bluuebunny/crossref_metadata_2025_split huggingface dataset:
Iterated Residuals and Time-Varying Covariate Effects in Cox Regression
Authors: Winnett Angela , Sasieni Peter 
Published: December 2004

SummaryThe Cox proportional hazards model, which is widely used for the analysis of treatment and prognostic effects with censored survival data, makes the assumption that the hazard ratio is constant over time. Nonparametric estimators have been developed for an extended model in which the hazard ratio is allowed to change over time. Estimators based on residuals are appealing as they are easy to use and relate in a simple way to the more restricted Cox model estimator. After fitting a Cox model and calculating the residuals, one can obtain a crude estimate of the time-varying coefficients by adding a smooth of the residuals to the initial (constant) estimate. Treating the crude estimate as the fit, one can re-estimate the residuals. Iteration leads to consistent estimation of the nonparametric time-varying coefficients. This approach leads to clear guidelines for residual analysis in applications. The results are illustrated by an analysis of the Medical Research Council’s myeloma trials, and by simulation.
Classical Model Selection via Simulated Annealing
Authors: Brooks S. P. , Friel N. , King R. 
Published: December 2004

SummaryThe classical approach to statistical analysis is usually based upon finding values for model parameters that maximize the likelihood function. Model choice in this context is often also based on the likelihood function, but with the addition of a penalty term for the number of parameters. Though models may be compared pairwise by using likelihood ratio tests for example, various criteria such as the Akaike information criterion have been proposed as alternatives when multiple models need to be compared. In practical terms, the classical approach to model selection usually involves maximizing the likelihood function associated with each competing model and then calculating the corresponding criteria value(s). However, when large numbers of models are possible, this quickly becomes infeasible unless a method that simultaneously maximizes over both parameter and model space is available. We propose an extension to the traditional simulated annealing algorithm that allows for moves that not only change parameter values but also move between competing models. This transdimensional simulated annealing algorithm can therefore be used to locate models and parameters that minimize criteria such as the Akaike information criterion, but within a single algorithm, removing the need for large numbers of simulations to be run. We discuss the implementation of the transdimensional simulated annealing algorithm and use simulation studies to examine its performance in realistically complex modelling situations. We illustrate our ideas with a pedagogic example based on the analysis of an autoregressive time series and two more detailed examples: one on variable selection for logistic regression and the other on model selection for the analysis of integrated recapture–recovery data.
A Note on the Prospective Analysis of Outcome-Dependent Samples
Authors: Chen Hua Yun 
Published: December 2004

SummaryTwo likelihood representations corresponding to the prospective and retrospective analyses of the case–control design are derived for general outcome-dependent samples with arbitrary discrete or continuous outcomes and possibly non-multiplicative models. Parameter identification in the general outcome-dependent design is reduced to the simple problem of parameter identification in the general odds ratio function. Both likelihoods are shown to generate the same profile likelihood for the common parameter of interest. Maximum likelihood estimators based on either likelihood are semiparametric efficient for the identifiable parameters.
A General Condition for Avoiding Effect Reversal after Marginalization
Authors: Cox D. R. , Wermuth Nanny 
Published: December 2004

SummaryThe paper examines the effect of marginalizing over a possibly unobserved background variable on the conditional relation between a response and an explanatory variable. In particular it is shown that some conclusions derived from least squares regression theory apply in general to testing independence for arbitrary distributions. It is also shown that the general condition of independence of the explanatory variable and the background ensures that monotonicity of dependence is preserved after marginalization. Relations with effect reversal and with collapsibility are sketched.
Die Evolution der bundesdeutschen Forschungs- und Technologiepolitik: Rückblick und Bestandsaufnahme
Authors: Fier Andreas , Harhoff Dietmar 
Published: December 2004

