bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ab‐initiosimulations of materials using VASP: Density‐functional theory and beyond
Authors: Hafner Jürgen 
Published: July 2008

AbstractDuring the past decade, computer simulations based on a quantum‐mechanical description of the interactions between electrons and between electrons and atomic nuclei have developed an increasingly important impact on solid‐state physics and chemistry and on materials science—promoting not only a deeper understanding, but also the possibility to contribute significantly to materials design for future technologies. This development is based on two important columns: (i) The improved description of electronic many‐body effects within density‐functional theory (DFT) and the upcoming post‐DFT methods. (ii) The implementation of the new functionals and many‐body techniques within highly efficient, stable, and versatile computer codes, which allow to exploit the potential of modern computer architectures. In this review, I discuss the implementation of various DFT functionals [local‐density approximation (LDA), generalized gradient approximation (GGA), meta‐GGA, hybrid functional mixing DFT, and exact (Hartree‐Fock) exchange] and post‐DFT approaches [DFT + U for strong electronic correlations in narrow bands, many‐body perturbation theory (GW) for quasiparticle spectra, dynamical correlation effects via the adiabatic‐connection fluctuation‐dissipation theorem (AC‐FDT)] in the Viennaab initiosimulation package VASP. VASP is a plane‐wave all‐electron code using the projector‐augmented wave method to describe the electron‐core interaction. The code uses fast iterative techniques for the diagonalization of the DFT Hamiltonian and allows to perform total‐energy calculations and structural optimizations for systems with thousands of atoms andab initiomolecular dynamics simulations for ensembles with a few hundred atoms extending over several tens of ps. Applications in many different areas (structure and phase stability, mechanical and dynamical properties, liquids, glasses and quasicrystals, magnetism and magnetic nanostructures, semiconductors and insulators, surfaces, interfaces and thin films, chemical reactions, and catalysis) are reviewed. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
The Hamilton—Waterloo problem: The case of triangle‐factors and one Hamilton cycle
Authors: Dinitz J.H. , Ling Alan C.H. 
Published: July 2008

AbstractThe Hamilton—Waterloo problem is to determine the existence of a 2‐factorization of K2n+1 in which r of the 2‐factors are isomorphic to a given 2‐factor R and s of the 2‐factors are isomorphic to a given 2‐factor S, with r + s=n. In this article we consider the case when R is a triangle‐factor, S is a Hamilton cycle and s = 1. We solve the problem completely except for 14 possible exceptions. This solves a major open case from the 2004 article of Horak et al. © 2008 Wiley Periodicals, Inc. J Combin Designs 17: 160–176, 2009
Anti‐histones antibodies in systemic lupus erythematosus: prevalence and frequency in neuropsychiatric lupus
Authors: Sun Xiao‐Yun , Shi Jinxia , Han Lei , Su Yin , Li Zhan‐Guo 
Published: July 2008

AbstractTo investigate the specificity, sensitivity, and concomitant presence of antibodies against histones (H), histone H1 (H1), and histone H3 (H3) in patients with systemic lupus erythematosus (SLE) and analyze their association with SLE. Serum IgG anti‐histones antibodies were detected by enzyme‐linked immunosorbent assay in 144 SLE patients consisting of 24 neuropsychiatric lupus (NPSLE), 65 lupus nephritis (LN), and 55 SLE, 100 other rheumatic diseases patients, as well as 40 healthy controls. Clinical and biological parameters of the patients were also evaluated. Anti‐H, anti‐H1, and anti‐H3 antibodies yielded a sensitivity of approximately 33% and a specificity of more than 93% for SLE, which was comparable to that found for anti‐double‐stranded DNA (anti‐dsDNa) antibodies. More significantly, anti‐histone antibody is found in approximately 50% of patients with NPSLE compared with LN. Moreover, the titers of anti‐histones antibodies of NPSLE patients were significantly higher than that of patients with SLE and LN. The sequential analysis revealed a close correlation of anti‐H and anti‐H1 antibodies with SLE disease activity. There was an approximate 30% positive rate of anti‐histones antibodies in 144 SLE patients lacking anti‐nucleosome, anti‐mDNA, anti‐Sm, and anti‐dsDNA antibodies. Antibodies to histones H1 and H3 are markers with high specificity of 93.6–96.4% for SLE. The anti‐histone antibody markers are prevalent in approximately 50% of NPSLE. Furthermore, there was a strong correlation with SLE disease activity index and levels of antibodies to histones and H1. J. Clin. Lab. Anal. 22:271–277, 2008. © 2008 Wiley‐Liss, Inc.
Estimation of vitamin B1 excretion in 24‐hr urine by assay of first‐morning urine
Authors: Ihara Hiroshi , Matsumoto Takayuki , Kakinoki Takashi , Shino Yoshio , Hashimoto Reiko , Hashizume Naotaka 
Published: July 2008

