bluuebunny/crossref_metadata_2025_split huggingface dataset:
An off‐line robot simulation toolbox
Authors: Kucuk Serdar , Bingul Zafer 
Published: January 2009

AbstractRobotics has gained popularity in education so many engineering schools are offering robotics courses. In this study, a novel robot toolbox, “ROBOLAB” is developed for the educational users to improve the understanding of robotics fundamentals through interactive real‐time simulation. To understand manipulator movement in 3‐D space with increasing number of joints is very difficult for engineering students; because the mathematical model between joint space and physical space becomes more complex. In order to overcome this complexity, ROBOLAB based on MATLAB Graphical User Interface (GUI) includes a library for the 16 different 6 degree of freedom (6‐DOF) fundamental serial robot manipulators. The user has option to view an animation of the robot manipulators with choosing one of them or to create own GUIs based on robot project. ROBOLAB provides valuable analysis tools to students and engineering professionals in which they can compute rotation and transformation matrix, forward and inverse kinematics, and trajectory planning. Additionally, it allows user to use powerful MATLAB features such as controlling over data and formatting. In order to illustrate the features of ROBOLAB, RS cylindrical robot manipulator is given here as an example. Usage of real industrial robots in laboratory may be a very expensive way to teach robotics courses. ROBOLAB may help students to accomplish the courses and projects involving robots with minimum cost and to see 3‐D space robot applications more effectively. © 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 18: 41–52, 2010; Published online in Wiley InterScience (www.interscience.wiley.com); DOI 10.1002/cae.20236
Synthesis and optical resolution of 1‐[(3‐carboxy‐1,1′‐biphenyl)‐2‐yl]‐1H‐pyrrole‐2‐carboxylic acid
Authors: Faigl Ferenc , Vas‐Feldhoffer Bernadett , Kudar Veronika , Czugler Mátyás , Pál Krisztina , Kubinyi Miklós 
Published: January 2009

AbstractSite selective mono‐ and dimetalation methods have been developed for the functionalization of 1‐[(1,1′‐biphenyl)‐2‐yl]‐1H‐pyrrole. Optical resolution of the prepared 1‐[(3‐carboxy‐1,1′‐biphenyl)‐2‐yl]pyrrole‐2‐carboxylic acid provided new atropisomeric 1‐arylpyrrole derivatives. The absolute configuration of the pure dicarboxylic acid enantiomers was determined by single crystal X‐ray diffraction and CD spectroscopy. Chirality 2009. © 2009 Wiley‐Liss, Inc.
Water‐soluble calix[4]resorcinarenes as chiral NMR solvating agents for bicyclic aromatic compounds
Authors: O'Farrell Courtney M. , Hagan Kaitlin A. , Wenzel Thomas J. 
Published: January 2009

AbstractWater‐soluble calix[4]resorcinarenes with proline, 3‐hydroxyproline, and 4‐hydroxyproline substituent groups are evaluated as chiral NMR solvating agents on a series of bicyclic aromatic compounds with naphthyl, indole, dihydroindole, and indane rings. The substrates interact with the calixresorcinarene through insertion of the aromatic ring into the cavity. Most of the substrates are analyzed as cationic species, although one anionic species is analyzed. All of the substrates exhibit enantiomeric discrimination in the 1H‐NMR spectrum with one or more of the calixresorcinarenes. In most cases, the hydroxyproline derivatives are more effective at causing enantiodifferentiation than the corresponding proline derivative. Presumably, the hydroxyl group on the proline moieties is involved in interactions with the substituent groups of the substrate that are important in creating chiral recognition. The enantiomeric discrimination in the 1H‐NMR spectrum is large enough for many resonances to permit the analysis of enantiomeric purity. Chirality 2009. © 2009 Wiley‐Liss, Inc.
Use of FOXJ1CreER2T mice for inducible deletion of embryonic node gene expression
Authors: Wang Shuyun , Ware Stephanie M. 
Published: January 2009

