bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel molecular targeted therapy for esophageal cancer
Authors: Schrump David S. , Nguyen Dao M. 
Published: November 2005

AbstractEsophageal cancers are highly lethal neoplasms which are generally refractory to conventional multidisciplinary interventions. Recent elucidation of the mechanisms of esophageal carcinogenesis, as well as preclinical studies utilizing chromatin remodeling agents and inhibitors of oncogene signaling in conjunction with conventional chemotherapeutic agents provide new opportunities for the development of potentially efficacious molecular targeted therapies for these malignancies. J. Surg. Oncol. 2005;92:257–261. © 2005 Wiley‐Liss, Inc.
Improving outcomes after esophagectomy: The impact of operative volume
Authors: Casson Alan G. , van Lanschot J. Jan B. 
Published: November 2005

AbstractOnce considered an uncommon malignancy, primary esophageal adenocarcinoma has increased steadily in incidence over the past three decades. Despite advances in multimodality therapy, the prognosis for this tumor is generally poor. Surgical resection and reconstruction of the upper gastrointestinal tract is the current standard of care for localized esophageal cancer, but despite advances in perioperative care, still remains a relatively high‐risk surgical procedure. Increasing numbers of reports published over the past decade have documented a clear volume‐outcome relationship for several complex surgical procedures, and in particular for esophagectomy. The clinical implications of this association are reviewed in this section. J. Surg. Oncol. 2005;92:262–266. © 2005 Wiley‐Liss, Inc.
Novel Supramolecular Polymers Based on Zinc‐Salen Chromophores for Efficient Light‐Emitting Diodes
Authors: Peng Qiang , Xie Minggui , Huang Yan , Lu Zhiyun , Cao Yong 
Published: November 2005

AbstractSummary: A novel series of supramolecular polymers based on zinc‐salen chromophores were readily prepared via ligand‐metal coordination. These polymers were characterized by FT‐IR, NMR, GPC and elemental analysis. All the polymers were readily soluble in common organic solvents and had substantially good thermal properties. Cyclic voltammetry revealed they had LUMO energy levels ranging from −3.20 to −3.23 eV and HOMO energy levels ranging from −6.13 to −6.15 eV. The polymer films can emit strong green photoluminescence (PL) with relatively high quantum efficiencies of 42–51%. Light‐emitting diodes with the configuration ITO/PEDOT/polymer/BCP/Alq3/LiF/Al were efficient green emitters, with maximum current efficiencies of 0.9–2.3 cd · A−1. The preliminary EL results thus suggest that these polymers are potential candidates for efficient green emission in polymer LEDs.Structures of polymers produced.magnified imageStructures of polymers produced.
Diffusion behavior in polymer–clay nanocomposites
Authors: Sorrentino A. , Tortora M. , Vittoria V. 
Published: November 2005

AbstractThis paper reviews our previous studies on the diffusion behavior in polymers clay nanocomposites. A geometric model for predicting the effective diffusivity through this type of systems as a function of clay sheets orientation, volume fraction, polymer clay interaction, and aspect ratio is proposed. Model predictions are compared to the effective diffusivity generated using random walk simulations as well as with predictions obtained from already existing theoretical models. Fair agreement is found between the model prediction and the results of numerical simulations. With respect to the already existing theoretical models, the present mathematical derivation seems more adequate to describe diffusion behavior in conventional nanocomposites systems (i.e. when fillers present very low values of volume to surface ratio). Experimental diffusion tests are discussed and interpreted with the aid of the proposed model. In addition to the aspect ratio and clay concentration, the polymer clay interactions as well as the sheets orientation are the factors controlling the barrier properties of polymer‐layered silicate nanocomposites. Good agreement was found in the case of samples containing exfoliated clay, whereas the model fails in the case of micro‐composites, in which the inorganic lamellae are agglomerated in clusters. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 265–274, 2006
Methyl dynamics for understanding hydrophobic core packing of dynamically different motifs of double‐stranded RNA binding domain of protein kinase R
Authors: Barnwal Ravi P. , Chaudhuri Tista R. , Nanduri S. , Qin J. , Chary K.V.R. 
Published: November 2005