Abstract We consider the development of German federal research and technology (R&T) policies since the 1960s and sketch the evolution of today's highly differentiated and complex set of policy instruments. Advances from economic theory and empirical results are reflected in this evolution, but have not necessarily been the driving force. In some instances, innovative policy instruments have been introduced in order to accommodate the state of the art in economic analysis; in other cases, such innovations have preceded a thorough analysis of the respective policy instruments. A major point of concern is the lack of comprehensive evaluation and cost-benefit analyses in R&T policies. In this regard, German policy practice lags behind well-established procedures in other countries.
Neuroendocrine and cardiovascular reactivity to stress in mid‐aged and older women: Long‐term temporal consistency of individual differences
Authors: Burleson Mary H. , Poehlmann Kirsten M. , Hawkley Louise C. , Ernst John M. , Berntson Gary G. , Malarkey William B. , Kiecolt‐Glaser Janice K. , Glaser Ronald , Cacioppo John T. 
Published: December 2004

AbstractWe report long‐term temporal consistency of stress‐related neuroendocrine and cardiovascular variables in mid‐aged and older women who performed mental math and speech stress tasks two times approximately 1 year apart. Epinephrine, norepinephrine, ACTH, cortisol, cardiac preejection period (PEP), respiratory sinus arrhythmia, heart rate (HR), blood pressure, and respiration rate were measured at baseline, after or during stressors, and 30 min posttask. Although there were exceptions, year‐to‐year Spearman coefficients showed mostly moderate to high consistency (rs≈.5–.8) for baseline, stressor, and posttask values. For reactivity, HR and PEP were most consistent (rs≈.65); consistency for other variables was moderate to low (rs≈.1–.4). Means of most variables changed from year to year. Results support the use of baseline, stressor, and posttask values in longitudinal studies.
Cerebral patterns of attentional habituation to emotional visual stimuli
Authors: Carretié Luis , Hinojosa José Antonio , Mercado Francisco 
Published: December 2004

AbstractAttentional habituation in response to emotional stimuli, an aspect of the interaction between cognitive and emotional processes that has received scant attention, was investigated. Event‐related potentials were recorded using a 60‐electrode array from 25 participants who attended to 120 presentations of three different picture types: emotionally negative (S−), positive (S+), and neutral (S0). The affective content of the stimulation was assessed, through questionnaires, by the participants themselves. N1 showed different patterns of habituation as a function of the stimulation: amplitudes indicated that S− was more resistant to habituation than S0 and S+. This pattern, which reflects a greater capacity of S− to attract and maintain the participant's attention, is interpreted as a manifestation of the “negativity bias,” a phenomenon that reflects an evolution‐favored set of mechanisms that facilitate a rapid and intense response to aversive events.
Auditory selective attention in young and elderly adults: The selection of single versus conjoint features
Authors: Gaeta Helen , Friedman David , Ritter Walter 
Published: December 2004

AbstractThe effects of aging on the behavioral and neurophysiological correlates of auditory selective attention were investigated when selection was between either unidimensional or multidimensional stimuli. Attentional processes were studied by recording event‐related brain potentials (ERPs) from 16 young (M=22 years) and 16 elderly adults (M=74 years) while they detected target tones based on a single location cue or a conjunction of location and pitch cues. Performance declined from the single‐ to the conjoint‐cue task for both age groups but more so for the elderly. The ERP data showed that both age groups used a hierarchical processing strategy to perform the conjoint‐cue task, but processing of the pitch dimension took longer for the elderly than for the young. The ERP data also showed that the scalp distribution of a late aspect of the waveform was more restricted in both anterior and posterior directions for the elderly. This suggests that frontal‐lobe dependent attentional processes may be less efficacious with aging.
Multiple visual memory phenomena in a memory search task
Authors: Fabiani Monica , Ho Jonathan , Stinard Alex , Gratton Gabriele 
Published: December 2004

AbstractThis paper reports evidence of the existence of multiple and distinct visual memory processes in a memory search task in which a divided field stimulus presentation was used at study (Experiments 1–3) and either a foveal (Experiments 1 and 2) or a lateralized (Experiment 3) stimulus presentation was used at test. These memory processes can be distinguished on the basis of (1) whether or not they are hemispherically organized; and (2) the locus of their underlying brain activity, as evidenced by the scalp distribution of the event‐related brain potentials and by the localization of the event‐related optical signal that accompany them. These memory effects are discussed in the context of visual form memory.
Children's meta‐perceptions and meta‐accuracy of acceptance and rejection by same‐sex and other‐sex peers
Authors: Bellmore Amy D. , Cillessen Antonius H. N. 
Published: December 2004

