of children who were eligible. The estimated number of doses administered and the vaccination coverage rate varied greatly from state to state. Children living in households with higher socioeconomic conditions were more likely to receive the vaccine. Conclusion. Ecologic studies had a limited ability to detect a significant increase in the population incidence rate of intussusception that could be attributed to RRV-TV because populations in these studies consisted primarily of children who did not receive the vaccine. The example from RRV-TV demonstrates some of the challenges of assessing the magnitude of the association between a vaccine and an uncommon or rare adverse event.
Completeness of Pediatric TB Reporting in New York City
Authors: San Gabriel Pablo , Saiman Lisa , Kaye Katherine , Silin Muriel , Onorato Ida , Schulte Joann 
Published: April 2003

Objectives. Accurate surveillance of tuberculosis (TB) in children is critical because such cases represent recent transmission, but surveillance is difficult as only 10% to 50% of cases are culture-confirmed. Hospital-based sources were used to develop alternative surveillance to assess completeness of reporting for pediatric TB in northern Manhattan and Harlem from 1993 through 1995. Methods. Alternative surveillance sources included ICD-9-CM hospital discharge codes for active TB and gastric aspirate reports. Cases identified by alternative surveillance were compared with cases previously reported to the New York City Department of Health (NYC DOH). Results. Alternative surveillance detected 25 cases of possible pediatric TB, of which four (16%) had never been reported to the NYC DOH and three (12%) had been reported as suspect cases, but had not fulfilled the criteria for a reportable case of pediatric TB. Of these seven newly counted cases, three were detected by ICD-9-CM codes, three by a gastric aspirate log book, and one by both. In contrast, 13 other cases had been reported to the NYC DOH, but were undetected by our alternative surveillance; eight of these could be verified with available medical records. Thus, the demographic and clinical characteristics of the 25 detected and the eight undetected cases with available medical records were evaluated in this study. Conclusions. Alternative surveillance proved effective, was complementary to the NYC DOH surveillance efforts, and increased the number of pediatric TB cases identified during the study period by 21%.
Ethylene Regulates Monomeric GTP-Binding Protein Gene Expression and Activity in Arabidopsis
Authors: Moshkov Igor E. , Mur Luis A.J. , Novikova Galina V. , Smith Aileen R. , Hall Michael A. 
Published: April 2003

AbstractEthylene rapidly and transiently up-regulates the activity of several monomeric GTP-binding proteins (monomeric G proteins) in leaves of Arabidopsis as determined by two-dimensional gel electrophoresis and autoradiographic analyses. The activation is suppressed by the receptor-directed inhibitor 1-methylcyclopropene. In theetr1-1 mutant, constitutive activity of all the monomeric G proteins activated by ethylene is down-regulated relative to wild type, and ethylene treatment has no effect on the levels of activity. Conversely, in the ctr1-1 mutant, several of the monomeric G proteins activated by ethylene are constitutively up-regulated. However, the activation profile of ctr1-1does not exactly mimic that of ethylene-treated wild type. Biochemical and molecular evidence suggested that some of these monomeric G proteins are of the Rab class. Expression of the genes for a number of monomeric G proteins in response to ethylene was investigated by reverse transcriptase-PCR. Rab8 andAra3 expression was increased within 10 min of ethylene treatment, although levels fell back significantly by 40 min. In theetr1-1 mutant, expression of Rab8 was lower than wild type and unaffected by ethylene; inctr1-1, expression of Rab8 was much higher than wild type and comparable with that seen in ethylene treatments. Expression in ctr1-1 was also unaffected by ethylene. Thus, the data indicate a role for monomeric G proteins in ethylene signal transduction.
Phloem-Localizing Sulfate Transporter, Sultr1;3, Mediates Re-Distribution of Sulfur from Source to Sink Organs in Arabidopsis
Authors: Yoshimoto Naoko , Inoue Eri , Saito Kazuki , Yamaya Tomoyuki , Takahashi Hideki 
Published: April 2003