AbstractDouble‐stranded RNA binding domains of human protein kinase R (dsRBD‐PKR) regulate distinct cellular functions and the fate of an RNA molecule in the cell. This highly homologous domains present in multiple copies in a number of species, exhibit individual and specific functional specificity. Number of NMR and X‐ray crystallographic structural studies reveals that such domains take a common α‐β‐β‐β‐α tertiary fold. However, the functional specificities of these domains could be due to the dynamics of the individual amino acid residues, as has been shown earlier in the case of backbone dynamics of 15N‐1H of dsRNA binding motifs (dsRBMs) of human protein kinase R (PKR) (Nanduri S, Rahman F, Williams BRG, Qin J. EMBO J 2000;19:5567–5574). To further investigate if the differences in dynamics of the two dsRBMs are restricted to only backbone, or if the side‐chain motions are also different to the extent of influencing their packing of the two hydrophobic cores, we have investigated the methyl group dynamics using 13C‐methyl relaxation measurements. The results show that the hydrophobic core of dsRBM1 is more tightly packed than dsRBM2, and it seems to undergo less fast scale motions in the subnanosecond regime. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Role of extracellular signal‐regulated protein kinase and phosphatidylinositol 3‐kinase in neuronal cell death and survival
Authors: Thiel Gerald , Bauer Inge , Rössler Oliver G. 
Published: November 2005

AbstractThe survival of neurons requires, at some point, the presence of neurotrophic factors and depends on competition for a limited supply of survival factors. The neurotrophin brain‐derived neurotrophic factor (BDNF) is the ligand for the TrkB neurotrophin receptor, the most abundant Trk receptor in the brain. Two key signaling pathways are induced following binding of BDNF to its cognate receptor that are characterized by the activation of extracellular signal‐regulated protein kinase (ERK) and phosphatidylinositol 3‐kinase (PI3 kinase). Many reports have assigned a cellular survival function to the activation of ERK and/or PI3 kinase, in line with the reported neuroprotective activity of neurotrophin receptor activation. The activation of PI3 kinase by BDNF represents the dominant survival pathway, whereas the ERK signaling pathway has no or only a marginal role. However, a sustained activation of ERK, lasting for several hours, protects neurons from growth factor deprivation‐induced cell death, indicating that the duration of ERK activation is of major importance for its neuroprotective biological function. The activation of ERK and PI3 kinase does not provide protection against oxidative glutamate toxicity. Thus, the biochemical events underlying neuronal cell death induction by the lack of trophic support or via oxidative stress are distinct.
Sex differences in cardiac and autonomic response to clinical and experimental pain in LBP patients
Authors: Tousignant‐Laflamme Yannick , Marchand Serge 
Published: November 2005

AbstractRehabilitation professionals are currently using heart rate (HR) in order to assess the sincerity of effort in certain evaluations. It has been shown that a relation exists between HR and pain but no study has measured cardiac response during both clinical and experimental pain among a patient population using an intra‐subject design. Thirty patients with low back pain (LBP) participated in this study including 16 men. Clinical pain was induced by applying a postero‐anterior pressure (PA) on a painful lumbar segment for 15 and 30 s in order to reproduce the patient's typical LBP at an intensity ranging between 50 and 70/100. Experimental pain was induced with a 15 s thermal stimulus at a temperature which reproduced the same pain intensity as the 15 s PA. For both reproduced clinical pain durations, we observed a rise in HR ranging between 8.5% and 12.67%. However, unlike men, women's cardiac response failed to show a constant rise in HR during the 30 s PA. For all subjects, the rise in HR was much lower during the experimental pain condition (p < 0.001), reaching only 5%. On the other hand, galvanic skin responses were significantly higher during the experimental pain condition (p < 0.001). During this same condition, women also had a greater rise in galvanic skin responses than men (p = 0.04). Finally, a significant correlation was found between both types of pain. These results suggest that pain induced during a clinical evaluation will produce a significant HR augmentation. However, heart rate variability analysis showed greater sympathetic cardiac regulation for men. The sex differences observed in this study call for caution when interpreting HR during pain assessment.
Combining indicator trends to assess ongoing changes in exploited fish communities: diagnostic of communities off the coasts of France
Authors: Rochet Marie-Joëlle , Trenkel Verena , Bellail Robert , Coppin Franck , Le Pape Olivier , Mahé Jean-Claude , Morin Jocelyne , Poulard Jean-Charles , Schlaich Ivan , Souplet Arnauld , Vérin Yves , Bertrand Jacques 
Published: November 2005

