bluuebunny/crossref_metadata_2025_split huggingface dataset:
A NEW NEUTROSOPHIC APPROACH TO IMAGE THRESHOLDING
Authors: CHENG H. D. , GUO YANHUI 
Published: May 2008

A neutrosophic set (Ns), a part of neutrosophy theory, studies the origin, nature, and scope of neutralities, as well as their interactions with different ideational spectra. The neutrosophic set is a powerful general formal framework that has been recently proposed. However, the neutrosophic set needs to be specified from a technical point of view. We apply the neutrosophic set in image domain and define some concepts and operations for image thresholding. The image G is transformed into Ns domain, which is described using three subsets T, I and F. The entropy in neutrosophic set is defined and employed to evaluate the indetermination. A new λ-mean operation is proposed to reduce the set's indetermination. Finally, the proposed method is employed to perform image thresholding. We have conducted experiments on a variety of images. The experimental results demonstrate that the proposed approach can select the thresholds automatically and effectively. Especially, it can process the "clean" images, the images with different kinds of noise and the images with multiple kinds of noise well without knowing the type of the noise, which is the most difficult task for image thresholding.
A Polarimetric Radar Forward Operator for Model Evaluation
Authors: Pfeifer M. , Craig G. C. , Hagen M. , Keil C. 
Published: May 2008

Abstract
A polarimetric radar forward operator has been developed as a tool for the systematic evaluation of microphysical parameterization schemes in high-resolution numerical weather prediction (NWP) models. The application of such a forward operator allows a direct comparison of the model simulations to polarimetric radar observations. While the comparison of observed and synthetic reflectivity gives information on the quality of quantitative precipitation forecasts, the information from the polarimetric quantities allows for a direct evaluation of the capacity of the NWP model to realistically describe the processes involved in the formation and interactions of the hydrometeors and, hence, the performance of the microphysical parameterization scheme. This information is expected to be valuable for detecting systematic model errors and hence improve model physics. This paper summarizes the technical characteristics of the synthetic polarimetric radar (SynPolRad). Different polarimetric radar quantities are computed from model forecasts using a T-matrix scattering code and ice phase hydrometeors are explicitly considered. To do so, the sensitivities of the scattering processes to the microphysical characteristics of different ice hydrometeors are investigated using sensitivity studies. Furthermore, beam propagation effects are considered, including attenuation and beam bending. The performance of SynPolRad and the consistence of the assumptions made in the derivation of the input parameters are illustrated in a case study. The resulting synthetic quantities as well as hydrometeor classification are compared with observations and are shown to be consistent with the model assumptions.
Diagnosing the Intercept Parameter for Exponential Raindrop Size Distribution Based on Video Disdrometer Observations: Model Development
Authors: Zhang Guifu , Xue Ming , Cao Qing , Dawson Daniel 
Published: May 2008

Abstract
The exponential distribution N(D) = N0 exp(−ΛD) with a fixed intercept parameter N0 is most commonly used to represent raindrop size distribution (DSD) in rainfall estimation and in single-moment bulk microphysics parameterization schemes. Disdrometer observations show that the intercept parameter is far from constant and systematically depends on the rain type and intensity. In this study, a diagnostic relation of N0 as a function of rainwater content W is derived based on two-dimensional video disdrometer (2DVD) measurements. The data reveal a clear correlation between N0 and W in which N0 increases as W increases. To minimize the effects of sampling error, a relation between two middle moments is used to derive the N0–W relation. This diagnostic relation has the potential to improve rainfall estimation and bulk microphysics parameterizations. A parameterization scheme for warm rain processes based on the diagnostic N0 DSD model is formulated and presented. The diagnostic N0-based parameterization scheme yields less evaporation and accretion for stratiform rain than that using fixed N0.
Comparing Reanalyses Using Analysis Increment Statistics
Authors: Fitzmaurice Jean , Bras Rafael L. 
Published: May 2008

