bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Neutral pH and Reduced Glucose Degradation Products in a New Peritoneal Dialysis Solution on Morphology of Peritoneal Membrane in Rats
Authors: Ikehara Osamu , Nishimura Hideki , Naito Takashi , Higuchi Chieko , Sanaka Tsutomu 
Published: March 2005

<i>Background:</i> In vitro studies have shown that pH and glucose degradation products (GDPs) in the dialysate are determinant factors for the biocompatibility of peritoneal dialysis (PD) treatment. The present study was thus designed to evaluate whether a newly developed PD solution, which features neutral pH levels and a low GDP concentration, influences tissue damage of the peritoneal membrane in an in vivo setting, and which factor is more critical to the histological changes. <i>Methods:</i> Rats were injected 3 times per day during 1 or 4 weeks with 10 ml of various PD fluids (group G, acidic pH, high GDPs; group S, neutral pH, low GDPs; or group A, acidic pH, low GDPs). When the experimental period was over, the mesothelial cell monolayers of the animals were taken and studied with population analysis, and peritoneal membranes were obtained from the abdominal wall for immunohistochemical examination with proliferating cell nuclear antigen (PCNA) and for measurement of thickness of the peritoneal specimens. <i>Results:</i> The density of the mesothelial cell monolayer and the number of fibroblast-like cells in group S were significantly less than in group G at 1 and 4 weeks’ injection. PCNA-positive nuclei in group S were significantly less than in group G for only the 1-week injection set (group G, 2.03 ± 0.95; group S, 0.85 ± 1.18 nuclei/1 × 10<sup>4</sup> µm<sup>2</sup>). At 4 weeks, the peritoneal thickness of group S (6.32 ± 0.53 µm) was significantly less than that of group G (7.94 ± 0.77 µm), There was no significant difference between groups S and A throughout the whole study period except for the result of the number of fibroblast-like cells. <i>Conclusion:</i> These results indicate that a PD solution with a neutral pH and low GDPs proved more biocompatible with the peritoneal membrane than a solution with an acidic pH and high GDPs. Furthermore, the level of the GDPs has more impact on tissue damage of the peritoneal membrane than the pH in the short term.
Isoflavones Improve Plasma Homocysteine Status and Antioxidant Defense System in Healthy Young Men at Rest but Do Not Ameliorate Oxidative Stress Induced by 80% VO<sub>2</sub>pk Exercise
Authors: Chen Chung-Yen , Bakhiet Raga M. , Hart Vanessa , Holtzman Golde 
Published: March 2005

<i>Aims:</i> (1) Determination of whether isoflavones, as antioxidants and estrogen-like substances, reduce the atherosclerotic process. (2) Assessment of isoflavone anti-atherosclerotic effectiveness by means of measuring plasma markers of atherosclerosis: homocysteine (Hcy), antioxidant status, and lipid peroxidation. (3) Testing of isoflavone antioxidant effectiveness in the presence and absence of oxidative stress induced by exercise. <i>Methods:</i> Thirty subjects paired by aerobic fitness level were randomly assigned to either a placebo or high-genistein isoflavone extract (HGI, 150 mg/day) treatment. Blood samples were collected before and within 5 min, after 30 min at 80% peak oxygen consumption (VO<sub>2</sub>pk) exercise, and before and after 4-week supplementation. <i>Results:</i> Plasma genistein and daidzein were significantly increased by 4-week HGI supplementation before and after exercise (p < 0.05). HGI decreased pre-exercise (pre-ex) plasma malondialdehyde (MDA) (p < 0.05) and Hcy (p = 0.01), and increased pre-ex blood total glutathione (TGSH) (p = 0.01), but did not diminish the increase of MDA and the decrease of TGSH due to the exercise. Furthermore, HGI supplementation enhanced pre-ex total antioxidant capacity (p < 0.05), but did not influence plasma vitamin C and E and uric acid concentrations. <i>Conclusion:</i> Isoflavones reduce plasma Hcy and have antioxidant activity in healthy young men. However, the effect of isoflavones on antioxidant systems may not be potent enough to diminish an abrupt surge of oxidative stress due to acute exercise.
Kosovo: Boundaries and the Liberal Dilemma
Authors: Johanson Märta 
Published: March 2005

