bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of cholesterol-lowering and antioxidant properties of sugar cane policosanols in hamsters and humans
Authors: Kassis Amira N. 
Published: May 2008

Atherosclerosis prevention is now a main focus of the scientific community and pharmaceutical industry. Sugar cane policosanols (SCPs) have gained increasing popularity over the last decade as a result of numerous studies conducted in Cuba that consider SCPs as a natural alternative to statin drugs. However, independent research on policosanols was not able to replicate cholesterol reductions reported by Cuban laboratories. No independent study to date has examined the cholesterol-lowering effect and antioxidant capacity of original SCPs in humans. In addition, since independent research was criticized because of the use of alternative policosanol formulations, the source and composition of policosanol mixtures are now at the core of the policosanol controversy. The aim of this thesis project was first to compare the composition and cholesterol-lowering effects of different SCP preparations in hamsters, and second to test the cholesterol-lowering efficacy, mechanism of action, and antioxidant capacity of the original Cuban SCP in hypercholesterolemic humans. In study 1, 48 male hamsters were randomly assigned to 4 groups for a period of 4 weeks: (i) non-cholesterol control, (ii) cholesterol control, (iii) original SCPs, and (iv) alternative SCPs. Hamsters were sacrificed and blood was collected at the end of the feeding period for lipid measurements. In study 2, 21 hypercholesterolemic volunteers consumed 10 mg·d–1 of SCPs or a placebo for a period of 28 days in a crossover trial. Plasma lipid levels and low-density lipoprotein (LDL) oxidation were measured at the start and end of supplementation phases. Cholesterol absorption and synthesis were assessed using a single-isotope, single-tracer technique and deuterium incorporation, respectively. There was no significant difference in cholesterol-lowering efficacy between hamsters in the original and alternative SCP groups relative to the control. Similarly, in hypercholesterolemic humans, supplementation with original SCPs did not significantly improve lipid parameters and no change in cholesterol absorption or synthesis was observed relative to the control. In vivo assessment of LDL oxidation showed no significant changes in oxidized LDL concentration relative to baseline and control. The present thesis disagrees with previous Cuban data on the cardio-protective role of SCPs in animals and humans and supports independent studies showing no cholesterol-lowering effect and no antioxidant capacity.
NMR analysis of lipoprotein particle size does not increase sensitivity to the effect of soy protein on CVD risk when compared with the traditional lipid profile
Authors: Santo Antonio S. , Cunningham Ariana M. , Alhassan Sofiya , Browne Richard W. , Burton Harold , Leddy John J. , Grandjean Peter W. , Horvath Steven M. , Horvath Peter J. 
Published: May 2008

The traditional lipid profile compared with nuclear magnetic resonance (NMR) may underestimate the risk for cardiovascular disease and may explain some of the discrepancies in results between studies analyzing the salubrious effects of soy. Our purpose was to compare the traditional lipid profile with NMR quantification of the number of lipoprotein particles, subclasses, and diameters or sizes in 30 sedentary males, between 18 and 30 years of age, consuming 1 of the following 3 supplements daily for 28 days: milk protein (Milk), isoflavone-poor soy protein (Soy–), or isoflavone-rich soy protein (Soy+). The study used a double-blind, parallel-arm design with random assignment to 1 of the 3 protein supplement groups. Fasting EDTA blood samples were collected at baseline and after 28 days of supplementation and analyzed for the number and size of very low-density lipoprotein (VLDL), low-density lipoprotein (LDL), and high-density lipoprotein (HDL) particles, respectively. Fasting serum samples were analyzed for concentrations of total cholesterol (TC), LDL cholesterol (LDL-C), total HDL cholesterol (HDL-C), HDL2-C, HDL3-C, triglycerides (TGs), free fatty acids (FFAs), and glucose. Fasting heparin blood samples were collected at baseline and after supplementation and analyzed for apolipoproteins A-I, A-II, B, C-II, C-III, and E, as well as hepatic and lipoprotein lipase concentrations. HDL3-C increased by 47.2% after Soy+ supplementation and hepatic lipase decreased 19.2% after Soy– supplementation (p < 0.05). HDL-C and apolipoproteins A-I and A-II were found to increase in all 3 groups (p < 0.05). Results support that NMR analysis of lipoprotein particle number and size are not more sensitive to the effect of soy protein on CVD risk compared with the traditional lipid profile. Furthermore, the lack of isoflavones in soy protein seems to have a deleterious effect on hepatic lipase.
The length dependency of maximum force development in rat medial gastrocnemius muscle in situ
Authors: de Ruiter Cornelis J. , Busé-Pot Tinelies E. , de Haan Arnold 
Published: May 2008

