Showing papers by "Ghent University published in 2007"
TL;DR: 2007 Guidelines for the Management of Arterial Hypertension : The Task Force for the management of Arterspertension of the European Society ofhypertension (ESH) and of theEuropean Society of Cardiology (ESC).
Abstract: 2007 Guidelines for the Management of Arterial Hypertension : The Task Force for the Management of Arterial Hypertension of the European Society of Hypertension (ESH) and of the European Society of Cardiology (ESC).
9,932 citations
TL;DR: It is concluded that ANI can accurately replace DDH values for strains for which genome sequences are available and reveal extensive gene diversity within the current concept of "species".
Abstract: DNA-DNA hybridization (DDH) values have been used by bacterial taxonomists since the 1960s to determine relatedness between strains and are still the most important criterion in the delineation of bacterial species. Since the extent of hybridization between a pair of strains is ultimately governed by their respective genomic sequences, we examined the quantitative relationship between DDH values and genome sequence-derived parameters, such as the average nucleotide identity (ANI) of common genes and the percentage of conserved DNA. A total of 124 DDH values were determined for 28 strains for which genome sequences were available. The strains belong to six important and diverse groups of bacteria for which the intra-group 16S rRNA gene sequence identity was greater than 94 %. The results revealed a close relationship between DDH values and ANI and between DNA-DNA hybridization and the percentage of conserved DNA for each pair of strains. The recommended cut-off point of 70 % DDH for species delineation corresponded to 95 % ANI and 69 % conserved DNA. When the analysis was restricted to the protein-coding portion of the genome, 70 % DDH corresponded to 85 % conserved genes for a pair of strains. These results reveal extensive gene diversity within the current concept of "species". Examination of reciprocal values indicated that the level of experimental error associated with the DDH method is too high to reveal the subtle differences in genome size among the strains sampled. It is concluded that ANI can accurately replace DDH values for strains for which genome sequences are available.
3,471 citations
TL;DR: This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest.
Abstract: Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules and (v) identifying enriched Gene Ontology annotations in the network. These steps provide a broad sample of the types of analyses performed by Cytoscape.
2,313 citations
TL;DR: Authors/Task Force Members: Giuseppe Mancia, co-Chairperson (Italy), Guy De Backer, Co-Chair person (Belgium), Anna Dominiczak (UK), Renata Cifkova (Czech Republic), Robert Fagard (Belgian), Giuseppi Germano (Italy) and Guido Grassi (Italy).
Abstract: Authors/Task Force Members: Giuseppe Mancia, Co-Chairperson (Italy), Guy De Backer, Co-Chairperson (Belgium), Anna Dominiczak (UK), Renata Cifkova (Czech Republic), Robert Fagard (Belgium), Giuseppe Germano (Italy), Guido Grassi (Italy), Anthony M. Heagerty (UK), Sverre E. Kjeldsen (Norway), Stephane Laurent (France), Krzysztof Narkiewicz (Poland), Luis Ruilope (Spain), Andrzej Rynkiewicz (Poland), Roland E. Schmieder (Germany), Harry A.J. Struijker Boudier (Netherlands), Alberto Zanchetti (Italy)
1,992 citations
TL;DR: The current state of scientific evidence for the individual components of the fear-avoidance model: pain severity, pain catastrophizing, attention to pain, escape/avoidance behavior, disability, disuse, and vulnerabilities is reviewed.
Abstract: Research studies focusing on the fear-avoidance model have expanded considerably since the review by Vlaeyen and Linton (Vlaeyen J. W. S. & Linton, S. J. (2000). Fear-avoidance and its consequences in chronic musculoskeletal pain: a state of the art. Pain, 85(3), 317--332). The fear-avoidance model is a cognitive-behavioral account that explains why a minority of acute low back pain sufferers develop a chronic pain problem. This paper reviews the current state of scientific evidence for the individual components of the model: pain severity, pain catastrophizing, attention to pain, escape/avoidance behavior, disability, disuse, and vulnerabilities. Furthermore, support for the contribution of pain-related fear in the inception of low back pain, the development of chronic low back pain from an acute episode, and the maintenance of enduring pain, will be highlighted. Finally, available evidence on recent clinical applications is provided, and unresolved issues that need further exploration are discussed.
