bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of sperm DNA vaccine on fertility of female mice
Authors: Naz Rajesh K. 
Published: April 2006

AbstractOur laboratory has identified a sperm‐specific dodecamer peptide sequence, designated as YLP12, vaccination with which causes a long‐term reversible immunocontraceptive effect in female mice. In the present study, the effects of YLP12 DNA vaccine were examined. YLP12 36 bp cDNA was cloned into pVAX1 vector to prepare the DNA vaccine. Two additional vaccine constructs were made by in frame cloning of one and two CpG repeats in the YLP12‐cDNA vaccine. Five groups of female mice were immunized intradermally by using gene gun with YLP12‐cDNA, YLP12‐cDNA‐CpG, YLP12‐cDNA‐CpG‐CpG, YLP12‐cDNA mixed with exogenous synthetic CpG oligodeoxynucleotide (ODN), or vector DNA alone, respectively. Vaccination with all three constructs and the YLP12 vaccine mixed with exogenous ODN raised antibody response both in the sera as well as locally in the vaginal tract. There was no antibody response in the mice injected with the vector alone. In sera, the highest titers were obtained for the IgG class for all constructs and formulation followed by IgA class. In vaginal washings the highest titers were obtained for the IgA class followed by IgG class. Within the IgG class, the titers for the IgG2a subclass were significantly greater than the IgG1 subclass. Immunization with all constructs and formulation caused a significant (P < 0.05 to <0.001) reduction (20–43%) in fertility of female mice. The highest reductions were seen in mice immunized with YLP12‐cDNA‐CpG‐CpG (two repeats) (43% reduction) and with the YLP12 vaccine administered with exogenous CpG ODN (42% reduction). T lymphocytes obtained from DNA‐vaccinated mice showed clearly distinguished comparative RT‐PCR analysis of cytokine mRNA expression for Th1 and Th2 immune responses compared to T lymphocytes obtained from control animals injected with vector DNA. Expression of both Th1 cytokines (IL‐2 and IFN‐gamma) and Th2 cytokines (IL‐4 and IL‐10) was enhanced after DNA vaccination as compared to controls, with a bias towards Th1 response. The immunocontraceptive effects were long‐lasting observed up to 1.3 years of the observation period and increased with time. These novel findings indicate that the intradermal immunization with a sperm‐specific DNA vaccine causes a long‐term circulating and local immune response resulting in immunocontraceptive effects in female mice. Mol. Reprod. Dev. © 2006 Wiley‐Liss, Inc.
Electron paramagnetic resonance imaging of tumor hypoxia: Enhanced spatial and temporal resolution for in vivo pO2 determination
Authors: Matsumoto Ken‐ichiro , Subramanian Sankaran , Devasahayam Nallathamby , Aravalluvan Thirumaran , Murugesan Ramachandran , Cook John A. , Mitchell James B. , Krishna Murali C. 
Published: April 2006

AbstractThe time‐domain (TD) mode of electron paramagnetic resonance (EPR) data collection offers a means of estimating the concentration of a paramagnetic probe and the oxygen‐dependent linewidth (LW) to generate pO2 maps with minimal errors. A methodology for noninvasive pO2 imaging based on the application of TD‐EPR using oxygen‐induced LW broadening of a triarylmethyl (TAM)‐based radical is presented. The decay of pixel intensities in an image is used to estimate T, which is inversely proportional to pO2. Factors affecting T in each pixel are critically analyzed to extract the contribution of dissolved oxygen to EPR line‐broadening. Suitable experimental and image‐processing parameters were obtained to produce pO2 maps with minimal artifacts. Image artifacts were also minimized with the use of a novel data collection strategy using multiple gradients. Results from a phantom and in vivo imaging of tumor‐bearing mice validated this novel method of noninvasive oximetry. The current imaging protocols achieve a spatial resolution of ∼1.0 mm and a temporal resolution of ∼9 s for 2D pO2 mapping, with a reliable oxygen resolution of ∼1 mmHg (0.12% oxygen in gas phase). This work demonstrates that in vivo oximetry can be performed with good sensitivity, accuracy, and high spatial and temporal resolution. Magn Reson Med, 2006. Published 2006 Wiley‐Liss, Inc.
The bi‐criteria doubly weighted center‐median path problem on a tree
Authors: Puerto J. , Rodríguez‐Chía A.M. , Tamir A. , Pérez‐Brito D. 
Published: April 2006

