bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of models for average bioequivalence in replicated crossover designs
Authors: Willavize Susan A. , Morgenthien Elizabeth A. 
Published: May 2006

AbstractAverage bioequivalence (ABE) has been the regulatory standard for bioequivalence (BE) since the 1990s. BE studies are commonly two‐period crossovers, but may also use replicated designs. The replicated crossover will provide greater power for the ABE assessment. FDA has recommended that ABE analysis of replicated crossovers use a model which includes terms for separate within‐ and between‐subject components for each formulation and which allows for a subject × formulation interaction component. Our simulation study compares the performance of four alternative mixed effects models: the FDA model, a three variance component model proposed by Ekbohm and Melander (EM), a random intercepts and slopes model (RIS) proposed by Patterson and Jones, and a simple model that contains only two variance components. The simple model fails (when not ‘true’) to provide adequate coverage and it accepts the hypothesis of equivalence too often. FDA and EM models are frequently indistinguishable and often provide the best performance with respect to coverage and probability of concluding BE. The RIS model concludes equivalence too often when both the within‐ and between‐subject variance components differ between formulations. The FDA analysis model is recommended because it provides the most detail regarding components of variability and has a slight advantage over the EM model in confidence interval length. Copyright © 2006 John Wiley & Sons, Ltd.
Assessing the zero‐field splitting in magnetic molecules by wave function‐based methods
Authors: de Graaf Coen , Sousa Carmen 
Published: May 2006

AbstractThe effect of spin‐orbit coupling is assessed through the spin‐orbit state interaction method. This method involves a two‐step procedure to include both dynamical electron correlation effects and spin‐orbit effects on the relative energies of the low‐lying electronic states. Accurate energies of the spin free states are obtained with the complete active space self‐consistent field/complete active space second‐order perturbation theory (CASSCF/CASPT2) procedure. Second, the spin‐orbit coupling is taken into account by interaction of the CASSCF states using the CASPT2 relative energies. The method is validated on the Co2+ ion in vacuum and in the ionic insulator CoO. Afterward the method is applied to CoCl2(PPh3)2 and the dinuclear complexes [TM2Cl6]2− (TM = Mn, Fe, Co). For the monomeric species, the results compare favorable with experimental data or fully relativistic benchmarks. We discuss the difficulties to interpret the dimer results in terms of the parameters that are usually derived from experiment. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Increase in DNA fragmentation and apoptosis-related gene expression in frozen-thawed bovine blastocysts
Authors: Park Sae Young , Kim Eun Young , Cui Xiang Shun , Tae Jin Cheol , Lee Won Don , Kim Nam Hyung , Park Se Pill , Lim Jin Ho 
Published: May 2006

SummaryEvaluation of apoptosis and expression level of apoptosis-related genes is useful for examining the variation in embryo quality according to environmental change. The objective of this study was to investigate DNA fragmentation and apoptosis-related gene expression patterns in frozen-thawed bovine blastocysts.In vitroproduced day 7 blastocysts were frozen by two different vitrification methods (conventional 0.25 ml straw or MVC straw). After thawing, DNA fragmentation of surviving embryos was examined by TUNEL assay, and the expression patterns of their apoptotic genes (survivin, Fas, Hsp 70 and caspase-3) were evaluated using real-time quantitative reverse transcriptase polymerase chain reaction.In vitrosurvival rates of frozen-thawed embryos were higher following the MVC vitrification method (88.2% re-expanded at 24 h, 77.1% hatching at 48 h) than the conventional (C) vitrification method (77.0% re-expanded at 24 h, 66.7% hatching at 48 h). However, both vitrified methods resulted in a significantly higher apoptotic index (C vitrification method 11.9%, MVC vitrification method 11.0%) than in non-frozen embryos (3.0%). Expression levels of survivin, Fas, caspase-3, and Hsp 70 were also increased in the frozen-thawed embryos compared with non-frozen embryos. These results indicate that the cryopreservation procedure might cause damage that results in an increase in DNA fragmentation and apoptosis-related gene transcription, reducing developmental capacity of frozen-thawed embryos.
Quality control of rainfall measurements in Cyprus
Authors: Golz Claudia , Einfalt Thomas , Michaelides Silas Chr. 
Published: May 2006

