bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stereoselection in the diels–alderase ribozyme: A molecular dynamics study
Authors: Bereźniak Tomasz , Jäschke Andres , Smith Jeremy C. , Imhof Petra 
Published: May 2012

AbstractThe Diels‐Alderase ribozyme is an in vitro‐evolved ribonucleic acid enzyme that catalyzes a [4 + 2] cycloaddition reaction between an anthracene diene and a maleimide dienophile. The ribozyme can in principle be used to selectively synthesize only one product enantiomer, depending on which of the two entrances to the catalytic pocket, “front” or “back”, the substrate is permitted to use. Here, we investigate stereoselection and substrate recognition in the ribozyme by means of multiple molecular dynamics simulations, performed on each of the two substrates individually in the pocket, on the reactant state, and on the product state. The results are consistent with a binding mechanism in which the maleimide likely binds first followed by the anthracene, which enters preferentially through the front door. The free energy profiles for anthracene binding indicate that the pre‐(R,R)‐enantiomer conformation is slightly preferred, in agreement with the experimentally observed small enantiomeric excess of the (R,R)‐enantiomer of the product. The reactant state is stabilized by the simultaneous presence of both substrates bound to their binding sites in the hydrophobic pocket as well as by stacking interactions between them. © 2012 Wiley Periodicals, Inc.
Adsorption of metadiiodobenzene on Cu(110): A theoretical study
Authors: Panosetti Chiara , Hofer Werner A. 
Published: May 2012

AbstractIn this work, we have computationally modeled the adsorption of 1,3‐diiodobenzene (meta‐diiodobenzene or m‐DIB) on Cu(1 1 0) by means of density functional theory including van der Waals interaction using Grimme's method. We have compared the adsorption energies and structures of 23 possible configurations of the physisorbed molecule. Furthermore, we have simulated STM images for the four most stable configurations using the Tersoff–Hamann approach at different bias voltages. We find that all the adsorption orientations have comparable energy, and we discuss the relative probabilities of experimental observation. We find that the adsorption induces small distortions in the molecular structure of the adsorbate and in some cases an adsorption‐induced symmetry breakdown occurs. We also find evidence that the most stable arrangement is actually a bistable system with interesting symmetry properties. © 2012 Wiley Periodicals, Inc.
The Physical, Chemical and Biological Effects by Room Temperature Ceramic Far‐infrared Ray Emitting Material Irradiated Water: A Pilot Study
Authors: Leung Ting‐Kai , Yang Jen‐Chang , Lin Yung‐Sheng 
Published: May 2012

AbstractFar infrared ray (FIR) is non‐ionizing electromagnetic radiation with wavelengths of 4‐16 μm. Ceramic far infrared ray emitting materials (cFIR) are sources of FIR that exhibit only non‐thermal effects at room temperature. Certain physical, chemical and biological effects of cFIR irradiation were investigated in this study that heretofore has not been well characterized. We demonstrated that cFIR irradiation reduced the size of water clusters, and significantly increased the freezing temperature of water. We also observed an increase in the volatility of a complex mixture of alcohol, water and solutes and recorded elevated total phenol in green tea infusions prepared using cFIR irradiated water. The effects of cFIR irradiated water on living cells were also investigated. The MC3T3‐E1 murine osteoblast cells grown in the presence of cFIR irradiated water exhibited anti‐oxidative effects on H2O2‐mediated toxicity, as evidenced by late stage increase in intracellular alkaline phosphatase. The presence of cFIR irradiated water also resulted in significant decrease in COX‐2 production in the chondrosarcoma cell line, SW1353, in response to lipopolysaccharide induction. Based on our findings, the possible anti‐inflammatory effects of cFIR irradiated water and implications of our study with regard to bone and joint health were discussed.
Crystal Structure of Lanthanide‐oxalate‐pyridine‐2,4‐dicarboxylate Coordination Polymers Suggesting the Reductive Coupling of Carbon Dioxide to Oxalate
Authors: Shen Fwu‐Ming , Lush Shie‐Fu 
Published: May 2012

AbstractUnder the hydrothermal conditions, Nd(NO3)3·6H2O reacted with pyridine‐2,4‐dicarboxylic acid (2,4‐pydcH2) to give a 2D co‐ordination polymer with the empirical formula of C16H18N2Nd2O18×H2O (1). Pr(NO3)3·6H2O also reacted with 2,4‐pydcH2 to give another 2D coordination polymer (C8H9NO9Pr)2·H2O (2). The structure of both polymers have been determined by X‐ray diffraction. X‐ray structural analyses show that both polymers contain bridging oxalate (C2O42−) ligands, which might have been formed by the coupling of two CO2−× radicals, released from pydc2− ligands.
All λ‐Designs with Small λ are Type‐1
Authors: Puliyambalath Naushad Pasha , Seress Ákos , Weisz Iván 
Published: May 2012

