bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the effects of image filtering in short‐term radar rainfall forecasting for hydrological applications
Authors: Van Horne Matthew P. , Vivoni Enrique R. , Entekhabi Dara , Hoffman Ross N. , Grassotti Christopher 
Published: August 2006

AbstractRadar rainfall nowcasting at short lead times has important hydrometeorological applications in the fields of weather prediction and flood forecasting. The predictability of rainfall events can vary significantly with scale as smaller storm features are less predictable than the storm envelope motion. As a result, various techniques have been developed for filtering a radar image and deriving short‐term forecasts from the more predictable, larger storm scales. In this study, the effects of image filtering on radar nowcasting performance using the Storm Tracker Nowcasting Model (STNM) are evaluated. Radar rainfall nowcasts are evaluated for three storms exhibiting varying degrees of organisation over the Arkansas‐Red River basin. In each case, it is found that the nowcast skill decreases with the forecast lead time, increases with the verification area used around a forecast location, and decreases with higher rainfall thresholds. Furthermore, it is demonstrated that a set of properly tuned filtering nowcasts are superior to simple ‘persistence’ and slightly better than ‘uniform advection’. At the scale of a large hydrologic basin (∼6000 km2), filter‐based nowcasting is shown to capture the temporal variation in rainfall amount and its spatial distribution based on a set of catchment‐based metrics. Finally, a method for relating changes in nowcasting skill to errors associated with storm dynamics not captured by image filtering techniques is evaluated. Copyright © 2006 John Wiley & Sons, Ltd.
Regulating Expression of Pyruvate Kinase in Bacillus subtilis for Control of Growth Rate and Formation of Acidic Byproducts
Authors: Pan Zhiwei , Zhu Tao , Domagalski Nathan , Khan Saleem , Koepsel Richard R. , Domach Michael M. , Ataai Mohammad M. 
Published: August 2006

AbstractOur prior work has shown that a pyk mutant of Bacillus subtilis exhibited diminished acidic byproduct accumulation, dramatically elevated phosphoenolpyruvate (PEP) pool, and reduced growth rate. To determine if a low acetate‐producing but fast‐growing strain of B. subtilis could be developed, we placed the expression of the pykgene under the control of an inducible promoter. Enzyme measurements proved that PYK activity of the inducible PYK mutant (iPYK) increases with the isopropyl‐β‐d‐thiogalactopyranoside concentration. Batch growth experiments showed that growth rate and acid formation are closely related to the induction level of pyk. Measurements of cell growth rate and acetate formation of the iPYK mutant at different induction levels revealed that a PYK activity of about 12% of wild‐type allows for good growth rate (0.4 h−1 versus 0.63 h−1 of wild‐type) and low acetate production (0.26 g/L versus 1.05 g/L of wild‐type). This is the first report to our knowledge of a metabolically engineered B. subtilis strain that allows good growth rate and low acid production in batch cultures. Finally, it was found that, by varying the pyk induction level, intracellular PEP concentration can be controlled over a wide range. The intracellular PEP concentration is intimately connected to the regulation of the transport of phosphotransferase system (PTS) sugars in the presence of glucose. Because there is no other method for modulating intracellular PEP levels, this finding represents a major advance in oneapos;s ability to dissect the function of the PTS and sugar metabolism in bacteria.
GenePro: a cytoscape plug-in for advanced visualization and analysis of interaction networks
Authors: Vlasblom James , Wu Samuel , Pu Shuye , Superina Mark , Liu Gina , Orsi Chris , Wodak Shoshana J. 
Published: August 2006

Abstract
Motivation: Analyzing the networks of interactions between genes and proteins has become a central theme in systems biology. Versatile software tools for interactively displaying and analyzing these networks are therefore very much in demand. The public-domain open software environment Cytoscape has been developed with the goal of facilitating the design and development of such software tools by the scientific community.
Results: We present GenePro, a plugin to Cytoscape featuring a set of versatile tools that greatly facilitates the visualization and analysis of protein networks derived from high-throughput interactions data and the validation of various methods for parsing these networks into meaningful functional modules.
Availability: The GenePro plugin is available at the website
contact: shuyepu@sickkids.ca
Suppression of LX Ribonuclease in Tomato Results in a Delay of Leaf Senescence and Abscission
Authors: Lers Amnon , Sonego Lilian , Green Pamela J. , Burd Shaul 
Published: August 2006

