bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Empirical Evaluation of normalization Methods for MicroRNA Arrays in a Liposarcoma Study
Authors: Qin Li-Xuan , Tuschl Tom , Singer Samuel 
Published: March 2013

Background Methods for array normalization, such as median and quantile normalization, were developed for mRNA expression arrays. These methods assume few or symmetric differential expression of genes on the array. However, these assumptions are not necessarily appropriate for microRNA expression arrays because they consist of only a few hundred genes and a reasonable fraction of them are anticipated to have disease relevance. Methods We collected microRNA expression profiles for human tissue samples from a liposarcoma study using the Agilent microRNA arrays. For a subset of the samples, we also profiled their microRNA expression using deep sequencing. We empirically evaluated methods for normalization of microRNA arrays using deep sequencing data derived from the same tissue samples as the benchmark. Results: In this study, we demonstrated array effects in microRNA arrays using data from a liposarcoma study. We found moderately high correlation between Agilent data and sequence data on the same tumors, with the Pearson correlation coefficients ranging from 0.6 to 0.9. Array normalization resulted in some improvement in the accuracy of the differential expression analysis. However, even with normalization, there is still a significant number of false positive and false negative microRNAs, many of which are expressed at moderate to high levels. Conclusions Our study demonstrated the need to develop more efficient normalization methods for microRNA arrays to further improve the detection of genes with disease relevance. Until better methods are developed, an existing normalization method such as quantile normalization should be applied when analyzing microRNA array data.
Space-Time Discontinuous Galerkin Method for Maxwell’s Equations
Authors: Xie Ziqing , Wang Bo , Zhang Zhimin 
Published: March 2013

AbstractA fully discrete discontinuous Galerkin method is introduced for solving time-dependent Maxwell’s equations. Distinguished from the Runge-Kutta discontinuous Galerkin method (RKDG) and the finite element time domain method (FETD), in our scheme, discontinuous Galerkin methods are used to discretize not only the spatial domain but also the temporal domain. The proposed numerical scheme is proved to be unconditionally stable, and a convergent rate is established under the L2-norm when polynomials of degree atmost r and k are used for temporal and spatial approximation, respectively. Numerical results in both 2-D and 3-D are provided to validate the theoretical prediction. An ultra-convergence of order in time step is observed numerically for the numerical fluxes w.r.t. temporal variable at the grid points.
Ionic Dialysance and Determination of Kt/V in on-line Hemodiafiltration with Simultaneous Pre- and Post-dilution
Authors: Créput Caroline , Toledano Daniel , Petitclerc Thierry 
Published: March 2013

Purpose A direct determination of Kt/V using ionic dialysance for estimating K and bio-impedancemetry for estimating V is compared with the usual indirect estimation based on the second generation Daugirdas equation during a new technique of hemodiafiltration with simultaneous pre- and postdilution (mixed-HDF). Methods In 31 informed consented patients, the urea distribution volume (V) is estimated by total body water (VBCM) measured by the Body Composition Monitor (BCM; Fresenius Medical Care, Bad Homburg, Germany) based on bio-impedance spectroscopy. The value (KOCM t)/VBCM is calculated during 114 mixed-HDF sessions (duration 4 hours) from the measurement of ionic dialysance KOCM by the OCM module, standard on the 5008 dialysis monitor (Fresenius Medical Care, Germany). The single pool (Kt/V)sp is determined from blood urea concentration measurements using the Daugirdas equation. Results Mixed-HDF is a very high-efficiency hemodialysis with a delivered dialysis dose Kt/V near from 2 per 4-hour session. (KOCM t)/VBCM (1.97 ± 0.28) is consistent with (Kt/V)sp (2.01 ± 0.34) with a correlation coefficient at 0.72. Conclusions Direct calculation of Kt/V from estimating K by OCM and V by BCM is consistent with the usual indirect estimation by the second generation Daugirdas equation. Therefore, the regular determination of V by BCM allows the estimation of single-pool Kt/V at each session without the need of blood sampling.
Mouse Colony Data Management
Authors: Donnelly Charles J. , Bult Carol J. 
Published: March 2013

AbstractIn this unit we discuss the importance of implementing a data management system for research animal colonies. We focus on drivers such as ethical considerations, cost, and data integrity. We also discuss keys to effective data management and important considerations for adopting or building a data management system, and present an overview of some of the currently available colony and laboratory data management systems. Curr. Protoc. Mouse Biol. 3:1‐8 © 2013 by John Wiley & Sons, Inc.
Acute Asthma Models to Ovalbumin in the Mouse
Authors: Daubeuf François , Frossard Nelly 
Published: March 2013