1,900 citations
TL;DR: The 2006 KDIGO Controversies Conference on CKD was convened to consider six major topics: CKD classification, CKD screening and surveillance, public policy for CKD, CVD and CVD risk factors as risk factors for development and progression of CKd, association of CKD with chronic infections, and (6) association of CJD with cancer.
1,316 citations
DSM1, Delft University of Technology2, University of Nottingham3, Technical University of Denmark4, Wageningen University and Research Centre5, University of Sheffield6, Utrecht University7, Biomax Informatics AG8, CLC bio9, University of Liverpool10, Ghent University11, University of Manchester12, University of Provence13, University of Groningen14, Pasteur Institute15, University of Amsterdam16, University of Angers17, Leiden University18, Radboud University Nijmegen19, University of Szeged20
TL;DR: The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid, and the sequenced genome revealed a large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors.
Abstract: The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis.
1,161 citations
TL;DR: It is concluded that uncertainty assessment is not just something to be added after the completion of the modelling work, but should be seen as a red thread throughout the modelling study starting from the very beginning.
Abstract: A terminology and typology of uncertainty is presented together with a framework for the modelling process, its interaction with the broader water management process and the role of uncertainty at different stages in the modelling processes. Brief reviews have been made of 14 different (partly complementary) methods commonly used in uncertainty assessment and characterisation: data uncertainty engine (DUE), error propagation equations, expert elicitation, extended peer review, inverse modelling (parameter estimation), inverse modelling (predictive uncertainty), Monte Carlo analysis, multiple model simulation, NUSAP, quality assurance, scenario analysis, sensitivity analysis, stakeholder involvement and uncertainty matrix. The applicability of these methods has been mapped according to purpose of application, stage of the modelling process and source and type of uncertainty addressed. It is concluded that uncertainty assessment is not just something to be added after the completion of the modelling work. Instead uncertainty should be seen as a red thread throughout the modelling study starting from the very beginning, where the identification and characterisation of all uncertainty sources should be performed jointly by the modeller, the water manager and the stakeholders.
1,112 citations
TL;DR: A high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir provides candidate genes implicated in traits relevant to grapevine cultivation, such as those influencing wine quality, via secondary metabolites, and those connected with the extreme susceptibility of grape to pathogens.
Abstract: Background. Worldwide, grapes and their derived products have a large market. The cultivated grape species Vitis vinifera has potential to become a model for fruit trees genetics. Like many plant species, it is highly heterozygous, which is an additional challenge to modern whole genome shotgun sequencing. In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented. Principal Findings. We estimate the genome size of V. vinifera to be 504.6 Mb. Genomic sequences corresponding to 477.1 Mb were assembled in 2,093 metacontigs and 435.1 Mb were anchored to the 19 linkage groups (LGs). The number of predicted genes is 29,585, of which 96.1% were assigned to LGs. This assembly of the grape genome provides candidate genes implicated in traits relevant to grapevine cultivation, such as those influencing wine quality, via secondary metabolites, and those connected with the extreme susceptibility of grape to pathogens. Single nucleotide polymorphism (SNP) distribution was consistent with a diffuse haplotype structure across the genome. Of around 2,000,000 SNPs, 1,751,176 were mapped to chromosomes and one or more of them were identified in 86.7% of anchored genes. The relative age of grape duplicated genes was estimated and this made possible to reveal a relatively recent Vitisspecific large scale duplication event concerning at least 10 chromosomes (duplication not reported before). Conclusions. Sanger shotgun sequencing and highly efficient sequencing by synthesis (SBS), together with dedicated assembly programs, resolved a complex heterozygous genome. A consensus sequence of the genome and a set of mapped marker loci were generated. Homologous chromosomes of Pinot Noir differ by 11.2% of their DNA (hemizygous DNA plus chromosomal gaps). SNP markers are offered as a tool with the potential of introducing a new era in the molecular breeding of grape.