Abstract
We present a method for combining individual indicator results into a comprehensive diagnostic of fishing impacts on fish populations and communities. A conceptual framework for interpreting combined trends in a set of simple indicators is proposed, relying beforehand on qualitative expectations anchored in ecological theory. The initial state of the community is first assessed using published information. Which combinations of trends are acceptable or undesirable is decided, depending on the initial status. The indicators are then calculated from a time-series and their time trends are estimated as the slopes of linear models. Finally, the test results are combined within the predefined framework, providing a diagnostic on the dynamics of fishing impacts on populations and communities. The method is demonstrated for nine coastal and shelf-sea fish communities monitored by French surveys. Most communities were persistently or increasingly impacted by fishing. In addition, climate change seems to have contributed to changes in East Atlantic communities.
Cet article propose une méthode utilisant des indicateurs pour élaborer un diagnostic sur les effets de la pêche sur les populations et les peuplements de poissons. Un cadre conceptuel permet d'interpréter les tendances conjointes d'indicateurs à partir de la théorie écologique. L'état initial du peuplement est d'abord évalué sur la base d'informations publiées. En fonction de l'état initial et des objectifs de gestion, les combinaisons des tendances sont qualifiées d'indésirables ou satisfaisantes. Les indicateurs sont ensuite estimés à partir de données de campagnes de pêches scientifiques: abondance et longueur moyenne d'une sélection de populations, nombre, biomasse totale, poids moyen et longueur moyenne dans le peuplement, et la pente du spectre de taille multispécifique. Les tendances temporelles de ces indicateurs sont testées au moyen d'un modèle linéaire, et les résultats des tests sont combinés en un diagnostic final. La méthode est mise en œuvre pour neuf peuplements de poissons côtiers et du plateau continental, suivis par des campagnes françaises. Il en résulte que la plupart de ces peuplements sont affectés par la pêche de manière stationnaire ou croissante. Par ailleurs, les changements climatiques dans l'Atlantique Nord-Est contribuent aussi à des modifications dans les peuplements de poissons de cette région.
Suicidal behaviour among primary-care patients with depressive disorders
Authors: VUORILEHTO M. S. , MELARTIN T. K. , ISOMETSÄ E. T. 
Published: November 2005

Background. Most national suicide prevention strategies set improved detection and management of depression in primary health care into a central position. However, suicidal behaviour among primary-care patients with depressive disorders has been seldom investigated.Method. In the Vantaa Primary Care Depression Study, a total of 1119 primary-care patients in the City of Vantaa, Finland, aged 20 to 69 years, were screened for depression with the Primary Care Evaluation of Mental Disorders (PRIME-MD) questionnaire. Depressive disorders were diagnosed with the Structured Clinical Interview for DSM-IV Axis I Disorders (SCID-I), and the 137 patients with depressive disorder were included in the study. Suicidal behaviour was investigated cross-sectionally and retrospectively in three time-frames: current, current depressive episode, and lifetime. Current suicidal ideation was measured with the Scale for Suicidal Ideation (SSI), and previous ideation and suicide attempts were evaluated based on interviews plus medical and psychiatric records.Results. Within their lifetimes, 37% (51/137) of the patients had seriously considered suicide and 17% (23/137) attempted it. Lifetime suicidal behaviour was independently and strongly predicted by psychiatric treatment history and co-morbid personality disorder, and suicidal behaviour within the current episode was predicted most effectively by severity of depression.Conclusions. Based on these findings and their convergence with studies of completed suicides, prevention of suicidal behaviour in primary care should probably focus more on high-risk subgroups of depressed patients, including those with moderate to severe major depressive disorder, personality disorder or a history of psychiatric care. Recognition of suicidal behaviour should be improved. The complex psychopathology of these patients in primary care needs to be considered in targeting preventive efforts.
Modeling genome evolution with a diffusion approximation of a birth-and-death process
Authors: Karev Georgy P. , Berezovskaya Faina S. , Koonin Eugene V. 
Published: November 2005