AbstractAlthough present in different organisms and conserved in their protein sequence, the biological functions of T2 ribonucleases (RNase) are generally unknown. Tomato (Lycopersicon esculentum) LX is a T2/S-like RNase and its expression is known to be associated with phosphate starvation, ethylene responses, and senescence and programmed cell death. In this study, LX function was investigated using antisense tomato plants in which the LX protein level was reduced. LX protein levels normally become elevated when leaves senesce and antisense inhibition of LX retarded the progression of senescence. Moreover, we observed a marked delay of leaf abscission in LX-deficient plants. This correlated with specific induction of LX protein in the tomato mature abscission zone tissue. LX RNase gene regulation and the consequences of antisense inhibition indicate that LX has an important functional role in both abscission and senescence.
Gibberellin Mobilizes Distinct DELLA-Dependent Transcriptomes to Regulate Seed Germination and Floral Development in Arabidopsis
Authors: Cao Dongni , Cheng Hui , Wu Wei , Soo Hui Meng , Peng Jinrong 
Published: August 2006

Abstract
Severe Arabidopsis (Arabidopsis thaliana) gibberellin (GA)-deficient mutant ga1-3 fails to germinate and is impaired in floral organ development. In contrast, the ga1-3 gai-t6 rga-t2 rgl1-1 rgl2-1 mutant confers GA-independent seed germination and floral development. This fact suggests that GA-regulated transcriptomes for seed germination and floral development are DELLA dependent. However, it is currently not known if all GA-regulated genes are GA regulated in a DELLA-dependent fashion and if a similar set of DELLA-regulated genes is mobilized to repress both seed germination and floral development. Here, we compared the global gene expression patterns in the imbibed seeds and unopened flower buds of the ga1-3 mutant with that of the wild type and of the ga1-3 gai-t6 rga-t2 rgl1-1 rgl2-1 mutant. We found that about one-half of total GA-regulated genes are apparently regulated in a DELLA-dependent fashion, suggesting that there might be a DELLA-independent or -partially-dependent component of GA-dependent gene regulation. A cross-comparison based on gene identity revealed that the GA-regulated DELLA-dependent transcriptomes in the imbibed seeds and flower buds are distinct from each other. Detailed ontology analysis showed that, on one hand, DELLAs differentially regulate the expression of different individual members of a gene family to run similar biochemical pathways in seeds and flower. Meanwhile, DELLAs control many functionally different genes to run specific pathways in seeds or flower buds to mark the two different developmental processes. Our data shown here not only confirm many previous reports but also single out some novel aspects of DELLA functions that are instructive to our future research.
Species Having C4 Single-Cell-Type Photosynthesis in the Chenopodiaceae Family Evolved a Photosynthetic Phosphoenolpyruvate Carboxylase Like That of Kranz-Type C4 Species
Authors: Lara María Valeria , Chuong Simon D.X. , Akhani Hossein , Andreo Carlos Santiago , Edwards Gerald E. 
Published: August 2006

Abstract
Spatial and temporal regulation of phosphoenolpyruvate carboxylase (PEPC) is critical to the function of C4 photosynthesis. The photosynthetic isoform of PEPC in the cytosol of mesophyll cells in Kranz-type C4 photosynthesis has distinctive kinetic and regulatory properties. Some species in the Chenopodiaceae family perform C4 photosynthesis without Kranz anatomy by spatial separation of initial fixation of atmospheric CO2 via PEPC from C4 acid decarboxylation and CO2 donation to Rubisco within individual chlorenchyma cells. We studied molecular and functional features of PEPC in two single-cell functioning C4 species (Bienertia sinuspersici, Suaeda aralocaspica) as compared to Kranz type (Haloxylon persicum, Salsola richteri, Suaeda eltonica) and C3 (Suaeda linifolia) chenopods. It was found that PEPC from both types of C4 chenopods displays higher specific activity than that of the C3 species and shows kinetic and regulatory characteristics similar to those of C4 species in other families in that they are subject to light/dark regulation by phosphorylation and display differential malate sensitivity. Also, the deduced amino acid sequence from leaf cDNA indicates that the single-cell functioning C4 species possesses a Kranz-type C4 isoform with a Ser in the amino terminal. A phylogeny of PEPC shows that isoforms in the two single-cell functioning C4 species are in a clade with the C3 and Kranz C4 Suaeda spp. with high sequence homology. Overall, this study indicates that B. sinuspersici and S. aralocaspica have a C4-type PEPC similar to that in Kranz C4 plants, which likely is required for effective function of C4 photosynthesis.
A Cytosolic Arabidopsis d-Xylulose Kinase Catalyzes the Phosphorylation of 1-Deoxy-d-Xylulose into a Precursor of the Plastidial Isoprenoid Pathway
Authors: Hemmerlin Andréa , Tritsch Denis , Hartmann Michael , Pacaud Karine , Hoeffler Jean-François , van Dorsselaer Alain , Rohmer Michel , Bach Thomas J. 
Published: August 2006