During many movements (e.g., running, jumping, and kicking) there is little time for skeletal muscles to build up force, thus rapid force development is important. The length dependency of isometric force development was investigated in maximally activated rat medial gastrocnemius muscles in situ with intact blood flow at 35 °C. Depending on time available for muscle activation, the length dependency of force development was expected to differ from that of the maximal isometric force (Fmax) reached much later during the contraction. During isometric force development in intact muscle–tendon preparations, the contractile elements actually shortened. Therefore, similar to previous findings on shortening contractions, it was hypothesized that maximal rate of force development (MRFD) would be obtained at a length below the optimum (Lo) for maximal isometric force production. To measure the effect of the entire time history of activation, force time integrals (FTIs) for different activation times (10–50 ms) were also calculated. The highest MRFD was obtained 1.94 ± 0.42 mm below (p < 0.05) Lo. When expressed relative to Fmax obtained at each individual length, the optimum was found at Lo – 4.4 mm. For FTI 10 ms and FTI 20 ms, optimum length was obtained at ~2 and 1 mm above (p < 0.05) Lo, respectively, whereas the optima for FTI 30, 40, and 50 ms were ~1 mm below (p < 0.05) Lo. In addition, at short lengths (< Lo – 4 mm) and for all activation times FTIs were relatively more decreased than Fmax. In conclusion, length dependency of force output during rapid force development differed from that of maximal isometric force; specifically, MRFD was obtained 2 mm below Lo.
DSD-Crasher
Authors: Csallner Christoph , Smaragdakis Yannis , Xie Tao 
Published: May 2008

DSD-Crasher is a bug finding tool that follows a three-step approach to program analysis:
D. Capture the program's intended execution behavior with dynamic invariant detection. The derived invariants exclude many unwanted values from the program's input domain.
S. Statically analyze the program within the restricted input domain to explore many paths.
D. Automatically generate test cases that focus on reproducing the predictions of the static analysis. Thereby confirmed results are feasible.
This three-step approach yields benefits compared to past two-step combinations in the literature. In our evaluation with third-party applications, we demonstrate higher precision over tools that lack a dynamic step and higher efficiency over tools that lack a static step.
Generic framework for design, modeling and simulation of cyber physical systems
Authors: Kim Ji Eun , Mosse Daniel 
Published: May 2008

Wireless technologies have contributed to extensive development of many kinds of applications that enable cost-effective and intelligent monitoring and control of physical environments, objects, activities such as smart buildings, home or industry automation, and remote patient care. These kinds of applications often require support of heterogeneous physical environments and large-scale systems mixing several different types of monitoring and control. In addition to heterogeneity and scalability support, mobility support is crucial in the development of these software systems.
Although much research has addressed design, modeling and simulation of such systems, most solutions usually do not cover all requirements from different domains. Rather, these solutions restrict the development environment and reduce flexibility of design by enforcing the use of a specific software platform and tightly-coupled tools.
This paper presents problems and challenges of Cyber Physical Systems (CPS) like the aforementioned applications, and discusses features and benefits of a generic framework to enable design, modeling and simulation of large-scale, heterogeneous CPS systems in an integrated manner.
Buildable evolution
Authors: Funes Pablo José 
Published: May 2008

