bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contractible subgraphs in k‐connected graphs
Authors: Jin Zemin , Yu Xingxing , Zhang Xiaoyan 
Published: December 2006

AbstractFor a graph G we define a graph T(G) whose vertices are the triangles in G and two vertices of T(G) are adjacent if their corresponding triangles in G share an edge. Kawarabayashi showed that if G is a k‐connected graph and T(G) contains no edge, then G admits a k‐contractible clique of size at most 3, generalizing an earlier result of Thomassen. In this paper, we further generalize Kawarabayashi's result by showing that if G is k‐connected and the maximum degree of T(G) is at most 1, then G admits a k‐contractible clique of size at most 3 or there exist independent edges e and f of G such that e and f are contained in triangles sharing an edge and G/e/f is k‐connected. © 2006 Wiley Periodicals, Inc. J Graph Theory 55: 121–136, 2007
Gas transport properties of asymmetric polyimide membranes prepared by ion‐beam irradiation
Authors: Sannomiya A. , Fukui K. , Nagaoka S. , Suzuki Y. , Iwaki M. , Kawakami H. 
Published: December 2006

AbstractIon beam irradiation has been widely used to modify the structure and properties of membrane surface layers. In this study, the gas permeability and selectivity of an asymmetric polyimide membrane modified by He ion irradiation were investigated using a high vacuum apparatus equipped with a Baratron absolute pressure gauge at 76 cmHg and 35 °C. Specifically, we estimated the effects of the gas diffusion and solubility on the gas permeation properties of the asymmetric membranes with the carbonized skin layer prepared by ion irradiation. The asymmetric polyimide membranes were prepared by a dry–wet phase inversion process, and the surface skin layer on the membrane was irradiated by He ions at fluences of 1 × 1015 to 5 × 1015 ions/cm2 at 50 keV. The increase in the gas permeability of the He+‐irradiated asymmetric polyimide membrane is entirely due to an increase in the gas diffusion, and the gas selectivity increases of the membranes were responsible for the high gas diffusion selectivities. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 262–269, 2007.
Computer‐Assisted Operative Planning in Adult Living Donor Liver Transplantation: A New Way to Resolve the Dilemma of the Middle Hepatic Vein
Authors: Radtke A. , Nadalin S. , Sotiropoulos G. C. , Molmenti E. P. , Schroeder T. , Valentin‐Gamazo C. , Lang H. , Bockhorn M. , Peitgen H.O. , Broelsch C. E. , Malagó M. 
Published: December 2006

AbstractAn adequate venous outflow is essential for securing viability of both graft and remnant in adult living donor liver transplantation (ALDLT). Seventy‐five potential live liver donors were evaluated for LDLT by means of an “all‐in‐one” CT, which defined the biliary tree, portal vein, hepatic artery, and hepatic vein anatomy. The acquired data sets were further analysed by means of the software HepaVision (MeVis, Germany). Only a minority (29%) of potential donors were found to have a vascular and biliary anatomy consistent with the classically described “normal” patterns. The vast majority (71%) had “anatomical variations”. Thirty‐nine (52%) donors underwent ALDLT hepatectomy. The right hepatic vein was dominant in 64 cases, representing 48 ± 6% of the total liver volume (TLV). The middle hepatic vein was dominant in 11 cases, making up 40 ± 8% of the TLV. The left hepatic vein was never dominant. The volume contribution of the middle hepatic vein (MHV) was 114–782 ml for the right and 87–419 ml for the left hemiliver. Computer‐assisted planning allows for the 3D reconstruction of the vascular and biliary anatomy, automatic calculation of the total and territorial liver volumes, and risk analysis of hepatic vein dominance relationships. This comprehensive data acquisition supports preoperative evaluation and provides a high degree of safety for donors and improved outcomes for recipients.
Impact of Patient‐ and Disease‐Specific Factors on SLNB in Breast Cancer Patients. Are Current Guidelines Justified?
Authors: Bembenek A. , Fischer J. , Albrecht H. , Kemnitz E. , Gretschel S. , Schneider U. , Dresel S. , Schlag P. M. 
Published: December 2006