AbstractA λ‐design is a family of subsets of such that for all and not all are of the same size. Ryser's and Woodall's λ‐design conjecture states that each λ‐design can be obtained from a symmetric block design by a certain complementation procedure. Our main result is that the conjecture is true when λ < 63. © 2012 Wiley Periodicals, Inc. J. Combin. Designs 20: 408–431, 2012
Early and Later Predictors of Outcome in Brief Therapy: The Role of Real Relationship
Authors: Gullo Salvatore , Lo Coco Gianluca , Gelso Charles 
Published: May 2012

ObjectivesThe study examined whether clients who continued longer in brief therapy reported stronger associations of real relationship and working alliance with therapy outcome than clients who received very brief treatment. It also examined whether real relationship and working alliance assessed early in treatment predicted outcome differently from that assessed later in therapy.MethodFifty clients (32 women; Mage = 22.3 years) were recruited from a university counseling center. Thirty‐two clients (very brief therapy) completed the post‐third session assessment of real relationship and working alliance, and 18 (brief therapy) had both the third and eighth assessment.ResultsThe real relationship scores (both client and therapist rating) were significantly correlated with outcome in the 18 brief therapy clients, but not in the 32 very brief therapy clients. We found significant correlations between outcome and Bond element of the working alliance in the 18 brief therapy clients, and between outcome and working alliance‐Task in the 32 very brief therapy clients.ConclusionsThese findings suggested that the strength of the early real relationship, as well as later real relationship, are highly associated with outcome for clients who continue brief therapy past its earliest stages. © 2012 Wiley Periodicals, Inc. J. Clin. Psychol. 00:1–6, 2012.
Dissecting Pin1 and phospho‐pRb regulation
Authors: Rizzolio Flavio , Caligiuri Isabella , Lucchetti Chiara , Fratamico Robert , Tomei Valentina , Gallo Gaia , Agelan Alexis , Ferrari Giovanni , Toffoli Giuseppe , Klein‐Szanto Andres J. , Giordano Antonio 
Published: May 2012

AbstractThe activity of the Retinoblastoma protein, the master regulator of the cell cycle, is finely regulated by phosphorylation. CDKs and cyclins are major players in phosphorylation and it has been recently discovered that the prolyl isomerase Pin1 is an essential protein that orchestrates this process. In this article, we report new findings regarding the role of Pin1 in the pRb pathway. Our data suggest that PI3K, CDKs, and the Pin1 axis have a critical role in sustaining the complete phosphorylation of pRb. Furthermore, we analyze the correlation between Pin1 and pRb phosphorylation in vivo. We show that, in human malignant glioma tissue microarrays (TMA) and in Pin1 knockout (KO) mice, there is a positive correlation between Pin1 and pRb phosphorylation. Prospectively, our findings suggest that the synergism between CDKs, Pin1, and PI3K inhibitors hold great promise for targeted pharmacological treatment of cancer patients, with the possibility of reaching high effectiveness at tolerated doses. J. Cell. Physiol. 228: 73–77, 2013. © 2012 Wiley Periodicals, Inc.
P2Y2 receptor promotes intestinal microtubule stabilization and mucosal re‐epithelization in experimental colitis
Authors: Degagné Émilie , Degrandmaison Jade , Grbic Djordje M. , Vinette Valérie , Arguin Guillaume , Gendron Fernand‐Pierre 
Published: May 2012

