bluuebunny/crossref_metadata_2025_split huggingface dataset:
A NEW FEATURE SELECTION METHOD FOR TEXT CLASSIFICATION
Authors: UCHYIGIT GULDEN , CLARK KEITH 
Published: April 2007

Text classification is the problem of classifying a set of documents into a pre-defined set of classes. A major problem with text classification problems is the high dimensionality of the feature space. Only a small subset of these words are feature words which can be used in determining a document's class, while the rest adds noise and can make the results unreliable and significantly increase computational time. A common approach in dealing with this problem is feature selection where the number of words in the feature space are significantly reduced. In this paper we present the experiments of a comparative study of feature selection methods used for text classification. Ten feature selection methods were evaluated in this study including the new feature selection method, called the GU metric. The other feature selection methods evaluated in this study are: Chi-Squared (χ2) statistic, NGL coefficient, GSS coefficient, Mutual Information, Information Gain, Odds Ratio, Term Frequency, Fisher Criterion, BSS/WSS coefficient. The experimental evaluations show that the GU metric obtained the best F1 and F2 scores. The experiments were performed on the 20 Newsgroups data sets with the Naive Bayesian Probabilistic Classifier.
An implementation of real-time 3D interactive drama
Authors: Szilas Nicolas , Barles Jason , Kavakli Manolya 
Published: April 2007

Interactive fiction and adventure video games are narrative genres which provide the player with the option of acting as the main character of the story. However these genres do not fully match the expectations of their authors and readers because the player cannot deeply affect the storyline.
This article describes a system integrating highly interactive narrative structures in a real-time 3D environment.
Based on a theoretical foundation of narrative and drama, an interactive drama engine (IDE) has been implemented. It comprises an action calculus system, a text-generation system, a behavior engine, an animation engine as well as an innovative adaptive user interface. The IDE is demonstrated with two scenarios.
Integrative Genomic Analysis of Small-Cell Lung Carcinoma Reveals Correlates of Sensitivity to Bcl-2 Antagonists and Uncovers Novel Chromosomal Gains
Authors: Olejniczak Edward T. , Van Sant Charles , Anderson Mark G. , Wang Gang , Tahir Stephen K. , Sauter Guido , Lesniewski Rick , Semizarov Dimitri 
Published: April 2007

Abstract
Cancer is a highly heterogeneous disease in terms of the genetic profile and the response to therapeutics. An early identification of a genomic marker in drug discovery may help select patients that would respond to treatment in clinical trials. Here we suggest coupling compound screening with comparative genomic hybridization analysis of the model systems for early discovery of genomic biomarkers. A Bcl-2 antagonist, ABT-737, has recently been discovered and shown to induce regression of solid tumors, but its activity is limited to a fraction of small-cell lung carcinoma (SCLC) models tested. We used comparative genomic hybridization on high-density single-nucleotide polymorphism genotyping arrays to carry out a genome-wide analysis of 23 SCLC cell lines sensitive and resistant to ABT-737. The screen revealed a number of novel recurrent gene copy number abnormalities, which were also found in an independent data set of 19 SCLC tumors and confirmed by real-time quantitative PCR. A previously unknown amplification was identified on 18q and associated with the sensitivity of SCLC cell lines to ABT-737 and another Bcl-2 antagonist. The region of gain contains Bcl-2 and NOXA, two apoptosis-related genes. Expression microarray profiling showed that the genes residing in the amplified region of 18q are also overexpressed in the sensitive lines relative to the resistant lines. Fluorescence in situ hybridization analysis of tumors revealed that Bcl-2 gain is a frequent event in SCLC. Our findings suggest that 18q21-23 copy number will be a clinically relevant predictor for sensitivity of SCLC to Bcl-2 family inhibitors. The 18q21-23 genomic marker may have a broader application in cancer because Bcl-2 is associated with apoptosis evasion and chemoresistance. (Mol Cancer Res 2007;5(4):331–39)
The Global Trend in Sea Surface Temperature from 20 Years of Advanced Very High Resolution Radiometer Data
Authors: Good S. A. , Corlett G. K. , Remedios J. J. , Noyes E. J. , Llewellyn-Jones D. T. 
Published: April 2007