1,005 citations
TL;DR: Adopting a theoretically based approach, it is shown for three languages that four dimensions are needed to satisfactorily represent similarities and differences in the meaning of emotion words.
Abstract: For more than half a century, emotion researchers have attempted to establish the dimensional space that most economically accounts for similarities and differences in emotional experience. Today, many researchers focus exclusively on two-dimensional models involving valence and arousal. Adopting a theoretically based approach, we show for three languages that four dimensions are needed to satisfactorily represent similarities and differences in the meaning of emotion words. In order of importance, these dimensions are evaluation-pleasantness, potency-control, activation-arousal, and unpredictability. They were identified on the basis of the applicability of 144 features representing the six components of emotions: (a) appraisals of events, (b) psychophysiological changes, (c) motor expressions, (d) action tendencies, (e) subjective experiences, and (f) emotion regulation.
963 citations
TL;DR: Three different uses of a recurrent neural network as a reservoir that is not trained but instead read out by a simple external classification layer are compared and a new measure for the reservoir dynamics based on Lyapunov exponents is introduced.
Bradley University1, University of Tartu2, National Institutes of Health3, University of California4, Pontifical Catholic University of Chile5, University of Louisville6, University of Latvia7, Pennsylvania State University8, Slovak Academy of Sciences9, University of San Carlos10, University of Malta11, Ghent University12, Clemson University13, Laval University14, University of Buenos Aires15, Osaka University16, Illinois State University17, National Autonomous University of Mexico18, University of Brasília19, University of Western Australia20, University of Lima21, Boğaziçi University22, University of Kassel23, York University24, University of Queensland25, Åbo Akademi University26, Al Akhawayn University27, University of Hawaii at Manoa28, University of Catania29, University of Otago30, University of Dhaka31, Chemnitz University of Technology32, Knox College33, Comenius University in Bratislava34, University of Rijeka35, University of Malaya36, Vilnius University37, American University of Beirut38, Kwangju Health College39, University of Salzburg40, Utrecht University41, National Computerization Agency42, City University of Hong Kong43, University of Idaho44, University of Zimbabwe45, University of Lisbon46, University of Central Lancashire47, Loyola Marymount University48, University of KwaZulu-Natal49, University of Granada50, University of Botswana51, Babeș-Bolyai University52, University of Cyprus53, University of Belgrade54, KPMG55, University of Montpellier56, University of Zurich57, University of Alabama58, Baylor University59, Queen's University Belfast60, University of Ljubljana61, University of Haifa62, University of La Serena63, Florida Atlantic University64, University of California, Davis65, University of Dar es Salaam66, Ramapo College67, Cyprus College68, Middle East Technical University69, Nicolaus Copernicus University in Toruń70, University of the South Pacific71, Vrije Universiteit Brussel72, University at Albany, SUNY73, University of the Aegean74, University of Lethbridge75, University of Vienna76, University of Hong Kong77, Yuan Ze University78, Charles University in Prague79, Chonnam National University80, Indian Institutes of Technology81
TL;DR: The Big Five Inventory (BFI) is a self-report measure designed to assess the high-order personality traits of Extraversion, Agreeableness, Conscientiousness, Neuroticism, and Openness as discussed by the authors.
Abstract: The Big Five Inventory (BFI) is a self-report measure designed to assess the high-order personality traits of Extraversion, Agreeableness, Conscientiousness, Neuroticism, and Openness. As part of the International Sexuality Description Project, the BFI was translated from English into 28 languages and administered to 17,837 individuals from 56 nations. The resulting cross-cultural data set was used to address three main questions: Does the factor structure of the English BFI fully replicate across cultures? How valid are the BFI trait profiles of individual nations? And how are personality traits distributed throughout the world? The five-dimensional structure was robust across major regions of the world. Trait levels were related in predictable ways to self-esteem, sociosexuality, and national personality profiles. People from the geographic regions of South America and East Asia were significantly different in openness from those inhabiting other world regions. The discussion focuses on limitations of t...
