bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysing and interpreting competing risk data
Authors: Pintilie Melania 
Published: August 2006

AbstractWhen competing risks are present, two types of analysis can be performed: modelling the cause specific hazard and modelling the hazard of the subdistribution. This paper contrasts these two methods and presents the benefits of each. The interpretation is specific to the analysis performed. When modelling the cause specific hazard, one performs the analysis under the assumption that the competing risks do not exist. This could be beneficial when, for example, the main interest is whether the treatment works in general. In modelling the hazard of the subdistribution, one incorporates the competing risks in the analysis. This analysis compares the observed incidence of the event of interest between groups. The latter analysis is specific to the structure of the observed data and it can be generalized only to another population with similar competing risks. Copyright © 2006 John Wiley & Sons, Ltd.
A nonlinear latent class model for joint analysis of multivariate longitudinal data and a binary outcome
Authors: Proust‐Lima Cécile , Letenneur Luc , Jacqmin‐Gadda Hélène 
Published: August 2006

AbstractWe consider a joint model for exploring association between several correlated longitudinal markers and a clinical event. A nonlinear growth mixture model exhibits the different latent classes of evolution of the latent quantity underlying the correlated longitudinal markers and a logistic regression models the probability of occurence of the clinical event according to the latent classes. By introducing a flexible nonlinear transformation including parameters to be estimated between each marker and the latent process, the model also deals with non‐Gaussian continuous markers. Through an application on cognitive ageing, the two advantages of the model are underlined: (1) the latent profiles of evolution associated with the clinical event are described including covariate effects in the longitudinal model but also in the probability of class membership and in the probability of occurence of the event, and (2) a diagnostic and a prognostic tools are derived from the model for early detection of the clinical event using any available information about the longitudinal markers. Copyright © 2006 John Wiley & Sons, Ltd.
Comparing the small sample performance of several variance estimators under competing risks
Authors: Braun Thomas M. , Yuan Zheng 
Published: August 2006

AbstractWe examine several variance estimators for cumulative incidence estimators that have been proposed over time, some of which are derived from asymptotic martingale or counting process theory, and some of which are developed from the moments of the multinomial distribution. There is little published work comparing these variance estimators, largely because the variance estimators are algebraically complex and difficult to interpret and all but one have yet to be programmed for a standard statistical package. Through simulation and application to real data, we compare the performance of six variance estimators in relation to each other and the bootstrap in order to confirm earlier reports of their performance and to provide future direction toward their application. We find that the multinomial‐moment‐based estimators have performance close to that of the bootstrap, and are quite accurate for estimating the variance, even in samples of 20 subjects. All but one of the martingale theory‐based estimators tend to perform poorly in small samples, tending to either overestimate or underestimate the empirical variance in samples of fewer than 100 subjects. Copyright © 2006 John Wiley & Sons, Ltd.
On estimating treatment effects under non‐compliance in randomized clinical trials: are intent‐to‐treat or instrumental variables analyses perfect solutions?
Authors: Bang Heejung , Davis Clarence E. 
Published: August 2006

AbstractIn this report, we compared four estimators (intent‐to‐treat, as treated, per protocol, and instrumental variables estimators) that are conventionally considered for treatment effect estimation by simulation under different non‐compliance scenarios in typical clinical trial settings. We found that intent‐to‐treat and instrumental variables estimators are not perfect and can be problematic in some situations although these two estimators carry desirable properties as we assume. Copyright © 2006 John Wiley & Sons, Ltd.
Improving fault prediction using Bayesian networks for the development of embedded software applications
Authors: Pérez‐Miñana Elena , Gras Jean‐Jacques 
Published: August 2006