AbstractHuman asthma is defined as a chronic inflammatory disease of the airways. Animal models are required to study asthma pathophysiology and identify and/or evaluate new therapeutic strategies. Several models of asthma have been developed in mice to mimic asthma symptoms, and can be divided in two groups as acute and chronic models. They are characterized by airway hyperresponsiveness (AHR), inflammation, and remodeling. Several experimental procedures have been implemented, the one mostly used being acute asthma models to ovalbumin. It comprises a sensitization step in the presence of aluminum hydroxide as an adjuvant, and a second step where mice are challenged with the allergen introduced directly into the airways to induce the modeled asthma features. This article describes procedures to efficiently and reproducibly obtain acute asthma features in mice, with ovalbumin as the allergen, which allow group comparisons and/or assessment of the activity of drug candidates. Curr. Protoc. Mouse Biol. 3:31‐37 © 2013 by John Wiley & Sons, Inc.
Realizing the Potential of ZnO with Alternative Non‐Metallic Co‐Dopants as Electrode Materials for Small Molecule Optoelectronic Devices
Authors: Kim Yong Hyun , Kim Jin Soo , Kim Won Mok , Seong Tae‐Yeon , Lee Jonghee , Müller‐Meskamp Lars , Leo Karl 
Published: March 2013

AbstractHigh performance indium tin oxide (ITO)‐free small molecule organic solar cells and organic light‐emitting diodes (OLEDs) are demonstrated using optimized ZnO electrodes with alternative non‐metallic co‐dopants. The co‐doping of hydrogen and fluorine reduces the metal content of ZnO thin films, resulting in a low absorption coefficient, a high transmittance, and a low refractive index as well as the high conductivity, which are needed for the application in organic solar cells and OLEDs. While the established metal‐doped ZnO films have good electrical and optical properties, their application in organic devices is not as efficient as other alternative electrode approaches. The optimized ZnO electrodes presented here are employed in organic solar cells as well as OLEDs and allow not only the replacement of ITO, but also significantly improve the efficiency compared to lab‐standard ITO. The enhanced performance is attributed to outstanding optical properties and spontaneously nanostructured surfaces of the ZnO films with non‐metallic co‐dopants and their straightforward integration with molecular doping technology, which avoids several common drawbacks of ZnO electrodes. The observations show that optimized ZnO films with non‐metallic co‐dopants are a promising and competitive electrode for low‐cost and high performance organic solar cells and OLEDs.
Acrylonitrile copolymers containing guanidine oligomer: Synthesis and use for the preparation of nonleaching antimicrobial acrylic fibers
Authors: Wei Da‐Fu , Zhou Ri‐Hui , Zhang You‐Wei , Guan Yong , Zheng An‐Na 
Published: March 2013

AbstractNonleaching acrylic fibers with permanent antibacterial activity were prepared via a combination of copolymerization and a wet‐blend‐spinning method. Specifically, poly[acrylonitrile‐co‐modified poly(hexamethylene guanidine hydrochloride)] [poly(AN‐co‐M‐PHMG)] copolymers containing a covalently connected antibacterial guanidine oligomer were first synthesized via the precipitation copolymerization of acrylonitrile (AN) with a modified poly(hexamethylene guanidine hydrochloride) (M‐PHMG) macromonomer in water. Then, modified acrylic fibers were prepared from a mixture of the copolymer and commercial fiber‐grade AN terpolymer via a wet‐spinning process with dimethyl sulfoxide as the solvent. The influences of the reaction time, temperature, pH value of the medium, and amount of initiator on the copolymerization and the effect of the copolymer content on the mechanical properties and antibacterial activity of the modified acrylic fibers were investigated in detail. The results show that the M‐PHMG macromonomer exhibited a lower reactivity than AN. The poly(AN‐co‐M‐PHMG) copolymer with a PHMG content of 5.49% and an intrinsic viscosity of 11.2 dL/g could be synthesized under optimized conditions. With increasing copolymer content, the tensile strength of the modified acrylic fibers decreased slightly, and the antibacterial activity increased. The modified acrylic fibers with a copolymer content of 50% (i.e., a PHMG content of 2.75%) exhibited both good mechanical properties and excellent antibacterial activity. The additional antibacterial function would surely enlarge the applications of the fiber. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013
Preparation of phosphorylated nata‐de‐coco for polymer electrolyte membrane applications
Authors: Radiman Cynthia Linaya , Rifathin Annisa 
Published: March 2013