AbstractThe ciliated cells of the node of the mouse embryo contribute to the establishment of left–right patterning via generation of leftward laminar fluid flow and initiation of a left‐sided morphogen gradient. Here, we identify FOXJ1CreER2T mice in which expression of Cre recombinase is directed to ciliated node cells. The data demonstrate that foxj1 is expressed specifically in the node throughout the developmental window critical for left–right patterning. In transgenic embryos, Cre expression is detected by immunohistochemistry in ciliated cells of the node. Rosa26R reporter mice, in which expression of lacZ is activated only after Cre‐mediated recombination, demonstrate strong and uniform labeling at the node when crossed with FOXJ1CreER2T mice. Cell labeling occurred as early as 0‐ to 2‐somite stages, specifically within cells of the node, and recombination was highly efficient in response to tamoxifen. FOXJ1CreER2T transgenic mice represent a new genetic tool for the analysis of node‐specific gene expression and will also be valuable in the study of node cell lineage and temporal cell fate mapping. genesis 47:132–136, 2009. © 2009 Wiley‐Liss, Inc.
Family history of cancer and nonmalignant lung diseases as risk factors for lung cancer
Authors: Gao Ying , Goldstein Alisa M. , Consonni Dario , Pesatori Angela C. , Wacholder Sholom , Tucker Margaret A. , Caporaso Neil E. , Goldin Lynn , Landi Maria Teresa 
Published: January 2009

AbstractFamily history (FH) of lung cancer is an established risk factor for lung cancer, but the modifying effect of smoking in relatives has been rarely examined. Also, the role of FH of nonmalignant lung diseases on lung cancer risk is not well known. We examined the role of FH of cancer and nonmalignant lung diseases in lung cancer risk overall, and by personal smoking, FH of smoking and histology in 1,946 cases and 2,116 population‐based controls within the Environment And Genetics in Lung cancer Etiology (EAGLE) study. Odds ratios (ORs) and 95% CI from logistic regression were calculated adjusting for age, gender, residence, education and cigarette smoking. FH of lung cancer in any family member was associated with increased lung cancer risk (OR = 1.57, 95% CI = 1.25–1.98). The odds associated with fathers', mothers' and siblings' history of lung cancer were 1.41, 2.14 and 1.53, respectively. The associations were generally stronger in never smokers, younger subjects and for the adenocarcinoma and squamous cell carcinoma subtypes. FH of chronic bronchitis and pneumonia was associated with increased (OR = 1.49, 95% CI = 1.23–1.80) and decreased (OR = 0.73, 95% CI = 0.61–0.87) lung cancer risk, respectively. FH of lung cancer and nonmalignant lung diseases affected lung cancer risk independently, and did not appear to be modified by FH of smoking. © 2009 UICC
Cancer/testis antigen CT45: Analysis of mRNA and protein expression in human cancer
Authors: Chen Yao‐Tseng , Hsu Melinda , Lee Peishan , Shin Sandra J. , Mhawech‐Fauceglia Paulette , Odunsi Kunle , Altorki Nasser K. , Song Chao‐Jun , Jin Bo‐Quan , Simpson Andrew J. , Old Lloyd J. 
Published: January 2009

AbstractCT45 is a cancer/testis gene that we previously identified by massively parallel signature sequencing. Encoded by a multigene family on chromosome X, CT45 showed restricted mRNA expression to normal testis and various cancers. In this study, monoclonal antibodies were generated against recombinant CT45 protein, and CT45 protein expression in normal and tumor tissues was evaluated by immunohistochemical analysis. In adult normal tissue, CT45 expression was restricted to testicular germ cells, detected as a nuclear protein mainly at the stage of primary spermatocytes. In tumors, CT45 protein expression correlated with the mRNA levels detected by quantitative RT‐PCR, and most lung cancer and ovarian cancers with CT45 mRNA at levels >1% of testicular expression were CT45 protein‐positive. In positive cases, CT45 showed expression patterns that ranged from diffuse strong staining to heterogeneous and patchy expression. In lung cancer, CT45 expression was least frequent in adenocarcinoma, more frequent in squamous cell carcinoma and neuroendocrine tumors. Using tissue microarrays, 376 lung cancer, 219 ovarian cancer and 155 breast cancer were evaluated for CT45 protein expression. The expression frequency was highest in ovarian cancer (37%), followed by lung cancer (13%) and lowest in breast cancer (<5%). Given the focal nature of CT45 expression in many cases, these numbers represented the minimal frequency of expression in these tumor types. In summary, the expression frequency and characteristics of CT45 expression are similar to other CT cancer vaccine targets currently in clinical trials, e.g., NY‐ESO‐1 and MAGE‐A, suggesting CT45 as a potentially useful cancer target. © 2009 UICC
Water channel proteins (later called aquaporins) and relatives: Past, present, and future
Authors: Benga Gheorghe 
Published: January 2009