AbstractBayesian network (BN) models can be used to predict the level of fault injection in the different phases of the software development process. This paper describes the techniques used by Motorola to develop BN fault prediction models using product, usage and process information. It also includes a procedure created to validate and calibrate the BN models. Statistical techniques are applied that provide a measurement of the quality of the predictions made by the models, and directions on how the models could be improved. The validation method described in this paper considers two alternative ways to produce an improved network. The first is based mainly on modifying the ranges of the existing nodes, adding interdependencies between them, and varying the weight values associated with each of the nodes that are used as inputs to the intermediate nodes of the BN model. The second possibility uses linear regression and principal component analysis to build the intermediate and output nodes of the network. The paper closes with some encouraging results, and outlines a number of unresolved questions. Copyright © 2006 John Wiley & Sons, Ltd.
Day Care Laparoscopic Cholecystectomy: A Feasibility Study in a Public Health Service Hospital in a Developing Country
Authors: Chauhan A. , Mehrotra M. , Bhatia P.K. , Baj B. , Gupta A.K. 
Published: August 2006

AbstractBackgroundDay care laparoscopic cholecystectomy (DCLC) has been shown to be safe in centers with adequate infrastructure for day care surgery in economically advanced countries. However, the feasibility of applying this concept in public health service hospitals in less developed and developing nation needs to studied. Unique protocols need to be developed and tested, taking into account local conditions and infrastructural constraints.Patients and methodsPatients less than 60 years old, graded I and II on the American Society of Anesthesiologists (ASA) physical status score, living within one hour traveling time and willing to make their own arrangements for a return to hospital in case of problems, were selected for DCLC.Results291 cases (78%) out of 373 laparoscopic cholecystectomies done in one calendar year were found suitable for DCLC. The most common cause for omitting from DCLC was that the patient lived out of the defined area (57%). Four of 291 (1.3%) cases were cancelled due to medical condition; 270/287 (96.1%) were discharged the same evening as surgery; 6 patients were converted to open surgery; and 11 did not meet the necessary discharge criteria. Eight of 270 (2.9%) required readmission out of which 3 (1.1%) required intervention. Overall, incidence of complication rate was 3.4%. Analysis of data showed that results were comparable to previously published studies, hence extrapolating that inclusion and discharge criteria used in the study are valid. However, there are certain social constraints which hinder truly universal application of DCLC.ConclusionsDCLC is a safe and technically feasible concept, even in public health service centers without dedicated ambulatory surgery units. It has potential for much economical and social benefit in these countries.
Relationship between quality management practices and knowledge transfer
Authors: Molina Luis M. , Lloréns‐Montes Javier , Ruiz‐Moreno Antonia 
Published: August 2006

AbstractThis paper analyzes the relationship between quality management (QM) and knowledge transfers. The study of QM was tackled by analyzing the degree of implementation of the different practices that compose it. Hypotheses are developed on the relationship between some QM practices and knowledge transfers. Both the proposed model and the hypotheses were tested on a sample of 197 Spanish firms. The results confirm the importance of the different QM practices on internal and external knowledge transfers.
Ground ice and slope sediments archiving late Quaternary paleoenvironment and paleoclimate signals at the margins of El'gygytgyn Impact Crater, NE Siberia
Authors: Schwamborn Georg , Meyer Hanno , Fedorov Grigory , Schirrmeister Lutz , Hubberten Hans-W. 
Published: August 2006

AbstractAn accumulation terrace close to the El'gygytgyn Impact Crater in northeastern Siberia contains stratigraphic and periglacial evidence of the paleoenvironmental and paleoclimatic history and permafrost dynamics during late Quaternary time. A succession of paleo active-layer deposits that mirror environmental changes records periods favorable for the establishment and growth of ice-wedge polygonal networks and sediment variations. These two elements of the periglacial landscape serve as complementary paleoenvironmental archives that can be traced back to ∼ 14,000 cal yr BP. The slope sediments and the ground ice contained therein have prominent relative maxima and minima in properties (grain size, total organic content, oxygen isotopes). They document a regional early Holocene thermal maximum at about 9000 cal yr BP, followed by a transition to slightly cooler conditions, and a subsequent transition to slightly warmer conditions after about 4000 cal yr BP. Results from sedimentary analysis resemble morphological and geochemical (oxygen and hydrogen isotopes) results from ice wedge studies, in which successive generations of ice-wedge polygonal networks record warmer winters in late Holocene time. Moreover, peaks of light soluble cation contents and quartz-grain surface textures reveal distinct traces of cryogenic weathering. We propose a conclusive sedimentation model illustrating terrace formation in a permafrost terrain.
Epidemiological tracing ofSalmonella entericaserotype Abortusovis from Spanish ovine flocks by PFGE fingerprinting
Authors: VALDEZATE S. , ASTORGA R. , HERRERA-LEÓN S. , PEREA A. , USERA M. A. , HUERTA B. , ECHEITA A. 
Published: August 2006