AbstractThe basic condition for using precipitation data from raingauges and radars is data quality control. This aspect is important for comparing and using rainfall data, for example in models. In the scope of the EU‐project VOLTAIRE (Validation of multisensors precipitation fields and numerical modelling in Mediterranean test sites) rain data from Cyprus have been analysed. Different quality control methods have been applied to the rainfall data of 158 raingauges and the data of 11 events (in 2002 and 2003) of the C‐Band radar in Kykkos. The first results of the use of ground clutter algorithms for radar data in Cyprus are presented in the paper. Copyright © 2006 Royal Meteorological Society.
Modelling dust transport over central eastern Australia
Authors: Leslie Lance M. , Speer Milton S. 
Published: May 2006

AbstractA ten‐year climatology has been prepared of dust days for central eastern Australia, from January 1995 to February 2004, using reports from the Australian Bureau of Meteorology's observational network. It was found that there had been a total of 55 dust days during this ten‐year period. Of these, 43 dust days were associated with cold fronts: 24 were classified as embedded in the zonal westerlies in the Great Australian Bight (GAB) or in westerlies derived from low pressure systems in the GAB, whereas the remaining 19 were associated with cold fronts over eastern Australia where high pressure systems in the GAB generated strong post‐frontal south to southeast winds. Three detailed case studies of dust storm generation and transport were modelled using a sophisticated coupled wind erosion prediction system. The model predictions in all three cases were found to be broadly consistent both with satellite images highlighting dust and the synoptic observations that reported dust. Antecedent land surface conditions are found to be critically important in generating dust, and their representation in the integrated prediction system is subsequently important in providing skilful model predictions of dust transport. Copyright © 2006 Royal Meteorological Society.
Detecting and nowcasting cloudiness using near‐surface temperatures on winter nights
Authors: Grimbacher Tobias , Schmid Willi 
Published: May 2006

AbstractA model to deduce cloudiness from automatic measurements of synoptic and road weather stations during winter nights is introduced. The (height‐adjusted) cloud amount of each station can be determined from near‐surface temperature measurements and precipitation information only. By using the difference between the air temperature at surface level and the air temperature 2 m above ground, a correlation coefficient is achieved of up to 0.91 between the calculated cloud amount and observations. The model is applied to a dense network in central Switzerland in order to obtain a two‐dimensional cloud map by interpolation. With the help of a tracking algorithm, the displacement of cloud patterns is nowcasted. The procedure was tested using data from winter 2003–4. It works successfully with a forecast range up to about 90 minutes. The results are used to predict a change in surface temperature (in cases with changing cloudiness), and thus allow nowcasting of slippery roads or ground frost. Copyright © 2006 Royal Meteorological Society.
Heat balance of an asphalt surface: observations and physically‐based simulations
Authors: Jansson C. , Almkvist E. , Jansson P‐E. 
Published: May 2006

AbstractA physically‐based 1‐D heat and mass transfer model was tested to estimate the heat fluxes of an asphalt surface. The model was run for two summer months for a road test site in southwest Sweden. Parameters for thermal properties, surface runoff, radiation and turbulent transfer were obtained from a description of the road stratification and from the literature. Coefficients of determination (r2) 0.94, 0.93 and 0.97 were obtained when simulated results were compared with observations of net radiation, heat flow below the surface and surface temperature respectively, all with slope coefficients close to unity. In addition, simulation results elucidated the role of water vapour transport through the asphalt‐soil profile and its effect on the latent heat flow from the surface. Problems were identified with closure of the heat balance in measurements based on discrepancy between simulated and observed sensible heat flux. Copyright © 2006 Royal Meteorological Society.
Existence of positive solutions for a semilinear elliptic problem with critical Sobolev and Hardy terms
Authors: Hirano Norimichi , Shioji Naoki 
Published: May 2006

Let

N
≥
4

N\geq 4

, let

2

∗

=
2
N

/

(
N
−
2
)

2^{\ast }=2N/(N-2)

and let

Ω
⊂

R

N

\Omega \subset \mathbb {R}^{N}

be a bounded domain with a smooth boundary

∂
Ω

\partial \Omega

. Our purpose in this paper is to consider the existence of solutions of the problem:
\[

{

−
Δ
u
−
μ

u

|
x

|
2

a
m
p
;
=
|
u

|

2
∗

−
1

a
m
p
;

a
m
p
;

in

Ω

,

u

a
m
p
;
>
0

a
m
p
;

a
m
p
;

in

Ω

,

u

a
m
p
;
=
0

a
m
p
;

a
m
p
;

on

∂
Ω

,

\left \{ \begin {aligned} -\Delta u - \mu \frac {u}{\vert x\vert ^2} &= \vert u\vert ^{2^\ast -1} && \text {in $\Omega $}, \\ u & > 0 && \text {in $\Omega $},\\ u & = 0 && \text {on $\partial \Omega $}, \end {aligned} \right .