The most interesting results in Artificial Life come about when some aspect of reality is captured. In the mid-1990s, Karl Sims energized the AL community with his ground-breaking work on evolved moving creatures [28, 29]. The life-like behavior of Sims' creatures resulted from combining evolved morphology with a physics simulation based on Featherstone's earlier work [9].
The question that begged asking was: can a similar thing be done in the physical world? Can we make creatures that walk out of the computer screen and into the room?
Two components were required: a language to evolve morphologies that have real-world counterparts, and a way to build them --- either in simulation or by automated building and testing. We set out to demonstrate that buildable evolution was possible using a readily available, cheap building system --- Lego bricks --- and an ad-hoc physics simulation that allowed us to study the interaction of the object with the physical world in silico; with respect to gravitational forces at least. The result [10, 14, 12, 13, 15, 16, 25, 23, 26, 24, 27] is a system that can evolve a variety of different shapes and is very easy to use, set up and replicate.
Here I present an overview of the evolvable Lego structures project. Coinciding with the publication of this article, the source code is being released to the community (demo.cs.brandeis.edu/pr/buildable/source).
Dominant Balances and Exchanges of the Atmospheric Water Cycle in the Reanalysis 2 at Diurnal, Annual, and Intraseasonal Time Scales
Authors: Ruane Alex C. , Roads John O. 
Published: May 2008

Abstract
Output from the National Centers for Environmental Prediction–Department of Energy (NCEP–DOE) Reanalysis 2 (R2) is passed through a broadband filter to determine the normalized covariances that describe the variance of the atmospheric water cycle at diurnal, annual, and intraseasonal (∼7–80 days) time scales. Vapor flux convergence is residually defined to close the water cycle between successive 3-hourly output times from 2002 to 2004, resulting in a balance between precipitation, evaporation, precipitable water tendency, and vertically integrated vapor flux convergence. The same balance holds at each time scale, allowing 100% of each variable’s temporal variance to be described by its covariance with other water cycle components in the same variance category. Global maps of these normalized covariances are presented to demonstrate the unique balances and exchanges that govern temporal variations in the water cycle.
The diurnal water cycle is found to be dominated by a land–sea contrast, with continents controlled thermodynamically through evaporation and the oceans following dynamic convergence. The annual time-scale features significant meridional structure, with the low latitudes described mostly through variability in convergence and the extratropics governed by the properties of advected continental and maritime air masses. Intraseasonal transients lack direct solar oscillations at the top of the atmosphere and are characterized by propagating dynamic systems that act to adjust the precipitable water content of unsaturated regions or exchange directly with precipitation in saturated areas.
By substituting the modeled precipitation with observation-based fields, a detailed description of the water cycle’s exchanges relating to the nocturnal precipitation maximum over the Midwest is obtained.
Comparison of Diurnal Variations in Precipitation Systems Observed by TRMM PR, TMI, and VIRS
Authors: Yamamoto Munehisa K. , Furuzawa Fumie A. , Higuchi Atsushi , Nakamura Kenji 
Published: May 2008

Abstract
Tropical Rainfall Measuring Mission (TRMM) data during June–August 1998–2003 are used to investigate diurnal variations of rain and cloud systems over the tropics and midlatitudes. The peak time of the coldest minimum brightness temperature derived from the Visible and Infrared Scanner (VIRS) and the maximum rain rate derived from the Precipitation Radar (PR) and the TRMM Microwave Imager (TMI) are compared. Time distributions are generally consistent with previous studies. However, it is found that systematic shifts in peak time relative to each sensor appeared over land, notably over western North America, the Tibetan Plateau, and oceanic regions such as the Gulf of Mexico. The peak time shift among PR, TMI, and VIRS is a few hours.
The relationships among the amplitude of diurnal variation, convective frequency, storm height, and rain amount are further investigated and compared to the systematic peak time shifts. The regions where the systematic shift appears correspond to large amplitude of diurnal variation, high convective frequency, and high storm height. Over land and over ocean near the coast, the relationships are rather clear, but not over open ocean.
The sensors likely detect different stages in the evolution of convective precipitation, which would explain the time shift. The PR directly detects near-surface rain. The TMI observes deep convection and solid hydrometeors, sensing heavy rain during the mature stage. VIRS detects deep convective clouds in mature and decaying stages. The shift in peak time particularly between PR (TMI) and VIRS varies by region.
Observations of Cross-Shelf Flow Driven by Cross-Shelf Winds on the Inner Continental Shelf
Authors: Fewings Melanie , Lentz Steven J. , Fredericks Janet 
Published: May 2008