SUMMARYSalmonella entericaserotype Abortusovis, an ovine host-specific serotype, rare in most countries, is responsible for epidemic abortion episodes in Spain. With the aim of surveillance and detection of the spread of specific clones, 55 Abortusovis isolates collected during 1996–2001 from flocks in 11 provinces, were studied usingXbaI–PFGE. Despite the fact that the strains were geographically and spatially related, PFGE demonstrated an epidemiologically acceptable discriminating power, identifying 20 clones (similarity, 52–96%). Clones Sabv6, 1, 5 were disseminated in seven, five and two areas respectively, while another 17 clones appeared in single places. Clones from nearby geographic regions showed a high relatedness (one band of difference in the PFGE profile) Sabv1-2-3, Sabv5-6, Sabv7-8, and Sabv13-14, suggesting a common ancestor. Co-isolation in the same flock (Sabv5-6, Sabv1-3, Sabv1-6) was detected. PFGE surveillance detected the predominance and widespread distribution of clone Sabv6 in 21 out of the 55 Abortusovis serotype episodes studied in Spain.
Investigations of Reaction Kinetics for Immobilized Enzymes—Identification of Parameters in the Presence of Diffusion Limitation
Authors: Berendsen Wouter R. , Lapin Alexei , Reuss Matthias 
Published: August 2006

AbstractA method is proposed for identification of kinetic parameters when diffusion of substrates is limiting in reactions catalyzed by immobilized enzymes. This method overcomes conventional sequential procedures, which assume immobilization does not affect the conformation of the enzyme and, thus, consider intrinsic and inherent kinetics to be the same. The coupled equations describing intraparticle mass transport are solved simultaneously using numerical methods and are used for direct estimation of kinetic parameters by fitting modeling results to time‐course measurements in a stirred tank reactor. While most traditional procedures were based on Michaelis‐Menten kinetics, the method presented here is applicable to more complex kinetic mechanisms involving multiple state variables, such as ping‐pong bi‐bi. The method is applied to the kinetic resolution of (R/S)‐1‐methoxy‐2‐propanol with vinyl acetate catalyzed by Candida antarctica lipase B. A mathematical model is developed consisting of irreversible ping‐pong bi‐bi kinetics, including competitive inhibition of both enantiomers. The kinetic model, which fits to experimental data over a wide range of both substrates (5–95%) and temperatures (5–56 °C), is used for simulations to study typical behavior of immobilized enzyme systems.
Solvated docking: introducing water into the modelling of biomolecular complexes
Authors: van Dijk Aalt D. J. , Bonvin Alexandre M. J. J. 
Published: August 2006