AbstractUrinary B1 (vitamin B1) excretion is commonly determined in 24‐hr urine specimens to obtain an estimate of nutritional status. The aim of our study was to investigate whether B1 in random urine specimens, corrected for the urine creatinine (Cr), can be substituted for B1 in 24‐hr urines. Collection of such hour urines is often fraught with errors; an alternative method is described here. All urine specimens voided over 24 hr were collected from 32 healthy adults as were the first‐morning urines from 30 healthy Japanese women. The B1 excretion was expressed as the ratio of B1 to Cr. Although the B1 excretion was expressed as the B1/Cr ratio, the B1 excretion varied with the urine volume and the time of urine collection. The B1/Cr ratio in random urine specimens not collected at a fixed time may mislead the evaluation of the nutritional status. We found that the B1/Cr ratio in the first‐morning urine correlated significantly with the ratio in 24‐hr urines (r=0.970, P<0.001) and also with the concentration of total B1 (B1 plus its phosphate esters) in whole blood (r=0.733, P<0.001). We conclude that the B1/Cr ratio in 24‐hr urines could be estimated by measuring the ratio in the first‐morning urine. J. Clin. Lab. Anal. 22:291‐294, 2008. © 2008 Wiley‐Liss, Inc.
Effect of Asian ginseng, Siberian ginseng, and Indian ayurvedic medicine Ashwagandha on serum digoxin measurement by digoxin III, a new digoxin immunoassay
Authors: Dasgupta Amitava , Tso Gertie , Wells Alice 
Published: July 2008

AbstractAsian ginseng, Siberian ginseng, and Indian Ayurvedic medicine Ashwagandha demonstrated modest interference with serum digoxin measurements by the fluorescent polarization immunoassay (FPIA). Recently, Abbott Laboratories marketed a new digoxin immunoassay, Digoxin III for application on the AxSYM analyzer. We studied potential interference of these herbal supplements on serum digoxin measurement by Digoxin III assay in vitro and compared our results with the values obtained by Tina‐quant assay. Aliquots of drug‐free serum pool were supplemented with various amounts of Asian ginseng, Siberian ginseng, or Ashwagandha approximating expected concentrations after recommended doses and overdoses of these herbal supplements in serum. Then digoxin concentrations were measured by the Digoxin III and Tina‐quant (Roche Diagnostics) assay. We also supplemented aliquots of a digoxin pool prepared from patients receiving digoxin with various amounts of these herbal supplements and then measured digoxin concentrations again using both digoxin immunoassays. We observed modest apparent digoxin concentrations when aliquots of drug‐free serum pool were supplemented with all three herbal supplements using Digoxin III assay (apparent digoxin in the range of 0.31–0.57 ng/ml), but no apparent digoxin concentration (except with the highest concentration of Ashwagandha supplement for both brands) was observed using the Tina‐quant assay. When aliquots of digoxin pool were further supplemented with these herbal supplements, digoxin concentrations were falsely elevated when measured by the new Digoxin III assay. For example, we observed 48.2% (1.63 ng/ml digoxin) increase in digoxin concentration when an aliquot of Digoxin pool 1 (1.10 ng/ml digoxin) was supplemented with 50 μl of Asian ginseng extract (Brand 2). Measuring free digoxin does not eliminate the modest interferences of these herbal supplements in serum digoxin measurement by the Digoxin III assay. J. Clin. Lab. Anal. 22:295–301, 2008. © 2008 Wiley‐Liss, Inc.
A simple, rapid, and convenient Luminex™‐compatible method of tissue isolation
Authors: Barclay Derek , Zamora Ruben , Torres Andres , Namas Rajaie , Steed David , Vodovotz Yoram 
Published: July 2008

AbstractVarious pathological conditions are associated with changes in multiple protein biomarkers, and these changes can be assessed using xMAP™ beads and the Luminex™ platform. Although this platform is most commonly utilized in the analysis of biomarkers in serum, plasma, or urine, it is often desirable to measure these analytes in tissues (e.g., biopsy specimens). We have developed a simple, rapid method of tissue isolation in which excised tissues are permeabilized in RNAlater™ at 4°C overnight, followed by Luminex™ analysis for inflammatory biomarkers (cytokines). This method was compared with flash‐freezing in both mouse liver and human debrided wound specimens, and may be of utility in other clinical settings. J. Clin. Lab. Anal. 22:278–281,
2008. © 2008 Wiley‐Liss, Inc.
Nontreponemal tests in the diagnosis of neurosyphilis: an evaluation of the Venereal Disease Research Laboratory (VDRL) and the Rapid Plasma Reagin (RPR) tests
Authors: Castro Rita , Prieto Emília Simões , da Luz Martins Pereira Filomena 
Published: July 2008