AbstractBackgroundThe evidence on which to base guidelines for sentinel lymph node biopsy (SLNB) in breast cancer is still limited. In order to facilitate the further implementation of renewed guidelines, we evaluated patient‐ and disease‐specific factors for their impact on the results of SLNB.Materials and methodsProspective data acquisition from patients undergoing surgery for primary invasive breast cancer was performed. All patients underwent SLNB using the radiocolloid or the combined technique. The association of patient‐ and disease‐specific factors to detection rate and false‐negative rate was calculated using univariate and multivariate analyses (P < 0.05 considered as significant). Calculation of the false‐negative rate was based on patients who underwent a backup axillary dissection.ResultsAmong 455 consecutively enrolled patients, a significant inverse association to the detection rate was found for extracapsular extension of non‐SLN metastases, body mass index (BMI), number of involved lymph nodes, pT category, tumor size, and age. A significant association to the false‐negative rate to identify macrometastases was found for pT category, tumor size, and grading. Other factors, such as prior surgery, multicentric tumor growth, or vascular invasion, showed no influence. A cut‐point analysis revealed that a tumor size of 2 cm separated the collective of patients with the highest significance in regard to the false‐negative rate (9% vs. 25%).ConclusionOur results indicate that SLNB can be safely used in elderly and obese patients with multicentric tumors and those having undergone prior surgery for benign breast disease. However, the method should be applied with caution in patients with tumors larger than 2 cm.
Breast Cancer Local Recurrence: Risk Factors and Prognostic Relevance of Early Time to Recurrence
Authors: Neri A. , Marrelli D. , Rossi S. , De Stefano A. , Mariani F. , De Marco G. , Caruso S. , Corso G. , Cioppa T. , Pinto E. , Roviello F. 
Published: December 2006

AbstractBackgroundLocal recurrence occurs in 10%–20% of patients treated with breast‐conserving surgery for stage I–II breast cancer. The aim of the present study was to investigate breast cancer local recurrence, potential risk factors, and prognostic impact.MethodsA total of 503 patients treated with breast‐conserving surgery were included in the study. All patients underwent axillary dissection and postoperative radiotherapy, and all patients had negative margins at pathological examination. Median follow‐up was 82 months. Local recurrence was classified as early when it occurred within 2 years from surgery. The risk factors for local recurrence and overall survival were estimated by univariate and multivariate analyses.ResultsForty‐six cases (9.1%) of local recurrence were observed, 11 of which occurred within 24 months of surgery; the other 35, sometime later. Statistically significant risk factors for local recurrence were premenopausal status, peritumoral vascular invasion, multifocality, and absence of estrogen receptors. Independent negative prognostic factors for overall survival at 5 and 10 years were N stage, absence of estrogen receptors, and early time to recurrence. Overall survival at 10 years was 10.0% for patients with early recurrence, 87.5% for patients with late recurrence, and 87.9% for patients without recurrence.ConclusionsNone of the studied clinicopathological characteristics alone is a determinant for the choice of surgical treatment. Younger patients treated with breast‐conserving surgery should receive aggressive postsurgical treatment and should be followed with an intensive follow‐up program when metastatic axillary lymph nodes, negative estrogen receptors, or peritumoral vascular invasion are present.
Iatrogenic Vascular Injuries in Varicose Vein Surgery: a Systematic Review
Authors: Rudström Håkan , Björck Martin , Bergqvist David 
Published: December 2006

AbstractBackgroundIatrogenic vascular injuries during varicose vein surgery are serious. The aim of this study was to investigate their nature and consequences.MethodA systematic literature research was performed.ResultsThe incidence is low (0.0017%–0.3%). We found 81 patients suffering from 87 vascular injuries—44 arterial and 43 deep vein injuries.ConclusionVascular injuries during varicose surgery are rare but serious. They are avoidable, and when they occur, early recognition is crucial.Bleeding is a common symptom, especially in deep venous injury. In our study, we reviewed the literature on 81 patients with 87 vascular injuries. Laceration or division of the femoral vein dominated venous injuries (28/43). Partial stripping of the femoral vein was not common (4/43) and occurred when the strip probe passed into the deep veins through a perforator. Arterial stripping predominated in arterial injuries (17/44) and happened when stripping distally during a primary operation, as reported by experienced surgeons, in nonobese women. Major arterial complications resulted in ischemia, often with diagnostic delay and poor reconstruction results. Only 30% (13/44) of arterial injuries were detected peroperatively. The amputation rate was 34% (15/44), but rose to 100% if combined with intra‐arterial sclerotherapy (5/5 cases). When stripping an artery below the femoral artery, the amputation rate was high (42%; 5/12) and morbidity severe (85%; 11/12). All fatal injuries (5 cases) were venous. Anatomic knowledge and awareness of the possibility of vascular complications should be preventive. Early detection by routine checking of arterial circulation is important.
Effect of mid‐late mouse fetus' microenvironment on the growth of tumor cells after intrauterine transplantation
Authors: Ma Fang , Zhou Lan , Fang Liao‐Qiong , Bai Jin , Zhao Jie , Wang Yuan , Wang Zhi‐Biao 
Published: December 2006