Abstract
Motivation: Interfacial water, which plays an important role in mediating biomolecular interactions, has been neglected in the modelling of biomolecular complexes.
Methods: We present a solvated docking approach that explicitly accounts for the presence of water in protein–protein complexes. Our solvated docking protocol is based on the concept of the first encounter complex in which a water layer is present in-between the molecules. It mimics the pathway from this initial complex towards the final assembly in which most waters have been expelled from the interface. Docking is performed from solvated biomolecules and waters are removed in a biased Monte Carlo procedure based on water-mediated contact propensities obtained from an analysis of high-resolution crystal structures.
Results: We demonstrate the feasibility of this approach for protein–protein complexes representing both ‘wet’ and ‘dry’ interfaces. Solvated docking leads to improvements both in quality and scoring. Water molecules are recovered that closely match the ones in the crystal structures.
Availabilty: Solvated docking will be made available in the future release of HADDOCK version 2.0 ().
Contact: a.m.j.j.bonvin@chem.uu.nl
Supplementary information: Supplementary Data are available at Bioinformatics Online.
Breeding seasonality and population dynamics of three rodent species in the Magamba Forest Reserve, Western Usambara Mountains, north‐east Tanzania
Authors: Makundi Rhodes H. , Massawe Apia W. , Mulungu Loth S. 
Published: August 2006

AbstractWe investigated breeding seasonality and population dynamics of three rodent species, Lophuromys flavopuncatus, Grammomys dolichurus and Praomys delectorum, in the Magamba Forest, Western Usambara Mountains, north‐east Tanzania. Capture–mark–recapture studies were conducted in 2002–2004. Reproductive conditions of males and females showed temporal variations, an indication of breeding seasonality. Animals were reproductively active between February and May. Rainfall in November–January was instrumental for the onset of breeding and continued throughout the wet season. The recruitment of new individuals born during the season led to highest population densities between end of May and August. Populations declined progressively towards the end of the dry season (September–October). Only P. delectorum showed a marked density increase during January–February, indicating greater survival and/or recruitment during the November–January rains. The study shows that despite a relatively stable environment of the forest reserve, rainfall has strong influence on reproduction and population dynamics, probably because of its effect on primary food resources.
Comparative phenology and growth of four Cenchrus ciliaris L. accessions established under arid bioclimate in Tunisia
Authors: Lobna Mnif , Mohamed Chaieb 
Published: August 2006

AbstractA phenological study is one of the first steps in understanding the function of ecosystems. This is because phenological events reflect the way in which the species exploit the so‐called favourable periods in order to gain carbon and to allocate photosynthetic products for growth and reproduction. The objective of the present work was to examine the phenology of reproduction and the above‐ground growth of several Cenchrus ciliaris accessions, growing under the arid bioclimate in Tunisia. These accessions collected in the south of Tunisia are: Bou Hedma (P1), Tozeur (P2), Raas Jedir (P3) and Sidi Toui (P4). It was demonstrated that an important phenological variability exists within the different accessions studied. The statistical analysis (correlation and principal component analysis) showed that the accession from Bou Hedma (P1) was the most precocious and vigorous one.
Population genetic structure of the common warthog (Phacochoerus africanus) in Uganda: evidence for a strong philopatry among warthogs and social structure breakdown in a disturbed population
Authors: Muwanika Vincent B. , Nyakaana Silvester , Siegismund Hans R. , Arctander Peter 
Published: August 2006

AbstractFine‐scale genetic structure of large mammals is rarely analysed. Yet it is potentially important in estimating gene flow between the now fragmented wildlife habitats and in predicting re‐colonization following local extinction events. In this study, we examined the extent to which warthog populations from five localities in Uganda are genetically structured using both mitochondrial control region sequence and microsatellite allele length variation. Four of the localities (Queen Elizabeth, Murchison Falls, Lake Mburo and Kidepo Valley) are national parks with relatively good wildlife protection practices and the other (Luwero), not a protected area, is characterized by a great deal of hunting. In the total sample, significant genetic differentiation was observed at both the mtDNA locus (FST = 0.68;P < 0.001) and the microsatellite loci (FST = 0.14;P < 0.001). Despite the relatively short geographical distances between populations, significant genetic differentiation was observed in all pair‐wise population comparisons at the two marker sets (mtDNAFST = 0.21–0.79,P < 0.001; microsatelliteFST = 0.074–0.191,P < 0.001). Significant heterozygote deficiency was observed at most loci within protected areas while no significant deviation from Hardy–Weinberg expectation was observed in the unprotected Luwero population. We explain these results in terms of: (i) a strong philopatry among warthogs, (ii) a Wahlund effect resulting from the sampling regime and (iii) break down of social structure in the disturbed Luwero population.
Expression of TCL1 and CD27 in primary cutaneous B‐cell lymphomas
Authors: Pescarmona E , Remotti D , Perez M , Monaco S , Pacchiarotti A , Faraggiana T , Russo G , Baroni C D 
Published: August 2006