TL;DR: The ability of the oncogene BMI1 to repress the INK4A-ARF locus requires its direct association and is dependent on the continued presence of the EZH2-containing Polycomb-Repressive Complex 2 (PRC2) complex.
Abstract: The p16INK4A and p14ARF proteins, encoded by the INK4A-ARF locus, are key regulators of cellular senescence, yet the mechanisms triggering their up-regulation are not well understood. Here, we show that the ability of the oncogene BMI1 to repress the INK4A-ARF locus requires its direct association and is dependent on the continued presence of the EZH2-containing Polycomb-Repressive Complex 2 (PRC2) complex. Significantly, EZH2 is down-regulated in stressed and senescing populations of cells, coinciding with decreased levels of associated H3K27me3, displacement of BMI1, and activation of transcription. These results provide a model for how the INK4A-ARF locus is activated and how Polycombs contribute to cancer.
TL;DR: The present document serves as a stand‐alone terminology update reflecting refinement and current advancement of knowledge on pediatric LUT function.
Abstract: Purpose: We updated the terminology in the field of pediatric lower urinary tract function. Materials and Methods: Discussions were held in the board of the International Children's Continence Society and an extensive reviewing process was done involving all members of the International Children's Continence Society, the urology section of the American Academy of Pediatrics, the European Society of Pediatric Urology, as well as other experts in the field. Results and Conclusions: New definitions and a standardized terminology are provided, taking into account changes in the adult sphere and new research results.
TL;DR: This work proposes a label-free biosensor based on microring cavities in Silicon-on-Insulator (SOI) that fits in an area below 10x10mum(2), and uses the avidin/biotin high affinity couple to demonstrate good repeatability and detection of protein concentrations down to 10ng/ml.
Abstract: Label-free biosensors attempt to overcome the stability and reliability problems of biosensors relying on the detection of labeled molecules We propose a label-free biosensor based on microring cavities in Silicon-on-Insulator (SOI) that fits in an area below 10x10mum(2) The resonance wavelength shift that occurs when the surroundings of a cavity is changed, is used for sensing While theoretically the performance for bulk refractive index changes is moderate (10(-5)), this device performs outstanding in terms of absolute molecular mass sensing (theoretical sensitivity of 1fg molecular mass) thanks to its extremely small dimensions We use the avidin/biotin high affinity couple to demonstrate good repeatability and detection of protein concentrations down to 10ng/ml Fabrication with Deep UV lithography allows for cheap mass production and integration with electronic functions for complete lab-on-chip devices
Newcastle University1, J. Craig Venter Institute2, University of Maryland, College Park3, University of Glasgow4, Technical University of Denmark5, University of Calgary6, Natural History Museum7, Ghent University8, University of Dundee9, University of Sassari10, University of California, Los Angeles11, Children's Hospital Oakland Research Institute12, Charles University in Prague13, University of Iowa14, University of Düsseldorf15, University of California, San Francisco16, University of Queensland17, QIMR Berghofer Medical Research Institute18, Chang Gung University19, University of Strathclyde20
TL;DR: The genome sequence of the protist Trichomonas vaginalis predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria.
Abstract: We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the similar to 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion, in conjunction with the shaping of metabolic pathways that likely transpired through lateral gene transfer from bacteria, and amplification of specific gene families implicated in pathogenesis and phagocytosis of host proteins may exemplify adaptations of the parasite during its transition to a urogenital environment. The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria.
TL;DR: It is shown that the effect of ethylene on root growth is largely mediated by the regulation of the auxin biosynthesis and transport-dependent local auxin distribution, and ethylene achieves a local activation of the Auxin signaling pathway and regulates root growth by both stimulating the aux in biosynthetic process and by modulating the auxIn transport machinery.