AbstractThe goals of this study were to examine children's meta‐perceptions and meta‐accuracy of acceptance and rejection in the peer group, the degree to which these perceptions vary by perceiver sex and sex of the reference group, and the association between these perceptions and children's actual functioning in the peer group. Participants were 644 fourth‐grade children. Meta‐perceptions and meta‐accuracy were derived from sociometric nominations of actual and perceived acceptance and rejection. Children more accurately perceived how they were seen by same‐sex peers than how they were seen by other‐sex peers. They also perceived more rejection than acceptance from other‐sex peers. Meta‐accuracy for rejection was low regardless of the sex of the reference group. Sex of the reference group significantly moderated the association between meta‐perceptions and meta‐accuracy of acceptance and rejection and children's actual peer relationships. These findings indicate the importance of examining these relatively understudied social cognitions in research with children and the importance of taking the sex of the reference group into account in future peer relations studies using peer nomination methods.
New Insights on the Structure of the Mouse Silver Locus and on the Function of the Silver Protein
Authors: SOLANO FRANCISCO , MARTÍNEZ‐ESPARZA MARÍA , JIMÉNEZ‐CERVANTES CELIA , HILL SIMON P. , LOZANO JOSÉ A. , GARCÍA‐BORRÓN JOSÉ C. 
Published: December 2004

The melanosomal proteins encoded by the silver locus play important roles in melanogenesis. The human locus yields two proteins, PMEL17 and GP100, by alternative mRNA splicing. The mouse si locus was reported to encode a Pmel17 protein, and later gp87, a GP100 homologue. When we re‐examined the products of wild‐type and silver‐mutant mouse si loci, RT‐PCR of wild‐type RNA and genomic DNA sequence accounted for gp87 but excluded the occurrence of Pmel17. Analysis of cDNA from the silver (si/si) melanocyte line, melan‐si, showed that the pathogenic mutation is a G to A substitution at nt 1808, which yields a premature stop codon and a predicted protein truncated in the C‐terminus. This was confirmed by reaction of a specific anti‐gp87 antiserum with si/si melanocyte extracts.To further explore gp87 function, we compared the DHICA oxidase activity of extracts from B16, melan‐si (heterozygous for the brown mutation and homozygous for the silver mutation) and Cloudman S91 cells (homozygous for the brown mutation), since both TRP1 and gp87 are thought to be involved in DHICA oxidation/polymerization. Cloudman extracts do not oxidize significantly DHICA and its methyl ester, supporting the involvement of native mouse TRP1 in DHICA oxidation. Extracts from B16 and melan‐si do not show significant differences for the oxidation of free acid and methylated dihydroxyindoles, indicating that the mechanism is not decarboxylative. Melan‐si extracts are very efficient in catalyzing dihydroxyindole oxidation, in spite of being heterozygous for the TRP1 mutation, consistent with a stablin effect for the wild‐type gp87 protein. On the other hand, aggregated and degraded forms of that mutant gp87 protein are found in the cytosolic fraction of melan‐si, suggesting that misrouting and aberrant processing of the gp87 and tyrosinase may also be related to the high DHICA oxidase activity of these melanocytes.
Photosynthates stimulate the UV‐B induced fungal anthraquinone synthesis in the foliose lichen Xanthoria parietina
Authors: SOLHAUG K. A. , GAUSLAA Y. 
Published: December 2004

