bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using the PRIMME eigensolver in materials science applications
Authors: Stathopoulos Andreas 
Published: July 2006

AbstractOne of the outstanding computational problems in materials science is the solution of large, Hermitian eigenvalue problems. The dimension of these problems can grow to several millions, while thousands of eigenvalues and eigenvectors must be computed. Applications that must maintain orthogonality in the eigenvector basis scale quadratically to the number of eigenvectors. In this paper, we present an overview of the state‐of‐the‐art in methods and software for eigenvalue computations, and demonstrate why our new package PRIMME fills an important gap in both methods and software. Moreover, we show that PRIMME includes two nearly optimal methods, and that it can be significantly faster than any existing method. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Computer simulations of protein translocation
Authors: Kirmizialtin Serdal , Huang Lei , Makarov Dmitrii E. 
Published: July 2006

AbstractMany biological processes involve translocation of protein molecules across pores. Shown in the cover picture of this issue is a snapshot from a computer simulation of the protein ubiquitin that is forced mechanically to enter a narrow cylindrical pore. As the force f applied at one end of the molecule pulls it along the pore, the confinement within the pore causes the protein to unfold. The ensuing changes in the protein's entropy and energy lead to a free energy barrier, which has to be surmounted for the translocation to occur. The magnitude of this barrier is estimated by Kirmizialtin et al. in the article [1]. The plot was generated by using the PyMol software.This paper is a presentation from the 1st Institute for the Theory of Advanced Materials in Information Technology Workshop on Computational Materials and Electronics held 20–22 October 2005 in Austin, USA. The present issue has been guest‐edited by James Chelikowsky and Alex Demkov. The background of the cover shows a photograph of the tower of the University of Texas at Austin. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The effect of FF-MAS on porcine cumulus–oocyte complex maturation, fertilization and pronucleus formation in vitro
Authors: Faerge Inger , Strejcek Frantisek , Laurincik Jozef , Rath Detlef , Niemann Heiner , Schellander Karl , Rosenkranz Christine , Hyttel Poul Maddox , Grøndahl Christian 
Published: July 2006

SummaryFollicular fluid meiosis-activating sterol (FF-MAS) has been isolated from the follicular fluid (FF) of several species including man. FF-MAS increases the quality of in vitro oocyte maturation, and thus the developmental potential of oocytes exposed to FF-MAS during in vitro maturation is improved. The aim of the present study was to investigate the effects of FF-MAS on porcine oocyte maturation and pronucleus formation in vitro. Porcine cumulus–oocyte complexes (COCs) were isolated from abattoir ovaries and in vitro matured for 48 h in NCSU 37 medium supplemented with 1 mg/l cysteine, 10 ng/ml epidermal growth factor and 50 μM 2-mercaptoethanol with or without 10% porcine follicular fluid (pFF). For the first 22 h, 1 mM db-cAMP and 10 I.E PMSG/hCG was added. The medium was supplemented with 1 μM, 3 μM, 10 μM, 30 μM or 100 μM FF-MAS dissolved in ethanol. After maturation the COCs were denuded mechanically using a fine glass pipette under constant pH and in vitro fertilized with fresh semen (5 × 105 spermatozoa/ml). The presumptive zygotes were evaluated 18 h after fertilization. The addition of pFF increased the monospermic as well as the polyspermic penetration of oocytes. In the absence of pFF, the addition of FF-MAS decreased the polyspermic penetration rate, whereas FF-MAS in combination with pFF decreased monospermic and increased polyspermic penetration. The degeneration rate of ova decreased in the presence of FF-MAS irrespective of the presence or absence of pFF. In the absence of pFF, FF-MAS at 3–10 μM increased the number of zygotes with advanced maternal pronuclear stages. In supraphysiological doses, i.e. 30–100 μM, FF-MAS dose-dependently and reversibly inhibited nuclear maturation in the absence of pFF.
Fazang (643–712) and Wuzhensi: With a Special Reference to his Daoist Ties
Authors: Chen Jinhua 
Published: July 2006

AbstractIn his biography for the Avatamsaka master Fazang (643–712), Tang Tae Ch'ǒnboksa kosaju pǒn'gyǒng taedǒk Pǒpjang hwasang chǒn (Ch. Tang Da Jianfusi gu sizhu fanjing dade Fazang heshang zhuan) (Biography for Upādhyāya Fazang, the Late Bhadanta-translator and Abbot of Great Jianfusi of the Tang) composed ca. 904, the Korean author Ch'oe Ch'iwon (Ch. Cui Zhiyuan, 857–904) reports a ritual that Fazang performed to pray for snow in order to prevent an imminent drought. The ritual was executed in the winter of 711, barely one year before Fazang's death, beside a pond at the scenic mountain range fifty li west of Chang'an – Mount Zhongnan.
Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities
Authors: Mokdad Ali , Leontis Neocles B. 
Published: July 2006

