bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular‐Beacon‐Based Tricomponent Probe for SNP Analysis in Folded Nucleic Acids
Authors: Nguyen Camha , Grimes Jeffrey , Gerasimova Yulia V. , Kolpashchikov Dmitry M. 
Published: September 2011

AbstractHybridization probes are often inefficient in the analysis of single‐stranded DNA or RNA that are folded in stable secondary structures. A molecular beacon (MB) probe is a short DNA hairpin with a fluorophore and a quencher attached to opposite sides of the oligonucleotide. The probe is widely used in real‐time analysis of specific DNA and RNA sequences. This study demonstrates how a conventional MB probe can be used for the analysis of nucleic acids that form very stable (Tm>80 °C) hairpin structures. Here we demonstrate that the MB probe is not efficient in direct analysis of secondary structure‐folded analytes, whereas a MB‐based tricomponent probe is suitable for these purposes. The tricomponent probe takes advantage of two oligonucleotide adaptor strands f and m. Each adaptor strand contains a fragment complementary to the analyte and a fragment complementary to a MB probe. In the presence of a specific analyte, the two adaptor strands hybridize to the analyte and the MB probe, thus forming a quadripartite complex. DNA strand f binds to the analyte with high affinity and unwinds its secondary structure. Strand m forms a stable complex only with the fully complementary analyte. The MB probe fluorescently reports the formation of the quadripartite associate. It was demonstrated that the DNA analytes folded in hairpin structures with stems containing 5, 6, 7, 8, 9, 11, or 13 base pairs can be detected in real time with the limit of detection (LOD) lying in the nanomolar range. The stability of the stem region in the DNA analyte did not affect the LOD. Analytes containing single base substitutions in the stem or in the loop positions were discriminated from the fully complementary DNA at room temperature. The tricomponent probe promises to simplify nucleic acid analysis at ambient temperatures in such applications as in vivo RNA monitoring, detection of pathogens, and single nucleotide polymorphism (SNP) genotyping by DNA microarrays.
Seasonal Thermal Energy Stores – Design, Operation and Applications
Authors: Marx Roman , Nußbicker‐Lux Janet , Bauer Dan , Heidemann Wolfgang , Drück Harald 
Published: September 2011

AbstractDie saisonale Speicherung von Solarwärme oder Abwärme aus Kraft‐Wärmekopplungsanlagen kann maßgeblich dazubeitragen, in zukünftigen Energiewandlungssystemen fossile Brennstoffe zu einem großen Anteil zu ersetzen. Solar unterstützte Nahwärmeversorgungsanlagen in Kombination mit Langzeit‐Wärmespeichern ermöglichen solare Deckungsanteile am Gesamtwärmebedarf von 50 % und mehr. Durch den Bau und Betrieb mehrerer Pilotanlagen zur solar unterstützten Nahwärmeversorgung mit saisonaler Wärmespeicherung in Deutschland seit 1996 konnten die hohen erzielbaren solaren Deckungsanteile bestätigt werden. Vier unterschiedliche Bauarten für Langzeit‐Wärmespeicher wurden entwickelt, unter realen Betriebsbedingungen getestet und langzeitüberwacht: Heißwasser‐, Kies/Wasser‐, Erdsonden‐ und Aquifer‐Wärmespeicher.
Petri Net Based Metabolic Network Parameters Fitting with GPU Acceleration
Authors: Gao Jun , Zhu Ruixin , Liu Qi , Cao Zhiwei 
Published: September 2011

Abstract Classical Petri net has been applied into biological analysis, especially as a qualitative model for biochemical pathways analysis, but lack of the ability for quantitative kinetic simulations. In our study, we presented an integration work of the qualitative model–Petri nets with the quantitative approach‐ordinary differential equations (ODEs) for the modeling and analysis of metabolic networks. As an application of our study, the computational modeling of arachidonic acid (AA) biochemical network was provided. A Petri net was set up to present the constraint‐based dynamic simulations on AA metabolic network combined with the validated ODEs model. Furthermore, Graphics Processing Unit (GPU) was adopted to accelerate the calculation of kinetic parameters unavailable from experiments. Our results have indicated that the proposed simulation method was practicable and useful with GPU acceleration, and provides new clues for the large‐scale qualitative and quantitative models of biochemical networks.
Development of a Rapid and Simultaneous Detection Method for Buprenorphine, Norbuprenorphine and Naloxone in Human Plasma Using Ultra‐high Performance Liquid Chromatography‐tandem Mass Spectrometer with Solid‐phase Extraction
Authors: Guo Qiaozhen , Du Zhenxia 
Published: September 2011