Abstract
The trend in sea surface temperature has been determined from 20 yr of Advanced Very High Resolution Radiometer Pathfinder data (version 5). The data span the period from January 1985 to December 2004, inclusive. The linear trends were calculated to be 0.18° ± 0.04° and 0.17° ± 0.05°C decade−1 from daytime and nighttime data, respectively. However, the measured trends were found to be somewhat smaller if version 4.1 of the Pathfinder data was used, or if the time series of data ended earlier. The influence of El Niño on global temperatures can be seen clearly in the data. However, it was not found to affect the trend measurements significantly. Evidence of cool temperatures after the eruption of Mount Pinatubo in 1991 was also observed.
Identification of heat shock protein 32 (Hsp32) as a novel survival factor and therapeutic target in neoplastic mast cells
Authors: Kondo Rudin , Gleixner Karoline V. , Mayerhofer Matthias , Vales Anja , Gruze Alexander , Samorapoompichit Puchit , Greish Khaled , Krauth Maria-Theresa , Aichberger Karl J. , Pickl Winfried F. , Esterbauer Harald , Sillaber Christian , Maeda Hiroshi , Valent Peter 
Published: April 2007

AbstractSystemic mastocytosis (SM) is a myeloid neoplasm characterized by increased survival and accumulation of neoplastic mast cells (MCs). In most patients, the D816V-mutated variant of KIT is detectable. We report here that heat shock protein 32 (Hsp32), also known as heme oxygenase-1 (HO-1), is a novel KIT-inducible survival factor in neoplastic MCs. As assessed by reverse transcription-polymerase chain reaction (RT-PCR), immunocytochemistry, and Western blotting, the KIT D816V+ MC line HMC-1.2 as well as highly enriched primary neoplastic MCs were found to express Hsp32 mRNA and the Hsp32 protein. Moreover, KIT D816V and stem cell factor (SCF)–activated wild-type KIT were found to induce Hsp32 promoter activity, expression of Hsp32 mRNA, and expression of the Hsp32 protein in Ba/F3 cells. Correspondingly, the KIT D816V-targeting drug PKC412 decreased the expression of Hsp32 as well as proliferation/survival in neoplastic MCs. The inhibitory effects of PKC412 on the survival of HMC-1.2 cells were counteracted by the HO-1 inductor hemin or lentiviral-transduced HO-1. Moreover, 2 Hsp32-targeting drugs, pegylated zinc protoporphyrin (PEG-ZnPP) and styrene maleic acid copolymer micelle-encapsulated ZnPP (SMA-ZnPP), were found to inhibit proliferation and to induce apoptosis in neoplastic MCs. Furthermore, both drugs were found to cooperate with PKC412 in producing growth inhibition. Together, these data show that Hsp32 is an important survival factor and interesting new therapeutic target in neoplastic MCs.
Mesostructured Silica with Bush-like Morphology and Its Transformation into Nanometer-sized Mesoporous Silica Particles
Authors: Kapoor Mahendra P , Kasama Yuuki , Yanagi Masaaki , Yokoyama Takuji , Nanbu Hironobu , Juneja Lekh R 
Published: April 2007

Abstract
A novel bush-like morphology of mesostructured silica having stems, branches, and leaves has been grown under mild basic conditions via auxiliary solvent evaporation induced self-assembly process.
Differential Binding of Poly(ADP-Ribose) Polymerase-1 and JunD/Fra2 Accounts for RANKL-Induced Tcirg1 Gene Expression During Osteoclastogenesis
Authors: Beranger Guillaume E , Momier David , Guigonis Jean-Marie , Samson Michel , Carle Georges F , Scimeca Jean-Claude 
Published: April 2007

Abstract
We studied Tcirg1 gene expression on RANKL-induced osteoclastic differentiation of the mouse model RAW264.7 cells. We identified a mechanism involving PARP-1 inhibition release and JunD/Fra-2 binding, which is responsible for Tcirg1 gene upregulation.
Introduction: The Tcirg1 gene encodes the a3 isoform of the V-ATPase a subunit, which plays a critical role in the resorption activity of the osteoclast. Using serial deletion constructs of the Tcirg1 gene promoter, we performed a transcriptional study to identify factor(s) involved in the regulation of the RANKL-induced gene expression.
Materials and Methods: The promoter activity of serial-deletion fragments of the Tcirg1 gene promoter was monitored throughout the RAW264.7 cells differentiation process. We next performed sequence analysis, EMSA, UV cross-linking, qPCR, and gel supershift experiments to identify the factor(s) interacting with the promoter.
Results: A deletion of the −1297−1244 region led to the disappearance of the RANKL-induced promoter activity. EMSA experiments showed the binding of two factors that undergo differential binding on RANKL treatment. Supershift experiments led us to identify the dimer JunD/Fra-2 as the binding activity associated with the −1297/−1268 Tcirg1 gene promoter sequence in response to RANKL. Moreover, we observed poly(ADP-ribose) polymerase-1 (PARP-1) binding to an adjacent site (−1270/−1256), and this interaction was disrupted after RANKL treatment.
Conclusions: We provide data that identify junD proto-oncogene (JunD) and Fos-related antigen 2 (Fra-2) as the activator protein-1 (AP-1) factors responsible for the RANKL-induced upregulation of the mouse Tcirg1 gene expression. Moreover, we identified another binding site for PARP-1 that might account for the repression of Tcirg1 gene expression in pre-osteoclastic cells.
Inflammatory Markers and Incident Fracture Risk in Older Men and Women: The Health Aging and Body Composition Study
Authors: Cauley Jane A , Danielson Michelle E , Boudreau Robert M , Forrest Kimberly Y Z , Zmuda Joseph M , Pahor Marco , Tylavsky Frances A , Cummings Steven R , Harris Tamara B , Newman Anne B 
Published: April 2007