Abstract: In plants, each developmental process integrates a network of signaling events that are regulated by different phytohormones, and interactions among hormonal pathways are essential to modulate their effect. Continuous growth of roots results from the postembryonic activity of cells within the root meristem that is controlled by the coordinated action of several phytohormones, including auxin and ethylene. Although their interaction has been studied intensively, the molecular and cellular mechanisms underlying this interplay are unknown. We show that the effect of ethylene on root growth is largely mediated by the regulation of the auxin biosynthesis and transport-dependent local auxin distribution. Ethylene stimulates auxin biosynthesis and basipetal auxin transport toward the elongation zone, where it activates a local auxin response leading to inhibition of cell elongation. Consistently, in mutants affected in auxin perception or basipetal auxin transport, ethylene cannot activate the auxin response nor regulate the root growth. In addition, ethylene modulates the transcription of several components of the auxin transport machinery. Thus, ethylene achieves a local activation of the auxin signaling pathway and regulates root growth by both stimulating the auxin biosynthesis and by modulating the auxin transport machinery.
TL;DR: The periphyton treatment technique is applicable to extensive systems, and the proteinaceous bio-flocs technology can be used in extensive as well as in intensive systems, which provide an inexpensive feed source and a higher efficiency of nutrient conversion of feed.
University of California, San Diego1, Stanford University2, United States Department of Energy3, Ghent University4, University of Arizona5, University of California, Los Angeles6, Scripps Research Institute7, Centre national de la recherche scientifique8, University of Mainz9, University of Massachusetts Medical School10, J. Craig Venter Institute11, University of Maryland, College Park12
TL;DR: It is speculated that this latter process may be involved in altering the cell-surface characteristics of each species, and selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size.
Abstract: The smallest known eukaryotes, at ≈1-μm diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri. This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms acting differently on different chromosomes and likely including acquisition of new genes through horizontal gene transfer. We speculate that this latter process may be involved in altering the cell-surface characteristics of each species. In addition, the genome of O. lucimarinus provides insights into the unique metal metabolism of these organisms, which are predicted to have a large number of selenocysteine-containing proteins. Selenoenzymes are more catalytically active than similar enzymes lacking selenium, and thus the cell may require less of that protein. As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size.
TL;DR: This article found that holding an extrinsic, relative to an intrinsic, work value orientation was associated with less positive outcomes (i.e., less satisfaction with, dedication to and vitality while on the job) and more negative outcomes (e.g., higher emotional exhaustion, short-lived satisfaction after successful goal-attainment, and turn-over intention).
Abstract: Using self-determination theory, two studies found that holding an extrinsic, relative to an intrinsic, work value orientation was associated with less positive outcomes (i.e. less satisfaction with, dedication to and vitality while on the job) and more negative outcomes (i.e. higher emotional exhaustion, short-lived satisfaction after successful goal-attainment, and turn-over intention). These relations were not limited to job outcomes, but also emerged using indicators of employees' general mental health. Moreover, income level did not moderate these relations. Study 2 found that holding an extrinsic, relative to an intrinsic, work value orientation was detrimental to employees' job outcomes because these orientations thwarted the satisfaction of the basic psychological needs for autonomy, competence and relatedness at work.
National Institutes of Health1, University of Pavia2, Thomas Jefferson University3, Tulane University4, Ghent University5, Shriners Hospitals for Children6, University of Copenhagen7, Turku University Hospital8, University of Oulu9, Cedars-Sinai Medical Center10, University of Verona11, University of Washington12, University of Leicester13
TL;DR: The data on genotype–phenotype relationships indicate that the two collagen chains play very different roles in matrix integrity and that phenotype depends on intracellular and extracellular events.