Abstract
Six-yr-long time series of winds, waves, and water velocity from a cabled coastal observatory in 12 m of water reveal the separate dependence of the cross-shelf velocity profile on cross-shelf and along-shelf winds, waves, and tides. During small waves, cross-shelf wind is the dominant mechanism driving the cross-shelf circulation after tides and tidal residual motions are removed. The along-shelf wind does not drive a substantial cross-shelf circulation. During offshore winds, the cross-shelf circulation is offshore in the upper water column and onshore in the lower water column, with roughly equal and opposite volume transports in the surface and bottom layers. During onshore winds, the circulation is nearly the reverse. The observed profiles and cross-shelf transport in the surface layer during winter agree with a simple two-dimensional unstratified model of cross-shelf wind stress forcing. The cross-shelf velocity profile is more vertically sheared and the surface layer transport is stronger in summer than in winter for a given offshore wind stress.
During large waves, the cross-shelf circulation is no longer roughly symmetric in the wind direction. For onshore winds, the cross-shelf velocity profile is nearly vertically uniform, because the wind- and wave-driven shears cancel; for offshore winds, the profile is strongly vertically sheared because the wind- and wave-driven shears have the same sign. The Lagrangian velocity profile in winter is similar to the part of the Eulerian velocity profile due to cross-shelf wind stress alone, because the contribution of Stokes drift to the Lagrangian velocity approximately cancels the contribution of waves to the Eulerian velocity.
Observation of the Diurnal Cycle in the Low Troposphere of West Africa
Authors: Lothon Marie , Saïd Frédérique , Lohou Fabienne , Campistron Bernard 
Published: May 2008

AbstractThe authors give an overview of the diurnal cycle of the low troposphere during 2006 at two different sites, Niamey (Niger) and Nangatchori (Benin). This study is partly based on the first observations of UHF wind profilers ever made in West Africa in the context of the African Monsoon Multidisciplinary Analysis (AMMA) project. Also used are the radiosoundings made in Niamey and ground station observations at Nangatchori, which allow for the study of the impact of the dynamics on the water vapor cycle and the turbulence observed at the ground.Profiler measurements revealed a very consistent year-round nocturnal low-level jet maximal around 0500 UTC and centered at 400-m above the ground, with wind speed around 15 m s−1. This jet comes either from the northeast during the dry season or from the southwest during the wet season, in relation with the position of the intertropical discontinuity. The radiosoundings made in Niamey highlight both the role of the nocturnal jet in bringing water vapor from the south during the night when the intertropical discontinuity has reached the vicinity of the considered area at the end of the dry season and the role of the daytime planetary boundary layer in mixing this water vapor within a larger depth of the troposphere. The planetary boundary layer processes play a large role in the diurnal cycle of the position of the intertropical discontinuity itself.The observations of turbulence made at the ground in Nangatchori showed that the best signature of the nocturnal jet close to surface can be seen in the turbulent kinetic energy and skewness of the air vertical velocity, rather than on the mean wind itself. They reveal the downward transport of momentum from the jet core aloft to the surface.
Rapid regulation of protein activity in fission yeast
Authors: Bøe Cathrine A , Garcia Ignacio , Pai Chen-Chun , Sharom Jeffrey R , Skjølberg Henriette C , Boye Erik , Kearsey Stephen , MacNeill Stuart A , Tyers Michael D , Grallert Beáta 
Published: May 2008

Abstract

Background
The fission yeast Schizosaccharomyces pombe is widely-used as a model organism for the study of a broad range of eukaryotic cellular processes such as cell cycle, genome stability and cell morphology. Despite the availability of extensive set of genetic, molecular biological, biochemical and cell biological tools for analysis of protein function in fission yeast, studies are often hampered by the lack of an effective method allowing for the rapid regulation of protein level or protein activity.

