bluuebunny/crossref_metadata_2025_split huggingface dataset:
Are Tropical Cyclones Less Effectively Formed by Easterly Waves in the Western North Pacific than in the North Atlantic?
Authors: Chen Tsing-Chang , Wang Shih-Yu , Yen Ming-Cheng , Clark Adam J. 
Published: April 2008

Abstract
It has been observed that the percentage of tropical cyclones originating from easterly waves is much higher in the North Atlantic (∼60%) than in the western North Pacific (10%–20%). This disparity between the two ocean basins exists because the majority (71%) of tropical cyclogeneses in the western North Pacific occur in the favorable synoptic environments evolved from monsoon gyres. Because the North Atlantic does not have a monsoon trough similar to the western North Pacific that stimulates monsoon gyre formation, a much larger portion of tropical cyclogeneses than in the western North Pacific are caused directly by easterly waves.
This study also analyzed the percentage of easterly waves that form tropical cyclones in the western North Pacific. By carefully separating easterly waves from the lower-tropospheric disturbances generated by upper-level vortices that originate from the tropical upper-tropospheric trough (TUTT), it is observed that 25% of easterly waves form tropical cyclones in this region. Because TUTT-induced lower-tropospheric disturbances often become embedded in the trade easterlies and resemble easterly waves, they have likely been mistakenly identified as easterly waves. Inclusion of these “false” easterly waves in the “true” easterly wave population would result in an underestimation of the percentage of easterly waves that form tropical cyclones, because the TUTT-induced disturbances rarely stimulate tropical cyclogenesis.
However, an analysis of monsoon gyre formation mechanisms over the western North Pacific reveals that 82% of monsoon gyres develop through a monsoon trough–easterly wave interaction. Thus, it can be inferred that 58% (i.e., 82% × 71%) of tropical cyclones in this region are an indirect result of easterly waves. Including the percentage of tropical cyclones that form directly from easterly waves (∼25%), it is found that tropical cyclones formed directly and indirectly from easterly waves account for over 80% of tropical cyclogeneses in the western North Pacific. This is more than the percentage that has been documented by previous studies in the North Atlantic.
Tropical Cyclone Inner-Core Kinetic Energy Evolution
Authors: Maclay Katherine S. , DeMaria Mark , Vonder Haar Thomas H. 
Published: April 2008

Abstract
Tropical cyclone (TC) destructive potential is highly dependent on the distribution of the surface wind field. To gain a better understanding of wind structure evolution, TC 0–200-km wind fields from aircraft reconnaissance flight-level data are used to calculate the low-level area-integrated kinetic energy (KE). The integrated KE depends on both the maximum winds and wind structure. To isolate the structure evolution, the average relationship between KE and intensity is first determined. Then the deviations of the KE from the mean intensity relationship are calculated. These KE deviations reveal cases of significant structural change and, for convenience, are referred to as measurements of storm size [storms with greater (less) KE for their given intensity are considered large (small)]. It is established that TCs generally either intensify and do not grow or they weaken/maintain intensity and grow. Statistical testing is used to identify conditions that are significantly different for growing versus nongrowing storms in each intensification regime. Results suggest two primary types of growth processes: (i) secondary eyewall formation and eyewall replacement cycles, an internally dominated process, and (ii) external forcing from the synoptic environment. One of the most significant environmental forcings is the vertical shear. Under light shear, TCs intensify but do not grow; under moderate shear, they intensify less but grow more; under very high shear, they do not intensify or grow. As a supplement to this study, a new TC classification system based on KE and intensity is presented as a complement to the Saffir–Simpson hurricane scale.
Perceiving hierarchy through intrinsic color structure
Authors: Puhalla Dennis M. 
Published: April 2008