AbstractSuccessful intrauterine transplantation (IUT) of stem cells for treatment of fetal defects in some animal models of human diseases has prompted us to study the mechanisms of transplantation, immunological tolerance and embryonic environment. The objective of this study was to determine whether intrauterine transplantation of tumor cells would affect the survival and growth of the tumor cells themselves as well as fetus development. A total of 2 × 106 H22 cells or S180 cells were transplanted into the amniotic or abdominal cavity of NIH mice on D9–D12 or D13–D18 of gestation. The adult and newborn NIH mice which were inoculated with the same number of H22 cells and S180 cells by intraperitoneal injection were used as positive controls for the cancer bearing control group while undisrupted fetuses of the same gestation were used as negative controls (i.e. for the normal development) group. The development of fetuses transplanted with tumor cells in utero was monitored by several developmental indices, and the tumor growth of them were observed by some distinctive bearing cancer index. The H22 transplanted group was further assessed for minimal cancer bearing by detection of alpha‐fetoprotein (AFP) using radioimmunoassay (RIA) and reverse transcription‐polymerase chain reaction (RT‐PCR). In addition, tumor burden and the development of the F1 generation of the mice by IUT were also investigated. Protein kinase C (PKC) and proliferating cell nuclear antigen (PCNA) of GFP‐expressing H22 cells transplanted in the uterus were analyzed under laser confocal microscopy. There was no significant difference in the developmental indices between the experimental and control groups. HE staining of the major organs, including liver, kidney, and lung, showed that these organs properly developed. No tumor ascites were found in those delivered mice after intrauterine transplantation with H22 cells and S180 cells. Furthermore, as minimal bearing cancer index for H22 cells, AFP expression analyzed by RIA and RT‐PCR indicated that no tumor cells were detected in the experimental groups. The F1 progenies developed normally without any signs of tumor development. Fluorescence analysis revealed that expression of PKC and PCNA was markedly reduced in the H22 cells after injection for 24, 48, and 72 h. Our study showed that the tumor cells did not grow in the mice by intrauterine transplantation, whereas transplantation of the same number of tumor cells resulted in obvious ascites tumor in the adult and newborn mice. Furthermore, the differentiation and proliferation of H22 cells changed dramatically after injection. Our results suggest that, while the embryonic transplantation of tumor cells does not affect fetal development, the survival and growth of implanted tumor cells may be significantly inhibited in the embryonic microenvironment.
The Rice Kinase Database. A Phylogenomic Database for the Rice Kinome
Authors: Dardick Christopher , Chen Johann , Richter Todd , Ouyang Shu , Ronald Pamela 
Published: December 2006

Abstract
The rice (Oryza sativa) genome contains 1,429 protein kinases, the vast majority of which have unknown functions. We created a phylogenomic database (http://rkd.ucdavis.edu) to facilitate functional analysis of this large gene family. Sequence and genomic data, including gene expression data and protein-protein interaction maps, can be displayed for each selected kinase in the context of a phylogenetic tree allowing for comparative analysis both within and between large kinase subfamilies. Interaction maps are easily accessed through links and displayed using Cytoscape, an open source software platform. Chromosomal distribution of all rice kinases can also be explored via an interactive interface.
Saponin Biosynthesis in Saponaria vaccaria. cDNAs Encoding β-Amyrin Synthase and a Triterpene Carboxylic Acid Glucosyltransferase
Authors: Meesapyodsuk Dauenpen , Balsevich John , Reed Darwin W. , Covello Patrick S. 
Published: December 2006

Abstract
Saponaria vaccaria (Caryophyllaceae), a soapwort, known in western Canada as cowcockle, contains bioactive oleanane-type saponins similar to those found in soapbark tree (Quillaja saponaria; Rosaceae). To improve our understanding of the biosynthesis of these saponins, a combined polymerase chain reaction and expressed sequence tag approach was taken to identify the genes involved. A cDNA encoding a β-amyrin synthase (SvBS) was isolated by reverse transcription-polymerase chain reaction and characterized by expression in yeast (Saccharomyces cerevisiae). The SvBS gene is predominantly expressed in leaves. A S. vaccaria developing seed expressed sequence tag collection was developed and used for the isolation of a full-length cDNA bearing sequence similarity to ester-forming glycosyltransferases. The gene product of the cDNA, classified as UGT74M1, was expressed in Escherichia coli, purified, and identified as a triterpene carboxylic acid glucosyltransferase. UGT74M1 is expressed in roots and leaves and appears to be involved in monodesmoside biosynthesis in S. vaccaria.
A Comprehensive Analysis of the 14-3-3 Interactome in Barley Leaves Using a Complementary Proteomics and Two-Hybrid Approach
Authors: Schoonheim Peter J. , Veiga Helena , da Costa Pereira Daniel , Friso Giulia , van Wijk Klaas J. , de Boer Albertus H. 
Published: December 2006