AbstractWater channels or water channel proteins (WCPs) are transmembrane proteins that have a specific three‐dimensional structure with a pore that can be permeated by water molecules. WCPs are large families (over 450 members) that are present in all kingdoms of life. The first WCP was discovered in the human red blood cell (RBC) membrane in 1980s. In 1990s other WCPs were discovered in plants, microorganisms, various animals, and humans; and it became obvious that the WCPs belong to the superfamily of major intrinsic proteins (MIPs, over 800 members). WCPs include three subfamilies: (a) aquaporins (AQPs), which are water specific (or selective water channels); (b) aquaglyceroporins (and glycerol facilitators), which are permeable to water and/or other small molecules; and (c) “superaquaporins” or subcellular AQPs. WCPs (and MIPs) have several structural characteristics which were better understood after the atomic structure of some MIPs was deciphered. The structure–function relationships of MIPs expressed in microorganisms (bacteria, archaea, yeast, and protozoa), plants, and some multicellular animal species [nematodes, insects, fishes, amphibians, mammals (and humans)] are described. A synthetic overview on the WCPs from RBCs from various species is provided. The physiological roles of WCPs in kidney, gastrointestinal system, respiratory apparatus, central nervous system, eye, adipose tissue, skin are described, and some implications of WCPs in various diseases are briefly presented. References of detailed reviews on each topic are given. This is the first review providing in a condensed form an overview of the whole WCP field that became in the last 20 years a very hot area of research in biochemistry and molecular cell biology, with wide and increasing implications. © 2009 IUBMB IUBMB Life, 61(2): 112–133, 2009
Biomimetic, bioactive etheric polyphosphazene‐poly(lactide‐co‐glycolide) blends for bone tissue engineering
Authors: Deng Meng , Nair Lakshmi S. , Nukavarapu Syam P. , Kumbar Sangamesh G. , Brown Justin L. , Krogman Nicholas R. , Weikel Arlin L. , Allcock Harry R. , Laurencin Cato T. 
Published: January 2009

AbstractThe long‐term goal of this work is to develop biomimetic polymer‐based systems for bone regeneration that both allow for neutral pH degradation products and have the ability to nucleate bonelike apatite. In this study, the etheric biodegradable polyphosphazene, poly[(50%ethyl glycinato)(50%methoxyethoxyethoxy)phosphazene] (PNEG50MEEP50) was blended with poly(lactide‐co‐glycolide) PLAGA and studied their ability to produce high‐strength degradable biomaterials with bioactivity. Accordingly, two blends with weight ratios of PNEG50MEEP50 to PLAGA 25:75 (BLEND25) and 50:50 (BLEND50) were fabricated using a mutual solvent approach. Increases in PNEG50MEEP50 content in the blend system resulted in decreased elastic modulus of 779 MPa when compared with 1684 MPa (PLAGA) as well as tensile strength 7.9 MPa when compared with 25.7 MPa (PLAGA). However, the higher PNEG50MEEP50 content in the blend system resulted in higher Ca/P atomic ratio of the apatite layer 1.35 (BLEND50) when compared with 0.69 (BLEND25) indicating improved biomimicry. Furthermore, these blends supported primary rat osteoblast adhesion and proliferation with an enhanced phenotypic expression when compared with PLAGA. These findings establish the suitability of PNEG50MEEP50‐PLAGA biodegradable blends as promising bioactive materials for orthopedic applications. © 2009 Wiley Periodicals, Inc. J Biomed Mater Res, 2010
Effects of mechanical load on the expression and activity of hyaluronidase in cultured synovial membrane cells
Authors: Kitamura Reiko , Tanimoto Kotaro , Tanne Yuki , Kamiya Takashi , Huang Yu‐Ching , Tanaka Nobuaki , Tanaka Eiji , Tanne Kazuo 
Published: January 2009