AbstractA simultaneous method was successfully established and validated for the separation and determination of buprenorphine (BP), its primary metabolite, nor‐buprenorphine (NBP) and a proposed co‐formulate, naloxone (NLX) in human plasma. The method used buprenorphine‐d4 (BP‐D4), nor‐buprenorphine‐d3 (NBP‐D3), naltrexone (NTX) as internal standards (ISs). 100 μL of plasma sample fortified with the ISs was cleaned up by solid‐phase extraction (SPE), and was then separated on a Waters AcquityTM BEH C18 column with gradient elution using methanol and water (containing 0.2% formic) at a flow rate of 0.25 mL·min−1. The mass spectrometer was used for detection and was operated in the positive electrospray ionization with multiple reaction monitoring (MRM) mode. The three compounds were effectively separated in 5 min. The linear ranges of the compounds were 0.1–25, 0.25–25 and 0.05–25 ng·mL−1 for BP, NBP and NLX, respectively, with r≧0.9935. The method had high sensitivity (the limits of detection were 0.02, 0.1 and 0.01 ng·mL−1 for BP, NBP and NLX, respectively) and high recoveries (≧97.6%). The result was shown to be linear and satisfactorily met current acceptance criteria for validation of bioanalytical method: intra and inter assay precisions within the required limits of ≦25% RSD. The LOQs fulfilled the LOQ requirements: precision≦25% RSD, and was fully validated according to the State Food and Drug Administration (SFDA) regulations. The results demonstrated that ultra‐high performance liquid chromatography‐tandem mass spectrometer (UPLC‐MS/MS) with SPE was a powerful detection tool and contributed to pharmaceutical analysis in biological matrices.
Novel Cross‐Linked Conducting Polythiophene with Yellow‐Green‐Light‐Emitting Properties and Good Thermal Stability
Authors: Lai Cunyuan , Guo Wenjuan , Tang Xinde , Zhang Guangyou , Pan Qiwei , Pei Meishan 
Published: September 2011

AbstractA novel conjugated polythiophene derivative with polymethacrylate attaching to the polymer backbone via an alkyl spacer was successfully synthesized. A methacrylate‐substituted thiophene monomer, 3‐(hexyl methacrylate)thiophene was prepared and polymerized by free radical polymerization, followed by an electrochemical polymerization. The resulting polymer as a yellow‐green‐light emitter, has potential applications in photoelectronics area.
Silicon Analogues of the Nonpeptidic GnRH Antagonist AG‐045572: Syntheses, Crystal Structure Analyses, and Pharmacological Characterization
Authors: Barnes Matthew J. , Burschka Christian , Büttner Matthias W. , Conroy Richard , Daiss Jürgen O. , Gray Ian C. , Hendrick Alan G. , Tam L. H. , Kuehn Diana , Miller David J. , Mills John S. , Mitchell Philip , Montana John G. , Muniandy Parameswary A. , Rapley Helen , Showell Graham A. , Tebbe David , Tacke Reinhold , Warneck Julie B. H. , Zhu Bin 
Published: September 2011

AbstractAG‐045572 (CMPD1, 1 a) is a nonpeptidic gonadotropin‐releasing hormone (GnRH) antagonist that has been investigated for the treatment of sex hormone‐related diseases. In the context of systematic studies on sila‐substituted drugs, the silicon analogue disila‐AG‐045572 (1 b) and its derivative 2 were prepared in multi‐step syntheses and characterized by elemental analyses (C, H, N), NMR spectroscopic studies (1H, 13C, 29Si), and single‐crystal X‐ray diffraction. The pharmacological properties of compounds 1 a, 1 b, and 2 were compared in terms of their in vitro potency at cloned human and rat GnRH receptors. Compounds 1 a and 2 were also examined in regard to their pharmacokinetics and in vivo efficacy in both castrated rat (luteinizing hormone (LH) suppression) and intact rat (testosterone suppression) models. The efficacy and pharmacokinetic profiles of 1 a and its silicon‐containing analogue 2 appear similar, indicating that replacement of the 5,6,7,8‐tetrahydronaphthalene ring system by the 1,3‐disilaindane skeleton led to retention of efficacy. Therefore, the silicon compound 2 represents a novel drug prototype for the design of potent, orally available GnRH antagonists suitable for once‐daily dosing.
Regularization of voxelwise autoregressive model for analysis of functional magnetic resonance imaging data
Authors: Ahmad Fayyaz , Maqbool M. , Lee Namgil 
Published: September 2011