Abstract
Summary: RNA atomic resolution structures have revealed the existance of different families of basepair interactions, each of which with its own isosteric sub-families. Ribostral (Ribonucleic Structural Aligner) is a user-friendly framework for analyzing, evaluating and viewing RNA sequence alignments with at least one available atomic resolution structure. It is the first of its kind that makes direct and easy- to-understand superposition of the isostericity matrices of basepairs observed in the structure onto sequence alignments, easily indicating allowed and unallowed substitutions at each BP position. Potential mistakes in the alignments can then be corrected using other sequence editing software. Ribostral has been developed and tested under Windows XP, and is capable of running on any PC or MAC platform with MATLAB 7.1 (SP3) or higher installed version. A stand-alone version is also available for the PC platform.
Availability:
Contact: mali@bgsu.edu
Supplementary information: A user manual is available on Ribostral website.
High Expression of CD105 as a Prognostic Predictor of Early Tongue Cancer
Authors: Chuang Hui‐Ching , Su Chih‐Ying , Huang Hsuang‐Ying , Chien Chih‐Yen , Chen Ching‐Mei , Huang Chao‐Cheng 
Published: July 2006

AbstractObjectives: The purpose of this article is to investigate the expressions of vascular endothelial growth factor (VEGF) and endoglin (CD105) in the biopsy tissues of squamous cell carcinoma of the tongue in early tumor stages and their relationship with the clinicopathologic features.Study Design and Methods: The authors conducted retrospective clinical and biologic studies. Immunohistochemistry was used to study the expressions of VEGF and CD105 in the biopsy tissues taken from 94 patients with T1 and T2 tongue cancers. The expressions of VEGF and CD105 were analyzed and correlated to the clinicopathologic features of these patients.Results: High expressions of VEGF and CD105 significantly correlated with a relatively advanced tumor stage (P = .001 and P < .001), positive nodal status (P < .001 and P < .001), presence of tumor necrosis (P = .022 and P = .01), and greater tumor thickness (P < .001 and P < .001), respectively. In addition, high expression of CD105 correlated with the presence of perineural invasion (P = .003). However, the expression of VEGF and CD105 did not significantly correlate with age, gender, vascular invasion, or histologic grading. The cumulative 5‐year disease‐free survival rate significantly correlated with low expression of VEGF (P = .003), CD105 (P < .001), positive nodal status (P < .001), a relatively advanced tumor stage (P = .024), greater tumor thickness (P = .023), and presence of tumor necrosis (P = .003). Nonetheless, Cox's regression analysis revealed that only the expression of CD105 was an independent prognostic predictor for survival (P < .001).Conclusions: Higher expression of either CD105 or VEGF in the tumor bed implicates a more aggressive potential for T1 and T2 tongue cancers, and the expression of CD105 is a useful predictive prognostic factor in early tongue cancer.
Expression of RANKL and OPG in Middle Ear Cholesteatoma Tissue
Authors: Jeong Jin‐Hyeok , Park Chul‐Won , Tae Kyung , Lee Seung‐Hwan , Shin Dae‐Hyun , Kim Kyung‐Rae , Park Yong‐Wook 
Published: July 2006

AbstractObjectives: The objective of this study was to investigate how the expression of the RANK‐RANKL‐OPG system mediates the formation and differentiation of osteoclasts and causes bone resorption in cholesteatoma.Methods: An immunohistochemical analysis was carried out in 22 cholesteatoma tissues obtained during middle ear surgery and 15 normal postauricular skin tissues to examine the expression of RANKL and OPG.Results: All 22 cases of cholesteatoma and the 15 cases of normal postauricular skin expressed RANKL and OPG. The count and rate of RANKL‐positive cells in cholesteatoma was significantly higher than in normal postauricular skin. The count and rate of OPG‐positive cells in normal postauricular skin was significantly higher than in cholesteatoma. The ratio of the positive expression rates of RANKL and OPG in cholesteatoma was statistically higher than in normal postauricular skin.Conclusions: We provide evidence suggesting that RANKL, which activates osteoclasts, plays a significant role in the mechanism of bone destruction in cholesteatoma, and that the ratio of RANKL to OPG may be a reliable indicator of bone destruction in cholesteatoma.
Simple electrostatic model improves designed protein sequences
Authors: Zollars Eric S. , Marshall Shannon A. , Mayo Stephen L. 
Published: July 2006