Color is an intrinsic visual attribute of form that functions as language and message. The purpose of this study was to investigate objectively structured color combinations as a means to communicate visual order for the purpose of reinforcing information hierarchy. Controlling the visual relationships of hue, value and chroma contrast can significantly assist a person's cognitive ability to assign importance and dominance to a controlled color structure. This research study provided significant findings supporting the hypothesis that intrinsic color structures can be formulated objectively; represent a visual hierarchy; and be perceived in an understandable order. Chi-square analysis for 99 participants was calculated for task effectiveness. To analyze task efficiency, three distinct ANOVA calculations were made for time variations. The documented findings of this study presented explicit evidence that addresses specific mechanisms for objective color ordering. The natural inferences of the study support the proposition that there is a natural relationship between objective color ordering principles and human perception.
Sequestration and homing of bone marrow-derived lineage negative progenitor cells in the lung during pneumococcal pneumonia
Authors: Suzuki Hisashi , Hogg James C , van Eeden Stephan F 
Published: April 2008

Abstract

Background
Bone marrow (BM)-derived progenitor cells have been shown to have the potential to differentiate into a diversity of cell types involved in tissue repair. The characteristics of these progenitor cells in pneumonia lung is unknown. We have previously shown that Streptococcus pneumoniae induces a strong stimulus for the release of leukocytes from the BM and these leukocytes preferentially sequester in the lung capillaries. Here we report the behavior of BM-derived lineage negative progenitor cells (Lin- PCs) during pneumococcal pneumonia using quantum dots (QDs), nanocrystal fluorescent probes as a cell-tracking technique.

Methods
Whole BM cells or purified Lin- PCs, harvested from C57/BL6 mice, were labeled with QDs and intravenously transfused into pneumonia mice infected by intratracheal instillation of Streptococcus pneumoniae. Saline was instilled for control. The recipients were sacrificed 2 and 24 hours following infusion and QD-positive cells retained in the circulation, BM and lungs were quantified.

Results
Pneumonia prolonged the clearance of Lin- PCs from the circulation compared with control (21.7 ± 2.7% vs. 7.7 ± 0.9%, at 2 hours, P < 0.01), caused preferential sequestration of Lin- PCs in the lung microvessels (43.3 ± 8.6% vs. 11.2 ± 3.9%, at 2 hours, P < 0.05), and homing of these cells to both the lung (15.1 ± 3.6% vs. 2.4 ± 1.2%, at 24 hours, P < 0.05) and BM as compared to control (18.5 ± 0.8% vs. 9.5 ± 0.4%, at 24 hours, P < 0.01). Very few Lin- PCs migrated into air spaces.

Conclusion
In this study, we demonstrated that BM-derived progenitor cells are preferentially sequestered and retained in pneumonic mouse lungs. These cells potentially contribute to the repair of damaged lung tissue.
EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries
Authors: Smith Robin P , Buchser William J , Lemmon Marcus B , Pardinas Jose R , Bixby John L , Lemmon Vance P 
Published: April 2008

Abstract

Background
Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds.

Results
We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization.

Conclusion
EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.
Identification of transcription factor contexts in literature using machine learning approaches
Authors: Yang Hui , Nenadic Goran , Keane John A 
Published: April 2008

Abstract

Background
Availability of information about transcription factors (TFs) is crucial for genome biology, as TFs play a central role in the regulation of gene expression. While manual literature curation is expensive and labour intensive, the development of semi-automated text mining support is hindered by unavailability of training data. There have been no studies on how existing data sources (e.g. TF-related data from the MeSH thesaurus and GO ontology) or potentially noisy example data (e.g. protein-protein interaction, PPI) could be used to provide training data for identification of TF-contexts in literature.

Results
In this paper we describe a text-classification system designed to automatically recognise contexts related to transcription factors in literature. A learning model is based on a set of biological features (e.g. protein and gene names, interaction words, other biological terms) that are deemed relevant for the task. We have exploited background knowledge from existing biological resources (MeSH and GO) to engineer such features. Weak and noisy training datasets have been collected from descriptions of TF-related concepts in MeSH and GO, PPI data and data representing non-protein-function descriptions. Three machine-learning methods are investigated, along with a vote-based merging of individual approaches and/or different training datasets. The system achieved highly encouraging results, with most classifiers achieving an F-measure above 90%.