Abstract
Reanalysis data are an important source of information for hydrometeorology applications, which use data assimilation to combine an imperfect atmospheric model with uncertain observations. However, uncertainty estimates are not normally provided with reanalyses. The model “first guess” (6-h forecast) is sometimes saved along with reanalysis estimates, which allows the calculation of the analysis increment (AI), defined as the analysis minus the model first guess. Analysis increment statistics could provide a quantitative index for comparing models in regions with sufficient observations. Monthly analysis increment statistics for the NCEP–NCAR Global Reanalysis 1 (NCEP-R1) and the NCEP/Department of Energy Global Reanalysis 2 (NCEP-R2) are computed for a North American and South American location for zonal and meridional wind and specific humidity at three atmospheric levels for 1998–2001. NCEP-R2 specific humidity was found to have a smaller mean monthly standard deviation of the analysis increment than NCEP-R1 at the North American location at the 300-mb level. The NCEP-R2 specific humidity monthly standard deviation at the South American location is much larger than NCEP-R1 for September–November 1998, which may be related to the transition to La Niña. For both zonal and meridional wind, the monthly AI standard deviations are similar for NCEP-R1 and NCEP-R2 at all atmospheric levels for the North American location. The South American location exhibits similar behavior for the wind AI statistics as for specific humidity: NCEP-R2 has a much larger monthly standard deviation of the AI for September–November 1998. The analysis increment statistics could be one method for quantitatively comparing reanalyses. First guess information should be available to the user in reanalysis archives.
Steel factor coordinately regulates the molecular signature and biologic function of hematopoietic stem cells
Authors: Kent David G. , Dykstra Brad J. , Cheyne Jay , Ma Elaine , Eaves Connie J. 
Published: May 2008

Abstract
Hematopoietic stem cells (HSCs) regenerated in vivo display sustained differences in their self-renewal and differentiation activities. Variations in Steel factor (SF) signaling are known to affect these functions in vitro, but the cellular and molecular mechanisms involved are not understood. To address these issues, we evaluated highly purified HSCs maintained in single-cell serum-free cultures containing 20 ng/mL IL-11 plus 1, 10, or 300 ng/mL SF. Under all conditions, more than 99% of the cells traversed a first cell cycle with similar kinetics. After 8 hours in the 10 or 300 ng/mL SF conditions, the frequency of HSCs remained unchanged. However, in the next 8 hours (ie, 6 hours before any cell divided), HSC integrity was sustained only in the 300 ng/mL SF cultures. The cells in these cultures also contained significantly higher levels of Bmi1, Lnk, and Ezh2 transcripts but not of several other regulators. Assessment of 21 first division progeny pairs further showed that only those generated in 300 ng/mL SF cultures contained HSCs and pairs of progeny with similar differentiation programs were not observed. Thus, SF signaling intensity can directly and coordinately alter the transcription factor profile and long-term repopulating ability of quiescent HSCs before their first division.
WHO classification and WPSS predict posttransplantation outcome in patients with myelodysplastic syndrome: a study from the Gruppo Italiano Trapianto di Midollo Osseo (GITMO)
Authors: Alessandrino Emilio Paolo , Della Porta Matteo Giovanni , Bacigalupo Andrea , Van Lint Maria Teresa , Falda Michele , Onida Francesco , Bernardi Massimo , Iori Anna Paola , Rambaldi Alessandro , Cerretti Raffaella , Marenco Paola , Pioltelli Pietro , Malcovati Luca , Pascutto Cristiana , Oneto Rosi , Fanin Renato , Bosi Alberto 
Published: May 2008