AbstractThe Venereal Disease Research Laboratory (VDRL) test has long been considered the best serological test for the diagnosis of neurosyphilis. The goal of this study was to find out if the Rapid Plasma Reagin (RPR) could be an alternative to the VDRL. Cerebrospinal fluid (CSF) and sera samples from patients in the following stages of syphilis were tested: 8 had symptomatic and 16 asymptomatic neurosyphilis, 4 were in the primary stage, 6 had secondary syphilis, and 92 were in the latent stage. We have also studied 61 samples from individuals with treated syphilis and 126 with other neurological diseases than neurosyphilis. All the CSF samples were studied with both RPR and VDRL tests. RPR and VDRL test results were mostly concordant. The specificity of these tests for current neurosyphilis was 99% for the VDRL and 99.3% for the RPR, whereas the sensitivity was 70.8 and 75%, respectively, for the VDRL and RPR. In view of these results it seems to us that the RPR could be an alternative to the VDRL in the diagnosis of neurosyphilis. J. Clin. Lab. Anal. 22:257–261, 2008. © 2008 Wiley‐Liss, Inc.
Validation of fecal elastase‐1 determination using immunoenzymatic assay in HIV‐infected patients
Authors: de Oliveira Claudia Giorgia Bronzatti , Affonso Fonseca Fernando Luiz , Stackunas Salotto Nicolle , Ambrosio Chicoli Felipe , Leopoldo Dória Pedro , Alessi Rudá , Zimberg Chehter Ethel 
Published: July 2008

AbstractPancreatic elastase‐1 is a proteolytic enzyme exclusively produced in the pancreas, is stable when passing through the bowel, and its determination is associated with chronic pancreatitis. The clinical diagnosis of pancreatitis is based on anamnesis, physical examination, radiological, sonographic, endoscopic, and laboratory findings. Nowadays, there is a test for the determination of fecal elastase‐1, by enzymatic reaction (enzyme‐linked immunosorbent assay, ELISA), which specifically determines human elastase‐1, promoting the pancreatic function evaluation. Parameters such as linearity, calibration curve, sensitivity, specificity, precision, accuracy, recovery, and receiver operator characteristic (ROC) curve are used to evaluate the test. The aim of this study was the validation of the immunoenzymatic assay (ELISA) and the use of its results in patients with HIV, alcoholics, and under antiretroviral therapy. The study involved 157 patients, 95 of them were HIV‐infected, and 62 were completely healthy. The elastase‐1 ELISA kit from Bioserv was used, and we noted that the obtained results were linear, sensitive, precise, and accurate. Moreover, our results suggest that this test can be a laboratory evaluation to determine the relationship of pancreatitis with alcohol use, but not its association with antiretroviral use in HIV patients (P=0.424). This test is useful to diagnose pathologies related to pancreatic insufficiency. J. Clin. Lab. Anal. 22:286‐290, 2008. © 2008 Wiley‐Liss, Inc.
Clinical laboratory automated urinalysis: comparison among automated microscopy, flow cytometry, two test strips analyzers, and manual microscopic examination of the urine sediments
Authors: Mayo S. , Acevedo D. , Quiñones‐Torrelo C. , Canós I. , Sancho M. 
Published: July 2008