Conclusions
The experimental results have shown that the proposed model can be used for identification of TF-related contexts (i.e. sentences) with high accuracy, with a significantly reduced set of features when compared to traditional bag-of-words approach. The results of considering existing PPI data suggest that there is not as high similarity between TF and PPI contexts as we have expected. We have also shown that existing knowledge sources are useful both for feature engineering and for obtaining noisy positive training data.
New challenges for text mining: mapping between text and manually curated pathways
Authors: Oda Kanae , Kim Jin-Dong , Ohta Tomoko , Okanohara Daisuke , Matsuzaki Takuya , Tateisi Yuka , Tsujii Jun'ichi 
Published: April 2008

Abstract

Background
Associating literature with pathways poses new challenges to the Text Mining (TM) community. There are three main challenges to this task: (1) the identification of the mapping position of a specific entity or reaction in a given pathway, (2) the recognition of the causal relationships among multiple reactions, and (3) the formulation and implementation of required inferences based on biological domain knowledge.

Results
To address these challenges, we constructed new resources to link the text with a model pathway; they are: the GENIA pathway corpus with event annotation and NF-kB pathway. Through their detailed analysis, we address the untapped resource, ‘bio-inference,’ as well as the differences between text and pathway representation. Here, we show the precise comparisons of their representations and the nine classes of ‘bio-inference’ schemes observed in the pathway corpus.

Conclusions
We believe that the creation of such rich resources and their detailed analysis is the significant first step for accelerating the research of the automatic construction of pathway from text.
Gene Ontology density estimation and discourse analysis for automatic GeneRiF extraction
Authors: Gobeill Julien , Tbahriti Imad , Ehrler Frédéric , Mottaz Anaïs , Veuthey Anne-Lise , Ruch Patrick 
Published: April 2008

Abstract

Background
This paper describes and evaluates a sentence selection engine that extracts a GeneRiF (Gene Reference into Functions) as defined in ENTREZ-Gene based on a MEDLINE record. Inputs for this task include both a gene and a pointer to a MEDLINE reference. In the suggested approach we merge two independent sentence extraction strategies. The first proposed strategy (LASt) uses argumentative features, inspired by discourse-analysis models. The second extraction scheme (GOEx) uses an automatic text categorizer to estimate the density of Gene Ontology categories in every sentence; thus providing a full ranking of all possible candidate GeneRiFs. A combination of the two approaches is proposed, which also aims at reducing the size of the selected segment by filtering out non-content bearing rhetorical phrases.

Results
Based on the TREC-2003 Genomics collection for GeneRiF identification, the LASt extraction strategy is already competitive (52.78%). When used in a combined approach, the extraction task clearly shows improvement, achieving a Dice score of over 57% (+10%).

Conclusions
Argumentative representation levels and conceptual density estimation using Gene Ontology contents appear complementary for functional annotation in proteomics.
Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio
Authors: Lintner Robert E , Mishra Pankaj K , Srivastava Poonam , Martinez-Vaz Betsy M , Khodursky Arkady B , Blumenthal Robert M 
Published: April 2008

Abstract

Background
Bacterial genome sequences are being determined rapidly, but few species are physiologically well characterized. Predicting regulation from genome sequences usually involves extrapolation from better-studied bacteria, using the hypothesis that a conserved regulator, conserved target gene, and predicted regulator-binding site in the target promoter imply conserved regulation between the two species. However many compared organisms are ecologically and physiologically diverse, and the limits of extrapolation have not been well tested. In E. coli K-12 the leucine-responsive regulatory protein (Lrp) affects expression of ~400 genes. Proteus mirabilis and Vibrio cholerae have highly-conserved lrp orthologs (98% and 92% identity to E. coli lrp). The functional equivalence of Lrp from these related species was assessed.