AbstractGiven a tree network T with n nodes, let 𝒫L be the subset of all discrete paths whose length is bounded above by a prespecified value L. We consider the location of a path‐shaped facility P ∈ 𝒫L, where customers are represented by the nodes of the tree. We use a bi‐criteria model to represent the total transportation cost of the customers to the facility. Each node is associated with a pair of nonnegative weights: the center‐weight and the median‐weight. In this doubly weighted model, a path P is assigned a pair of values (MAX(P),SUM(P)), which are, respectively, the maximum center‐weighted distance and the sum of the median‐weighted distances from P to the nodes of the tree. Viewing 𝒫L and the planar set {(MAX(P),SUM(P)) : P ∈ 𝒫L} as the decision space and the bi‐criteria or outcome space respectively, we focus on finding all the nondominated points of the bi‐criteria space. We prove that there are at most 2n nondominated outcomes, even though the total number of efficient paths can be Ω(n2), and they can all be generated in O(n log n) optimal time. We apply this result to solve the cent‐dian model, whose objective is a convex combination of the weighted center and weighted median functions. We also solve the restricted models, where the goal is to minimize one of the two functions MAX or SUM, subject to an upper bound on the other one, both with and without a constraint on the length of the path. All these problems are solved in linear time, once the set of nondominated outcomes has been obtained, which in turn, results in an overall complexity of O(n log n). The latter bounds improve upon the best known results by a factor of O(log n). © 2006 Wiley Periodicals, Inc. NETWORKS, Vol. 47(4), 237–247 2006
Investigation of fracture mechanism on liquid crystalline epoxy networks arranged by a magnetic field
Authors: Harada Miyuki , Akamatsu Naoki , Ochi Mitsukazu , Tobita Masayuki 
Published: April 2006

AbstractA liquid crystalline epoxy resin was cured under non‐ and 10T‐magnetic fields, and polydomain and monodomain networks were obtained, respectively. The fracture toughness of these systems was evaluated and it was clarified that the toughness of the magnetic field system showed a higher value. To investigate the toughening mechanism, polarized micro FTIR measurements were carried out. As a result, it was clarified that their mechanisms were quiet different. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1406–1412, 2006
Unfolding transition state and intermediates of the tumor suppressor p16INK4a investigated by molecular dynamics simulations
Authors: Interlandi Gianluca , Settanni Giovanni , Caflisch Amedeo 
Published: April 2006

AbstractThe ankyrin repeat is one of the most common protein motifs and is involved in protein–protein interactions. It consists of 33 residues that assume a β‐hairpin helix‐loop‐helix fold. Mutagenesis and kinetic experiments (Φ‐value analysis of the folding transition state) have shown that the tumor suppressor p16INK4a, a four‐repeat protein, unfolds sequentially starting from the two N‐terminal repeats. Here, the flexibility of p16INK4a at room temperature and its unfolding mechanism at high temperature have been investigated by multiple molecular dynamics runs in explicit water for a total simulation time of 0.65 μs. The transition state ensemble (TSE) of p16INK4a was identified by monitoring both the deviation from the experimental Φ values and sudden conformational changes along the unfolding trajectories. Conformations in the TSE have a mainly unstructured second repeat whereas the other repeats are almost completely folded. A rigid‐body displacement of the first repeat involving both a rotation and translation is observed in all molecular dynamics simulations at high temperature. The Trp15, Pro75, and Ala76 side‐chains are more buried in the TSE than the native state. The sequential unfolding starting at the second repeat is in agreement with the mutagenesis studies whereas the displacement of the first repeat and the presence of nonnative interactions at the TSE are simulation results which supplement the experimental data. Furthermore, the unfolding trajectories reveal the presence of two on‐pathway intermediates with partial α‐helical structure. Finally, on the basis of the available experimental and simulation results we suggest that in modular proteins the shift of the folding TSE toward the native structure upon reduction of the number of tandem repeats is consistent with the Hammond effect. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Xα‐DVM modelling of oxygen transport in YBa2Cu3O7‐δ and SrFeO3
Authors: Yuryeva Elmira I. 
Published: April 2006