AbstractUrinalysis is one of the habitual clinical laboratory procedures, which implies that one of the largest sample volumes currently requires significant labor to examine microscopic sediments. Different analyzers currently used to perform this task have been compared with the manual microscopic sediment examination. The Atlas Clinitek 10 (Bayer Corporation, Diagnostics Division, Tarrytown, NY) and Urisys 2400 (Hitachi Science Systems Ltd., Ibaraki, Japan) test strips analyzers and two automated urinalysis systems, Sysmex UF‐100 (Sysmex Corporation Kobe, Japan) and IRIS iQ200 (International Imaging Remote Systems, Chatsworth, CA), have been considered. We assessed the concordance between the results obtained from 652 freshly collected urine samples for erythrocytes (RBC), leukocytes (WBC), squamous epithelial cells (EC), nitrites/bacteria, and crystals using the methodologies mentioned. A principal components analysis was performed in order to examine the correlation between these parameters. Instrument accuracy was also assessed. The Spearman's statistic (p) showed an adequate agreement between methods for RBC (iQ200=0.473; UF‐100=0.439; Atlas=0.525; Urisys=0.539), WBC (iQ200=0.695; UF‐100=0.761; Atlas=0.684: Urisys=0.620), and bacteria/nitrites (iQ200=0.538; UF‐100=0.647; Atlas=0.532; Urisys=0.561) counts. By applying the Wilcoxon and McNemar tests, a concordance degree was found between 82–99 and 52–95% for the values obtained from the two test strips analyzers considered and from the iQ200 and UF‐100 systems, respectively. From these results, we can conclude that both test strips analyzers are similar and, on the other hand, that automated urinalysis is needed to improve precision and the response time; but sometimes manual microscopic revisions are required, mainly when flags, because of crystals, are detected. J. Clin. Lab. Anal. 22:262–270, 2008. © 2008 Wiley‐Liss, Inc.
Comparison between a liquid chromatography‐tandem mass spectrometry assay and a fluorescent polarization immunoassay to measure whole blood everolimus concentration in heart and renal transplantations
Authors: Dailly Eric , Deslandes G. , Hourmant M. , Petit T. , Renaud C. , Treilhaud M. , Jolliet P. 
Published: July 2008

AbstractVarious methods [fluorescent polarization immunoassay (FPIA) and liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) assay] are used for therapeutic drug monitoring of everolimus. The aim of this study is to compare these assays in renal and heart transplantation. The correlation between results was investigated by linear regression in 44 patients (24 heart recipients and 20 renal recipients—137 samples). The comparison between assays was performed by a paired t‐test. A highly significant correlation was found between FPIA and LC‐MS/MS in heart and renal recipients [FPIA=0.851 × LC‐MS/MS+1.773r2=0.8738 (P<0.001)]. Paired t‐tests did not show a significant difference between everolimus whole blood concentrations in the populations of heart and renal recipients or heart recipients or renal recipients. FPIA and LC‐MS/MS assays gave consistent overall results although some significant differences were observed in some samples between these methods indicating that FPIA assay has limitations that deserve further investigations. J. Clin. Lab. Anal. 22:282‐285, 2008. © 2008 Wiley‐Liss, Inc.
Prognostic potential of a PSA complex in sera of prostate cancer patients with α2‐macroglobulin deficiency
Authors: Kanoh Yuhsaku , Ohara Tadashi , Egawa Shin , Baba Shiro , Akahoshi Tohru 
Published: July 2008

AbstractWe previously reported on a number of cases of metastatic prostate cancer (PCa) in which serum α2‐macroglobulin (α2M) levels were markedly decreased to less than 20 mg/dl (α2M deficiency). In order to elucidate the relative proportions of free and a prostate‐specific antigen (PSA) complex in PCa patients with α2M deficiency, we have assessed serum α2M and total PSA levels, and ratios of free PSA to total PSA (F/T ratios) at each stage of PCa. Moreover, the PSA reactivity profile was determined on fractionated serum specimens of PCa patients using high‐performance liquid chromatography (HPLC) using a TSKG‐3000 SWXL column. Measurement of α2M concentration was performed by laser‐nephelometry. PSA levels were determined by enzyme immunoassay, free PSA by radioimmunoassay. In those PCa patients with α2M deficiency, serum α2M and F/T ratios were lower, whereas PSA levels were higher when compared with those PCa patients without α2M deficiency (P<0.05). PSA elution profiles on HPLC columns revealed two major peaks. The proportion of PSA‐antichymotrypsin (PSA‐ACT) increased, whereas the proportion of free PSA decreased in PCa patients with α2M deficiency as compared with those PCa patients without α2M deficiency. F/T ratios were significantly lower in PCa patients with α2M deficiency than in those PCa patients without α2M deficiency. PSA‐ACT and F/T ratio may be useful for monitoring bone metastasis in PCa. J. Clin. Lab. Anal. 22:302–306, 2008. © 2008 Wiley‐Liss, Inc.
Inhibitory effects of starvation on prothoracic gland cell DNA synthesis during the last larval instar of the silkworm, Bombyx mori
Authors: Chen Chien‐Hung , Gu Shi‐Hong 
Published: July 2008