\]
where

0
>
μ
>
(

N
−
2

2

)

2

.

0>\mu >(\frac {N-2}{2})^{2}.
A remark on the existence of suitable vector fields related to the dynamics of scalar semi-linear parabolic equations
Authors: Hang Fengbo , Jiang Huiqiang 
Published: May 2006

In 1992, P. Poláčik showed that one could linearly imbed any vector field into a scalar semi-linear parabolic equation on

Ω
\Omega

with Neumann boundary condition provided that there exists a smooth vector field

Φ
=

(

ϕ

1

,
⋯
,

ϕ

n

)

\Phi =\left ( \phi _{1},\cdots ,\phi _{n}\right )

on

Ω
¯

\overline {\Omega }

such that
\[

{

rank
⁡

(
Φ

(
x
)

,

∂

1

Φ

(
x
)

,
⋯
,

∂

n

Φ

(
x
)

)

=
n
for all
x
∈

Ω
¯

,

∂
Φ

∂
ν

=
0
on
∂
Ω
.

\left \{ \begin {array} [c]{l} \operatorname {rank}\left ( \Phi \left ( x\right ) ,\partial _{1}\Phi \left ( x\right ) ,\cdots ,\partial _{n}\Phi \left ( x\right ) \right ) =n\text { for all }x\in \overline {\Omega }, \frac {\partial \Phi }{\partial \nu }=0\text { on }\partial \Omega \text {.} \end {array} \right .

\]
In this short paper, we give a classification of all the domains on which one may find such a type of vector field.
On the arithmetic of tight closure
Authors: Brenner Holger , Katzman Mordechai 
Published: May 2006

We provide a negative answer to an old question in tight closure theory by showing that the containment

x
3

y
3

∈
(

x
4

,

y
4

,

z
4

)
∗

x^3y^3 \in (x^4,y^4,z^4)^*

in

K

[
x
,
y
,
z
]

/

(

x
7

+

y
7

−

z
7

)

\mathbb {K}[x,y,z]/(x^7+y^7-z^7)

holds for infinitely many but not for almost all prime characteristics of the field

K

\mathbb {K}

. This proves that tight closure exhibits a strong dependence on the arithmetic of the prime characteristic. The ideal

(
x
,
y
,
z
)
⊂

K

[
x
,
y
,
z
,
u
,
v
,
w
]

/

(

x
7

+

y
7

−

z
7

,
u

x
4

+
v

y
4

+
w

z
4

+

x
3

y
3

)

(x,y,z) \subset \mathbb {K}[x,y,z,u,v,w]/(x^7+y^7-z^7, ux^4+vy^4+wz^4+x^3y^3)

has then the property that the cohomological dimension fluctuates arithmetically between

0
0

and

1
1

.
Cobounding odd cycle colorings
Authors: Kozlov Dmitry 
Published: May 2006

We prove that the

(
n
−
2
)

(n-2)

nd power of the Stiefel-Whitney class of the space of all

n
n

-colorings of an odd cycle is

0
0

by presenting a cochain whose coboundary is the desired power of the class. This gives a very short self-contained combinatorial proof of a conjecture by Babson and the author.
BDT: an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock
Authors: Vaqué Montserrat , Arola Anna , Aliagas Carles , Pujadas Gerard 
Published: May 2006

Abstract
Motivation: AutoGrid/AutoDock is one of the most popular software packages for docking, but its automation is not trivial for tasks such as (1) the virtual screening of a library of ligands against a set of possible receptors; (2) the use of receptor flexibility and (3) making a blind-docking experiment with the whole receptor surface. This is an obstacle for research teams in the fields of Chemistry and the Life Sciences who are interested in conducting this kind of experiment but do not have enough programming skills. To overcome these limitations, we have designed BDT, an easy-to-use graphic interface for AutoGrid/AutoDock.
Availability: BDT is available for free, upon request, for non-commercial research.
Supplementary information:
Contact: gerard.pujadas@urv.cat
Imprint of evolutionary conservation and protein structure variation on the binding function of protein tyrosine kinases
Authors: Verkhivker Gennady M. 
Published: May 2006