AbstractFuel cells are being developed to overcome the global energy crisis. The objective of this research is to prepare an environmental‐friendly and cheap material as the polymer electrolyte membrane. Coconut water was fermented by Acetobacter xylinum to produce nata‐de‐coco and the phosphorylation was carried out by microwave‐assisted reaction. The resulting membranes are characterized by ion exchange capacity, contact angle, proton conductivity, swelling index, methanol permeability, mechanical properties measurement and morphological analysis. At the optimum phosphorylation condition using 17.35 mmol of phosphoric acid, membrane showed a proton conductivity of 1.2 × 10−2 S/cm and a methanol permeability of 2.3 × 10−6 cm2/s. The tensile strength of the produced membranes increases significantly and the arrangement of the cellulosic fibers are kept well‐aligned. It is concluded that a green and sustainable natural resources can be used for preparing electrolyte membrane. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013
FTY720 Ameliorates Murine Sclerodermatous Chronic Graft‐Versus‐Host Disease by Promoting Expansion of Splenic Regulatory Cells and Inhibiting Immune Cell Infiltration Into Skin
Authors: Huu Doanh Le , Matsushita Takashi , Jin Guihua , Hamaguchi Yasuhito , Hasegawa Minoru , Takehara Kazuhiko , Fujimoto Manabu 
Published: March 2013

ObjectiveSphingosine 1‐phosphate (S1P) exerts a variety of activities in immune, inflammatory, and vascular systems. S1P plays an important role in systemic sclerosis (SSc) pathogenesis. Regulation of S1P in fibrotic diseases as well as in SSc was recently reported. FTY720, an oral S1P receptor modulator, has been shown to be a useful agent for the prevention of transplant rejection and autoimmune diseases. Murine sclerodermatous chronic graft‐versus‐host disease (GVHD) is a model for human sclerodermatous chronic GVHD and SSc. We undertook this study to investigate the effects of FTY720 in murine sclerodermatous chronic GVHD.MethodsFTY720 was orally administered to allogeneic recipient mice from day 0 to day 20 (short‐term, early‐treatment group), from day 0 to day 42 (full‐term, early‐treatment group), or from day 22 to day 42 (delayed‐treatment group) after bone marrow transplantation.ResultsDelayed administration of FTY720 attenuated, and early administration of FTY720 inhibited, the severity and fibrosis in murine sclerodermatous chronic GVHD. With early treatment, FTY720 induced expansion of splenic myeloid‐derived suppressor cells, Treg cells, and Breg cells. Vascular damage in chronic GVHD was inhibited by FTY720 through down‐regulating serum levels of S1P and soluble E‐selectin. FTY720 inhibited infiltration of immune cells into skin. Moreover, FTY720 diminished the expression of messenger RNA for monocyte chemotactic protein 1, macrophage inflammatory protein 1α, RANTES, tumor necrosis factor α, interferon‐γ, interleukin‐6 (IL‐6), IL‐10, IL‐17A, and transforming growth factor β1 in the skin.ConclusionFTY720 suppressed the immune response by promoting the expansion of regulatory cells and reducing vascular damage and infiltration of immune cells into the skin. Taken together, these results have important implications for the potential use of FTY720 in the treatment of sclerodermatous chronic GVHD and SSc in humans.
Enhanced Rho‐Associated Protein Kinase Activation in Patients With Systemic Lupus Erythematosus
Authors: Isgro Josephine , Gupta Sanjay , Jacek Elzbieta , Pavri Tanya , Duculan Roland , Kim Mimi , Kirou Kyriakos A. , Salmon Jane E. , Pernis Alessandra B. 
Published: March 2013

ObjectiveRho‐associated protein kinases (ROCKs) have been implicated in the pathogenesis of cardiovascular and renal disorders. We recently showed that ROCKs could regulate the differentiation of murine Th17 cells and the production of interleukin‐17 (IL‐17) and IL‐21, two cytokines associated with systemic lupus erythematosus (SLE). The goal of this study was to assess ROCK activation in human Th17 cells and to evaluate ROCK activity in SLE patients.MethodsAn enzyme‐linked immunosorbent assay (ELISA)–based ROCK activity assay was used to evaluate ROCK activity in human cord blood CD4+ T cells differentiated under Th0 or Th17 conditions. We then performed a cross‐sectional analysis of 28 SLE patients and 25 healthy matched controls. ROCK activity in peripheral blood mononuclear cell (PBMC) lysates was determined by ELISA. Cytokine and chemokine profiles were analyzed by ELISA.ResultsHuman cord blood CD4+ T cells differentiated under Th17 conditions expressed higher levels of ROCK activity than did CD4+ T cells stimulated under Th0 conditions. Production of IL‐17 and IL‐21 was inhibited by the addition of a ROCK inhibitor. SLE PBMCs expressed significantly higher levels of ROCK activity than did healthy control PBMCs (1.25 versus 0.56; P = 0.0015). Sixteen SLE patients (57%) expressed high levels of ROCK (optical density at 450 nm >1). Disease duration, lymphocyte count, and azathioprine use were shown to be significant independent predictors of ROCK activity in multivariable analyses.ConclusionConsistent with previous results in the murine system, increased ROCK activation was associated with Th17 cell differentiation. Moreover, enhanced ROCK activity was observed in a subgroup of SLE patients. These data support the concept that the ROCK pathway could represent an important therapeutic target for SLE.
Familial Mediterranean Fever in Heterozygotes: Are We Able to Accurately Diagnose the Disease in Very Young Children?
Authors: Hentgen Véronique , Grateau Gilles , Stankovic‐Stojanovic Katia , Amselem Serge , Jéru Isabelle 
Published: March 2013