Abstract
The inflammation of aging hypothesis purports that aging is the accumulation of damage, which results, in part, from chronic activation of inflammation process. We tested this hypothesis in relationship to fractures in 2985 men and women enrolled in the Health ABC study. Results showed that subjects with the greatest number of inflammatory markers have the highest risk of fracture.
Introduction: Cytokines play major roles in regulating bone remodeling in the bone microenvironment, but their relationship to fractures is uncertain.
Materials and Methods: The study population includes 2985 well-functioning white and black women and men (42%, black; 51%, women) 70–79 yr of age enrolled in the Health Aging and Body Composition Study. Inflammatory markers were measured in frozen serum using standardized assays. We measured interleukin (IL-6), TNFα, C-reactive protein (CRP), and soluble receptors (IL-2 sR, IL-6 sR, TNF sR1and TNF sR2).Cytokine-soluble receptors were measured in a subset (n = 1430). Total hip BMD was measured by DXA. During 5.8 ± 1.6 yr of 95% complete follow-up, incident fractures were confirmed in 268 subjects. The risk of fracture was compared among subjects with the highest inflammatory markers (quartile 4) versus lower levels (quartiles 1, 2, and 3) using proportional hazard models.
Results and Conclusions: Subjects who fractured were more likely to be white and female. Baseline markers of inflammation were higher among subjects who subsequently experienced an incident fracture. In multivariate models, the relative risk of fracture (95% CIs) for subjects with the highest inflammatory markers (quartile 4) compared with those with lower inflammatory markers (quartiles 1, 2, and 3) was 1.34 (0.99, 1.82) for CRP; 1.28 (0.95–1.74) for IL-6; 1.28 (0.97–1.70) for TNFα; 1.52 (1.04–2.21) for IL-2 sR; 1.33 (0.90–1.96) for IL-6 sR; 1.73 (1.18–2.55) for TNF sR1 and 1.48 (1.01–2.20) for TNF sR2. In subjects with three or more (out of seven) high inflammatory markers, the relative risk of fracture was 2.65 (1.44–4.89) in comparison with subjects with no elevated markers. (p trend = 0.001). We conclude that elevated inflammatory markers are prognostic for fractures, extending the inflammation hypothesis of aging to osteoporotic fractures.
Long-term Follow-up of 414 HIV-Infected Romanian Children and Adolescents Receiving Lopinavir/Ritonavir-Containing Highly Active Antiretroviral Therapy
Authors: Kline Mark W. , Rugina Sorin , Ilie Margareta , Matusa Rodica F. , Schweitzer Ana-Maria , Calles Nancy R. , Schwarzwald Heidi L. 
Published: April 2007