AbstractThis study reports the construction of a simple and elegant method to improve the detection of brain regions with increased neuronal activity in functional magnetic resonance imaging (fMRI). The main advantages of the method are regularization of voxelwise autoregressive parameters and accurate estimation of parameters and statistical inferences as compared to the conventional restricted maximum likelihood (ReML) method, where each voxel uses the two voxel‐wide (global) hyperparameters. The model is tested for its accuracy and efficiency in analysis of fMRI data for stimulated and real brains of healthy individuals. Receiver operating characteristic curves are used to show that the proposed method is superior to the conventional ReML method. The proposed method will improve the diagnostic accuracy of fMRI studies in the human brain. © 2011 Wiley Periodicals, Inc. Concepts Magn Reson Part A 38: 187–196, 2011.
Tensors and rotations in NMR
Authors: Mueller Leonard J. 
Published: September 2011

AbstractThe transformation of second‐rank Cartesian tensors under rotation plays a fundamental role in the theoretical description of nuclear magnetic resonance experiments, providing the framework for describing anisotropic phenomena such as single crystal rotation patterns, tensor powder patterns, sideband intensities under magic‐angle sample spinning, and as input for relaxation theory. Here, two equivalent procedures for effecting this transformation—direct rotation in Cartesian space and the decomposition of the Cartesian tensor into irreducible spherical tensors that rotate in subgroups of rank 0, 1, and 2—are reviewed. In a departure from the standard formulation, the explicit use of the spherical tensor basis for the decomposition of a spatial Cartesian tensor is introduced, helping to delineate the rotational properties of the basis states from those of the matrix elements. The result is a uniform approach to the rotation of a physical system and the corresponding transformation of the spatial components of the NMR Hamiltonian, expressed as either Cartesian or spherical tensors. This clears up an apparent inconsistency in the NMR literature, where the rotation of a spatial tensor in spherical tensor form has typically been partnered with the inverse rotation in Cartesian form to produce equivalent transformations. © 2011 Wiley Periodicals, Inc. Concepts Magn Reson Part A 38: 221–235, 2011.
A randomized trial of internet‐based versus traditional sexual counseling for couples after localized prostate cancer treatment
Authors: Schover Leslie R. , Canada Andrea L. , Yuan Ying , Sui Dawen , Neese Leah , Jenkins Rosell , Rhodes Michelle M. 
Published: September 2011

AbstractBACKGROUND:After treatment for prostate cancer, multidisciplinary sexual rehabilitation involving couples appears more promising than traditional urologic treatment for erectile dysfunction (ED). The authors of this report conducted a randomized trial comparing traditional or internet‐based sexual counseling with waitlist (WL) control.METHODS:Couples were randomized adaptively to a 3‐month WL, a 3‐session face‐to‐face format (FF), or an internet‐based format (WEB1). A second internet‐based group (WEB2) was added to examine the relation between web site use and outcomes. At baseline, post‐WL, post‐treatment, and 6‐month, and 12‐month follow‐up assessments, participants completed the International Index of Erectile Function (IIEF), the Female Sexual Function Index (FSFI), the Brief Symptom Inventory‐18 to measure emotional distress, and the abbreviated Dyadic Adjustment Scale.RESULTS:Outcomes did not change during the WL period. Of 115 couples that were randomized to FF or WEB1 and 71 couples in the WEB2 group, 34% dropped out. Neither drop‐outs nor improvements in outcomes differed significantly between the 3 treatment groups. In a linear mixed‐model analysis that included all participants, mean ± standard deviation IIEF scores improved significantly across time (baseline, 29.7 ± 17.9; 12 months, 36.2 ± 22.4; P < .001). FSFI scores also improved significantly (baseline, 15.4 ± 8.5; 12 months, 18.2 ± 10.7; P = .034). Better IIEF scores were associated with finding an effective medical treatment for ED and normal female sexual function at baseline. In the WEB2 group, IIEF scores improved significantly more in men who completed >75% of the intervention.CONCLUSIONS:An internet‐based sexual counseling program for couples was as effective as a brief, traditional sex therapy format in producing enduring improvements in sexual outcomes after prostate cancer. Cancer 2011;. © 2011 American Cancer Society.
Sunitinib‐induced hyperparathyroidism
Authors: Baldazzi Valentina , Tassi Renato , Lapini Alberto , Lunghi Alice , Garofoli Eleonora , Caruso Salvatore , Carini Marco , Mazzanti Roberto 
Published: September 2011