Aims To investigate by immunohistochemical analysis the expression of the TCL1 oncogene product and of CD27 in 25 cases of primary cutaneous B‐cell lymphomas (PCBCL) classified according to the World Health Organization–European Organization for Research and Treatment of Cancer classification of cutaneous lymphomas. In B‐cell ontogenesis TCL1 is mainly expressed by ‘naive’ B lymphocytes and by a subset of germinal centre B cells, whereas CD27 is expressed by a subset of germinal centre B cells, ‘memory’ B lymphocytes and plasma cells, suggesting that their expression in physiological conditions is mutually exclusive.Methods and results Overall, TCL1 was expressed in 5/25 cases (20%) and CD27 in 15/25 cases (60%). Furthermore, 7/25 cases (28%) were TCL1– and CD27– and 2/25 cases (8%) were TCL1+ and CD27+. In particular, primary cutaneous follicle‐centre lymphomas (10 cases) showed a variable expression of both TCL1 and CD27, whereas primary cutaneous marginal‐zone B‐cell lymphomas (eight cases) showed, with the exception of a single case, a definite CD27+/TCL1– profile.Conclusions These findings indicate: (i) the TCL1 oncogene product is uncommonly expressed in PCBCL (20% of cases, mainly of the follicle‐centre subtype); (ii) in contrast, CD27 is often expressed in PCBCL (60% of cases), mainly of the marginal‐zone subtype; (iii) the coexpression of TCL1 and CD27 may be seldom observed in PCBCL (8% of cases); (iv) PCBCL does not seem to show, in terms of either TCL1 or CD27 expression, significant differences compared with its systemic counterparts.
Synovitis score: discrimination between chronic low‐grade and high‐grade synovitis
Authors: Krenn V , Morawietz L , Burmester G‐R , Kinne R W , Mueller‐Ladner U , Muller B , Haupl T 
Published: August 2006

Aims : To standardize the histopathological assessment of synovial membrane specimens in order to contribute to the diagnostics of rheumatic and non‐rheumatic joint diseases.Methods and results : Three features of chronic synovitis (enlargement of lining cell layer, cellular density of synovial stroma, leukocytic infiltrate) were semiquantitatively evaluated (from 0, absent to 3, strong) and each feature was graded separately. The sum provided the synovitis score, which was interpreted as follows: 0–1, no synovitis; 2–4, low‐grade synovitis; 5–9, high‐grade synovitis. Five hundred and fifty‐nine synovectomy specimens were graded by two independent observers. Clinical diagnoses were osteoarthrosis (n = 212), post‐traumatic arthritis (n = 21), rheumatoid arthritis (n = 246), psoriatic arthritis (n = 22), reactive arthritis (n = 9), as well as controls (n = 49) from autopsies of patients without joint damage. Median synovitis scores when correlated with clinical diagnoses were: controls 1.0, osteoarthritis 2.0, post‐traumatic arthritis 2.0, psoriatic arthritis 3.5, reactive arthritis 5.0 and rheumatoid arthritis 5.0. The scores differed significantly between most disease groups, especially between degenerative and rheumatic diseases. A high‐grade synovitis was strongly associated with rheumatic joint diseases (P < 0.001, sensitivity 61.7%, specificity 96.1%). The correlation between the two observers was high (r = 0.941).Conclusion : The proposed synovitis score is based on well‐defined, reproducible histopathological criteria and may contribute to diagnosis in rheumatic and non‐rheumatic joint diseases.