Results
Heterologous Lrp regulated gltB, livK and lrp transcriptional fusions in an E. coli background in the same general way as the native Lrp, though with significant differences in extent. Microarray analysis of these strains revealed that the heterologous Lrp proteins significantly influence only about half of the genes affected by native Lrp. In P. mirabilis, heterologous Lrp restored swarming, though with some pattern differences. P. mirabilis produced substantially more Lrp than E. coli or V. cholerae under some conditions. Lrp regulation of target gene orthologs differed among the three native hosts. Strikingly, while Lrp negatively regulates its own gene in E. coli, and was shown to do so even more strongly in P. mirabilis, Lrp appears to activate its own gene in V. cholerae.

Conclusion
The overall similarity of regulatory effects of the Lrp orthologs supports the use of extrapolation between related strains for general purposes. However this study also revealed intrinsic differences even between orthologous regulators sharing >90% overall identity, and 100% identity for the DNA-binding helix-turn-helix motif, as well as differences in the amounts of those regulators. These results suggest that predicting regulation of specific target genes based on genome sequence comparisons alone should be done on a conservative basis.
Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato
Authors: Datema Erwin , Mueller Lukas A , Buels Robert , Giovannoni James J , Visser Richard GF , Stiekema Willem J , van Ham Roeland CHJ 
Published: April 2008

AbstractBackgroundTomato (Solanum lycopersicon) and potato (S. tuberosum) are two economically important crop species, the genomes of which are currently being sequenced. This study presents a first genome-wide analysis of these two species, based on two large collections of BAC end sequences representing approximately 19% of the tomato genome and 10% of the potato genome.ResultsThe tomato genome has a higher repeat content than the potato genome, primarily due to a higher number of retrotransposon insertions in the tomato genome. On the other hand, simple sequence repeats are more abundant in potato than in tomato. The two genomes also differ in the frequency distribution of SSR motifs. Based on EST and protein alignments, potato appears to contain up to 6,400 more putative coding regions than tomato. Major gene families such as cytochrome P450 mono-oxygenases and serine-threonine protein kinases are significantly overrepresented in potato, compared to tomato. Moreover, the P450 superfamily appears to have expanded spectacularly in both species compared toArabidopsis thaliana, suggesting an expanded network of secondary metabolic pathways in theSolanaceae. Both tomato and potato appear to have a low level of microsynteny withA. thaliana. A higher degree of synteny was observed withPopulus trichocarpa, specifically in the region between 15.2 and 19.4 Mb onP. trichocarpachromosome 10.ConclusionThe findings in this paper present a first glimpse into the evolution of Solanaceous genomes, both within the family and relative to other plant species. When the complete genome sequences of these species become available, whole-genome comparisons and protein- or repeat-family specific studies may shed more light on the observations made here.
Apoptosis induction in Jurkat cells and sCD95 levels in women's sera are related with the risk of developing cervical cancer
Authors: Aguilar-Lemarroy Adriana , Romero-Ramos Jose E , Olimon-Andalon Vicente , Hernandez-Flores Georgina , Lerma-Diaz Jose M , Ortiz-Lazareno Pablo C , Morgan-Villela Gilberto , del Toro-Arreola Susana , Bravo-Cuellar Alejandro , Jave-Suarez Luis F 
Published: April 2008