Abstract
We evaluated the impact of World Health Organization (WHO) classification and WHO classification–based Prognostic Scoring System (WPSS) on the outcome of patients with myelodysplastic syndrome (MDS) who underwent allogeneic stem cell transplantation (allo-SCT) between 1990 and 2006. Five-year overall survival (OS) was 80% in refractory anemias, 57% in refractory cytopenias, 51% in refractory anemia with excess blasts 1 (RAEB-1), 28% in RAEB-2, and 25% in acute leukemia from MDS (P = .001). Five-year probability of relapse was 9%, 22%, 24%, 56%, and 53%, respectively (P < .001). Five-year transplant-related mortality (TRM) was 14%, 39%, 38%, 34%, and 44%, respectively (P = .24). In multivariate analysis, WHO classification showed a significant effect on OS (P = .017) and probability of relapse (P = .01); transfusion dependency was associated with a reduced OS (P = .01) and increased TRM (P = .037), whereas WPSS showed a prognostic significance on both OS (P = .001) and probability of relapse (P < .001). In patients without excess blasts, multilineage dysplasia and transfusion dependency affected OS (P = .001 and P = .009, respectively), and were associated with an increased TRM (P = .013 and P = .031, respectively). In these patients, WPSS identified 2 groups with different OS and TRM. These data suggest that WHO classification and WPSS have a relevant prognostic value in posttransplantation outcome of MDS patients.
Molecular evolution of Cide family proteins: Novel domain formation in early vertebrates and the subsequent divergence
Authors: Wu Congyang , Zhang Yinxin , Sun Zhirong , Li Peng 
Published: May 2008

AbstractBackgroundCide family proteins including Cidea, Cideb and Cidec/Fsp27, contain an N-terminal CIDE-N domain that shares sequence similarity to the N-terminal CAD domain (NCD) of DNA fragmentation factors Dffa/Dff45/ICAD and Dffb/Dff40/CAD, and a unique C-terminal CIDE-C domain. We have previously shown that Cide proteins are newly emerged regulators closely associated with the development of metabolic diseases such as obesity, diabetes and liver steatosis. They modulate many metabolic processes such as lipolysis, thermogenesis and TAG storage in brown adipose tissue (BAT) and white adipose tissue (WAT), as well as fatty acid oxidation and lipogenesis in the liver.ResultsTo understand the evolutionary process of Cide proteins and provide insight into the role of Cide proteins as potential metabolic regulators in various species, we searched various databases and performed comparative genomic analysis to study the sequence conservation, genomic structure, and phylogenetic tree of the CIDE-N and CIDE-C domains of Cide proteins. As a result, we identified signature sequences for the N-terminal region of Dffa, Dffb and Cide proteins and CIDE-C domain of Cide proteins, and observed that sequences homologous to CIDE-N domain displays a wide phylogenetic distribution in species ranging from lower organisms such as hydra (Hydra vulgaris) and sea anemone (Nematostella vectensis) to mammals, whereas the CIDE-C domain exists only in vertebrates. Further analysis of their genomic structures showed that although evolution of the ancestral CIDE-N domain had undergone different intron insertions to various positions in the domain among invertebrates, the genomic structure ofCidefamily in vertebrates is stable with conserved intron phase.ConclusionBased on our analysis, we speculate that in early vertebrates CIDE-N domain was evolved from the duplication of NCD of Dffa. The CIDE-N domain somehow acquired the CIDE-C domain that was formed around the same time, subsequently generating the Cide protein. Subsequent duplication and evolution have led to the formation of different Cide family proteins that play unique roles in the control of metabolic pathways in different tissues.
Trait-trait dynamic interaction: 2D-trait eQTL mapping for genetic variation study
Authors: Sun Wei , Yuan Shinsheng , Li Ker-Chau 
Published: May 2008