AbstractThe reasons for oxygen transport in YBa2Cu3O7‐δ and SrFeO3 were investigated, using the Xα‐discrete variation method. Reduced binding energy and other parameters of the electronic energy structure were calculated for a number of crystal fragments within the T and O phases of YBa2Cu3O7‐δ and the cubic phase of SrFeO3. The following results were obtained: (i) test calculations of reduced binding energy confirmed that high temperature should be a condition of existence of the T phase, as compared with the O phase of YBa2Cu3O7‐δ; (ii) an increase in temperature up to ∼400°C points to the beginning of the Jahn–Teller dynamic effect in SrFeO3; and (iii) transport of neutral and charged oxygen atoms results in distributions of stable and unstable oxygen vacancies, respectively. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Optimization of strong and weak coordinates
Authors: Swart Marcel , Matthias Bickelhaupt F. 
Published: April 2006

AbstractWe present a new scheme for the geometry optimization of equilibrium and transition state structures that can be used for both strong and weak coordinates. We use a screening function that depends on atom‐pair distances to differentiate strong coordinates from weak coordinates. This differentiation significantly accelerates the optimization of these coordinates, and thus of the overall geometry. An adapted version of the delocalized coordinates setup is used to generate automatically a set of internal coordinates that is shown to perform well for the geometry optimization of systems with weak and strong coordinates. For the Baker test set of 30 molecules, we need only 173 geometry cycles with PW91/TZ2P calculations, which compares well with the best previous attempts reported in literature. For the localization of transition state structures, we generate the initial Hessian matrix, using appropriate force constants from a database. In this way, one avoids the explicit computation of the Hessian matrix. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Some design issues of strata‐matched non‐randomized studies with survival outcomes
Authors: Mazumdar Madhu , Tu Donsheng , Zhou Xi Kathy 
Published: April 2006

AbstractNon‐randomized studies for the evaluation of a medical intervention are useful for quantitative hypothesis generation before the initiation of a randomized trial and also when randomized clinical trials are difficult to conduct. A strata‐matched non‐randomized design is often utilized where subjects treated by a test intervention are matched to a fixed number of subjects treated by a standard intervention within covariate based strata. In this paper, we consider the issue of sample size calculation for this design. Based on the asymptotic formula for the power of a stratified log‐rank test, we derive a formula to calculate the minimum number of subjects in the test intervention group that is required to detect a given relative risk between the test and standard interventions. When this minimum number of subjects in the test intervention group is available, an equation is also derived to find the multiple that determines the number of subjects in the standard intervention group within each stratum. The methodology developed is applied to two illustrative examples in gastric cancer and sarcoma. Copyright © 2006 John Wiley & Sons, Ltd.
Much ado about nothing: a comparison of the performance of meta‐analytical methods with rare events
Authors: Bradburn Michael J. , Deeks Jonathan J. , Berlin Jesse A. , Russell Localio A. 
Published: April 2006