AbstractP2Y2 receptor expression is increased in intestinal epithelial cells (IECs) during inflammatory bowel diseases (IBDs). In this context, P2Y2 stimulates PGE2 release by IECs, suggesting a role in wound healing. For this study, we have used the non‐cancerous IEC‐6 cell line. IEC‐6 cell migration was determined using Boyden chambers and the single‐edged razor blade model of wounding. The receptor was activated using ATP, UTP, or 2‐thioUTP. Pharmacological inhibitors, a blocking peptide, a neutralizing antibody and interfering RNAs were used to characterize the signaling events. Focal adhesions and microtubule (MT) dynamics were determined by immunofluorescence using anti‐vinculin and anti‐acetylated‐α‐tubulin antibodies, respectively. In vivo, the dextran sodium sulfate mouse model of colitis was used to characterize the effects of P2Y2 agonist 2‐thioUTP on remission. We showed that P2Y2 increased cell migration and wound closure by recruiting Go protein with the cooperation of integrin αv. Following P2Y2 activation, we demonstrated that GSK3β activity was inhibited in response to Akt activation. This leads to MT stabilization and increased number of focal adhesions. In vivo, P2Y2 activation stimulates remission, as illustrated by a reduction in the disease activity index values and histological scores as compared to control mice. These findings highlight a novel function for this receptor in IECs. They also illustrate that P2Y receptors could be targeted for the development of innovative therapies for the treatment of IBDs. J. Cell. Physiol. 228: 99–109, 2013. © 2012 Wiley Periodicals, Inc.
MRT letter: A fast and easy method for general fluorescent staining of cultured cells on transparent or opaque supports
Authors: Gayoso Manuel J. 
Published: May 2012

AbstractDevelopment of cell‐based therapy entails the use of different types of materials as support for cultured cells. Some of these materials are opaque. For a general microscope study of cell cultures prepared on transparent supports, Giemsa stain with bright field microscopy is useful. With opaque supports or scaffolds, epifluorescence microscopy is necessary. The method the authors describe uses eosin Y to stain cytoplasm and DAPI to stain nuclei under fluorescence microscopy. This method provides easy and fast fluorescent staining for a general morphological study of cultured cells on transparent or opaque supports. Microsc. Res. Tech. 2012. © 2012 Wiley Periodicals, Inc.
Pancyclicity of 4‐Connected, Claw‐Free, P10‐Free Graphs
Authors: Ferrara Michael , Morris Timothy , Wenger Paul 
Published: May 2012

AbstractA graph G is said to be pancyclic if G contains cycles of all lengths from 3 to . We show that if G is 4‐connected, claw‐free, and P10‐free, then G is either pancyclic or it is the line graph of the Petersen graph. This implies that every 4‐connected, claw‐free, P9‐free graph is pancyclic, which is best possible and extends a result of Gould et al. Pancyclicity in 3‐connected graphs: Pairs of forbidden subgraphs, [J Graph Theory 47 (2004), 183–202].
A Note on Degenerate and Spectrally Degenerate Graphs
Authors: Alon Noga 
Published: May 2012

AbstractA graph G is called spectrally d‐degenerate if the largest eigenvalue of each subgraph of it with maximum degree D is at most . We prove that for every constant M there is a graph with minimum degree M, which is spectrally 50‐degenerate. This settles a problem of Dvořák and Mohar (Spectrally degenerate graphs: Hereditary case, arXiv: 1010.3367).
The Merrifield–Simmons Conjecture Holds for Bipartite Graphs
Authors: Trinks Martin 
Published: May 2012

AbstractLet be a graph and the number of independent (vertex) sets of G. Then the Merrifield–Simmons conjecture states that the sign of the term only depends on the parity of the distance of the vertices in G. We prove that the conjecture holds for bipartite graphs by considering a generalization of the term, where vertex subsets instead of vertices are deleted.
3D MRI provides improved visualization and detection of aortic arch plaques compared to transesophageal echocardiography
Authors: Harloff Andreas , Brendecke Stefanie Marie , Simon Jan , Assefa Dawit , Wallis Wolf , Helbing Thomas , Weber Johannes , Frydrychowicz Alex , Vach Werner , Weiller Cornelius , Markl Michael 
Published: May 2012

AbstractPurpose:To compare 3D magnetic resonance imaging (3D MRI) with transesophageal echocardiography (TEE) for the detection of complex aortic plaques (≥4 mm thick, ulcerated, or containing mobile thrombi).Materials and Methods:In all, 99 consecutive patients with acute cryptogenic stroke and ≥3 mm thick aortic plaques in TEE were prospectively included. 3D MRI comprised T1‐weighted bright blood MRI with complete aortic coverage (spatial resolution 1 mm3). Wall thickness and occurrence of complex plaques in ascending aorta (AAo), aortic arch (AA), and descending aorta (DAo) and image quality for each segment was rated for MRI and TEE.Results:MRI detected more complex plaques than TEE (MRI vs. TEE): AAo 13 vs. 7; AA 37 vs. 11; differences were smaller in the DAo: 101 vs. 70. Image quality was higher for MRI in AAo and AA (P < 0.001) and superior for TEE in DAo (P < 0.001). MRI revealed additional complex plaques in the proximal aorta in 19 of 58 patients (32.8%) categorized as cryptogenic after complete routine diagnostics including TEE.Conclusion:Due to improved visualization of the aorta 3D MRI allows to detect more complex plaques than TEE. This renders 3D MRI particularly valuable for patients with cryptogenic stroke and for trials evaluating optimal treatment in aortic atherosclerosis. J. Magn. Reson. Imaging 2012;36:604–611. © 2012 Wiley Periodicals, Inc.
Comparison of MRI and 18F‐NaF PET/CT in patients with patellofemoral pain
Authors: Draper Christine E. , Quon Andrew , Fredericson Michael , Besier Thor F. , Delp Scott L. , Beaupre Gary S. , Gold Garry E. 
Published: May 2012