AbstractA common position adopted by international lawyers on State borders is that they should be changed as little as possible, as allowing too much scope for changes to borders risks opening up a Pandora's box of unending claims. The liberal position on international boundaries posits that the location of a State's external boundaries matters little anyway, as the liberal State can function within any borders. The article attempts to provide a critique of these positions, and argues that another approach to borders, and particularly to boundaries at the dissolution of States, is needed. The liberal assumption does not adequately respond to boundary changes in non-liberal States. Differences between borders, and the importance attached to these differences in different contexts, have attracted little attention by international lawyers. Because the same solution often tends to lead to different results in different contexts, attempting to apply Public International Law rules, such as a modern version of uti possidetis, to boundaries in all cases of State dissolutions and new State formations, forms not only an insuf ficient response, but might in fact risk contravening obligations under the UN Charter to maintain international peace and security. The con flicts over the republican boundaries of the Socialist Federal Republic of Yugoslavia (SFRY) in the early 1990s exemplify that an automatic conversion of federal boundaries into international ones risks undermining long-term peaceful solutions. The final status of Kosovo, and the issue of its borders, remains a challenge for the international community. In light of the recent tensions in Kosovo existing territorial and political assumptions need to be reexamined, in order that the solution adopted for the territory accord with international obligations set out under the UN Charter.
Is Environmental CAPE Important in the Determination of Maximum Possible Hurricane Intensity?
Authors: Persing John , Montgomery Michael T. 
Published: March 2005

Abstract
In numerical simulations using an axisymmetric, cloud-resolving hurricane model, hurricane intensity shows quasi-steady-state behavior. This quasi-steady intensity is interpreted as the maximum possible intensity (MPI) of the model.
Within the literature, numerical demonstrations have confirmed theoretically anticipated influences on hurricane intensity such as sea surface temperature, outflow temperature, and surface exchange coefficients of momentum and enthalpy. Here these investigations are extended by considering the role of environmental convective available potential energy (CAPE) on hurricane intensity. It is found that environmental CAPE (independent of changes to the outflow level) has no significant influence on numerically simulated maximum hurricane intensity. Within this framework, MPI theories that are sensitive to environmental CAPE should be discarded.
Atmospheric Stability in a Generalized Barotropic Model
Authors: Mitas Christos M. , Robinson Walter A. 
Published: March 2005

Abstract
An empirical modification of conventional barotropic dynamics is implemented to study the low-frequency variability (LFV) of the upper troposphere. Using the conservation of potential vorticity, generalized spectral barotropic operators that apply at single isentropic levels are constructed. In initial value calculations the empirical model shows improvement in skill compared to the conventional barotropic model, but it does not do significantly better than persistence. For short times, however, the empirically modified model shows a much closer resemblance to the observed streamfunction tendency. Overall, it is a significantly more accurate representation of the atmosphere than the conventional barotropic model.
Normal, optimal, and singular modes of the modified model are calculated. The modes of the empirically modified model are more stable and more difficult to excite than those of the barotropic model. These results are consistent with previous studies that found barotropic dynamics deficient for the quantitative description of LFV. The singular modes of the modified operator have very similar patterns but explain less variance than those of the barotropic operator, which is consistent with the difficulty in detecting optimal patterns in observations. The modified barotropic operator is also more normal than the barotropic operator, and thus less variable.
A Parameterization of the Effective Layer Emission for Infrared Radiation Calculations
Authors: Chou Ming-Dah , Lee Kyu-Tae 
Published: March 2005

Abstract
The impact of the vertical integration of radiative transfer on cooling rate calculations is studied for different numerical schemes. One involves the effective emitting temperature of a layer (scheme A), and the other involves temperatures at the interface between layers (scheme B). It is found that when there are large variations of temperature and humidity in the lower troposphere, the cooling rate profiles computed with the different schemes exhibit little resemblance. When the mean layer temperature is used for the effective emitting temperature (scheme A2), the cooling rate oscillates greatly from one layer to the next. On the other hand, the cooling rate computed with scheme B varies very little with height even for the case with large vertical variations of temperature and humidity. The reason for the large cooling rate oscillation in scheme A2 is due to the use of a single effective emitting temperature for both upward and downward fluxes, which is true only for an isothermal layer. The overly smoothed cooling profile for scheme B is caused by the interpolation of level temperatures from layer temperatures. The interpolation has a smoothing effect on the vertical distribution of temperature and, hence, cooling rate.
The transmission function averaged over a spectral band decreases exponentially with the square root of absorber amount. Based on this relationship, the effective emitting temperature of a layer is parameterized separately for computing upward and downward fluxes (scheme A1). Using the parameterization, the large oscillation of the cooling rate profile of scheme A2 is substantially reduced, while the problem of overly smoothing when using scheme B is eliminated. In addition, to be more accurate, the speed of computation using scheme A2 is higher than that using scheme B.
Shear Instability Wave along a Snowband: Instability Structure, Evolution, and Energetics Derived from Dual-Doppler Radar Data
Authors: Kawashima Masayuki , Fujiyoshi Yasushi 
Published: March 2005