Abstract: Osteogenesis imperfecta (OI) is a generalized disorder of connective tissue characterized by fragile bones and easy susceptibility to fracture. Most cases of OI are caused by mutations in type I collagen. We have identified and assembled structural mutations in type I collagen genes (COL1A1 and COL1A2, encoding the proalpha1(I) and proalpha2(I) chains, respectively) that result in OI. Quantitative defects causing type I OI were not included. Of these 832 independent mutations, 682 result in substitution for glycine residues in the triple helical domain of the encoded protein and 150 alter splice sites. Distinct genotype-phenotype relationships emerge for each chain. One-third of the mutations that result in glycine substitutions in alpha1(I) are lethal, especially when the substituting residues are charged or have a branched side chain. Substitutions in the first 200 residues are nonlethal and have variable outcome thereafter, unrelated to folding or helix stability domains. Two exclusively lethal regions (helix positions 691-823 and 910-964) align with major ligand binding regions (MLBRs), suggesting crucial interactions of collagen monomers or fibrils with integrins, matrix metalloproteinases (MMPs), fibronectin, and cartilage oligomeric matrix protein (COMP). Mutations in COL1A2 are predominantly nonlethal (80%). Lethal substitutions are located in eight regularly spaced clusters along the chain, supporting a regional model. The lethal regions align with proteoglycan binding sites along the fibril, suggesting a role in fibril-matrix interactions. Recurrences at the same site in alpha2(I) are generally concordant for outcome, unlike alpha1(I). Splice site mutations comprise 20% of helical mutations identified in OI patients, and may lead to exon skipping, intron inclusion, or the activation of cryptic splice sites. Splice site mutations in COL1A1 are rarely lethal; they often lead to frameshifts and the mild type I phenotype. In alpha2(I), lethal exon skipping events are located in the carboxyl half of the chain. Our data on genotype-phenotype relationships indicate that the two collagen chains play very different roles in matrix integrity and that phenotype depends on intracellular and extracellular events.
TL;DR: Evidence is found that the priming of pericycle cells for lateral root initiation might take place in the basal meristem, correlating with elevated auxin sensitivity in this part of the root, and auxin responsiveness oscillates with peaks of expression at regular intervals of 15 hours.
Abstract: In plants, the developmental mechanisms that regulate the positioning of lateral organs along the primary root are currently unknown. We present evidence on how lateral root initiation is controlled in a spatiotemporal manner in the model plant Arabidopsis thaliana. First, lateral roots are spaced along the main axis in a regular left-right alternating pattern that correlates with gravity-induced waving and depends on AUX1, an auxin influx carrier essential for gravitropic response. Second, we found evidence that the priming of pericycle cells for lateral root initiation might take place in the basal meristem, correlating with elevated auxin sensitivity in this part of the root. This local auxin responsiveness oscillates with peaks of expression at regular intervals of 15 hours. Each peak in the auxin-reporter maximum correlates with the formation of a consecutive lateral root. Third, auxin signaling in the basal meristem triggers pericycle cells for lateral root initiation prior to the action of INDOLE-3-ACETIC ACID14 (SOLITARY ROOT).
TL;DR: In selected patients with pathologically proven stage IIIA-N2 NSCLC and a response to induction chemotherapy, surgical resection did not improve overall or progression-free survival compared with radiother- apy, and radiotherapy should be considered the preferred locoregional treatment for these patients.
Abstract: Background : Induction chemotherapy before surgical resection increases survival compared with surgical resection alone in patients with stage IIIA-N2 non–small-cell lung cancer (NSCLC). We hypothesized that, following a response to induction chemotherapy, surgical resection would be superior to thoracic radiotherapy as locoregional therapy. Methods : Selected patients with histologic or cytologic proven stage IIIA-N2 NSCLC were given three cycles of platinum- based induction chemotherapy. Responding patients were subsequently randomly assigned to surgical resection or radiotherapy. Survival curves were estimated using Kaplan–Meier analyses from time of randomization. Results : Induction chemotherapy resulted in a response rate of 61% (95% confidence interval [CI] = 57% to 65%) among the 579 eligible patients. A total of 167 patients were allocated to resection and 165 to radiotherapy. Of the 154 (92%) patients who underwent surgery, 14% had an exploratory thoracotomy, 50% a radical resection, 42% a pathologic downstaging, and 5% a pathologic complete response; 4% died after surgery. Postoperative radiotherapy was administered to 62 (40%) of patients in the surgery arm. Among the 154 (93%) irradiated patients, overall compliance to the radiotherapy prescription was 55%, and grade 3/4 acute and late esophageal and pulmonary toxic effects occurred in 4% and 7%; one patient died of radiation pneumonitis. Median and 5-year overall survival for patients randomly assigned to resection versus radiotherapy were 16.4 versus 17.5 months and 15.7% versus 14%, respectively (hazard ratio = 1.06, 95% CI = 0.84 to 1.35). Rates of progression-free survival were also similar in both groups. Conclusion : In selected patients with pathologically proven stage IIIA-N2 NSCLC and a response to induction chemotherapy, surgical resection did not improve overall or progression-free survival compared with radiother- apy. In view of its low morbidity and mortality, radiotherapy should be considered the preferred locoregional treatment for these patients.