BACKGROUND. There are no published reports of the long-term safety and effectiveness of highly active antiretroviral therapy for children and adolescents living in resource-limited settings or of large cohorts of HIV-infected children and adolescents treated long-term (&gt;48 weeks) with lopinavir/ritonavir-containing highly active antiretroviral therapy.
OBJECTIVES. The purpose of this work was to evaluate the long-term outcomes of treatment of HIV-infected children and adolescents with lopinavir/ritonavir-containing highly active antiretroviral therapy in a resource-limited setting.
METHODS. We studied an inception cohort of 414 HIV-infected children receiving lopinavir/ritonavir-containing highly active antiretroviral therapy between November 2001 and August 2006 at the Romanian-American Children's Center in Constanta, Romania. The center provides comprehensive primary and HIV specialty care and treatment to all known HIV-infected children and adolescents living in Constanta. We measured safety and effectiveness by the percentage of children remaining on treatment, rates of mortality, and changes in plasma HIV RNA concentrations and CD4+ lymphocyte counts.
RESULTS. The study population consisted predominantly of antiretroviral drug–experienced older children and adolescents with advanced HIV disease. Treatment was well tolerated, with 337 children (81%) remaining on therapy after a median duration of &gt;4 years. Thirty-seven deaths occurred; the death rate compared favorably to prospectively collected historical data. The most recent on-treatment plasma HIV RNA concentration was &lt;400 copies per milliliter in 192 of 265 children tested. The mean baseline CD4+ lymphocyte count was 292 cells per microliter (n = 299); the mean change from baseline was +266 (n = 284), +317 (n = 260), +343 (n = 176), and +270 cells per microliter (n = 121) after 1, 2, 3, and 4 years of treatment, respectively.
CONCLUSIONS. Highly active antiretroviral therapy can be administered safely and effectively to children and adolescents in resource-limited settings. Lopinavir/ritonavir-containing highly active antiretroviral therapy is a safe, effective, and durable treatment option for antiretroviral drug–experienced older children and adolescents with advanced HIV disease.
CD41+/CD45+ Cells Without Acetylcholinesterase Activity Are Immature and a Major Megakaryocytic Population in Murine Bone Marrow
Authors: Matsumura-Takeda Kuniko , Sogo Shinji , Isakari Yoshimasa , Harada Yasuo , Nishioka Kinue , Kawakami Takuma , Ono Toshihide , Taki Takao 
Published: April 2007

Abstract
Murine megakaryocytes (MKs) are defined by CD41/CD61 expression and acetylcholinesterase (AChE) activity; however, their stages of differentiation in bone marrow (BM) have not been fully elucidated. In murine lineage-negative (Lin−)/CD45+ BM cells, we found CD41+ MKs without AChE activity (AChE−) except for CD41++ MKs with AChE activity (AChE+), in which CD61 expression was similar to their CD41 level. Lin−/CD41+/CD45+/AChE− MKs could differentiate into AChE+, with an accompanying increase in CD41/CD61 during in vitro culture. Both proplatelet formation (PPF) and platelet (PLT) production for Lin−/CD41+/CD45+/AChE− MKs were observed later than for Lin−/CD41++/CD45+/AChE+ MKs, whereas MK progenitors were scarcely detected in both subpopulations. GeneChip and semiquantitative polymerase chain reaction analyses revealed that the Lin−/CD41+/CD45+/AChE− MKs are assigned at the stage between the progenitor and PPF preparation phases in respect to the many MK/PLT-specific gene expressions, including β1-tubulin. In normal mice, the number of Lin−/CD41+/CD45+/AChE− MKs was 100 times higher than that of AChE+ MKs in BM. When MK destruction and consequent thrombocytopenia were caused by an antitumor agent, mitomycin-C, Lin−/CD41+/CD45+/AChE− MKs led to an increase in AChE+ MKs and subsequent PLT recovery with interleukin-11 administration. It was concluded that MKs in murine BM at least in part consist of immature Lin−/CD41+/CD45+/AChE− MKs and more differentiated Lin−/CD41++/CD45+/AChE+ MKs. Immature Lin−/CD41+/CD45+/AChE− MKs are a major MK population compared with AChE+ MKs in BM and play an important role in rapid PLT recovery in vivo.
Disclosure of potential conflicts of interest is found at the end of this article.
IMT504, the Prototype of the Immunostimulatory Oligonucleotides of the PyNTTTTGT Class, Increases the Number of Progenitors of Mesenchymal Stem Cells Both In Vitro and In Vivo: Potential Use in Tissue Repair Therapy
Authors: Hernando Insúa Andrés , Montaner Alejandro D. , Rodriguez Juan M. , Elías Fernanda , Fló Juan , López Ricardo A. , Zorzopulos Jorge , Hofer Erica L. , Chasseing Norma A. 
Published: April 2007