AbstractHyaluronan (HA) has lubricating and buffering functions in joints. Mechanical load is a regulatory factor of HA metabolism in joints, and HA synthesis by synovial membrane cells is modulated by mechanical load. However, the effects of mechanical load on HA catabolism by hyaluronidase (HYAL) in synovial membrane cells remain unclear. The purpose of this study was to evaluate the effects of cyclic tensile load on the expression and activity of HYAL in synovial membrane cells. A cyclic tensile load of 22.8% cell elongation was applied to cultured rabbit synovial membrane cells for 3 to 48 h with or without cycloheximide. HYAL1 and HYAL2 mRNA levels were evaluated by means of real‐time polymerase chain reaction (PCR) analysis. HYAL activity in the cell culture was analyzed by means of HA zymography with or without HYAL2‐small interfering (si) RNA. Levels of both HYAL1 and HYAL2 mRNA were up‐regulated significantly (p < 0.01) by the cyclic tensile load with or without cycloheximide. HYAL activity was detected in the loaded cell cultures and was suppressed substantially by HYAL2‐siRNA. HYAL activity was undetectable in unloaded cell cultures. These results show that a cyclic tensile load induces the expression and activity of HYAL in synovial membrane cells, suggesting that increased HYAL by mechanical load affects HA catabolism in synovial fluid. © 2009 Wiley Periodicals, Inc. J Biomed Mater Res, 2010
Theoretical study on the gas‐phase reaction mechanism between nickel monoxide and methane for syngas production
Authors: Yang Hua‐Qing , Qin Song , Qin Song , Hu Chang‐Wei 
Published: January 2009

AbstractThe comprehensive mechanism survey on the gas‐phase reaction between nickel monoxide and methane for the formation of syngas, formaldehyde, methanol, water, and methyl radical has been investigated on the triplet and singlet state potential energy surfaces at the B3LYP/6‐311++G(3df, 3pd)//B3LYP/6‐311+G(2d, 2p) levels. The computation reveals that the singlet intermediate HNiOCH3 is crucial for the syngas formation, whereas two kinds of important reaction intermediates, CH3NiOH and HNiOCH3, locate on the deep well, while CH3NiOH is more energetically favorable than HNiOCH3 on both the triplet and singlet states. The main products shall be syngas once HNiOCH3 is created on the singlet state, whereas the main products shall be methyl radical if CH3NiOH is formed on both singlet and triplet states. For the formation of syngas, the minimal energy reaction pathway (MERP) is more energetically preferable to start on the lowest excited singlet state other than on the ground triplet state. Among the MERP for the formation of syngas, the rate‐determining step (RDS) is the reaction step for the singlet intermediate HNiOCH3 formation involving an oxidative addition of NiO molecule into the CH bond of methane, with an energy barrier of 120.3 kJ mol−1. The syngas formation would be more effective under higher temperature and photolysis reaction condition. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009
Laser‐based in situ techniques: Novel methods for generating extreme conditions in TEM samples
Authors: Taheri Mitra L. , Lagrange Thomas , Reed Bryan W. , Armstrong Michael R. , Campbell Geoffrey H. , DeHope William J. , Kim Judy S. , King Wayne E. , Masiel Daniel J. , Browning Nigel D. 
Published: January 2009