AbstractElectrostatic interactions are important for both protein stability and function, including binding and catalysis. As protein design moves into these areas, an accurate description of electrostatic energy becomes necessary. Here, we show that a simple distance‐dependent Coulombic function parameterized by a comparison to Poisson‐Boltzmann calculations is able to capture some of these electrostatic interactions. Specifically, all three helix N‐capping interactions in the engrailed homeodomain fold are recovered using the newly parameterized model. The stability of this designed protein is similar to a protein forced by sequence restriction to have beneficial electrostatic interactions.
Regional differences in adhesive tape stripping of human skin
Authors: Tokumura Fumio , Yoshiura Yumi , Homma Takeyasu , Nukatsuka Hiroshi 
Published: July 2006

Background/purpose: The regional differences in acrylic adhesive tape stripping of human skin were evaluated.Methods: Two kinds of adhesive tape with different water vapor permeabilities were applied to the flexor side of the forearm and the cheek, palm and sole in eight healthy male volunteers. Dermal peeling force was measured at 1 and 6 h after application. Simultaneously, the electrical conductance of the skin beneath the applied tape and the amount of stripped corneocytes on the removed tape were measured.Results and conclusion: The regional difference in dermal peeling force of the permeable tape was large and that of the occlusive tape was small. The dermal peeling force of the permeable tape was high in the order of the palm, sole, cheek and forearm and individual differences among subjects in dermal peeling force of tape applied to the palm was large. The regional difference in dermal peeling force was considered to be related to fluid accumulation beneath the applied tape and the amount of stripped corneocytes. On the other hand, that the dermal peeling force of the occlusive tape was low and the regional difference was small may have been caused by fluid accumulation from the skin beneath the applied tape on all regions.
Safety of sodium fluorescein for in vivo study of skin
Authors: O'goshi Ken‐ichiro , Serup Jørgen 
Published: July 2006

Background/purpose: Epicutaneous labeling or intradermal injection of the fluorescent sodium fluorescein is being used increasingly to investigate skin conditions in vivo when using non‐invasive devices such as confocal scanning laser microscopy. Sodium fluorescein was used intravenously for decades for the examination of the vasculature of the ocular fundus (fluorescein angiography) and as eye drops for diagnosis of corneal erosions. The objective of this article is to systematically review the literature on fluorescein and conclude its safety in cutaneous research to support research planning and evaluations by ethics committees.Methods: A number of databases and the literature about safety and toxicity of fluorescein in animal and human studies were searched and analyzed.Results: Side effects or adverse events reported in the literature were related to intravenous bolus injection. Transient nausea and vomiting may occur. Other adverse events such as vasovagal reaction, cardiac or respiratory effects and anaphylaxes are extremely rare but may be fatal. Intradermal injection may cause mild itch or pain; systemic adverse event was reported. Epicutaneous labeling is associated with no reported problem. A typical local dose is several magnitudes of order smaller than a typical intravenous dose.Conclusion: Fluorescein has been used for many years in medicine for diagnostic purposes and is widely safe, albeit intravenous bolus injection may cause serious adverse reactions. In the literature, we could not trace reports of local or systemic side effects of topical sodium fluorescein except itch and pain on intradermal injection, however, dependent on the fluorescein preparation used. Local dermal application of fluorescein for in vivo study of skin may be considered widely safe.
Inhibitory effect of coenzyme Q1 on eukaryotic DNA polymerase γ and DNA topoisomerase II activities on the growth of a human cancer cell line
Authors: Yonezawa Yuko , Kuriyama Isoko , Fukuoh Atsushi , Muta Tsuyoshi , Kang Dongchon , Takemura Masaharu , Kato Ikuo , Yoshida Hiromi , Mizushina Yoshiyuki 
Published: July 2006