AbstractActivation of DNA synthesis in prothoracic gland cells of the silkworm, Bombyx mori, during the middle stages of the last larval instar appears to be nutrition dependent, with starvation on day 3 of the last larval instar inhibiting its dramatic increase. The possible cellular mechanism causing the inhibition of DNA synthesis owing to starvation was further examined by determining changes in the growth‐promoting activity of the hemolymph and the responsiveness of gland cells to starvation. The results showed that on starvation, the activity of the growth‐promoting factor in the hemolymph did not greatly decrease until 2 days after starvation had begun. However, the dramatic increase in the responsiveness of gland cells (the ability to synthesize DNA when exposed to the hemolymph growth factor), which normally occurs on day 4 of the last instar, was not observed when starvation was begun on day 3. A dramatic increase in gland cell size was observed in control larvae during later stages of the last larval instar. However, with starvation beginning on day 3, gland cell size was maintained at lower levels compared with those of control larvae, indicating that the inhibition of DNA synthesis is indeed related to the inhibition of cell size. From these results, it was assumed that alterations in growth factor receptors and downstream signaling may be related to the inhibition of DNA synthesis by starvation and that the deficiency in growth‐promoting factor signaling may guarantee that the growth of endoreplicative tissues in these larvae ceases. J. Exp. Zool. 309A:399–406, 2008. © 2008 Wiley‐Liss, Inc.
Lung ventilation during treadmill locomotion in a semi‐aquatic turtle, Trachemys scripta
Authors: Landberg Tobias , Mailhot Jeffrey D. , Brainerd Elizabeth L. 
Published: July 2008

AbstractIt is reasonable to presume that locomotion should have a mechanical effect on breathing in turtles. The turtle shell is rigid, and when the limbs protract and retract, air in the lungs should be displaced. This expectation was met in a previous study of the green sea turtle, Chelonia mydas; breathing completely ceased during terrestrial locomotion (Jackson and Prange, 1979. J Comp Physiol 134:315–319). In contrast, another study found no direct effect of locomotion on ventilation in the terrestrial box turtle, Terrapene carolina (Landberg et al., 2003. J Exp Biol 206:3391–3404). In this study we measured lung ventilation during treadmill locomotion in a semi‐aquatic turtle, the red‐eared slider, Trachemys scripta. Sliders breathed almost continuously during locomotion and during brief pauses between locomotor bouts. Tidal volume was relatively small (∼1 mL) during locomotion and approximately doubled during pauses. Minute ventilation was, however, not significantly smaller during locomotion because breath frequency was higher than that during the pauses. We found no consistent evidence for phase coupling between breathing and locomotion indicating that sliders do not use locomotor movements to drive breathing. We also found no evidence for a buccal‐pump mechanism. Sliders, like box turtles, appear to use abdominal musculature to breathe during locomotion. Thus, locomotion affects lung ventilation differently in the three turtle species studied to date: the terrestrial Te. carolina shows no measurable effect of locomotion on ventilation; the semi‐aquatic Tr. scripta breathes with smaller tidal volumes during locomotion; and the highly aquatic C. mydas stops breathing completely during terrestrial locomotion. J. Exp. Zool. 311A:551–562, 2009. © 2008 Wiley‐Liss, Inc.
Lung and metabolic development in mammals: contribution to the reconstruction of the marsupial and eutherian morphotype
Authors: Szdzuy Kirsten , Zeller Ulrich 
Published: July 2008

AbstractMarsupials represent only 6% of all living mammals. Marsupialia and Placentalia are distinguished mainly by their modes of reproduction. In particular, the differences in the stage of development of the neonates may be one explanation for the divergent evolutionary success. In this respect one important question is whether the survivability of the neonate depends on the degree of maturation of the respiratory system relative to the metabolic capacity at the time of birth. Therefore, this review highlights the differences in lung morphology and metabolic development of extant Marsupialia and Placentalia. The Marsupial neonate is born with a low birth weight and is highly immature. The neonatal lung is characterized by large terminal sacs, a poorly developed bronchial system and late formation of alveoli. Marsupialia have a low metabolic rate at birth and attain adult metabolic rate and thermoregulatory capacity late in postnatal development. In contrast, the eutherian neonate is born with a relative high birth weight and is always more mature than marsupial neonates. The neonatal lung has small terminal sacs, the bronchial system is well developed and the formation of alveoli begins few days after birth. Placentalia have a high metabolic rate at birth and attain adult metabolic rate and thermoregulatory capacity early in postnatal development. The differences in the developmental degree of the newborn lung between Marsupialia and Placentalia have consequences for their metabolic and thermoregulatory capacity. These differences could be advantageous for Placentalia in the changing environments in which they evolved.J. Exp. Zool. (Mol. Dev. Evol.) 312B:555–578, 2009. © 2008 Wiley‐Liss, Inc.