AbstractPurpose:To determine whether bone metabolic activity corresponds to bone and cartilage damage in patients with patellofemoral pain.Materials and Methods:We acquired magnetic resonance imaging (MRI) and 18F‐NaF positron emission tomography (PET) / computed tomography (CT) scans of the knees of 22 subjects. We compared locations of increased tracer uptake on the 18F‐NaF PET images to bone marrow edema and cartilage damage visualized on MRI.Results:We found that increased bone activity on 18F‐NaF PET does not always correspond to structural damage in the bone or cartilage as seen on MRI.Conclusion:Our results suggest that 18F‐NaF PET/CT may provide additional information in patellofemoral pain patients compared to MRI. J. Magn. Reson. Imaging 2012;36:928–932. © 2012 Wiley Periodicals, Inc.
Optimizing the functional diffusion map using Monte Carlo simulations
Authors: Reischauer Carolin , Gutzeit Andreas , Vorburger Robert S. , Froehlich Johannes M. , Binkert Christoph A. , Boesiger Peter 
Published: May 2012

AbstractPurpose:To optimize the diagnostic accuracy of the functional diffusion map for monitoring tumor treatment response in cancer patients.Materials and Methods:Using Monte Carlo simulations, measurement precision of the apparent diffusion coefficient (ADC), and particularly accuracy of threshold determination from healthy reference tissue, are evaluated by investigating the repeatability limit of the ADC as a function of different degrees of diffusion weighting of the sequence. Phantom and in‐vivo experiments are performed to verify and illustrate the results of the simulations.Results:While diagnostic accuracy of the functional diffusion map is hardly diminished by differing values of the T2 relaxation time in tumor and reference tissue, it is shown to be impaired by differing ADCs, resulting in erroneously determined segmentation thresholds. This problem can be addressed by decreasing the maximum b‐factor and increasing the number of signal averages at the maximum b‐factor or, alternatively, the number of b‐factors while favoring schemes with higher b‐factors. Phantom experiments confirm the results of the simulations. In‐vivo data are presented to illustrate the effect of sequence optimization on the diagnostic accuracy of the functional diffusion map.Conclusion:The present work demonstrates that the diagnostic accuracy of the functional diffusion map can be impaired by inaccurate segmentation thresholds and derives means for its optimization that will increase the fidelity of future clinical studies. J. Magn. Reson. Imaging 2012;36:1002–1009. ©2012 Wiley Periodicals, Inc.
Sensitive detection of drug vapors using an ion funnel interface for secondary electrospray ionization mass spectrometry
Authors: Meier Lukas , Berchtold Christian , Schmid Stefan , Zenobi Renato 
Published: May 2012

AbstractIn this study, we use an ion funnel (IF) at ambient pressure to enhance the sensitivity of secondary electrospray ionization (SESI). Atenolol, salbutamol and cocaine as test compounds are delivered to the SESI interface in the gas phase and are charged with three nano electrosprays. In our experiments, we show that the compounds can be detected at concentrations in the low pptv range, which is an increase of two orders of magnitude compared with the results without the IF. With a standard SESI interface, the compounds could not be detected at all. With the use of the SESI IF interface for the headspace analysis of bananas and limes, we can detect many more compounds and at higher intensities than with a standard SESI interface. Copyright © 2012 John Wiley & Sons, Ltd.
Chemical composition, nutritional and toxicological evaluation of rice (Oryza sativa) grown in fly ash amended soils
Authors: Bhaskarachary Kandlakunta , Ramulu Punna , Udayasekhararao Paruchuri , Bapurao Sangras , Kamala Krishnaswamy , Syed Qadri , Udaykumar Putcha , Sesikeran Boindala 
Published: May 2012