Abstract
This study describes the identification of over 150 target proteins of the five 14-3-3 isoforms in 7-d-old barley (Hordeum vulgare) cv Himalaya seedlings using yeast two-hybrid screens complemented with 14-3-3 protein affinity purification and tandem mass spectrometry. Independent experiments for a subset of genes confirmed the yeast two-hybrid interactions, demonstrating a low false positive identification rate. These combined approaches resulted in the identification of more than 150 putative targets; 15% were previously reported to be 14-3-3 interactors, including, for example, Serpin, RF2A, WPK4 kinase, P-type proton-translocating adenosine triphosphatase, EF1A, glutamine synthetase, and invertases. The affinity purification resulted in 30 interactors, of which 44% function in metabolism, while the yeast two-hybrid screens identified 132 different proteins, with 35% of the proteins involved in signal transduction. A number of proteins have a well-described function in hormonal signaling, such as the auxin transport protein PIN1 and NPH3 and components of the brassinosteroid pathway, such as the receptor kinase BAK1 (OsPERK1) and BRI1-kinase domain-interacting protein 129. However, 14-3-3 interactions with these signal mediators have not been confirmed in the affinity purification. Confirmations of the 14-3-3 interaction with the three ABF-like transcription factors are shown using far western analysis. Also, a REPRESSION OF SHOOT GROWTH ortholog named RF2A was identified; these transcription factors play important roles in the abscisic acid and gibberellin pathways, respectively. We speculate that 14-3-3 proteins have a role in cross talk between these hormonal pathways. The specificity and complementary nature of both the affinity purification and the yeast two-hybrid approaches is discussed.
Nitrogen-Dependent Posttranscriptional Regulation of the Ammonium Transporter AtAMT1;1
Authors: Yuan Lixing , Loqué Dominique , Ye Fanghua , Frommer Wolf B. , von Wirén Nicolaus 
Published: December 2006

Abstract
Ammonium transporter (AMT) proteins of the AMT family mediate the transport of ammonium across plasma membranes. To investigate whether AMTs are regulated at the posttranscriptional level, a gene construct consisting of the cauliflower mosaic virus 35S promoter driving the Arabidopsis (Arabidopsis thaliana) AMT1;1 gene was introduced into tobacco (Nicotiana tabacum). Ectopic expression of AtAMT1;1 in transgenic tobacco lines led to high transcript levels and protein levels at the plasma membrane and translated into an approximately 30% increase in root uptake capacity for 15N-labeled ammonium in hydroponically grown transgenic plants. When ammonium was supplied as the major nitrogen (N) form but at limiting amounts to soil-grown plants, transgenic lines overexpressing AtAMT1;1 did not show enhanced growth or N acquisition relative to wild-type plants. Surprisingly, steady-state transcript levels of AtAMT1;1 accumulated to higher levels in N-deficient roots and shoots of transgenic tobacco plants in spite of expression being controlled by the constitutive 35S promoter. Moreover, steady-state transcript levels were decreased after addition of ammonium or nitrate in N-deficient roots, suggesting a role for N availability in regulating AtAMT1;1 transcript abundance. Nitrogen deficiency-dependent accumulation of AtAMT1;1 mRNA was also observed in 35S:AtAMT1;1-transformed Arabidopsis shoots but not in roots. Evidence for a regulatory role of the 3′-untranslated region of AtAMT1;1 alone in N-dependent transcript accumulation was not found. However, transcript levels of AtAMT1;3 did not accumulate in a N-dependent manner, even though the same T-DNA insertion line atamt1;1-1 was used for 35S:AtAMT1;3 expression. These results show that the accumulation of AtAMT1;1 transcripts is regulated in a N- and organ-dependent manner and suggest mRNA turnover as an additional mechanism for the regulation of AtAMT1;1 in response to the N nutritional status of plants.
An Integrated View of Gene Expression and Solute Profiles ofArabidopsisTumors: A Genome-Wide Approach
Authors: Deeken Rosalia , Engelmann Julia C. , Efetova Marina , Czirjak Tina , Müller Tobias , Kaiser Werner M. , Tietz Olaf , Krischke Markus , Mueller Martin J. , Palme Klaus , Dandekar Thomas , Hedrich Rainer 
Published: December 2006