AbstractFor rare outcomes, meta‐analysis of randomized trials may be the only way to obtain reliable evidence of the effects of healthcare interventions. However, many methods of meta‐analysis are based on large sample approximations, and may be unsuitable when events are rare. Through simulation, we evaluated the performance of 12 methods for pooling rare events, considering estimability, bias, coverage and statistical power. Simulations were based on data sets from three case studies with between five and 19 trials, using baseline event rates between 0.1 and 10 per cent and risk ratios of 1, 0.75, 0.5 and 0.2. We found that most of the commonly used meta‐analytical methods were biased when data were sparse. The bias was greatest in inverse variance and DerSimonian and Laird odds ratio and risk difference methods, and the Mantel–Haenszel (MH) odds ratio method using a 0.5 zero‐cell correction. Risk difference meta‐analytical methods tended to show conservative confidence interval coverage and low statistical power at low event rates. At event rates below 1 per cent the Peto one‐step odds ratio method was the least biased and most powerful method, and provided the best confidence interval coverage, provided there was no substantial imbalance between treatment and control group sizes within trials, and treatment effects were not exceptionally large. In other circumstances the MH OR without zero‐cell corrections, logistic regression and the exact method performed similarly to each other, and were less biased than the Peto method. Copyright © 2006 John Wiley & Sons, Ltd.
Interval estimation for rank correlation coefficients based on the probit transformation with extension to measurement error correction of correlated ranked data
Authors: Rosner Bernard , Glynn Robert J. 
Published: April 2006

AbstractThe Spearman (ρs) and Kendall (τ) rank correlation coefficient are routinely used as measures of association between non‐normally distributed random variables. However, confidence limits for ρs are only available under the assumption of bivariate normality and for τ under the assumption of asymptotic normality of . In this paper, we introduce another approach for obtaining confidence limits for ρs or τ based on the arcsin transformation of sample probit score correlations. This approach is shown to be applicable for an arbitrary bivariate distribution. The arcsin‐based estimators for ρs and τ (denoted by s,a, a) are shown to have asymptotic relative efficiency (ARE) of 9/π2 compared with the usual estimators s and when ρs and τ are, respectively, 0.In some nutritional applications, the Spearman rank correlation between nutrient intake as assessed by a reference instrument versus nutrient intake as assessed by a surrogate instrument is used as a measure of validity of the surrogate instrument. However, if only a single replicate (or a few replicates) are available for the reference instrument, then the estimated Spearman rank correlation will be downwardly biased due to measurement error. In this paper, we use the probit transformation as a tool for specifying an ANOVA‐type model for replicate ranked data resulting in a point and interval estimate of a measurement error corrected rank correlation. This extends previous work by Rosner and Willett for obtaining point and interval estimates of measurement error corrected Pearson correlations. Copyright © 2006 John Wiley & Sons, Ltd.
A dose–response test via closed‐form solutions for constrained MLEs in survival/sacrifice experiments
Authors: Kim Wonkuk , Ahn Hongshik , Moon Hojin 
Published: April 2006

AbstractIn most survival–sacrifice experiments in animal carcinogenicity studies, the onset of the tumour of interest is not clinically observable. Due to the complexity of constraints for a biological justification, recently developed methods for estimating the tumour onset function and tumour‐specific survival function employ computer‐intensive numerical solutions. In this paper, closed‐form solutions for nonparametric maximum likelihood estimators are derived under explicit and implicit inequality constraints obtained from the monotonicity of the survival functions. Our methods do not require cause‐of‐death information. The proposed methods can be used to estimate the tumour onset function and the survival function of the tumour of interest. We use the proposed estimators for the development of our new dose–response trend test. A modification of the Poly‐k test is made by replacing the time‐ at‐risk weight to a function of the tumour onset survival function. The weighted least square regression method is applied to the estimated survival functions in order to construct a dose–response trend test. A simulation study is conducted to evaluate the performance of the proposed test and compare it with existing trend tests. A real example is used to illustrate the methods. Copyright © 2006 John Wiley & Sons, Ltd.
Integrated development and maintenance for the release, delivery, deployment, and customization of product software: a case study in mass‐market ERP software
Authors: Jansen Slinger , Ballintijn Gerco , Brinkkemper Sjaak , van Nieuwland Arco 
Published: April 2006

AbstractThe maintenance of enterprise application software at a customer site is a complex task for software vendors. This complexity results in a significant amount of work and risk. This article presents a case study of a product software vendor that tries to reduce this complexity by integrating product data management (PDM), software configuration management (SCM), and customer relationship management (CRM) into one system. The case study shows that by combining these management areas in a single software knowledge base, software maintenance processes can be automated and improved, thereby enabling a software vendor of enterprise resource planning software to serve a large number of customers with many different product configurations. Copyright © 2006 John Wiley & Sons, Ltd.
Effect of pericardiotomy on exercise-induced pulmonary hypertension in the horse
Authors: Textor JA , Ducharme NG , Gleed RD , Hackett RP , Erb HN , Mitchell L , Soderholm LV 
Published: April 2006