21 Oct 2007
TL;DR: A survey of existing Java performance evaluation methodologies is presented and the importance of statistically rigorous data analysis for dealing with non-determinism is discussed, and approaches to quantify startup as well as steady-state performance are advocated.
Abstract: Java performance is far from being trivial to benchmark because it is affected by various factors such as the Java application, its input, the virtual machine, the garbage collector, the heap size, etc. In addition, non-determinism at run-time causes the execution time of a Java program to differ from run to run. There are a number of sources of non-determinism such as Just-In-Time (JIT) compilation and optimization in the virtual machine (VM) driven by timer-based method sampling, thread scheduling, garbage collection, and various. There exist a wide variety of Java performance evaluation methodologies usedby researchers and benchmarkers. These methodologies differ from each other in a number of ways. Some report average performance over a number of runs of the same experiment; others report the best or second best performance observed; yet others report the worst. Some iterate the benchmark multiple times within a single VM invocation; others consider multiple VM invocations and iterate a single benchmark execution; yet others consider multiple VM invocations and iterate the benchmark multiple times. This paper shows that prevalent methodologies can be misleading, and can even lead to incorrect conclusions. The reason is that the data analysis is not statistically rigorous. In this paper, we present a survey of existing Java performance evaluation methodologies and discuss the importance of statistically rigorous data analysis for dealing with non-determinism. We advocate approaches to quantify startup as well as steady-state performance, and, in addition, we provide the JavaStats software to automatically obtain performance numbers in a rigorous manner. Although this paper focuses on Java performance evaluation, many of the issues addressed in this paper also apply to other programming languages and systems that build on a managed runtime system.
TL;DR: The ability of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid to inhibit root cell elongation was significantly enhanced in the presence of auxin, suggesting that by upregulating auxin biosynthesis, ethylene facilitates its ability to inhibitRoot cell expansion.
Abstract: Ethylene represents an important regulatory signal for root development. Genetic studies in Arabidopsis thaliana have demonstrated that ethylene inhibition of root growth involves another hormone signal, auxin. This study investigated why auxin was required by ethylene to regulate root growth. We initially observed that ethylene positively controls auxin biosynthesis in the root apex. We subsequently demonstrated that ethylene-regulated root growth is dependent on (1) the transport of auxin from the root apex via the lateral root cap and (2) auxin responses occurring in multiple elongation zone tissues. Detailed growth studies revealed that the ability of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid to inhibit root cell elongation was significantly enhanced in the presence of auxin. We conclude that by upregulating auxin biosynthesis, ethylene facilitates its ability to inhibit root cell expansion.
TL;DR: The computational approach to the Hirshfeld atom in a molecule is critically investigated, and several difficulties are highlighted, and it is shown that these difficulties are mitigated by an alternative, iterative version, of the HirShfeld partitioning procedure.
Abstract: The computational approach to the Hirshfeld [Theor. Chim. Acta 44, 129 (1977)] atom in a molecule is critically investigated, and several difficulties are highlighted. It is shown that these difficulties are mitigated by an alternative, iterative version, of the Hirshfeld partitioning procedure. The iterative scheme ensures that the Hirshfeld definition represents a mathematically proper information entropy, allows the Hirshfeld approach to be used for charged molecules, eliminates arbitrariness in the choice of the promolecule, and increases the magnitudes of the charges. The resulting "Hirshfeld-I charges" correlate well with electrostatic potential derived atomic charges.