AbstractTransformation of plant cells with T-DNA of virulent agrobacteria is one of the most extreme triggers of developmental changes in higher plants. For rapid growth and development of resulting tumors, specific changes in the gene expression profile and metabolic adaptations are required. Increased transport and metabolic fluxes are critical preconditions for growth and tumor development. A functional genomics approach, using the Affymetrix whole genome microarray (∼22,800 genes), was applied to measure changes in gene expression. The solute pattern of Arabidopsis thaliana tumors and uninfected plant tissues was compared with the respective gene expression profile. Increased levels of anions, sugars, and amino acids were correlated with changes in the gene expression of specific enzymes and solute transporters. The expression profile of genes pivotal for energy metabolism, such as those involved in photosynthesis, mitochondrial electron transport, and fermentation, suggested that tumors produce C and N compounds heterotrophically and gain energy mainly anaerobically. Thus, understanding of gene-to-metabolite networks in plant tumors promotes the identification of mechanisms that control tumor development.
The CauliflowerOrGene Encodes a DnaJ Cysteine-Rich Domain-Containing Protein That Mediates High Levels of β-Carotene Accumulation
Authors: Lu Shan , Van Eck Joyce , Zhou Xiangjun , Lopez Alex B. , O'Halloran Diana M. , Cosman Kelly M. , Conlin Brian J. , Paolillo Dominick J. , Garvin David F. , Vrebalov Julia , Kochian Leon V. , Küpper Hendrik , Earle Elizabeth D. , Cao Jun , Li Li 
Published: December 2006

AbstractDespite recent progress in our understanding of carotenogenesis in plants, the mechanisms that govern overall carotenoid accumulation remain largely unknown. The Orange (Or) gene mutation in cauliflower (Brassica oleracea var botrytis) confers the accumulation of high levels of β-carotene in various tissues normally devoid of carotenoids. Using positional cloning, we isolated the gene representing Or and verified it by functional complementation in wild-type cauliflower. Or encodes a plastid-associated protein containing a DnaJ Cys-rich domain. The Or gene mutation is due to the insertion of a long terminal repeat retrotransposon in the Or allele. Or appears to be plant specific and is highly conserved among divergent plant species. Analyses of the gene, the gene product, and the cytological effects of the Or transgene suggest that the functional role of Or is associated with a cellular process that triggers the differentiation of proplastids or other noncolored plastids into chromoplasts for carotenoid accumulation. Moreover, we demonstrate that Or can be used as a novel genetic tool to induce carotenoid accumulation in a major staple food crop. We show here that controlling the formation of chromoplasts is an important mechanism by which carotenoid accumulation is regulated in plants.
The Coactivator Function ofArabidopsisNPR1 Requires the Core of Its BTB/POZ Domain and the Oxidation of C-Terminal Cysteines
Authors: Rochon Amanda , Boyle Patrick , Wignes Tracy , Fobert Pierre R. , Després Charles 
Published: December 2006

AbstractNONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (NPR1) regulates systemic acquired resistance (SAR) in Arabidopsis thaliana, and current models propose that after treatment with salicylic acid (SA), Cys-82 and Cys-216 of NPR1 are reduced, leading to nuclear import. The interaction of nucleus-localized NPR1 with TGA transcription factors results in the activation of defense genes, including the SAR marker PATHOGENESIS-RELATED-1 (PR-1), and the deployment of SAR. Little is known about how TGA factors or NPR1 regulate transcription or whether a TGA-NPR1 complex forms on DNA. We show that TGA2 and NPR1 are recruited to PR-1 independently of each other and of SA treatment. Consistent with the result that a triple knockout in TGA2/5/6 derepresses PR-1, in vivo plant transcription assays revealed that TGA2 is not an autonomous transcription activator but is a transcriptional repressor in both untreated and SA-treated cells. However, after stimulation with SA, TGA2 is incorporated into a transactivating complex with NPR1, forming an enhanceosome that requires the core of the NPR1 BTB/POZ domain (residues 80 to 91) and the oxidation of NPR1 Cys-521 and Cys-529. These Cys residues are found in a new type of transactivation domain that we term Cys-oxidized. These data further our understanding of the mechanism by which TGA2 and NPR1 activate Arabidopsis PR-1.