Abstract
Motivation: In our previous studies, we developed discrete-space birth, death and innovation models (BDIMs) of genome evolution. These models explain the origin of the characteristic Pareto distribution of paralogous gene family sizes in genomes, and model parameters that provide for the evolution of these distributions within a realistic time frame have been identified. However, extracting the temporal dynamics of genome evolution from discrete-space BDIM was not technically feasible. We were interested in obtaining dynamic portraits of the genome evolution process by developing a diffusion approximation of BDIM.
Results: The diffusion version of BDIM belongs to a class of continuous-state models whose dynamics is described by the Fokker–Plank equation and the stationary solution could be any specified Pareto function. The diffusion models have time-dependent solutions of a special kind, namely, generalized self-similar solutions, which describe the transition from one stationary distribution of the system to another; this provides for the possibility of examining the temporal dynamics of genome evolution. Analysis of the generalized self-similar solutions of the diffusion BDIM reveals a biphasic curve of genome growth in which the initial, relatively short, self-accelerating phase is followed by a prolonged phase of slow deceleration. This evolutionary dynamics was observed both when genome growth started from zero and proceeded via innovation (a potential model of primordial evolution), and when evolution proceeded from one stationary state to another. In biological terms, this regime of evolution can be tentatively interpreted as a punctuated-equilibrium-like phenomenon whereby evolutionary transitions are accompanied by rapid gene amplification and innovation, followed by slow relaxation to a new stationary state.
Contact: koonin@ncbi.nlm.nih.gov
Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics
Authors: Collyn F. , Guy L. , Marceau M. , Simonet M. , Roten C.-A. H. 
Published: November 2005

AbstractMotivation: Lateral gene transfer is a major mechanism contributing to bacterial genome dynamics and pathovar emergence via pathogenicity island (PAI) spreading. However, since few of these genomic exchanges are experimentally reproducible, it is difficult to establish evolutionary scenarios for the successive PAI transmissions between bacterial genera. Methods initially developed at the gene and/or nucleotide level for genomics, i.e. comparisons of concatenated sequences, ortholog frequency, gene order or dinucleotide usage, were combined and applied here to homologous PAIs: we call this approach comparative PAI genometrics.Results: YAPI, a Yersinia PAI, and related islands were compared with measure evolutionary relationships between related modules. Through use of our genometric approach designed for tracking codon usage adaptation and gene phylogeny, an ancient inter-genus PAI transfer was oriented for the first time by characterizing the genomic environment in which the ancestral island emerged and its subsequent transfers to other bacterial genera.Contact: claude-alain.roten@unil.chSupplementary information:
Evaluation of the Antimicrobial Activities of Plant Oxylipins Supports Their Involvement in Defense against Pathogens
Authors: Prost Isabelle , Dhondt Sandrine , Rothe Grit , Vicente Jorge , Rodriguez Maria José , Kift Neil , Carbonne Francis , Griffiths Gareth , Esquerré-Tugayé Marie-Thérèse , Rosahl Sabine , Castresana Carmen , Hamberg Mats , Fournier Joëlle 
Published: November 2005

Abstract
Plant oxylipins are a large family of metabolites derived from polyunsaturated fatty acids. The characterization of mutants or transgenic plants affected in the biosynthesis or perception of oxylipins has recently emphasized the role of the so-called oxylipin pathway in plant defense against pests and pathogens. In this context, presumed functions of oxylipins include direct antimicrobial effect, stimulation of plant defense gene expression, and regulation of plant cell death. However, the precise contribution of individual oxylipins to plant defense remains essentially unknown. To get a better insight into the biological activities of oxylipins, in vitro growth inhibition assays were used to investigate the direct antimicrobial activities of 43 natural oxylipins against a set of 13 plant pathogenic microorganisms including bacteria, oomycetes, and fungi. This study showed unequivocally that most oxylipins are able to impair growth of some plant microbial pathogens, with only two out of 43 oxylipins being completely inactive against all the tested organisms, and 26 oxylipins showing inhibitory activity toward at least three different microbes. Six oxylipins strongly inhibited mycelial growth and spore germination of eukaryotic microbes, including compounds that had not previously been ascribed an antimicrobial activity, such as 13-keto-9(Z),11(E),15(Z)-octadecatrienoic acid and 12-oxo-10,15(Z)-phytodienoic acid. Interestingly, this first large-scale comparative assessment of the antimicrobial effects of oxylipins reveals that regulators of plant defense responses are also the most active oxylipins against eukaryotic microorganisms, suggesting that such oxylipins might contribute to plant defense through their effects both on the plant and on pathogens, possibly through related mechanisms.
A Wound-Responsive and Phospholipid-Regulated Maize Calcium-Dependent Protein Kinase
Authors: Szczegielniak Jadwiga , Klimecka Maria , Liwosz Aneta , Ciesielski Arkadiusz , Kaczanowski Szymon , Dobrowolska Grażyna , Harmon Alice C. , Muszyńska Grażyna 
Published: November 2005