ObjectiveFamilial Mediterranean fever (FMF) is an autosomal‐recessive autoinflammatory disease due to mutations in MEFV. Descriptions of disease manifestations among patients carrying a single mutated MEFV allele are becoming more frequent, although no data are available on the long‐term outcome. We undertook this study to assess the accuracy of clinical diagnosis in children carrying a single mutated MEFV allele with symptoms of recurrent autoinflammatory disorder.MethodsWe performed a retrospective single‐center study of 33 patients with autoinflammatory disorders age <6 years at disease onset with 1 mutated MEFV allele. The phenotype of the patients was investigated in detail, and the clinical picture and outcome of 18 patients with an initial FMF diagnosis according to current clinical criteria were compared to those of 25 homozygous or compound heterozygous FMF patients.ResultsNo major differences in presenting signs or initial response to colchicine were observed between patient groups. During followup, heterozygotes had a milder disease course compared to homozygotes and were less prone than homozygotes to experience new clinical signs of FMF. At puberty, clinical signs of FMF completely disappeared in 5 of 18 heterozygotes, allowing them to discontinue colchicine without recurrence of symptoms or increases in inflammatory marker levels.ConclusionOur data suggest that the clinical diagnosis of FMF in very young heterozygous children should be made with caution. At this young age they can present with an FMF‐like disease—similar to that seen in patients carrying 2 mutated alleles—that is not necessarily predictive of life‐long illness.
In Situ Analysis of Interleukin–23– and Interleukin‐12–Positive Cells in the Spine of Patients With Ankylosing Spondylitis
Authors: Appel Heiner , Maier Rene , Bleil Janine , Hempfing Axel , Loddenkemper Christoph , Schlichting Uwe , Syrbe Uta , Sieper Joachim 
Published: March 2013

ObjectiveThe interleukin‐12 (IL‐12) family of cytokines has been suggested to play a critical role in inflammatory autoimmune diseases, and recent studies analyzing peripheral blood and synovial fluid from patients with spondyloarthritides suggest that IL‐23 might be a proinflammatory factor in these disorders. This study was undertaken to investigate the presence and source of IL‐23 in the spines of patients with ankylosing spondylitis (AS).MethodsThe frequency of IL‐23–positive and IL‐12–positive cells within the subchondral bone marrow and within fibrous tissue replacing normal bone marrow in facet joints of patients with AS was analyzed by immunohistochemistry. The origin of IL‐23–positive cells was determined by double staining of CD163+ macrophages, CD68+ macrophages, CD1a+ dendritic cells, tryptase‐positive mast cells, myeloperoxidase‐positive cells, CD20+ B cells, and CD3+ T cells. Findings in 28 facet joints from 22 AS patients were compared with those in 20 facet joints from 13 patients with osteoarthritis (OA) and 10 normal control specimens.ResultsThe frequency of IL‐23–positive cells in subchondral bone marrow from the joints of AS patients (mean ± SD 42.50 ± 32.81/high‐power field [hpf]) was significantly increased compared to that in subchondral bone marrow from OA patients (OA 15.63 ± 29.90/hpf) (P = 0.0017) or controls (19.36 ± 16.8/hpf) (P = 0.03). Myeloperoxidase‐positive cells and, to a lesser extent, macrophages and dendritic cells were found to be the origin of IL‐23 in the bone marrow. In AS and OA patients, the frequency of IL‐23–positive cells was significantly higher than that of IL‐12–positive cells (P < 0.001 in both patient groups). Within fibrous tissue from AS and OA facet joints, IL‐23 was predominantly produced by CD163+ macrophages (mean ± SD 0.64 ± 0.59/hpf and 4.36 ± 3.4/hpf, respectively) and CD68+ macrophages (2.3 ± 0.65/hpf and 6.54 ± 4.1/hpf, respectively).ConclusionIL‐23 is expressed in the subchondral bone marrow and in fibrous tissue replacing bone marrow in facet joints of patients with AS. It might have a role in inflammatory processes and in chronic changes in AS joints, which makes it an interesting potential therapeutic target in this disease.
Structural Tailoring Effects on the Magnetic Behavior of Symmetric and Asymmetric Cubane‐Type Ni complexes
Authors: Ponomaryov Alexey N. , Kim Namseok , Hwang Jaewon , Nojiri Hiroyuki , van Tol Johan , Ozarowski Andrew , Park Jena , Jang Zeehoon , Suh Byoungjin , Yoon Sungho , Choi Kwang‐Yong 
Published: March 2013