AbstractBackgroundCurrently, there is clear evidence that apoptosis plays an important role in the development and progression of tumors. One of the best characterized apoptosis triggering systems is the CD95/Fas/APO-1 pathway; previous reports have demonstrated high levels of soluble CD95 (sCD95) in serum of patients with some types of cancer. Cervical cancer is the second most common cancer among women worldwide. As a first step in an attempt to design a minimally invasive test to predict the risk of developing cervical cancer in patients with precancerous lesions, we used a simple assay based on the capacity of human serum to induce apoptosis in Jurkat cells. We evaluated the relationship between sCD95 levels and the ability to induce apoptosis in Jurkat cells in cervical cancer patients and controls.MethodsJurkat cells were exposed to serum from 63 women (20 healthy volunteers, 21 with cervical intraepithelial neoplasia grade I [CIN 1] and 22 with cervical-uterine carcinoma). The apoptotic rate was measured by flow cytometry using Annexin-V-Fluos and Propidium Iodide as markers. Serum levels of sCD95 and soluble CD95 ligand (sCD95L) were measured by ELISA kits.ResultsWe found that serum from almost all healthy women induced apoptosis in Jurkat cells, while only fifty percent of the sera from women with CIN 1 induced cell death in Jurkat cells. Interestingly, only one serum sample from a patient with cervical-uterine cancer was able to induce apoptosis, the rest of the sera protected Jurkat cells from this killing. We were able to demonstrate that elimination of Jurkat cells was mediated by the CD95/Fas/Apo-1 apoptotic pathway. Furthermore, the serum levels of sCD95 measured by ELISA were significantly higher in women with cervical cancer.ConclusionOur results demonstrate that there is a strong correlation between low levels of sCD95 in serum of normal women and higher apoptosis induction in Jurkat cells. We suggest that an analysis of the apoptotic rate induced by serum in Jurkat cells and the levels of sCD95 in serum could be helpful during the prognosis and treatment of women detected with precancerous lesions or cervical cancer.
Jorge Basadre’s “Peruvian History of Peru,” Or the Poetic Aporia of Historicism
Authors: Thurner Mark 
Published: April 2008

Abstract
This article examines the historicist thought of Jorge Basadre (1903–1980). Basadre was Peru’s leading twentieth-century historian, and his brilliant and voluminous opus continues to exert a strong influence in Peru today. Basadre developed a “theory of Peru” that creatively drew upon concepts developed by European philosophers (Pascal, Fichte, Hegel, Dilthey, Renan, Ortega y Gasset, and Croce) but which was singularly Peruvian, since as an affirmative historicist apprehension of the collective subject or self named “Peru” it was “homologous with its own formation.” Nevertheless, this article argues that Basadre’s homologous “Peruvian history of Peru” admits ahistorical heterogeneity or “the abyss” as its founding (un)reason for being.
Association of an A/C single nucleotide polymorphism in programmed cell death-ligand 1 gene with Graves' disease in Japanese patients.
Authors: Hayashi Mina , Kouki Tsuyoshi , Takasu Nobuyuki , Sunagawa Sumito , Komiya Ichiro 
Published: April 2008

ObjectiveProgrammed cell death-1 (PD-1) and its ligands (PD-L1 and PD-L2) inhibit T-cell proliferation and activation. This inhibition down-regulates the immune responses. The association of a PD-L1 polymorphism with Graves' disease (GD) was studied.DesignThe association of an A/C polymorphism at position 8923 in PD-L1 intron 4 with GD was studied.PatientsThe study included 327 GD patients and 192 controls, of which 252 GD patients were followed over 5–10 years.MeasurementsPD-L1 intron 4 position 8923 A/C polymorphism was typed using the PCR-restriction fragment length polymorphism method.ResultsThe A/C genotype frequencies were significantly different between GD patients and controls. The A/C and C/C frequencies were higher in GD patients than in controls. The A/A frequencies were lower in GD patients than in controls. C-allele frequency was higher in GD patients than in controls. A total of 252 GD patients were followed over 5–10 years; 200 had discontinued antithyroid drugs (ATD) while 52 continued to take ATD. Of these 200, 176 continued to be in remission and 24 had relapsed into hyperthyroidism. Significant differences in the duration of positive TBII, positive thyroid-stimulating antibodies, and ATD treatment were noted between the patients in remission and those that had relapsed. Significant differences in the A- and C-allele frequencies were noted between the two. The C-allele frequency was higher in GD patients who did not achieve remission than in those who achieved remission.ConclusionAn A/C polymorphism at position 8923 in PD-L1 is associated with GD. The PD-L1 polymorphism plays a role in GD development. GD patients with the C allele at position 8923 in PD-L1 gene had difficulty in achieving remission.