Coenzyme Q (CoQ) is an isoprenoid quinine that functions as an electron carrier in the mitochondrial respiratory chain in eukaryotes. CoQ having shorter isoprenoid chains, especially CoQ1 and CoQ2, selectively inhibited the in vitro activity of eukaryotic DNA polymerase (pol) γ, which is a mitochondrial pol. These compounds did not influence the activities of nuclear DNA replicative pols such as α, δ and ɛ, and nuclear DNA repair‐related pols such as β, η, ι, κ and λ. CoQ also inhibited DNA topoisomerase II (topo II) activity, although the enzymatic characteristics, including modes of action, amino acid sequences and three‐dimensional structures, were markedly different from those of pol γ. These compounds did not inhibit the activities of procaryotic pols such as Escherichia coli pol I, and other DNA metabolic enzymes such as human immunodeficiency virus reverse transcriptase, T7 RNA polymerase and bovine deoxyribonuclease I. CoQ1, which has the shortest isoprenoid chains, had the strongest inhibitory effect on pol γ and topo II activities among CoQ1–CoQ10, with 50% inhibitory concentration (IC50) values of 12.2 and 15.5 µM, respectively. CoQ1 could prevent the growth of human promyelocytic leukemia cells, HL‐60, and the 50% lethal dose (LD50) value was 14.0 µM. The cells were halted at S phase and G1 phase in the cell cycle, and suppressed mitochondrial proliferation. From these results, the relationship between the inhibition of pol γ/topo II and cancer cell growth by CoQ is discussed. (Cancer Sci 2006; 97: 716–723)
Effects of salbutamol and glyceryl trinitrate on large arterial stiffness are similar between patients with hypertension and adults with normal blood pressure
Authors: Waring W. Stephen , Sinclair Hannah M. , Webb David J. 
Published: July 2006

What is already known about this subject

Assessment of endothelial function gives prognostic information and allows risk stratification among patients with hypertension.
Existing techniques for determining endothelial function involve invasive methods that are not widely applicable beyond a research environment.
A simple non‐invasive pulse wave analysis (PWA) method for assessing endothelial function has recently been described, but its applicability in clinical practice is uncertain.

What this study adds

Application of the PWA technique to patients with established hypertension is feasible, but endothelial dysfunction was not detected.
Possible discrepancies between different agonists used to assess endothelial function might be important and need further consideration.

AimsEndothelial function is characteristically impaired in patients with hypertension. Endothelial function was assessed in men and women with hypertension using a recently described, non‐invasive method.MethodsTwenty patients and 20 controls received salbutamol 400 µg and glyceryl trinitrate (GTN) 500 µg in a two‐way randomized, single‐blind study. Effects on augmentation index (AIx) were assessed using pulse wave analysis (PWA).ResultsResponses (absolute AIx reduction and 95% confidence interval) to salbutamol were 8.4% (6.2, 10.6) and 8.3% (7.0, 9.6) in patients and controls, respectively, and those to GTN were 13.6% (10.8, 16.4) and 15.5% (13.0, 17.0), respectively.ConclusionsSystemic arterial responses to endothelium‐dependent and ‐independent vasodilators are preserved in patients with mild, uncomplicated hypertension, indicating normal large arterial endothelial function.
Oral zinc sulfate in the treatment of rosacea: A double‐blind, placebo‐controlled study
Authors: Sharquie Khalifa E. , Najim Rafid A. , Al‐Salman Hala N. 
Published: July 2006

AbstractBackground  Rosacea is a skin problem not uncommonly encountered world‐wide. There is a need for an effective and well‐tolerated treatment for this disease.Objective  To evaluate the efficacy and side‐effects of zinc sulfate in rosacea in a randomized, controlled, double‐blind trial.Patients and methods  Patients with rosacea who attended the outpatient Clinic of Dermatology and Venereology in Baghdad Teaching Hospital were recruited into this study between October 2002 and August 2004. A disease severity score was calculated for each patient. The patients were randomly allocated to receive either zinc sulfate 100 mg or identical placebo capsules three times per day. Zinc sulfate and placebo capsules were given in a double‐blind manner. Following 3 months of starting the treatment, the patients crossed over, i.e. patients on placebo crossed over to zinc sulfate and those on zinc sulfate crossed over to placebo.Results  Twenty‐five patients with rosacea were included in this study: 16 (64%) females and nine (36%) males. Nineteen patients completed the study: 11 (58%) females and eight (42%) males. Patient age ranged from 21 to 64 years with a mean ± SD of 48.2 ± 9.3 years. Duration of the disease ranged from 1 to 14 years with a mean ± SD of 4.4 ± 3.2 years. In the group started on zinc sulfate, the score before therapy ranged from 5 to 11 with a mean ± SD of 8 ± 2.0. The mean started to decrease directly after the first month of therapy with zinc sulfate to a significantly lower level. After shifting to placebo treatment, the mean started to rise gradually in the fifth month but remained significantly lower than the levels before therapy. In the group started on placebo, the score before therapy ranged from 5 to 9 with a mean ± SD of 7 ± 1.3. The mean remained high in the first 3 months of therapy while the patients were on placebo. After shifting to zinc sulfate, the mean started to decrease after the fourth month to significantly low levels. No important side‐effects were reported apart from mild gastric upset in three (12%) patients on zinc sulfate.Conclusion  Zinc sulfate was found to be a good option in the treatment of rosacea, as it was safe, effective and lacking important side‐effects.
Mechanism by which a novel non‐thiazolidinedione peroxisome proliferator‐activated receptor γ agonist, FK614, ameliorates insulin resistance in Zucker fatty rats
Authors: Minoura H. , Takeshita S. , Kimura C. , Hirosumi J. , Takakura S. , Kawamura I. , Seki J. , Manda T. , Mutoh S. 
Published: July 2006