AbstractUsing two kinds of carboxylate ligands with small but significant differences in steric size, symmetric and asymmetric FeII and NiII cubanes have been synthesized in a controlled fashion. Fast sweeping pulsed field measurements showed magnetization hysteresis loops for two cubane‐type molecular complexes, [Ni4(μ‐OMe)4(O2CAr4F‐Ph)4(HOMe)8] and [Ni4(μ‐OMe)4(O2CArTol)4(HOMe)6], thus suggesting single‐molecule magnet behavior. To differentiate the magnetic properties between the symmetric and asymmetric cubanes, detailed electron paramagnetic resonance (EPR) measurements were performed. From the EPR data, taken at various frequencies and temperatures, zero‐field splitting parameters D, E, and other higher‐order parameters for both cubane samples were extracted. Compared to the symmetric Ni‐cubane, the asymmetric one shows an increase in the D and E values by about 20 %, thereby suggesting structural engineering effects on the magnetic properties. By using the magnetic parameters determined by EPR, a static magnetization curve at 2 K and a temperature dependence of the magnetic susceptibility were simulated. A good agreement between theoretical and experimental data confirms the validity of the values obtained from EPR measurements.
Passivity Based Attitude Control of Rigid Bodies
Authors: Wang Hanlei , Xie Yongchun 
Published: March 2013

AbstractIn this paper, we present a tutorial on passivity based attitude control that has been investigated over the past two decades. Both regulation control and adaptive tracking control for the attitude motion of rigid bodies are discussed under a unified passivity framework. Our attention is mainly confined to the attitude control schemes that are based on the passivity notion. Output feedback attitude control, attitude synchronization, and some open problems are also discussed.
Transcription activator‐like effector nucleases (TALENs): A highly efficient and versatile tool for genome editing
Authors: Sun Ning , Zhao Huimin 
Published: March 2013

AbstractTranscription activator‐like effector (TALE) nucleases (TALENs) have recently emerged as a revolutionary genome editing tool in many different organisms and cell types. The site‐specific chromosomal double‐strand breaks introduced by TALENs significantly increase the efficiency of genomic modification. The modular nature of the TALE central repeat domains enables researchers to tailor DNA recognition specificity with ease and target essentially any desired DNA sequence. Here, we comprehensively review the development of TALEN technology in terms of scaffold optimization, DNA recognition, and repeat array assembly. In addition, we provide some perspectives on the future development of this technology. Biotechnol. Bioeng. 2013; 110: 1811–1821. © 2013 Wiley Periodicals, Inc.
ChemInform Abstract: Predicted Lithium—Boron Compounds under High Pressure.
Authors: Peng Feng , Miao Maosheng , Wang Hui , Li Quan , Ma Yanming 
Published: March 2013

AbstractThe existence of Li3B2, Li2B, Li4B, and Li6B that might be experimentally synthesizable over a wide range of pressures is predicted by an unbiased structure search method based on particle‐swarm optimization algorithms in combination with DFT calculations.
ChemInform Abstract: Neutron Diffraction and Observation of Superconductivity for Tungsten Borides, WB and W2B4.
Authors: Kayhan Mehmet , Hildebrandt Erwin , Frotscher Michael , Senyshyn Anatoliy , Hofmann Kathrin , Alff Lambert , Albert Barbara 
Published: March 2013

AbstractThe title compounds are investigated by neutron diffraction and magnetic measurements.
ChemInform Abstract: Catalysis of Nickel Ferrite for Photocatalytic Water Oxidation Using [Ru(bpy)3]2+ and S2O82‐.
Authors: Hong Dachao , Yamada Yusuke , Nagatomi Takaharu , Takai Yoshizo , Fukuzumi Shunichi 
Published: March 2013

AbstractNiFe2O4 is an excellent catalyst for photocatalytic water oxidation with Na2S2O8 as a sacrificial oxidant and [Ru(bpy)3]2+ as a photosensitizer.