Abstract
Bone marrow (BM)-derived adult mesenchymal stem cells (MSCs) have the capacity to differentiate in vitro into different cell lines. This makes them a likely source for application in tissue repair therapies. Here, we report evidence indicating that, both in vivo and in vitro, IMT504, the prototype of the PyNTTTTGT class of immunostimulatory oligonucleotides, significantly increases the number of fibroblast colony-forming units (CFU-Fs) that originate MSCs. When rat BM cells were cultured with IMT504, the mean number of CFU-Fs increased about three times as compared with untreated controls (CFU-F: 19 ± 6.3 vs. 6.8 ± 2.0/2 × 106 seeded BM cells, p = .03). Furthermore, rats inoculated with IMT504 had a significantly higher number of CFU-Fs both in BM (CFU-F: 124 ± 33 vs. 38 ± 17/femur, p = .04) and in peripheral blood (animals with detectable CFU-Fs in circulation 8/12 vs. 2/12, p = .04) as compared with untreated animals. On the other hand, BM-derived adherent cells either treated in vitro with IMT504 or obtained from animals injected with IMT504 possess the capacity to differentiate to the osteogenic and adipogenic cell lineages as regular MSCs. Finally, we found that repair of a bone defect was accelerated in rats injected with IMT504 as compared with control animals (area with consolidated bone: 80% ± 6.4% vs. 49% ± 3.5%, p = .03, n = 10 rats per group). Importantly, when two human BM were cultured in the presence of IMT504, the mean number of fibroblastic adherent colonies also increased as compared with controls. These results suggest the possibility of clinical use of IMT504 in bone, and presumably other, tissue repair therapies.
Disclosure of potential conflicts of interest is found at the end of this article.
Genome-Wide Differential Gene Expression Profiling of Human Bone Marrow Stromal Cells
Authors: Jeong Ju Ah , Ko Kyung-Min , Bae Sohyun , Jeon Choon-Ju , Koh Gou Young , Kim Hoeon 
Published: April 2007

Abstract
Bone marrow stromal cells (BMSCs) reside in bone marrow and provide a lifelong source of new cells for various connective tissues. Although human BMSCs are regarded as highly suitable for the development of cell therapeutics and regenerative medicine, the molecular factors and the networks of signaling pathways responsible for their biological properties are as yet unclear. To gain a comprehensive understanding of human BMSCs at the transcriptional level, we have performed DNA microarray-based, genome-wide differential gene expression analysis with the use of peripheral blood-derived mononuclear cells (MNCs) as a baseline. The resulting molecular profile of BMSCs was revealed to share no meaningful overlap with those of other human stem cell types, suggesting that the cells might express a unique set of genes for their stemness. By contrast, the distinct molecular signature, consisting of 92 different genes whose expression strengths are at least 50-fold higher in BMSCs compared with MNCs, was shown to encompass largely a gene subset of umbilical cord blood-derived adherent cells, suggesting that adherent cells derived from bone marrow and umbilical cord blood may be defined by a common set of genes, regardless of their origin. Intriguingly, a large number of these genes, particularly ones for extracellular matrix products, coincide with normal or tumor endothelium-specific markers. Taken together, our results here provide a BMSC-specific genetic catalog that may facilitate future studies on molecular mechanisms governing core properties of these cells.
Disclosure of potential conflicts of interest is found at the end of this article.
Geomorphology-based interpretation of sedimentation rates from radiodating, lower passaic river, New Jersey, USA
Authors: Erickson Michael J , Barnes Charles R , Henderson Matthew R , Romagnoli Robert , Firstenberg Clifford E 
Published: April 2007

Abstract
Analysis of site geomorphology and sedimentation rates as an indicator of long-term bed stability is central to the evaluation of remedial alternatives for depositional aquatic environments. In conjunction with various investigations of contaminant distribution, sediment dynamics, and bed stability in the Passaic River Estuary, 121 sediment cores were collected in the early 1990s from the lower 9.7 km of the Passaic River and analyzed for lead-210 (210Pb), cesium-137 (137Cs), and other analytes. This paper opportunistically uses the extensive radiochemical dataset to examine the spatial patterns of long-term sedimentation rates in, and associated geomorphic aspects of, this area of the river. For the purposes of computing sedimentation rates, the utility of the 210Pb and 137Cs depositional profiles was assessed to inform appropriate interpretation. Sedimentation rates were computed for 90 datable cores by 3 different methods, depending on profile utility. A sedimentation rate of 0 was assigned to 17 additional cores that were not datable and for which evidence of no deposition exists. Sedimentation patterns were assessed by grouping results within similar geomorphic areas, delineated through inspection of bathymetric data. On the basis of channel morphology, results reflect expected patterns, with the highest sedimentation rates observed along point bars and channel margins. The lowest rates of sedimentation (and the largest percentage of undatable cores) were observed in the areas along the outer banks of channel bends. Increasing sedimentation rates from upstream to downstream were noted. Average and median sedimentation rates were estimated to be 3.8 and 3.7 cm/y, respectively, reflecting the highly depositional nature of the Passaic River estuary. This finding is consistent with published descriptions of long-term geomorphology for Atlantic Coastal Plain estuaries.