Aim:  The aim of this study was to examine the mechanism by which a novel non‐thiazolidinedione (TZD) peroxisome proliferator‐activated receptor (PPAR) γ agonist, FK614, ameliorates insulin resistance in Zucker fatty rats.Methods:  FK614 (1, 3.2 or 10 mg/kg) and a TZD PPARγ agonist, pioglitazone (1, 3.2 or 10 mg/kg), were orally administered to Zucker fatty rats (genetically obese and insulin resistant) once a day for 14 days, and an oral glucose tolerance test was performed. The expression levels of various genes in the white adipose tissue (WAT) of Zucker fatty rats treated with FK614 (3.2 mg/kg), pioglitazone (10 mg/kg) and another TZD PPARγ agonist, rosiglitazone (3.2 mg/kg), were determined using a real‐time reverse transcription–polymerase chain reaction method. Morphometric analysis of the WAT of Zucker fatty rats treated with FK614 (3.2 mg/kg) and pioglitazone (10 mg/kg) was performed. Glucose transport activity in the isolated soleus muscle of FK614‐treated Zucker fatty rats was also investigated.Results:  FK614 and pioglitazone both improved glucose tolerance in Zucker fatty rats. FK614 significantly increased the expression levels of acyl CoA oxidase, a PPAR‐responsive gene, and adipocyte fatty acid–binding protein (aP2), an adipocyte differentiation marker gene, in epididymal WAT. It also significantly decreased the level of gene expression of tumour necrosis factor‐α, an insulin resistance–inducing factor in retroperitoneal WAT, as did pioglitazone and rosiglitazone. FK614 and pioglitazone both significantly increased the total number of adipocytes and decreased their average size in WAT, mainly by increasing the number of small adipocytes. Additionally, administration of FK614 to Zucker fatty rats enhanced insulin sensitivity for glucose uptake in the soleus muscle.Conclusion:  This study suggests the possibility that FK614 induces adipocyte differentiation in Zucker fatty rats by stimulating PPARγin vivo, thereby changing the character of WAT and improving insulin sensitivity throughout the body.
Are Business Services Immune to the Business Cycle?
Authors: KIRK ROBERT 
Published: July 2006

ABSTRACTShould an economic development strategy target the business services industry to insulate the local economy from the business cycle? The relationship between business services employment (SIC 73) and measures of the business cycle is analyzed at national and metropolitan‐area levels. At the national level, certain components of business services are not immune to the business cycle while others are. At the metropolitan level, certain characteristics of the metropolitan area and its industrial structure are identified which would result in business services employment being procyclical or not immune to the business cycle.
Regional Population Growth Rate Differences: Note
Authors: NISSAN EDWARD , CAVENY REGINA 
Published: July 2006

ABSTRACTThis note investigates regional population growth in the U.S. for 1959‐84, taking into account four city sizes and three time periods. It is found that the growth is largest in city size (0.5 ‐ 1.0) million and (1.0 ‐ 2.0) million. Over time, the growth is largest in the less urbanized regions.
Valuation Analysis of Commercial Real Estate Using the Nearest Neighbors Appraisal Technique
Authors: ISAKSON HANS R. 
Published: July 2006

ABSTRACTThe Nearest Neighbors Appraisal Technique (NNAT) is pitted against the traditional real estate appraisal process and ordinary least squares (OLS) estimates of value for various types of commercial real estate in Dallas, Texas. Additionally, time is explicitly entered into NNAT. NNAT estimates of value are significantly more accurate than the traditional appraisal process for all types of commercial real estate, it is significantly more accurate than OLS estimates for retail and miscellaneous properties, and it is more accurate, but not significantly so, than OLS estimates for other types of commercial real estate.