Abstract
Plants are able to integrate exogenous 1-deoxy-d-xylulose (DX) into the 2C-methyl-d-erythritol 4-phosphate pathway, implicated in the biosynthesis of plastidial isoprenoids. Thus, the carbohydrate needs to be phosphorylated into 1-deoxy-d-xylulose 5-phosphate and translocated into plastids, or vice versa. An enzyme capable of phosphorylating DX was partially purified from a cell-free Arabidopsis (Arabidopsis thaliana) protein extract. It was identified by mass spectrometry as a cytosolic protein bearing d-xylulose kinase (XK) signatures, already suggesting that DX is phosphorylated within the cytosol prior to translocation into the plastids. The corresponding cDNA was isolated and enzymatic properties of a recombinant protein were determined. In Arabidopsis, xylulose kinases are encoded by a small gene family, in which only two genes are putatively annotated. The additional gene is coding for a protein targeted to plastids, as was proved by colocalization experiments using green fluorescent protein fusion constructs. Functional complementation assays in an Escherichia coli strain deleted in xk revealed that the cytosolic enzyme could exclusively phosphorylate xylulose in vivo, not the enzyme that is targeted to plastids. xk activities could not be detected in chloroplast protein extracts or in proteins isolated from its ancestral relative Synechocystis sp. PCC 6803. The gene encoding the plastidic protein annotated as “xylulose kinase” might in fact yield an enzyme having different phosphorylation specificities. The biochemical characterization and complementation experiments with DX of specific Arabidopsis knockout mutants seedlings treated with oxo-clomazone, an inhibitor of 1-deoxy-d-xylulose 5-phosphate synthase, further confirmed that the cytosolic protein is responsible for the phosphorylation of DX in planta.
The Balance between Cell Division and Endoreplication Depends on E2FC-DPB, Transcription Factors Regulated by the Ubiquitin-SCFSKP2A Pathway inArabidopsis
Authors: del Pozo Juan C. , Diaz-Trivino Sara , Cisneros Nerea , Gutierrez Crisanto 
Published: August 2006

AbstractThe balance between cell proliferation, cell cycle arrest, and differentiation needed to maintain the organogenetic program depends on the coordination of gene expression, posttranslational modification, and specific proteolysis of cell cycle regulators. The G1/S and G2/M transitions are critical checkpoints controlled, in part, by cyclin-dependent kinases in the retinoblastoma (RBR)/E2F/DP pathway. Arabidopsis thaliana DPB is regulated by phosphorylation and targeted to proteasome-mediated proteolysis by the SCFSKP2A complex. In addition, DPB interacts in vivo with E2FC, because ectopic coexpression of E2FC and DPB produces severe developmental defects. To understand E2FC/DPB heterodimer function, we analyzed the effect of reducing E2FC mRNA levels with RNA interference. The e2fc-R plants developed organs with more but smaller cells and showed increased cell cycle marker gene expression and increased proliferative activity in developing leaves, meristems, and pericycle cells. This last feature produces plants with more lateral roots, consistent with an E2FC role in restricting lateral root initiation. The e2fc-R plants also show marked reductions in ploidy levels of mature leaves. These results indicate that the transition from cell division to the endocycle is sensitive to different pathways, E2FC/DPB being one of them. Our results show that E2FC/DPB is a key factor in controlling the balance between cell proliferation and the switch to the endocycle program.
Higher‐level phylogeny of the Ithomiinae (Lepidoptera: Nymphalidae): classification, patterns of larval hostplant colonization and diversification
Authors: Willmott Keith R. , Freitas André V. L. 
Published: August 2006