TL;DR: The non-apoptotic functions of caspases suggest that they may become activated independently of – or without – inducing an apoptotic cascade, and the existence of non-catalytic caspase-like molecules further supports the non-proteolytic functions ofcaspases in the regulation of cell survival, proliferation, differentiation and inflammation.
Abstract: Caspases, a family of evolutionarily, conserved cysteinyl proteases, mediate both apoptosis and inflammation through aspartate-specific cleavage of a wide number of cellular substrates. Most substrates of apoptotic caspases have been conotated with cellular dismantling, while inflammatory caspases mediate the proteolytic activation of inflammatory cytokines. Through detailed functional analysis of conditional caspase-deficient mice or derived cells, caspase biology has been extended to cellular responses such as cell differentiation, proliferation and NF-kappaB activation. Here, we discuss recent data indicating that non-apoptotic functions of caspases involve proteolysis exerted by their catalytic domains as well as non-proteolytic functions exerted by their prodomains. Homotypic oligomerization motifs in the latter mediate the recruitment of adaptors and effectors that modulate NF-kappaB activation. The non-apoptotic functions of caspases suggest that they may become activated independently of--or without--inducing an apoptotic cascade. Moreover, the existence of non-catalytic caspase-like molecules such as human caspase-12, c-FLIP and CARD-only proteins further supports the non-proteolytic functions of caspases in the regulation of cell survival, proliferation, differentiation and inflammation.
TL;DR: This review aims to provide the reader with a concise overview of these novel MMP functions in relation to leukocyte migration.
Abstract: The action of matrix metalloproteinases (MMPs) was originally believed to be restricted to degradation of the extracellular matrix; however, in recent years, it has become evident that these proteases can modify many nonmatrix substrates, such as cytokines and chemokines. The use of MMP-deficient animals has revealed that these proteases can indeed influence the progression of various inflammatory processes. This review aims to provide the reader with a concise overview of these novel MMP functions in relation to leukocyte migration.
TL;DR: The total landscape species richness of all groups was most strongly affected by increased proximity of semi-natural habitat patches and the effect of increased habitat diversity appeared to be of secondary importance to total species richness but caused a shift in the relative contribution of α and β diversity towards the latter.
Abstract: 1. Agricultural intensification poses a serious threat to biodiversity as a consequence of increased land-use intensity, decreased landscape heterogeneity and reduced habitat diversity. Although there is interest in the preservation of total species richness of an agricultural landscape (γ diversity), the effects of intensification have been assessed primarily by species richness at a local scale (α diversity). This ignores species richness between local communities (β diversity), which is an important component of total species richness. 2. In this study, measures of land-use intensity, landscape structure and habitat diversity were related to γ, α and β diversity of wild bees (Apoidea), carabid beetles (Carabidae), hoverflies (Syrphidae), true bugs (Heteroptera) and spiders (Araneae) within 16 local communities in 24 temperate European agricultural landscapes. 3. The total landscape species richness of all groups was most strongly affected by increased proximity of semi-natural habitat patches. Bees also decreased in landscapes with a high intensity of farmland management, demonstrating additive effects of both factors. 4. Separating total species diversity into components, the decrease in total species richness could be attributed primarily to a decrease in species diversity between local communities. Species richness of the local communities of all investigated groups decreased with increasing land-use intensity and, in the case of spiders, decreasing proximity of the semi-natural habitat patches. 5. The effect of increased habitat diversity appeared to be of secondary importance to total species richness but caused a shift in the relative contribution of α and β diversity towards the latter.
TL;DR: In this article, a survey of 3,314 private sector and 409 public sector employees in Belgium showed that the differences in hierarchical level are more important determinants of work motivation than sectoral differences.
Abstract: This study contributes to our understanding of the differences in work motivation between the public and private sectors. Data from a survey of 3,314 private sector and 409 public sector employees in Belgium strongly confirm previous research showing that public sector employees are less extrinsically motivated. Differences in hierarchical level are more important determinants of work motivation than sectoral differences. In addition, most observed differences can be wholly or partially explained by differences in job content, not by the sector itself. Evidence is presented to show that motivational differences can be explained by a positive choice of work–life balance.