ABSTRACTSynthesis of the cortical anthraquinone pigment parietin (= physcion) was studied in acetone‐rinsed, parietin‐free Xanthoria parietina thalli. UV‐B induced the synthesis, which increased linearly with UV‐B (log‐transformed) to the highest applied UV‐B level (1.8 W m−2). At natural UV‐B levels (0.75 W m−2), parietin resynthesis occurred at a constant pace (106 mg m−2 d−1) during a 14‐d period at 220 µmol m−2 s−1 PAR. Under these conditions, 56% of the natural parietin content prior to extraction was resumed, accounting for 10% of total net carbon gain. In the presence of UV‐B, the remaining results were consistent with the hypothesis assuming that photosynthates regulate the pace at which parietin is synthesized by the mycobiont. Resynthesis was rapid when photosynthesis was activated by light, or when certain carbohydrates were added exogenously. Additions of ribitol, the carbohydrate delivered from the photobiont, increased the parietin resynthesis substantially. Mannitol, the main fungal polyol, was significantly less effective. Furthermore, parietin resynthesis in X. parietina was depressed at high and low hydration when net photosynthesis is depressed. Therefore, the photobiont regulates the parietin resynthesis pace in its mycobiont partner by the delivery of photosynthates. In conclusion, both lichen bionts play important roles in the synthesis of parietin, which probably acts as a PAR‐ rather than a UV‐B‐screen.
Genetic dissection of cotton physiological responses to arid conditions and their inter‐relationships with productivity
Authors: SARANGA Y. , JIANG C.‐X. , WRIGHT R. J. , YAKIR D. , PATERSON A. H. 
Published: December 2004

ABSTRACTTesting of the extent to which different complex traits share common genetic control provides a means to distinguish associations that are truly diagnostic of genetic potential for improved adaptation to abiotic stress, from incidental phenotypic correlations. In two generations of progeny from a cross between Gossypium hirsutum and Gossypium barbadense, quantitative trait loci (QTL) mapping was used to evaluate correspondence in genetic control of selected physiological measures and productivity under water‐limited and well‐watered environments, respectively. A total of 33 QTLs were detected for five physiological variables [osmotic potential (OP), carbon isotope ratio (δ13C; indicator of water use efficiency), canopy temperature, chlorophyll a and b], and 46 QTLs for five measures of crop productivity [dry matter, seed cotton yield (SC), harvest index, boll weight, and boll number]. QTL likelihood intervals for high SC and low OP corresponded in three genomic regions, two of which mapped to homoeologous locations on the two subgenomes of tetraploid cotton. QTLs for δ13C showed only incidental association with productivity, indicating that high water use efficiency can be associated with either high or low productivity. Different cotton species have evolved different alleles related to physiological responses and productivity under water deficit, which may permit the development of genotypes that are better‐adapted to arid conditions.
Detection by PCR of Candidatus Liberibacter asiaticus, the bacterium causing citrus huanglongbing in vector psyllids: application to the study of vector–pathogen relationships
Authors: Hung T.‐H. , Hung S.‐C. , Chen C.‐N. , Hsu M.‐H. , Su H.‐J. 
Published: December 2004

Citrus huanglongbing (HLB), previously called greening, is a serious citrus disease in Asia, eastern and southern Africa. It is caused by Candidatus Liberibacter asiaticus (Las), a phloem‐limited, nonculturable bacterium transmitted by the Asian citrus psyllid (Diaphorina citri) in Asia. A PCR‐based assay was developed for monitoring Las in vector psyllids using a rapid DNA extraction from psyllid bodies and PCR amplification. The entire procedure for Las detection in psyllids can be completed within 5 h. Using this method, Las can be accurately detected in psyllid adults as well as nymphs in different instar stages. The assay is sensitive enough for Las detection in single‐psyllid extract from adult, fifth, fourth and third instars. In a transovarial transmission experiment, Las was not detected in eggs or in offspring produced by Las‐carrying psyllid females. In a retention test, the Las‐carrying psyllids remained Las‐positive for 12 weeks after they were moved to common jasmine orange, a Las‐immune plant. From these experimental results it was concluded that Las persists in the Asian citrus psyllid vector, but is not transovarially transmitted by the vector. These data help in understanding epidemiological characteristics of Las and psyllids in citrus HLB.
Spread of Sugarcane yellow leaf virus in sugarcane plants and fields on the island of Réunion
Authors: Rassaby L. , Girard J.‐C. , Lemaire O. , Costet L. , Irey M. S. , Kodja H. , Lockhart B. E. L. , Rott P. 
Published: December 2004