AbstractBACKGROUND: The purpose of the present study was to evaluate nutritional and toxicological aspects of rice grown in fly ash amended soils. Rice was grown on soils with fly ash (200 t ha−1) and without fly ash at two different geographical locations of India.RESULTS: One kilogram each of 36 samples randomly collected from three replicates of rice grown with and without fly ash was subjected to various analytical techniques to determine the nutrient composition, mineral and heavy metal content. Moisture, protein and ash content of the rice samples showed no difference between fly ash treated and controls. Similar observations were also made on trace and heavy elements. Further, the rice grown on soils treated with fly ash was incorporated in the diet at 90% level and was fed to Wistar/NIN rats for 26 weeks for carrying out protein and toxicological evaluation.CONCLUSION: Results indicated that there is no difference between rice samples grown in soils with or without fly ash. Studies also clearly indicated that there were no adverse effects on hematological, biochemical or histopathological parameters when rice was fed to rats for 6 months. This indicates that rice grown on fly ash treated soils may be safe for human consumption. Copyright © 2012 Society of Chemical Industry
Alleviation of chilling injury in postharvest tomato fruit by preconditioning with ultraviolet irradiation
Authors: Liu Changhong , Jahangir Muhammad Muzammil , Ying Tiejin 
Published: May 2012

AbstractBACKGROUND: Tomato fruit is usually stored at low temperatures for delayed ripening and extended shelf life. However, tomato fruit is susceptible to chilling injury when exposed to low temperatures. In this study, the potential effects of preconditioning with UV‐C or UV‐B irradiation on chilling injury of postharvest tomato fruit were investigated.RESULTS: Mature–green tomato fruit were exposed to 4 kJ m−2 UV‐C or 20 kJ m−2 UV‐B irradiation and stored for 20 days at 2 °C and subsequently 10 days at 20 °C. UV irradiation was effective in reducing chilling injury index and delaying ethylene peak. Furthermore, UV irradiation preserved storage quality as manifested by reduced weight loss, better retention of firmness, and higher contents of total soluble solids, soluble protein and soluble sugar during subsequent storage at 20 °C. UV‐C irradiation significantly delayed the development of the red colour after 10 days of storage at 20 °C. On the other hand, UV irradiation decreased total phenolics content and antioxidant capacity, suggesting possibly reduced stress response to low temperature resulted from enhanced physiological adaptation by UV preconditioning.CONCLUSION: Our results suggest that preconditioning with UV‐C or UV‐B irradiation in appropriate doses had a positive effect on alleviating chilling injury in postharvest tomato fruit. Copyright © 2012 Society of Chemical Industry
Effect of bevacizumab added preoperatively to oxaliplatin on liver injury and complications after resection of colorectal liver metastases
Authors: van der Pool Anne E.M. , Marsman Hendrick A. , Verheij Joanne , Ten Kate Fibo J. , Eggermont Alexander M.M. , IJzermans Jan N.M. , Verhoef Cornelis 
Published: May 2012

AbstractBackgroundChemotherapy (CTx) before resection of colorectal liver metastases (CRLM) may cause hepatic injury and postoperative complications. To ascertain whether adding bevacizumab, a monoclonal antibody against VEGF, to oxaliplatin‐based CTx has an influence on liver injury and postoperative complications.MethodsPatients with CRLM who received neoadjuvant CTx and underwent resection between 2003 and 2008 were analyzed whether or not they received bevacizumab added to oxaliplatin‐based CTx.ResultsThe total study group existed of 104 patients: 53 patients received oxaliplatin‐based CTx and 51 patients received oxaliplatin‐based CTx and bevacizumab. The overall complication rate (29%) was not significantly different between the two groups. The bevacizumab group exhibited less moderate sinusoidal dilatation (8% vs. 28%, P = 0.01). No difference in complication rate was found between patients given fewer than six cycles of oxaliplatin‐based CTx and those given six or more cycles, or between patients with a short (<5 weeks) interval between the last dose of oxaliplatin and resection and those in which the interval was longer.ConclusionBevacizumab added to oxaliplatin‐based CTx may protect against moderate sinusoidal dilatation without significantly influencing morbidity. Neither duration of oxaliplatin‐based CTx nor the time interval between cessation of oxaliplatin‐based CTx and surgery were associated with postoperative complications. J. Surg. Oncol. 2012; 106:892–897. © 2012 Wiley Periodicals, Inc.