Abstract
For the effective recycling of nutrients, vascular plants transport pooled inorganic ions and metabolites through the sieve tube. A novel sulfate transporter gene, Sultr1;3, was identified as an essential member contributing to this process for redistribution of sulfur source in Arabidopsis.Sultr1;3 belonged to the family of high-affinity sulfate transporters, and was able to complement the yeast sulfate transporter mutant. The fusion protein of Sultr1;3 and green fluorescent protein was expressed by theSultr1;3 promoter in transgenic plants, which revealed phloem-specific expression ofSultr1;3 in Arabidopsis. Sultr1;3-green fluorescent protein was found in the sieve element-companion cell complexes of the phloem in cotyledons and roots. Limitation of external sulfate caused accumulation of Sultr1;3mRNA both in leaves and roots. Movement of 35S-labeled sulfate from cotyledons to the sink organs was restricted in the T-DNA insertion mutant of Sultr1;3. These results provide evidence that Sultr1;3 transporter plays an important role in loading of sulfate to the sieve tube, initiating the source-to-sink translocation of sulfur nutrient in Arabidopsis.
Tolerance of Mannitol-Accumulating Transgenic Wheat to Water Stress and Salinity
Authors: Abebe Tilahun , Guenzi Arron C. , Martin Bjorn , Cushman John C. 
Published: April 2003

Abstract
Previous work with model transgenic plants has demonstrated that cellular accumulation of mannitol can alleviate abiotic stress. Here, we show that ectopic expression of the mtlD gene for the biosynthesis of mannitol in wheat improves tolerance to water stress and salinity. Wheat (Triticum aestivum L. cv Bobwhite) was transformed with the mtlD gene of Escherichia coli. Tolerance to water stress and salinity was evaluated using calli and T2 plants transformed with (+mtlD) or without (−mtlD) mtlD. Calli were exposed to −1.0 MPa of polyethylene glycol 8,000 or 100 mm NaCl. T2plants were stressed by withholding water or by adding 150 mm NaCl to the nutrient medium. Fresh weight of −mtlD calli was reduced by 40% in the presence of polyethylene glycol and 37% under NaCl stress. Growth of +mtlD calli was not affected by stress. In −mtlD plants, fresh weight, dry weight, plant height, and flag leaf length were reduced by 70%, 56%, 40%, and 45% compared with 40%, 8%, 18%, and 29%, respectively, in +mtlD plants. Salt stress reduced shoot fresh weight, dry weight, plant height, and flag leaf length by 77%, 73%, 25%, and 36% in −mtlD plants, respectively, compared with 50%, 30%, 12%, and 20% in +mtlD plants. However, the amount of mannitol accumulated in the callus and mature fifth leaf (1.7–3.7 μmol g−1 fresh weight in the callus and 0.6–2.0 μmol g−1 fresh weight in the leaf) was too small to protect against stress through osmotic adjustment. We conclude that the improved growth performance of mannitol-accumulating calli and mature leaves was due to other stress-protective functions of mannitol, although this study cannot rule out possible osmotic effects in growing regions of the plant.
Suppression of a Vegetative MADS Box Gene of Potato Activates Axillary Meristem Development
Authors: Rosin Faye M. , Hart Jennifer K. , Van Onckelen Harry , Hannapel David J. 
Published: April 2003

Abstract
Potato MADS box 1 (POTM1) is a member of the SQUAMOSA-like family of plant MADS box genes isolated from an early stage tuber cDNA library. The RNA ofPOTM1 is most abundant in vegetative meristems of potato (Solanum tuberosum), accumulating specifically in the tunica and corpus layers of the meristem, the procambium, the lamina of new leaves, and newly formed axillary meristems. Transgenic lines with reduced levels of POTM1 mRNA exhibited decreased apical dominance accompanied by a compact growth habit and a reduction in leaf size. Suppression lines produced truncated shoot clusters from stem buds and, in a model system, exhibited enhanced axillary bud growth instead of producing a tuber. This enhanced axillary bud growth was not the result of increased axillary bud formation. Tuber yields were reduced and rooting of cuttings was strongly inhibited inPOTM1 suppression lines. Both starch accumulation and the activation of cell division occurred in specific regions of the vegetative meristems of the POTM1 transgenic lines. Cytokinin levels in axillary buds of a transgenic suppression line increased 2- to 3-fold. These results imply that POTM1mediates the control of axillary bud development by regulating cell growth in vegetative meristems.
Expression and Function of Cell Wall-Bound Cationic Peroxidase in Asparagus Somatic Embryogenesis
Authors: Takeda Hiroyuki , Kotake Toshihisa , Nakagawa Naoki , Sakurai Naoki , Nevins Donald J. 
Published: April 2003