AbstractBACKGROUND:Sunitinib malate is an orally bioavailable tyrosine kinase inhibitor that is active against many tyrosine kinase receptors involving crucial pathways in both healthy tissues and malignant tissues. Because its use in clinical practice is quite recent, many of its possible side effects remain unknown. In this report, the authors describe the incidence of new‐onset hyperparathyroidism in a cohort of patients with metastatic renal cell carcinoma who received treatment with sunitinib.METHODS:Twenty‐six patients who received first‐line sunitinib for metastatic renal cell carcinoma were enrolled in this study for a mineral and parathyroid function assessment. Plasma levels of intact parathyroid hormone; serum levels of calcium, phosphorus, 25‐hydroxyvitamin D3, and 1,25‐dihydrovitamin D3; and urinary 24‐hour calcium and phosphorus excretion all were measured in each patient. Biochemical evaluations were performed before the beginning of treatment and at the end of each sunitinib treatment period.RESULTS:Eighteen of 26 patients (69.2%) developed hyperparathyroidism with normal serum calcium levels, and 6 of them developed hypophosphatemia. Patients presented with a mean elevation of parathyroid hormone after 2.2 cycles of sunitinib. The levels of 25‐OH vitamin D3 were stable over the course of treatment, whereas 1,25‐OH vitamin D3 levels were increased in 5 hyperparathyroid patients. Those who presenting with elevated parathyroid hormone levels had low or undetectable urinary calcium levels. Parathyroid hormone elevation usually persisted but did not progress during long‐term therapy with sunitinib. Permanent treatment interruption resulted in a resolution of hyperparathyroidism.CONCLUSIONS:Hyperparathyroidism developed in an high percentage of patients on sunitinib. Therefore, the authors concluded that sunitinib may affect parathyroid function and bone mineral homeostasis, possibly resulting in abnormal bone remodeling. Cancer 2012;118: 3165–72. © 2011 American Cancer Society.
Antioxidant supplement use after breast cancer diagnosis and mortality in the Life After Cancer Epidemiology (LACE) cohort
Authors: Greenlee Heather , Kwan Marilyn L. , Kushi Lawrence H. , Song Jun , Castillo Adrienne , Weltzien Erin , Quesenberry Charles P. , Caan Bette J. 
Published: September 2011

AbstractBACKGROUND:There is concern that antioxidant supplement use during chemotherapy and radiation therapy may decrease treatment effects, yet the effects of such supplements on recurrence and survival are largely unknown.METHODS:The authors prospectively examined the associations between antioxidant use after breast cancer (BC) diagnosis and BC outcomes in 2264 women in the Life After Cancer Epidemiology (LACE) cohort. The cohort included women who were diagnosed with early stage, primary BC from 1997 to 2000 who enrolled, on average, 2 years postdiagnosis. Baseline data were collected on antioxidant supplement use since diagnosis and other factors. BC recurrence and mortality were ascertained, and hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated using delayed entry Cox proportional hazards models. All tests of statistical significance were 2‐sided.RESULTS:Antioxidant supplement use after diagnosis was reported by 81% of women. Among antioxidant users, frequent use of vitamin C and vitamin E was associated with a decreased risk of BC recurrence (vitamin C: HR, 0.73; 95% CI, 0.55‐0.97; vitamin E: HR, 0.71; 95% CI, 0.54‐0.94); and vitamin E use was associated with a decreased risk of all‐cause mortality (HR, 0.76; 95% CI, 0.58‐1.00). Conversely, frequent use of combination carotenoids was associated with increased risk of death from BC (HR, 2.07; 95% CI, 1.21‐3.56) and all‐cause mortality (HR, 1.75; 95% CI, 1.13‐2.71).CONCLUSIONS:Frequent use of vitamin C and vitamin E in the period after BC diagnosis was associated with a decreased likelihood of recurrence, whereas frequent use of combination carotenoids was associated with increased mortality. The effects of antioxidant supplement use after diagnosis likely differ by type of antioxidant. Cancer 2012. © 2011 American Cancer Society.
Phase 2 study of bevacizumab plus erlotinib in patients with advanced hepatocellular cancer
Authors: Philip Philip A. , Mahoney Michelle R. , Holen Kyle D. , Northfelt Donald W. , Pitot Henry C. , Picus Joel , Flynn Patrick J. , Erlichman Charles 
Published: September 2011