AbstractWe present a higher‐level phylogenetic hypothesis for the diverse neotropical butterfly subfamily Ithomiinae, inferred from one of the largest non‐molecular Lepidoptera data sets to date, including 106 species (105 ingroup) and 353 characters (306 informative) from adult and immature stage morphology and ecology. Initial analyses resulted in 1716 most parsimonious trees, which were reduced to a single tree after successive approximations character weighting. The inferred phylogeny was broadly consistent with other past and current work. Although some deeper relationships are uncertain, tribal‐level clades were generally strongly supported, with two changes required to existing classification. The tribe Melinaeini is polyphyletic andAthesis + Patriciarequire a new tribe. Methonashould be removed from Mechanitini into the restored tribe Methonini. Dircennini was paraphyletic in analyses of all data but monophyletic based on adult morphology alone, and its status remains to be confirmed.Hypothyris,Episcada,Godyris,HypoleriaandGretaare paraphyletic. A simulation analysis showed that relatively basal branches tended to have higher partitioned Bremer support for immature stage characters. Larval hostplant records were optimized on to a reduced, generic‐level phylogeny and indicate that ithomiines moved from Apocynaceae to Solanaceae twice, or that Tithoreini re‐colonized Apocynaceae after a basal shift to Solanaceae. Ithomiine clades have specialized on particular plant clades suggesting repeated colonization of novel hostplant niches consistent with adaptive radiation. The shift toSolanum, comprising 70% of neotropical Solanaceae, occurs at the base of a clade containing 89% of all ithomiines, and is interpreted as the major event in the evolution of ithomiine larval hostplant relationships.© The Willi Hennig Society 2006.
Rejecting “the given” in systematics
Authors: Kearney Maureen , Rieppel Olivier 
Published: August 2006

AbstractHow morphology and systematics come together through morphological analysis, homology hypotheses and phylogenetic analysis is a topic of continuing debate. Some contemporary approaches reject biological evaluation of morphological characters and fall back on an atheoretical and putatively objective (but, in fact, phenetic) approach that defers to the test of congruence for homology assessment. We note persistent trends toward an uncritical empiricism (where evidence is believed to be immediately “given” in putatively theory‐free observation) and instrumentalism (where hypotheses of primary homology become mere instruments with little or no empirical foundation for choosing among competing phylogenetic hypotheses). We suggest that this situation is partly a consequence of the fact that the test of congruence and the related concept of total evidence have been inappropriately tied to a Popperian philosophy in modern systematics. Total evidence is a classical principle of inductive inference and does not imply a deductive test of homology. The test of congruenceby itselfis based philosophically on a coherence theory of truth (coherentism in epistemology), which is unconcerned with empirical foundation. We therefore argue that coherence of character statements (congruence of characters) is a necessary, but not a sufficient, condition to support or refute hypotheses of homology or phylogenetic relationship. There should be at least some causal grounding for homology hypotheses beyond mere congruence. Such causal grounding may be achieved, for example, through empirical investigations of comparative anatomy, developmental biology, functional morphology and secondary structure.© The Willi Hennig Society 2006.
The how and why of branch support and partitioned branch support, with a new index to assess partition incongruence
Authors: Brower Andrew V. Z. 
Published: August 2006

AbstractAn introduction and step‐by‐step guide to the calculation of branch support (BS) and partitioned branch support (PBS) is provided, along with a new summary measure of conflict among data partitions, the partition congruence index (PCI). Patterns of PCI vs. BS are compared for two data matrices from butterflies. PCI is a close mirror of BS unless BY is relatively low and there is a lot of conflict among data partitions, in which case PCI becomes negative. Some theoretical concerns relating to PBS are noted.© The Willi Hennig Society 2006.
Report on the Ohio State University workshops in phylogenetic methods
Authors: Abdul‐Salim Kobinah , Daly Marymegan , Freudenstein John V. , Wenzel John W. 
Published: August 2006

AbstractA three‐part series of workshops in phylogenetic methods was held at the Ohio State University in September and December 2005. The first two were sponsored by the OSU Mathematical Biosciences Institute (MBI), and focused on phylogeography and phylogenetic data, and phylogenetic analysis of large data sets respectively. These workshops highlighted theoretical and practical aspects of phylogeographic inferences using model‐based approaches (e.g. likelihood and Bayesian MCMC), as well as current approaches to analyzing large datasets using both parsimony and model‐based methods. The third workshop was sponsored by OSU systematics faculty, and was intended to provide practical training in current tools of phylogenetic analysis at the beginning and intermediate levels. The success of these workshops emphasizes the need for greater interaction between those involved in theoretical and empirical phylogenetic research. Further workshops, such as these, would serve to bring a practical understanding of these methods to as broad an audience as possible.© The Willi Hennig Society 2006.
Staging performance of carbon‐11 choline positron emission tomography/computed tomography in patients with bone and soft tissue sarcoma: Comparison with conventional imaging
Authors: Tateishi Ukihide , Yamaguchi Umio , Maeda Testuo , Seki Kunihiko , Terauchi Takashi , Kawai Akira , Arai Yasuaki , Moriyama Noriyuki , Kakizoe Tadao 
Published: August 2006