Results
In order to be able to regulate protein function, we have made use of a previous finding that the hormone binding domain of steroid receptors can be used as a regulatory cassette to subject the activity of heterologous proteins to hormonal regulation. The approach is based on fusing the protein of interest to the hormone binding domain (HBD) of the estrogen receptor (ER). The HBD tag will attract the Hsp90 complex, which can render the fusion protein inactive. Upon addition of estradiol the protein is quickly released from the Hsp90 complex and thereby activated. We have tagged and characterised the induction of activity of four different HBD-tagged proteins. Here we show that the tag provided the means to effectively regulate the activity of two of these proteins.

Conclusion
The estradiol-regulatable hormone binding domain provides a means to regulate the function of some, though not all, fission yeast proteins. This system may result in very quick and reversible activation of the protein of interest. Therefore it will be a powerful tool and it will open experimental approaches in fission yeast that have previously not been possible. Since fission yeast is a widely-used model organism, this will be valuable in many areas of research.
Analysis of the distribution of functionally relevant rare codons
Authors: Widmann Michael , Clairo Marie , Dippon Jürgen , Pleiss Jürgen 
Published: May 2008

Abstract

Background
The substitution of rare codons with more frequent codons is a commonly applied method in heterologous gene expression to increase protein yields. However, in some cases these substitutions lead to a decrease of protein solubility or activity. To predict these functionally relevant rare codons, a method was developed which is based on an analysis of multisequence alignments of homologous protein families.

Results
The method successfully predicts functionally relevant codons in fatty acid binding protein and chloramphenicol acetyltransferase which had been experimentally determined. However, the analysis of 16 homologous protein families belonging to the α/β hydrolase fold showed that functionally rare codons share no common location in respect to the tertiary and secondary structure.

Conclusion
A systematic analysis of multisequence alignments of homologous protein families can be used to predict rare codons with a potential impact on protein expression. Our analysis showed that most genes contain at least one putative rare codon rich region. Rare codons located near to those regions should be excluded in an approach of improving protein expression by an exchange of rare codons by more frequent codons.
Short-term pacing in the mouse alters cardiac expression of connexin43
Authors: Kontogeorgis Andrianos , Kaba Riyaz A , Kang Eunice , Feig Jonathan E , Gupta Pritha P , Ponzio Marc , Liu Fangyu , Rindler Michael J , Wit Andrew L , Fisher Edward A , Peters Nicholas S , Gutstein David E 
Published: May 2008

Abstract

Background
Cardiac insults such as ischemia, infarction, hypertrophy and dilatation are often accompanied by altered abundance and/or localization of the connexin43 gap junction protein, which may predispose towards arrhythmic complications. Models of chronic dyssynchronous cardiac activation have also been shown to result in redistribution of connexin43 in cardiomyocytes. We hypothesized that alterations in connexin43 expression and localization in the mouse heart might be induced by ventricular pacing over a short period of time.

Results
The subdiaphragmatic approach was used to pace a series of wild type mice for six hours before the hearts were removed for analysis. Mice were paced at 10–15% above their average anesthetized sinus rate and monitored to ensure 1:1 capture. Short-term pacing resulted in a significant reduction in connexin43 mRNA abundance, a partial redistribution of connexin43 from the sarcolemma to a non-sarcolemmal fraction, and accumulation of ubiquitinated connexin43 without a significant change in overall connexin43 protein levels. These early pacing-induced changes in connexin43 expression were not accompanied by decreased cardiac function, prolonged refractoriness or increased inducibility into sustained arrhythmias.

Conclusion
Our data suggest that short-term pacing is associated with incipient changes in the expression of the connexin43 gap junction, possibly including decreased production and a slowed rate of degradation. This murine model may facilitate the study of early molecular changes induced by pacing and may ultimately assist in the development of strategies to prevent gap junction remodeling and the associated arrhythmic complications of cardiac disease.