AbstractThe dynamic transmission electron microscope (DTEM) is introduced as a novel tool for in situ processing of materials. Examples of various types of dynamic studies outline the advantages and differences of laser‐based heating in the DTEM in comparison to conventional (resistive) heating in situ TEM methods. We demonstrate various unique capabilities of the drive laser, namely, in situ processing of nanoscale materials, rapid and high temperature phase transformations, and controlled thermal activation of materials. These experiments would otherwise be impossible without the use of the DTEM drive laser. Thus, the potential of the DTEM as a new technique to process and characterize the growth of a myriad of micro and nanostructures is demonstrated. Microsc. Res. Tech., 2009. Published 2009 Wiley‐Liss, Inc.
The cytoplasmic and transmembrane domains of secretor type α1,2fucosyltransferase confer atypical cellular localisation
Authors: Christiansen Dale , Milland Julie , Dodson Hayley C. , Lazarus Brooke D. , Sandrin Mauro S. 
Published: January 2009

AbstractCarbohydrate structures influence many aspects of cell biology. Manipulating the glycosyltransferase enzymes, that sequentially add carbohydrate moieties to proteins and lipids as they pass through the Golgi and secretory pathway, can alter these carbohydrate epitopes. We previously demonstrated that the eight amino acid cytoplasmic tail of α1,2fucosyltransferase (FT) contained a sequence for Golgi localisation. In this study, we examined the localisation of the closely related secretor type α1,2fucosyltransferase (Sec) which has a smaller, yet apparently unrelated, five amino acid cytoplasmic tail. In contrast to the Golgi localisation of FT, Sec displayed atypical cytoplasmic vesicular‐like staining. However, replacing just the five amino acid tail of Sec with FT was sufficient to relocalise the enzyme to a perinuclear region with Golgi‐like staining. The biological significance of this relocalisation was this chimaeric enzyme was more effective than FT at competing for N‐Acetyl‐lactosamine and thus was superior in reducing expression of the Galα(1,3)Gal xenoepitope. Copyright © 2009 John Wiley & Sons, Ltd.
Differentiation of well‐differentiated hepatocellular carcinomas from other hepatocellular nodules in cirrhotic liver: Value of SPIO‐enhanced MR imaging at 3.0 Tesla
Authors: Park Hee Sun , Lee Jeong‐Min , Kim Se Hyung , Chang Samuel , Kim Soo Jin , Han Joon Koo , Choi Byung Ihn 
Published: January 2009

AbstractPurposeTo determine the diagnostic value of superparamagnetic iron oxide (SPIO)‐enhanced MRI for the differentiation of well‐differentiated hepatocellular carcinomas (WD‐HCCs) from other hepatocellular nodules in cirrhotic liver.Materials and MethodsThis study included 114 patients with 216 histologically confirmed hepatocellular nodules, i.e., 23 dysplastic nodules (DNs), 37 WD‐HCCs, and 156 moderately or poorly differentiated HCCs (MD‐/PD HCCs), who underwent SPIO‐enhanced MRI at 3.0T. MRI included T2‐weighted fast‐spin echo and T2*‐weighted gradient recalled echo (GRE) sequences before and after administration of ferucarbotran. The contrast‐to‐noise ratio (CNR) of the lesion was calculated. Reviewers analyzed signal intensity (SI) of the nodules and their enhancement features on SPIO‐enhanced images. Sensitivity, specificity, positive predictive value, negative predictive value, and accuracy in the diagnosis of WD‐HCC were also calculated.ResultsThe mean CNR of WD‐HCC was significantly higher than that of DN on T2*‐weighted image. Incomplete high SI on SPIO‐enhanced T2*‐weighted images were seen in 56.8% of WD‐HCC. The most prevalent enhancement features of WD‐HCCs on SPIO‐enhanced T2*‐weighted images, were iso SI with high SI foci [32.5% (12/37)] and homogenous subtle high SI [24.3% (9/37)]. Alternatively, 22 of 23 DNs (95.7%) showed low‐ or iso SI, and 145 of 156 (94.9%) MD‐/PD HCCs showed strong high SI. When iso SI with high SI foci or subtle homogenous high SI nodule was considered as diagnostic criteria for WD‐HCC, we could identify 56.8% of the WD‐HCCs but only 4.4% of the DNs and 3.2% of the MD‐/PD HCCs.ConclusionWD‐HCCs have characteristic enhancement features that differentiate them from DNs and MD‐/PD HCCs on SPIO‐enhanced 3.0T MRI. The lesion conspicuity was better on T2*‐weighted images than that on T2‐weighted images. J. Magn. Reson. Imaging 2009;29:328–335. © 2009 Wiley‐Liss, Inc.
Estimates of glomerular filtration rate from MR renography and tracer kinetic models
Authors: Bokacheva Louisa , Rusinek Henry , Zhang Jeff L. , Chen Qun , Lee Vivian S. 
Published: January 2009