The spread of Sugarcane yellow leaf virus (SCYLV) in sugarcane plants was studied on Réunion using virus‐infected cuttings from four cultivars (R570, R575, R577 and R579). One month after the germination of cuttings in an insect‐proof glasshouse, SCYLV was detected by reverse‐transcription polymerase chain reaction (RT‐PCR) and tissue‐blot immunoassay (TBIA) in the leaves, shoots and roots of all cultivars. The distribution of SCYLV in the whole plant did not vary over a 10‐ to 11‐month period of growth. In addition, the spread of SCYLV in sugarcane fields on Réunion was investigated during a survey conducted from 1998 to 2001. Samples were taken in three sugarcane‐growing areas, and TBIA was used to detect SCYLV in the three major cultivars (R570, R575 and R579). The percentage of infected stalks varied according to cultivar and growing area, but remained relatively stable for a given cultivar in a given growing area over the 30‐month survey period. Cultivar R575 was the most infected cultivar in all three growing areas (mean of 98% infected stalks). The percentage of infected stalks ranged from 16 to 94% in cv. R570 and from 21 to 92% in cv. R579. These results suggested that on Réunion: (i) infected sugarcane stools do not recover from the disease after harvesting; and (ii) the virus is mainly propagated by planting infected cuttings. SCYLV was detected by RT‐PCR in the aphid Melanaphis sacchari, a potential vector of this virus. Two months after planting virus‐free plants of susceptible cv. R575 in a field surrounded by sugarcane infected with SCYLV, 14% of plants were found infected with the virus. Four months later, 25% of plants were found infected with SCYLV, but no new infections were detected between 6 and 12 months after planting. In the first ratoon crop, 42% of plants were infected with SCYLV after 6 months of growth. Spatial distribution of infected plants suggested that, on Réunion, a small window of time (between 0 and 2 months after planting cuttings) exists during which primary infection can occur. Based on the results obtained in this study, the use of clean planting material for some cultivars and the use of tolerant cultivars should be an efficient means of controlling sugarcane yellow leaf on Réunion.
A Note on the Adaptive Control of False Discovery Rates
Authors: Black M. A. 
Published: December 2004

SummaryThe use of a fixed rejection region for multiple hypothesis testing has been shown to outperform standard fixed error rate approaches when applied to control of the false discovery rate. In this work it is demonstrated that, if the original step-up procedure of Benjamini and Hochberg is modified to exercise adaptive control of the false discovery rate, its performance is virtually identical to that of the fixed rejection region approach. In addition, the dependence of both methods on the proportion of true null hypotheses is explored, with a focus on the difficulties that are involved in the estimation of this quantity.
Degenerative Endometrial Changes do not Change the Functional Capacity of Immigrating Uterine Neutrophils in Mares
Authors: Zerbe H , Engelke F , Klug E , Schoon H‐A , Leibold W 
Published: December 2004

ContentsAn endometritis model was used to investigate the influence of degenerative endometrial changes (endometrosis) on functional parameters of uterine neutrophils in the horse. Six hours after intrauterine application of recombinant human interleukin‐8 (rhIL‐8), the uteri of 15 mares were flushed with phosphate‐buffered saline. Quantitative and qualitative flow cytometric assays were then made to determine the absolute numbers, viability, phenotype, generation of reactive oxygen species (ROS), and phagocytic activity of immigrated polymorphonuclear neutrophilic granulocytes (PMN). Recombinant hIL‐8 attracted similarly high numbers of similarly viable PMN into the uteri of mares with or without degenerative endometrial changes. Compared with blood PMN, immigrated uterine neutrophils displayed significantly upregulated expression of CD11a/CD18 (LFA‐1) on uterine PMN whereas major histocompatibility complex class I molecules were expressed at lower densities. The ability to phagocytose opsonized streptococci did not differ between uterine and blood PMN. However, uterine PMN displayed a higher capacity to generate ROS. On average, uterine PMN of mares with degenerative endometrial changes showed phenotypical and functional characteristics similar to those of mares with a histologically healthy endometrium. Therefore, degenerative endometrial changesper sedid not reduce the functional capacity of equine uterine neutrophils in mares.