Abstract
This article presents a detailed analysis of a meso-γ-scale (∼17 km wavelength) shear instability wave along a snowband using a series of dual-Doppler radar data. The wave developed along a low-level shear line that formed under the strain wind field caused by an adjacent mesoscale vortex. The horizontal wind shear across the line was largest at lower levels, and the eddy-component horizontal winds and the retrieved pressure anomaly showed a bottom-intensified structure as well. The resultant vertical pressure gradient force was found to be responsible for the enhancement of alternating updrafts and downdrafts that were subsequently related to the formation of the reflectivity core/gap structure of the wave.
Eddy kinetic energy (EKE) budgets of the evolving disturbance were investigated using time series of retrieved kinematic and thermodynamic data. The wave grew at an approximately constant growth rate for about 40 min from its onset. The EKE in this quasi-linear growth period was primarily generated by the horizontal shear that decreased with height. The pressure work was found to remove about two-thirds of this generation in the layer below 1 km, while in the upper layer it was constructive to EKE generation and comparable to the generation of EKE by horizontal shear. These results indicate that the source of EKE was basically located at low levels and the energy was transported upward mainly by the pressure work. After the quasi-linear growth period, horizontal shear generation rapidly decreased and EKE peaked. The buoyancy generation of EKE was small but positive in the quasi-linear growth period, then became negative because of the development of thermally indirect circulations.
Holes and Entrainment in Stratocumulus
Authors: Gerber H. , Frick G. , Malinowski S. P. , Brenguier J-L. , Burnet F. 
Published: March 2005

Abstract
Aircraft flights through stratocumulus clouds (Sc) during the Dynamics and Chemistry of Marine Stratocumulus II (DYCOMS-II) study off the California coast found narrow in-cloud regions with less liquid water content (LWC) and cooler temperatures than average background values. The regions are named cloud holes and are assumed to be a result of water evaporated by the entrainment of dryer air from above the Sc. While such features have been noted previously, this study provided a unique opportunity to investigate in much greater detail the nature of the holes, as well as their relationship to the entrainment rate, because high-speed temperature and LWC probes with maximum spatial resolution of 10 cm were flown together for the first time. Nine long-duration flights were made through mostly unbroken Sc for which conditional sampling was used to identify the location and size of the holes. The holes are concentrated near cloud top, their average width near cloud top is about 5 m, their relative length distribution is nearly constant for all flights, and they can penetrate hundreds of meters deep into the Sc before being lost by mixing. Entrainment velocities at cloud top are estimated from measurements of fluxes of reduced LWC and vapor mixing ratios in holes, the fraction of cloud area covered by holes, and the total water jump between cloud top and the free atmosphere. Rates as large as 10 mm s−1 are found for nocturnal flights, and these rates are about 3 times larger than for daytime flight segments. The rates correlate best with the size of the buoyancy jump above the Sc; the present conditional-sampling approach for measuring the rates gives larger rates than the “flux jump” rates determined by others for the same flights by a factor of about 2. The stability criterion for all Sc predicts thinning and breakup of the Sc, which does not occur. The minimal amount of cloud-top evaporative cooling caused by entrainment contributes little to the top-down convection dominated by radiative cooling during nocturnal flights; however, evaporative cooling caused by the mixing of holes as they subduct with the large-scale eddy circulation in the Sc may contribute, but with an as-of-yet unknown amount.
PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information
Authors: Angly Florent , Rodriguez-Brito Beltran , Bangor David , McNairnie Pat , Breitbart Mya , Salamon Peter , Felts Ben , Nulton James , Mahaffy Joseph , Rohwer Forest 
Published: March 2005

Abstract
Background
Phages, viruses that infect prokaryotes, are the most abundant microbes in the world. A major limitation to studying these viruses is the difficulty of cultivating the appropriate prokaryotic hosts. One way around this limitation is to directly clone and sequence shotgun libraries of uncultured viral communities (i.e., metagenomic analyses). PHACCS http://phage.sdsu.edu/phaccs, Phage Communities from Contig Spectrum, is an online bioinformatic tool to assess the biodiversity of uncultured viral communities. PHACCS uses the contig spectrum from shotgun DNA sequence assemblies to mathematically model the structure of viral communities and make predictions about diversity.

Results
PHACCS builds models of possible community structure using a modified Lander-Waterman algorithm to predict the underlying contig spectrum. PHACCS finds the most appropriate structure model by optimizing the model parameters until the predicted contig spectrum is as close as possible to the experimental one. This model is the basis for making estimates of uncultured viral community richness, evenness, diversity index and abundance of the most abundant genotype.