AbstractPurposeTo compare six methods for calculating the single‐kidney glomerular filtration rate (GFR) from T1‐weighted magnetic resonance (MR) renography (MRR) against reference radionuclide measurements.Materials and MethodsIn 10 patients, GFR was determined using six published methods: the Baumann–Rudin model (BR), the Patlak–Rutland method (PR), the two‐compartment model without bolus dispersion (2C) and with dispersion (2CD), the three‐compartment model (3CD), and the distributed parameter model (3C‐IRF). Reference single‐kidney GFRs were measured by radionuclide renography. The coefficient of variation of GFR (CV) was determined for each method by Monte Carlo analyses for one healthy and one dysfunctional kidney at a noise level (σn) of 2%, 5%, and 10%.ResultsGFR estimates in patients varied from 6% overestimation (BR) to 50% underestimation (PR and 2CD applied to cortical data). Correlations with reference GFRs ranged from R = 0.74 (2CD, cortical data) to R = 0.85 (BR). In simulations, the lowest CV was produced by 3C‐IRF in healthy kidney (1.7σn) and by PR in diseased kidney ((2.2–2.4)σn). In both kidneys the highest CV was obtained with 2CD ((5.9–8.2)σn) and with 3CD in diseased kidney (8.9σn at σn = 10%).ConclusionGFR estimates depend on the renal model and type of data used. Two‐ and three‐compartment models produce comparable GFR correlations. J. Magn. Reson. Imaging 2009;29:371–382. © 2009 Wiley‐Liss, Inc.
Coronary anomalies assessed by whole‐heart isotropic 3D magnetic resonance imaging for cardiac morphology in congenital heart disease
Authors: Beerbaum Philipp , Sarikouch Samir , Laser Kai‐Thorsten , Greil Gerald , Burchert Wolfgang , Körperich Hermann 
Published: January 2009

AbstractPurposeTo determine the value of whole‐heart three‐dimensional magnetic resonance imaging (MRI) for coronary artery imaging in children/adolescents with congenital heart disease (CHD).Materials and MethodsForty children/adolescents (median age: 14 years, range 2.6–25.8) with CHD underwent free‐breathing navigator‐gated isotropic three‐dimensional steady‐state free‐precession (3D‐SSFP) MRI for cardiac morphology. Two observers independently evaluated visibility of origin, course, vessel lengths, image quality (IQ), and contrast between coronary lumen and myocardium. A subgroup was compared with cardiac catheter.ResultsThe total scan time was 6.3 ± 3.2 minutes (mean ± SD, at mean heart rate 76 ± 15/min). The mean vessel length for right coronary artery (RCA) by observer 1 was 97 ± 43 mm (observer 2: 94 ± 37 mm), for left main and anterior descending artery (LM/LAD) 91 ± 40 mm (observer 2: 90 ± 40 mm), and for left circumflex artery (LCX) 64 ± 28mm (observer 2: 66 ± 28 mm). The mean vessel contrast was 0.34 ± 0.05 (range: 0.23–0.45; maximum = 1, minimum = 0). On a 4‐level score (1 = nondiagnostic, 4 = excellent), mean IQ scores ranged between 2.3–2.9 (±0.8–1.0). Both observers agreed on the presence/proximal course of RCA in 40/40, LM/LAD in 38/40, and LCX in 36/40 patients. There was complete agreement with invasive coronary angiography available in 12/40 patients (six anomalies).ConclusionIsotropic whole‐heart 3D‐MRI for cardiac morphology allows reliable discrimination between normal and abnormal coronary anatomy in children/adolescents with CHD. J. Magn. Reson. Imaging 2009;29:320–327. © 2009 Wiley‐Liss, Inc.