The present study was conducted to compare the diagnostic accuracy between carbon‐11 choline (11C‐choline) positron emission tomography (PET)/computed tomography (CT) and conventional imaging for the staging of bone and soft tissue sarcomas. Sixteen patients who underwent 11C‐choline PET/CT prior to treatment were evaluated retrospectively for staging accuracy. Conventional imaging methods consisted of 99,mTc‐hydroxymethylene diphosphonate bone scintigraphy, chest CT and magnetic resonance imaging of the primary site. The images were reviewed and a consensus was reached by two board‐certified radiologists who were unaware of any clinical or radiological information using hard‐copy films and multimodality computer platform. Tumor stage was confirmed by histological examination and/or by an obvious progression in number and/or size of the lesions on follow‐up examinations. Reviewers examining both 11C‐choline PET/CT and conventional imaging classified T stage in all patients. Interpretation based on 11C‐choline PET/CT, the Node (N) stage was correctly diagnosed in all patients, whereas the accuracy of conventional imaging in N stage was 63%. Tumor Node Metastasis (TNM) stage was assessed correctly with 11C‐choline PET/CT in 15 of 16 patients (94%) and with conventional imaging in eight of 16 patients (50%). The overall TNM staging and N staging accuracy of 11C‐choline PET/CT were significantly higher than that of conventional imaging (P < 0.05). 11C‐choline PET/CT is more accurate than conventional imaging regarding clinical staging of patients with bone and soft tissue sarcomas. A whole body 11C‐choline PET/CT might be acceptable for imaging studies of tumor staging prior to treatment. (Cancer Sci 2006; 97: 1125–1128)
Estrogen‐mediated post transcriptional down‐regulation of P‐glycoprotein in MDR1‐transduced human breast cancer cells
Authors: Mutoh Kazuyoshi , Tsukahara Satomi , Mitsuhashi Junko , Katayama Kazuhiro , Sugimoto Yoshikazu 
Published: August 2006

The human multidrug resistance gene 1 (MDR1) encodes the plasma membrane P‐glycoprotein (P‐gp/ABCB1) that functions as an efflux pump for various anticancer agents. We recently reported that estrogens down‐regulate the expression of breast cancer resistance protein (BCRP/ABCG2). In our present study we demonstrate that estrogens also down‐regulate P‐gp expression in the MDR1‐transduced, estrogen receptor α (ER‐α)‐positive human breast cancer cells, MCF‐7/MDR and T‐47D/MDR. The P‐gp expression levels in MCF‐7/MDR cells treated with 100 pM estradiol were found to be 10–20‐fold lower than the levels in these same cells that were cultured without estradiol. In contrast, estradiol did not affect the P‐gp expression levels in the ER‐α‐negative cancer cells, MDA‐MB‐231/MDR and NCI/ADR‐RES. Estrone and diethylstilbestrol were also found to down‐regulate P‐gp in MCF‐7/MDR cells, but progesterone treatment did not produce this effect. Tamoxifen reversed the estradiol‐mediated down‐regulation of P‐gp in MCF‐7/MDR cells, suggesting that ER‐α activity is necessary for the effects of estradiol upon P‐gp. However, estradiol was found not to alter the MDR1 transcript levels in either MCF‐7/MDR and T‐47D/MDR cells, suggesting that post‐transcriptional mechanisms underlie its effects upon P‐gp down‐regulation. MCF‐7/MDR cells also showed eight‐fold higher sensitivity to vincristine when treated with 100 pM estradiol, than when treated with 1 pM estradiol. These results may serve to provide a better understanding of the expression control of ABC transporters, and possibly allow for the establishment of new cancer chemotherapy strategies that would control P‐gp expression in breast cancer cells and thereby increase their sensitivity to MDR1‐related anticancer agents. (Cancer Sci 2006; 97: 1198–1204)