AbstractThe role of cardiac function or dysfunction in the pathogenesis of exercise-induced pulmonary hypertension and haemorrhage in horses has been minimally investigated. We hypothesize that pericardiotomy would enhance diastolic function and attenuate pulmonary vascular pressures in maximally exercising horses. Our objective was to evaluate diastolic function and cardiopulmonary pressures before and after pericardiotomy, at rest and at maximal exercise. Study design was both self- and externally controlled. Five horses underwent pericardiotomy after a baseline exercise test. They subsequently performed the same exercise protocol at 1 week and 13 weeks post-operatively. An external, unoperated control group of five horses performed the same experimental protocol. Pulmonary arterial pressure (PAP), pulmonary artery wedge pressure (PWP), right ventricular pressure, heart rate (HR) and oesophageal pressure were measured continuously at rest and at maximal exercise; maximum rates of ventricular pressure decrease (−dP/dtmax), relaxation half-time (t1/2), time constant of isovolumic relaxation (τ) and pulmonary capillary pressures (PcapP) were derived. Statistical analysis was performed using two-tailed Wilcoxon's signed-rank and rank-sum tests, with significance set atP<0.05. No significant differences were found in any variable after pericardiotomy was performed or between the experimental and external control groups. We conclude that during a 13-week study period, pericardiotomy does not alter pulmonary or ventricular pressures or rate of ventricular relaxation in the resting or maximally exercising horse. Results indicate that, in past and future studies requiring an open pericardium in normal horses, the cardiopulmonary parameters measured here are not affected by reduced pericardial pressure.
Infuse: A TDMA Based Data Dissemination Protocol for Sensor Networks
Authors: Kulkarni Sandeep S. , Arumugam Mahesh 
Published: April 2006

Reliable dissemination of bulk data is one of the important problems in sensor networks. For example, programming or upgrading the software in sensors at run-time requires reliable dissemination of a new program across the network. In this paper, we present Infuse, a time division multiple access (TDMA) based reliable data dissemination protocol. Infuse takes two input parameters: the choice of the recovery algorithm (from one of two presented in this paper) to deal with unexpected channel errors (e.g., message corruption, varying signal strength), and whether a sensor should listen only to a subset of its neighbors to reduce the amount of active radio time. Based on these parameters, we obtain four possible versions of Infuse. We compare the performance of these versions to assist a designer in selecting the appropriate version based on the network characteristics. Furthermore, we demonstrate Infuse in the context of network programming.
Variation in performance of elite cyclists from race to race
Authors: Paton Carl D. , Hopkins Will G. 
Published: April 2006

AbstractThe race‐to‐race variation in performance of a top athlete determines the smallest change in performance affecting the athlete's chances of winning. We report here the typical variation in competition times of elite cyclists in various race series. Repeated‐measures analysis of log‐transformed official race times provided the typical variation in a cyclist's performance as a coefficient of variation. The typical variation of a top cyclist (and its 95% likely limits) was 0.4% (0.3–0.5%) in World Cup road races, 0.7% (0.7–0.8%) in Tour de France road races, 1.2% (0.8–2.2%) in the Kilo, 1.3% (0.9–2.4%) in road time trials, 1.7% (1.2–2.6%) in Tour de France time trials, and 2.4% (2.1–2.8%) in World Cup mountain biking. Cyclist interdependence arising from team tactics and pack riding probably accounts for the lower variability in performance of cyclists in road races and precludes estimation of the smallest worthwhile change in performance time for cyclists in these events. The substantial differences in variability between the remaining events, where riders act independently of each other, arise from various event‐specific aspects. For these events the smallest worthwhile changes in performance time (∼0.5×typical variation) are ∼0.5% in the Kilo, ∼0.6% in road time trials, and ∼1.2% in mountain‐bike races.