AbstractBackgroundMany studies have shown that the abundance level of gene expression is heritable. Analogous to the traditional genetic study, most researchers treat the expression of one gene as a quantitative trait and map it to expression quantitative trait loci (eQTL). This is 1D-trait mapping. 1D-trait mapping ignores the trait-trait interaction completely, which is a major shortcoming.ResultsTo overcome this limitation, we study the expression of a pair of genes and treat the variation in their co-expression pattern as a two dimensional quantitative trait. We develop a method to find gene pairs, whose co-expression patterns, including both signs and strengths, are mediated by genetic variations and map these 2D-traits to the corresponding genetic loci. We report several applications by combining 1D-trait mapping with 2D-trait mapping, including the contribution of genetic variations to the perturbations in the regulatory mechanisms of yeast metabolic pathways.ConclusionOur approach of 2D-trait mapping provides a novel and effective way to connect the genetic variation with higher order biological modules via gene expression profiles.
Gene discovery in an invasive tephritid model pest species, the Mediterranean fruit fly, Ceratitis capitata
Authors: Gomulski Ludvik M , Dimopoulos George , Xi Zhiyong , Soares Marcelo B , Bonaldo Maria F , Malacrida Anna R , Gasperi Giuliano 
Published: May 2008

AbstractBackgroundThe medfly,Ceratitis capitata, is a highly invasive agricultural pest that has become a model insect for the development of biological control programs. Despite research into the behavior and classical and population genetics of this organism, the quantity of sequence data available is limited. We have utilized an expressed sequence tag (EST) approach to obtain detailed information on transcriptome signatures that relate to a variety of physiological systems in the medfly; this information emphasizes on reproduction, sex determination, and chemosensory perception, since the study was based on normalized cDNA libraries from embryos and adult heads.ResultsA total of 21,253 high-quality ESTs were obtained from the embryo and head libraries. Clustering analyses performed separately for each library resulted in 5201 embryo and 6684 head transcripts. Considering an estimated 19% overlap in the transcriptomes of the two libraries, they represent about 9614 unique transcripts involved in a wide range of biological processes and molecular functions. Of particular interest are the sequences that share homology withDrosophilagenes involved in sex determination, olfaction, and reproductive behavior. The medflytransformer2(tra2) homolog was identified among the embryonic sequences, and its genomic organization and expression were characterized.ConclusionThe sequences obtained in this study represent the first major dataset of expressed genes in a tephritid species of agricultural importance. This resource provides essential information to support the investigation of numerous questions regarding the biology of the medfly and other related species and also constitutes an invaluable tool for the annotation of complete genome sequences. Our study has revealed intriguing findings regarding the transcript regulation oftra2and other sex determination genes, as well as insights into the comparative genomics of genes implicated in chemosensory reception and reproduction.
Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae
Authors: Vongsangnak Wanwipa , Olsen Peter , Hansen Kim , Krogsgaard Steen , Nielsen Jens 
Published: May 2008

Abstract

Background
Since ancient times the filamentous fungus Aspergillus oryzae has been used in the fermentation industry for the production of fermented sauces and the production of industrial enzymes. Recently, the genome sequence of A. oryzae with 12,074 annotated genes was released but the number of hypothetical proteins accounted for more than 50% of the annotated genes. Considering the industrial importance of this fungus, it is therefore valuable to improve the annotation and further integrate genomic information with biochemical and physiological information available for this microorganism and other related fungi. Here we proposed the gene prediction by construction of an A. oryzae Expressed Sequence Tag (EST) library, sequencing and assembly. We enhanced the function assignment by our developed annotation strategy. The resulting better annotation was used to reconstruct the metabolic network leading to a genome scale metabolic model of A. oryzae.

Results
Our assembled EST sequences we identified 1,046 newly predicted genes in the A. oryzae genome. Furthermore, it was possible to assign putative protein functions to 398 of the newly predicted genes. Noteworthy, our annotation strategy resulted in assignment of new putative functions to 1,469 hypothetical proteins already present in the A. oryzae genome database. Using the substantially improved annotated genome we reconstructed the metabolic network of A. oryzae. This network contains 729 enzymes, 1,314 enzyme-encoding genes, 1,073 metabolites and 1,846 (1,053 unique) biochemical reactions. The metabolic reactions are compartmentalized into the cytosol, the mitochondria, the peroxisome and the extracellular space. Transport steps between the compartments and the extracellular space represent 281 reactions, of which 161 are unique. The metabolic model was validated and shown to correctly describe the phenotypic behavior of A. oryzae grown on different carbon sources.