Conclusion
PHACCS analysis of four different environmental phage communities suggests that the power law is an important rank-abundance form to describe uncultured viral community structure. The estimates support the fact that the four phage communities were extremely diverse and that phage community biodiversity and structure may be correlated with that of their hosts.
Using equilibrium frequencies in models of sequence evolution
Authors: Knudsen Bjarne , Miyamoto Michael M 
Published: March 2005

Abstract
Background
The f factor is a new parameter for accommodating the influence of both the starting and ending states in the rate matrices of "generalized weighted frequencies" (+gwF) models for sequence evolution. In this study, we derive an expected value for f, starting from a nearly neutral model of weak selection, and then assess the biological interpretation of this factor with evolutionary simulations.

Results
An expected value of f = 0.5 (i.e., equal dependency on the starting and ending states) is derived for sequences that are evolving under the nearly neutral model of this study. However, this expectation is sensitive to violations of its underlying assumptions as illustrated with the evolutionary simulations.

Conclusion
This study illustrates how selection, drift, and mutation at the population level can be linked to the rate matrices of models for sequence evolution to derive an expected value of f. However, as f is affected by a number of factors that limit its biological interpretation, this factor should normally be estimated as a free parameter rather than fixed a priori in a +gwF analysis.
Angiogenesis in cancer of unknown primary: clinicopathological study of CD34, VEGF and TSP-1
Authors: Karavasilis Vasilis , Malamou-Mitsi Vasiliki , Briasoulis Evangelos , Tsanou Elena , Kitsou Evangelia , Kalofonos Haralambos , Fountzilas George , Fotsis Theodore , Pavlidis Nicholas 
Published: March 2005

Abstract
Background
Cancer of unknown primary remains a mallignancy of elusive biology and grim prognosis that lacks effective therapeutic options. We investigated angiogenesis in cancer of unknown primary to expand our knowledge on the biology of these tumors and identify potential therapeutic targets.

Methods
Paraffin embedded archival material from 81 patients diagnosed with CUP was used. Tumor histology was adenocarcinoma (77%), undifferentiated carcinoma (18%) and squamous cell carcinoma (5%). The tissue expression of CD34, VEGF and TSP-1 was assessed immunohistochemically by use of specific monoclonal antibodies and was analyzed against clinicopathological data.

Results
VEGF expression was detected in all cases and was strong in 83%. Stromal expression of TSP-1 was seen in 80% of cases and was strong in 20%. The expression of both proteins was not associated with any clinical or pathological parameters. Tumor MVD was higher in tumors classified as unfavorable compared to more favorable and was positively associated with VEGF and negatively with TSP-1.

Conclusion
Angiogenesis is very active and expression of VEGF is almost universal in cancers of unknown primary. These findings support the clinical investigation of VEGF targeted therapy in this clinical setting.
Orientation determination by wavelets matching for 3D reconstruction of very noisy electron microscopic virus images
Authors: Saad Ali Samir 
Published: March 2005

Abstract
Background
In order to perform a 3D reconstruction of electron microscopic images of viruses, it is necessary to determine the orientation (Euler angels) of the 2D projections of the virus. The projections containing high resolution information are usually very noisy. This paper proposes a new method, based on weighted-projection matching in wavelet space for virus orientation determination. In order to speed the retrieval of the best match between projections from a model and real virus particle, a hierarchical correlation matching method is also proposed.

Results
A data set of 600 HSV-1 capsid particle images in different orientations was used to test the proposed method. An initial model of about 40 Å resolutions was used to generate projections of an HSV-1 capsid. Results show that a significant improvement, in terms of accuracy and speed, is obtained for the initial orientation estimates of noisy herpes virus images. For the bacteriophage (P22), the proposed method gave the correct reconstruction compared to the model, while the classical method failed to resolve the correct orientations of the smooth spherical P22 viruses.

Conclusion
This paper introduces a new method for orientation determination of low contrast images and highly noisy virus particles. This method is based on weighted projection matching in wavelet space, which increases the accuracy of the orientations. A hierarchical implementation of this method increases the speed of orientation determination. The estimated number of particles needed for a higher resolution reconstruction increased exponentially. For a 6 Å resolution reconstruction of the HSV virus, 50,000 particles are necessary. The results show that the proposed method reduces the amount of data needed in a reconstruction by at least 50 %. This may result in savings 2 to 3 man-years invested in acquiring images from the microscope and data processing. Furthermore, the proposed method is able to determine orientations for some difficult particles like P22 with accuracy and consistency. Recently a low PH sindbis capsid was determined with the proposed method, where other methods based on the common line fail.