Abstract
Motivation: According to the models of divergent molecular evolution, the evolvability of new protein function may depend on the induction of new phenotypic traits by a small number of mutations of the binding site residues. Evolutionary relationships between protein kinases are often employed to infer inhibitor binding profiles from sequence analysis. However, protein kinases binding profiles may display inhibitor selectivity within a given kinase subfamily, while exhibiting cross-activity between kinases that are phylogenetically remote from the prime target. The emerging insights into kinase function and evolution combined with a rapidly growing number of publically available crystal structures of protein kinases complexes have motivated structural bioinformatics analysis of sequence–structure relationships in determining the binding function of protein tyrosine kinases.
Results: In silico profiling of Imatinib mesylate and PD-173955 kinase inhibitors with protein tyrosine kinases is conducted on kinome scale by using evolutionary analysis and fingerprinting inhibitor–protein interactions with the panel of all publically available protein tyrosine kinases crystal structures. We have found that sequence plasticity of the binding site residues alone may not be sufficient to enable protein tyrosine kinases to readily evolve novel binding activities with inhibitors. While evolutionary signal derived solely from the tyrosine kinase sequence conservation can not be readily translated into the ligand binding phenotype, the proposed structural bioinformatics analysis can discriminate a functionally relevant kinase binding signal from a simple phylogenetic relationship. The results of this work reveal that protein conformational diversity is intimately linked with sequence plasticity of the binding site residues in achieving functional adaptability of protein kinases towards specific drug binding. This study offers a plausible molecular rationale to the experimental binding profiles of the studied kinase inhibitors and provides a theoretical basis for constructing functionally relevant kinase binding trees.
Contact: gverkhiv@ucsd.edu
Supplementary information: The supplementary material contains the details of the phylogenetic analysis of protein tyrosine kinases, including phylogenetic dendrograms of protein tyrosine kinases based on sequence alignments of the kinases catalytic domain and evolutionary conservation profiles of the binding site residues. This section provides a more detailed description of the Monte Carlo binding simulations, including energetic model and simulated tempering technique generalized for ligand–protein binding dynamics with the multiple protein tyrosine kinase structures.
SNPStats: a web tool for the analysis of association studies
Authors: Solé Xavier , Guinó Elisabet , Valls Joan , Iniesta Raquel , Moreno Víctor 
Published: May 2006

Abstract
Summary: A web-based application has been designed from a genetic epidemiology point of view to analyze association studies. Main capabilities include descriptive analysis, test for Hardy–Weinberg equilibrium and linkage disequilibrium. Analysis of association is based on linear or logistic regression according to the response variable (quantitative or binary disease status, respectively). Analysis of single SNPs: multiple inheritance models (co-dominant, dominant, recessive, over-dominant and log-additive), and analysis of interactions (gene–gene or gene–environment). Analysis of multiple SNPs: haplotype frequency estimation, analysis of association of haplotypes with the response, including analysis of interactions.
Availability: . Source code for local installation is available under GNU license.
Contact: v.moreno@iconcologia.net
Supplementary Information: Figures with a sample run are available on Bioinformatics online. A detailed online tutorial is available within the application.
Fructose Administration Increases Intraoperative Core Temperature by Augmenting Both Metabolic Rate and the Vasoconstriction Threshold
Authors: Mizobe Toshiki , Nakajima Yasufumi , Ueno Hiroshi , Sessler Daniel I. 
Published: May 2006

Background
The authors tested the hypothesis that intravenous fructose ameliorates intraoperative hypothermia both by increasing metabolic rate and the vasoconstriction threshold (triggering core temperature).

Methods
Forty patients scheduled to undergo open abdominal surgery were divided into two equal groups and randomly assigned to intravenous fructose infusion (0.5 g . kg(-1) . h(-1) for 4 h, starting 3 h before induction of anesthesia and continuing for 4 h) or an equal volume of saline. Each treatment group was subdivided: Esophageal core temperature, thermoregulatory vasoconstriction, and plasma concentrations were determined in half, and oxygen consumption was determined in the remainder. Patients were monitored for 3 h after induction of anesthesia.

Results
Patient characteristics, anesthetic management, and circulatory data were similar in the four groups. Mean final core temperature (3 h after induction of anesthesia) was 35.7 degrees +/- 0.4 degrees C (mean +/- SD) in the fructose group and 35.1 degrees +/- 0.4 degrees C in the saline group (P = 0.001). The vasoconstriction threshold was greater in the fructose group (36.2 degrees +/- 0.3 degrees C) than in the saline group (35.6 degrees +/- 0.3 degrees C; P < 0.001). Oxygen consumption immediately before anesthesia induction in the fructose group (214 +/- 18 ml/min) was significantly greater than in the saline group (181 +/- 8 ml/min; P < 0.001). Oxygen consumption was 4.0 l greater in the fructose patients during 3 h of anesthesia; the predicted difference in mean body temperature based only on the difference in metabolic rates was thus only 0.4 degrees C. Epinephrine, norepinephrine, and angiotensin II concentrations and plasma renin activity were similar in each treatment group.