Conclusion
A much enhanced annotation of the A. oryzae genome was performed and a genome-scale metabolic model of A. oryzae was reconstructed. The model accurately predicted the growth and biomass yield on different carbon sources. The model serves as an important resource for gaining further insight into our understanding of A. oryzae physiology.
Carbenoxolone induced depression of rhythmogenesis in the pre-Bötzinger Complex
Authors: Elsen Frank P , Shields Edward J , Roe Matthew T , VanDam Richard J , Kelty Jonathan D 
Published: May 2008

Abstract

Background
Carbenoxolone (CBX), a gap junction uncoupler, alters the functioning of the pre-Bötzinger Complex (preBötC), a central pattern generating neuronal network important for the production of respiratory rhythm in mammals. Even when isolated in a 1/2 mm-thick slice of medulla oblongata from neonatal mouse the preBötC continues producing periodic bursts of action potentials, termed population bursts that are thought to be important in generating various patterns of inspiration, in vivo. Whether gap junction communication contributes to preBötC rhythmogenesis remains unresolved, largely because existing gap junction uncouplers exert numerous non-specific effects (e.g., inhibition of active transport, alteration of membrane conductances). Here, we determined whether CBX alters preBötC rhythmogenesis by altering membrane properties including input resistance (Rin), voltage-gated Na+ current (INa), and/or voltage-gated K+ current (IK), rather than by blocking gap junction communication. To do so we used a medullary slice preparation, network-level recordings, whole-cell voltage clamp, and glycyrrhizic acid (GZA; a substance used as a control for CBX, since it is similar in structure and does not block gap junctions).

Results
Whereas neither of the control treatments [artificial cerebrospinal fluid (aCSF) or GZA (50 μM)] noticeably affected preBötC rhythmogenesis, CBX (50 μM) decreased the frequency, area and amplitude of population bursts, eventually terminating population burst production after 45–60 min. Both CBX and GZA decreased neuronal Rin and induced an outward holding current. Although neither agent altered the steady state component of IK evoked by depolarizing voltage steps, CBX, but not GZA, increased peak INa.

Conclusion
The data presented herein are consistent with the notion that gap junction communication is important for preBötC rhythmogenesis. By comparing the effects of CBX and GZA on membrane properties our data a) demonstrate that depression of preBötC rhythmogenesis by CBX results from actions on another variable or other variables; and b) show that this comparative approach can be used to evaluate the potential contribution of other non-specific actions (e.g., Ca++ conductances or active transport) of CBX, or other uncouplers, in their alteration of preBötC rhythmogenesis, or the functioning of other networks.
Global expression profiling in leaves of free-growing aspen
Authors: Sjödin Andreas , Wissel Kirsten , Bylesjö Max , Trygg Johan , Jansson Stefan 
Published: May 2008

AbstractBackgroundGenomic studies are routinely performed on young plants in controlled environments which is very different from natural conditions. In reality plants in temperate countries are exposed to large fluctuations in environmental conditions, in the case of perennials over several years. We have studied gene expression in leaves of a free-growing aspen (Populus tremula) throughout multiple growing seasonsResultsWe show that gene expression during the first month of leaf development was largely determined by a developmental program although leaf expansion, chlorophyll accumulation and the speed of progression through this program was regulated by the temperature. We were also able to define "transcriptional signatures" for four different substages of leaf development. In mature leaves, weather factors were important for gene regulation.ConclusionThis study shows that multivariate methods together with high throughput transcriptional methods in the field can provide additional, novel information as to plant status under changing environmental conditions that is impossible to mimic in laboratory conditions. We have generated a dataset that could be used to e.g. identify marker genes for certain developmental stages or treatments, as well as to assess natural variation in gene expression.