AbstractBACKGROUND:Epidermal growth factor receptor (EGFR) and vascular endothelial growth factor (VEGF) are rational targets for therapy in hepatocellular cancer (HCC).METHODS:Patients with histologically proven HCC and not amenable to curative or liver directed therapy were included in this 2‐stage phase 2 trial. Eligibility included an Eastern Cooperative Oncology Group (ECOG) performance status (PS) of 0 or 1 and Child's Pugh score of A or B, and 1 prior systemic therapy. Patients received erlotinib 150 mg daily and bevacizumab 10 mg/kg on days 1 and 15 every 28 days. Objective tumor response was the primary end point.RESULTS:Twenty‐seven patients with advanced HCC (median age, 60 years) were enrolled in this multi‐institutional study. The proportion of patients with Child's A classification was 74%. One patient had a confirmed partial response and 11 (48%) achieved stable disease. Median time to disease progression was 3.0 months (95% confidence interval [CI], 1.8‐7.1). Median survival time was 9.5 months (95% CI, 7.1‐17.1). Grade 3 toxicities included rash, hypertension, fatigue, and diarrhea.CONCLUSIONS:In this trial, erlotinib combined with bevacizumab had minimal activity in patients with advanced HCC based on objective response and progression‐free survival. The role of targeting EGFR and VEGF in HCC needs further evaluation in molecularly selected patients. Cancer 2012. © 2011 American Cancer Society.
Vector‐valued optimal Lipschitz extensions
Authors: Sheffield Scott , Smart Charles K. 
Published: September 2011

AbstractConsider a bounded open set
$\font\open=msbm10 at 10pt\def\R{\hbox{\open R}}U \subset \R^n$
and a Lipschitz function $\font\open=msbm10 at 10pt\def\R{\hbox{\open R}}g: \partial U \to \R^m$. Does this function always have a canonical optimal Lipschitz extension to all of U? We propose a notion of optimal Lipschitz extension and address existence and uniqueness in some special cases. In the case n = m = 2, we show that smooth solutions have two phases: in one they are conformal and in the other they are variants of infinity harmonic functions called infinity harmonic fans. We also prove existence and uniqueness for the extension problem on finite graphs. © 2011 Wiley Periodicals, Inc.
From Micro to Macro: Access to Long‐Range Li+ Diffusion Parameters in Solids via Microscopic 6, 7Li Spin‐Alignment Echo NMR Spectroscopy
Authors: Wilkening Martin , Heitjans Paul 
Published: September 2011

AbstractThe development of highly conductive solids is a rapidly growing research area in materials science. In particular, the study of Li‐ion conductors is driven by the ambitious effort to design powerful lithium‐ion batteries. A deeper understanding of Li dynamics in solids requires the availability of a large set of complementary techniques to probe Li self‐diffusion on different length and time‐scales. We report on 7Li as well as 6Li spin‐alignment echo (SAE) nuclear magnetic resonance (NMR) spectroscopy, which is capable of probing long‐range diffusion parameters from a microscopic, that is, atomic‐scale, point of view. So far, variable‐temperature SAE NMR spectroscopy has been applied to a number of polycrystalline and glassy Li‐ion conductors. The materials investigated serve as model systems to unravel the interesting features of the technique in determining reliable Li jump rates and hopping activation energies. In particular, the latter are compared with those probed by macroscopic techniques such as dc‐conductivity measurements that are sensitive to long‐range translational motions.
Noble‐Metal‐Based Catalysts Supported on Zeolites and Macro‐Mesoporous Metal Oxide Supports for the Total Oxidation of Volatile Organic Compounds
Authors: Barakat Tarek , Rooke Joanna C. , Tidahy Haingomalala Lucette , Hosseini Mahsa , Cousin Renaud , Lamonier Jean‐François , Giraudon Jean‐Marc , De Weireld Guy , Su Bao‐Lian , Siffert Stéphane 
Published: September 2011

AbstractThe use of porous materials to eliminate volatile organic compounds (VOCs) has proven very effective towards achieving sustainability and environmental protection goals. The activity of zeolites and macro–mesoporous metal‐oxide supports in the total oxidation of VOCs has been investigated, with and without noble‐metal deposition, to develop highly active catalyst systems where the formation of by‐products was minimal. The first catalysts employed were zeolites, which offered a good activity in the oxidation of VOCs, but were rapidly deactivated by coke deposition. The effects of the acido‐basicity and ionic exchange of these zeolites showed that a higher basicity was related to exchanged ions with lower electronegativities, resulting in better catalytic performances in the elimination of VOCs. Following on from this work, noble metals were deposited onto macro–mesoporous metal‐oxide supports to form mono and bimetallic catalysts. These were then tested in the oxidation of toluene to study their catalytic performance and their deactivation process. PdAu/TiO2 and PdAu/TiO2‐ZrO280/20 catalysts demonstrated the best activity and life span in the oxidation of toluene and propene and offered the lowest temperatures for a 50 % conversion of VOCs and the lowest coke content after catalytic testing. Different characterization techniques were employed to explain the changes occurring in catalyst structure during the oxidation of toluene and propene.