Abstract
Using protein sequence data obtained from a calcium- and phospholipid-regulated protein kinase purified from maize (Zea mays), we isolated a cDNA encoding a calcium-dependent protein kinase (CDPK), which we designated ZmCPK11. The deduced amino acid sequence of ZmCPK11 includes the sequences of all the peptides obtained from the native protein. The ZmCPK11 sequence contains the kinase, autoregulatory, and calmodulin-like domains typical of CDPKs. Transcripts for ZmCPK11 were present in every tested organ of the plant, relatively high in seeds and seedlings and lower in stems, roots, and leaves. In leaves, kinase activity and ZmCPK11 mRNA accumulation were stimulated by wounding. The level of ZmCPK11 is also increased in noninjured neighboring leaves. The results suggest that the maize protein kinase is involved in a systemic response to wounding. Bacterially expressed glutathione S-transferase (GST)-ZmCPK11 was catalytically active in a calcium-dependent manner. Like the native enzyme, GST-ZmCPK11 was able to phosphorylate histone III-S and Syntide 2. Phosphorylation of histone was stimulated by phosphatidylserine, phosphatidylinositol, and phosphatidic acid, whereas phosphatidylcholine, lysophosphatidylcholine, phosphatidylethanolamine, diolein, and cardiolipin did not increase the enzymatic activity. Autophosphorylation of GST-ZmCPK11 was stimulated by calcium and by phosphatidic acid and, to a lesser extent, by phosphatidylserine. Phosphatidylcholine did not affect autophosphorylation. These data unequivocally identify the maize phospholipid- and calcium-regulated protein kinase, which has protein kinase C-like activity, as a CDPK, and emphasize the potential that other CDPKs are regulated by phospholipids in addition to calcium.
Sucrose-Specific Induction of Anthocyanin Biosynthesis in Arabidopsis Requires the MYB75/PAP1 Gene
Authors: Teng Sheng , Keurentjes Joost , Bentsink Leónie , Koornneef Maarten , Smeekens Sjef 
Published: November 2005

Abstract
Sugar-induced anthocyanin accumulation has been observed in many plant species. We observed that sucrose (Suc) is the most effective inducer of anthocyanin biosynthesis in Arabidopsis (Arabidopsis thaliana) seedlings. Other sugars and osmotic controls are either less effective or ineffective. Analysis of Suc-induced anthocyanin accumulation in 43 Arabidopsis accessions shows that considerable natural variation exists for this trait. The Cape Verde Islands (Cvi) accession essentially does not respond to Suc, whereas Landsberg erecta is an intermediate responder. The existing Landsberg erecta/Cvi recombinant inbred line population was used in a quantitative trait loci analysis for Suc-induced anthocyanin accumulation (SIAA). A total of four quantitative trait loci for SIAA were identified in this way. The locus with the largest contribution to the trait, SIAA1, was fine mapped and using a candidate gene approach, it was shown that the MYB75/PAP1 gene encodes SIAA1. Genetic complementation studies and analysis of a laboratory-generated knockout mutation in this gene confirmed this conclusion. Suc, in a concentration-dependent way, induces MYB75/PAP1 mRNA accumulation. Moreover, MYB75/PAP1 is essential for the Suc-mediated expression of the dihydroflavonol reductase gene. The SIAA1 locus in Cvi probably is a weak or loss-of-function MYB75/PAP1 allele. The C24 accession similarly shows a very weak response to Suc-induced anthocyanin accumulation encoded by the same locus. Sequence analysis showed that the Cvi and C24 accessions harbor mutations both inside and downstream of the DNA-binding domain of the MYB75/PAP1 protein, which most likely result in loss of activity.