Conclusions
Preoperative fructose infusion helped to maintain normothermia by augmenting both metabolic heat production and increasing the vasoconstriction threshold.
Comparison of Three Disposable Extraglottic Airway Devices in Spontaneously Breathing Adults
Authors: van Zundert André , Al-Shaikh Baha , Brimacombe Joseph , Koster Jurgen , Koning Dick , Mortier Eric P. 
Published: May 2006

Background
The authors compared three disposable extraglottic airway devices in spontaneously breathing anesthetized adults: the LMA-Unique (LMA-U; The Laryngeal Mask Company, San Diego, CA), the Soft Seal laryngeal mask (SS-LM; Portex Ltd., Hythe, United Kingdom), and the Cobra perilaryngeal airway (Cobra-PLA; Engineered Medical Systems, Inc. Indianapolis, IN).

Methods
Three hundred twenty consecutive adults (American Society of Anesthesiologists physical status I-III; aged 18-80 yr) were randomly allocated for airway management with one of the three devices. Anesthesia was with fentanyl-propofol for induction and a sevoflurane-nitrous oxide-oxygen-fentanyl mixture for maintenance. Intraoperative data were collected by an unblinded observer about ease of insertion, effective airway time, oropharyngeal leak pressure, anatomical position (determined with a rigid endoscope), intracuff pressure changes, and airway trauma. Data were collected by a blinded observer about sore throat, dysphagia, and dysphonia 2 h after surgery.

Results
Insertion was easier with the LMA-U and SS-LM than with the Cobra-PLA (P < 0.02), but the overall failure rates were similar. Effective airway times were similar among groups. Oropharyngeal leak pressure was lower with the LMA-U than with the SS-LM and Cobra-PLA (P < 0.001). Intracuff pressure increased during surgery with all extraglottic airway devices. Anatomical position was better with the Cobra-PLA than with the SS-LMA (P < 0.001) and better with the SS-LM than with LMA-U (P < 0.001). Blood staining was detected more frequently with the Cobra-PLA than with the LMA-U and SS-LM (P < 0.001), but there were no differences in airway morbidity.

Conclusion
The LMA-U and SS-LM are easier to insert and cause less trauma than the Cobra-PLA, but the Cobra-PLA has a more effective seal than the LMA-U and better endoscopically determined anatomical position than the LMA-U and SS-LM.
Additive Effects of Sevoflurane and Propofol on γ-Aminobutyric Acid Receptor Function
Authors: Sebel Luke E. , Richardson James E. , Singh Sunil P. , Bell Shannon V. , Jenkins Andrew 
Published: May 2006

Background
Previous studies have shown that propofol and sevoflurane enhance the function of gamma-aminobutyric acid type A (GABAA) receptors. However, it is not known whether these two drugs modulate the same molecular pathways. In addition, little is known about receptor function in the presence of both propofol and sevoflurane. The aim of this study was to better understand the interactions of propofol and sevoflurane with the GABAA receptor.

Methods
Wild-type alpha1, beta(2), gamma(2s) GABA(A) receptor subunit complementary DNAs were transfected into human embryonic kidney cells grown on glass coverslips using a calcium phosphate transfection method. After transfection (36-72 h), cells were whole cell patch clamped and exposed to combinations of the following: 0.3-1,000 microm gamma-aminobutyric acid (GABA), 0-10 microm propofol, and 0-1,650 microm sevoflurane. Chemicals were delivered to the cells using two 10-channel infusion pumps and a rapid solution exchanger.

Results
Both propofol and sevoflurane alone enhanced the amplitude of GABA(A) receptor responses to submaximal concentrations of GABA in a dose-dependent manner. The enhancement was underpinned by an increase in the apparent affinity of the receptor for GABA. Coapplication of both anesthetics further enhanced the apparent affinity of the receptor for GABA.

Conclusions
Response surface modeling of the potentiation of GABA responses (0.3-1,000 microm) by sevoflurane and propofol revealed that the two anesthetics modulated receptor function in an additive manner. These results are consistent with recent mutagenesis studies, suggesting that these two drugs have separate binding sites and converging pathways of action on the GABAA receptor.