Abstract
Cultured asparagus (Asparagus officinalis L. cv Y6) cells induced to regenerate into whole plants through somatic embryogenesis secreted a 38-kD protein into cell walls. The full-length cDNA sequence of this protein (Asparagus officinalisperoxidase 1 [AoPOX1]) determined by reverse transcriptase-polymerase chain reaction showed similarity with plant peroxidases.AoPOX1 transcripts were particularly abundant during early somatic embryogenesis. To evaluate the in vivo function of AoPOX1 protein, purified recombinant AoPOX1 protein was reacted with a series of phenolic substrates. The AoPOX1 protein was effective in the metabolism of feruloyl (o-methoxyphenol)-substituted substrates, including coniferyl alcohol. The reaction product of coniferyl alcohol was fractionated and subjected to gas chromatography-mass spectrometry analysis and 1H-nuclear magnetic resonance analysis, indicating that the oxidation product of coniferyl alcohol in the presence of AoPOX1 was dehydrodiconiferyl alcohol. The concentration of dehydrodiconiferyl alcohol in the cultured medium of the somatic embryos was in the range of 10−8 m. Functions of the AoPOX1 protein in the cell differentiation are discussed.
Seasonal and Perennial Changes in the Distribution of Water in the Sapwood of Conifers in a Sub-Frigid Zone
Authors: Utsumi Yasuhiro , Sano Yuzou , Funada Ryo , Ohtani Jun , Fujikawa Seizo 
Published: April 2003

Abstract
An analysis was made of progressive changes in patterns of cavitation in the sapwood of three species of conifer (Larix kaempferi, Abies sachalinensis, and Picea jezoensis) that were growing in a sub-frigid zone. In all three conifers, all tracheids of the newly forming outermost annual ring were filled with water or cytoplasm during the period from May to August. However, many tracheids in the transition zone from earlywood to latewood lost water in September, presumably through drought-induced cavitation. Cavitated tracheids tended to be continuously distributed in a tangential direction. Subsequently, some earlywood tracheids of the outermost annual ring lost water during the period from January to March. This was associated with freeze-thaw cycles. In the second and third annual rings from the cambium of all three conifers, the lumina of most tracheids in the transition zone from earlywood to latewood contained no water. In contrast, some latewood tracheids near the annual ring boundary and many earlywood tracheids retained water in their lumina. The third annual ring had more cavitated tracheids than the second annual ring. Our observations indicated that cavitation progressed gradually in the tracheids of the conifers and that they were never refilled once cavitation had occurred. The region involved in water transport in conifers did not include the entire sapwood and differed among annual rings.
N-Acylethanolamine Signaling in Tobacco Is Mediated by a Membrane-Associated, High-Affinity Binding Protein
Authors: Tripathy Swati , Kleppinger-Sparace Kathryn , Dixon Richard A. , Chapman Kent D. 
Published: April 2003

AbstractN-Acylethanolamines (NAEs) are fatty acid derivatives found as minor constituents of animal and plant tissues, and their levels increase 10- to 50-fold in tobacco (Nicotiana tabacum) leaves treated with fungal elicitors. Infiltration of tobacco leaves with submicromolar to micromolar concentrations ofN-myristoylethanolamine (NAE 14:0) resulted in an increase in relative phenylalanine ammonia-lyase (PAL) transcript abundance within 8 h after infiltration, and this PAL activation was reduced after co-infiltration with cannabinoid receptor antagonists (AM 281 and SR 144528). A saturable, high-affinity specific binding activity for [3H]NAE 14:0 was identified in suspension-cultured tobacco cells and in microsomes from tobacco leaves (apparent K d of 74 and 35 nm,respectively); cannabinoid receptor antagonists reduced or eliminated specific [3H]NAE 14:0 binding, consistent with the physiological response. N-Oleoylethanolamine activatedPAL2 expression in leaves and diminished [3H]NAE 14:0 binding in microsomes, whereasN-linoleoylethanolamine did not activatePAL2 expression in leaves, and did not affect [3H]NAE 14:0 binding in microsomes. The nonionic detergent dodecylmaltoside solubilized functional [3H]NAE 14:0-binding activity from tobacco microsomal membranes. The dodecylmaltoside-solubilized NAE-binding activity retained similar, but not identical, binding properties to the NAE-binding protein(s) in intact tobacco microsomes. Additionally, high-affinity saturable NAE-binding proteins were identified in microsomes isolated from Arabidopsis and Medicago truncatula tissues, indicating the general prevalence of these binding proteins in plant membranes. We propose that plants possess an NAE-signaling pathway with functional similarities to the “endocannabinoid” pathway of animal systems and that this pathway, in part, participates in xylanase elicitor perception in tobacco.