bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simultaneous miRNA and mRNA transcriptome profiling of human myoblasts reveals a novel set of myogenic differentiation-associated miRNAs and their target genes
Authors: Dmitriev Petr , Barat Ana , Polesskaya Anna , O’Connell Mary J , Robert Thomas , Dessen Philippe , Walsh Thomas A , Lazar Vladimir , Turki Ahmed , Carnac Gilles , Laoudj-Chenivesse Dalila , Lipinski Marc , Vassetzky Yegor S 
Published: April 2013

AbstractBackgroundmiRNA profiling performed in myogenic cells and biopsies from skeletal muscles has previously identified miRNAs involved in myogenesis.ResultsHere, we have performed miRNA transcriptome profiling in human affinity-purified CD56+ myoblasts induced to differentiatein vitro. In total, we have identified 60 miRNAs differentially expressed during myogenic differentiation. Many were not known for being differentially expressed during myogenic differentiation. Of these, 14 (miR-23b, miR-28, miR-98, miR-103, miR-107, miR-193a, miR-210, miR-324-5p, miR-324-3p, miR-331, miR-374, miR-432, miR-502, and miR-660) were upregulated and 6 (miR-31, miR-451, miR-452, miR-565, miR-594 and miR-659) were downregulated. mRNA transcriptome profiling performed in parallel resulted in identification of 6,616 genes differentially expressed during myogenic differentiation.ConclusionsThis simultaneous miRNA/mRNA transcriptome profiling allowed us to predict with high accuracy target genes of myogenesis-related microRNAs and to deduce their functions.
Morphological and functional differentiation in BE(2)-M17 human neuroblastoma cells by treatment with Trans-retinoic acid
Authors: Andres Devon , Keyser Brian M , Petrali John , Benton Betty , Hubbard Kyle S , McNutt Patrick M , Ray Radharaman 
Published: April 2013

Abstract

Background
Immortalized neuronal cell lines can be induced to differentiate into more mature neurons by adding specific compounds or growth factors to the culture medium. This property makes neuronal cell lines attractive as in vitro cell models to study neuronal functions and neurotoxicity. The clonal human neuroblastoma BE(2)-M17 cell line is known to differentiate into a more prominent neuronal cell type by treatment with trans-retinoic acid. However, there is a lack of information on the morphological and functional aspects of these differentiated cells.

Results
We studied the effects of trans-retinoic acid treatment on (a) some differentiation marker proteins, (b) types of voltage-gated calcium (Ca2+) channels and (c) Ca2+-dependent neurotransmitter ([3H] glycine) release in cultured BE(2)-M17 cells. Cells treated with 10 μM trans-retinoic acid (RA) for 72 hrs exhibited marked changes in morphology to include neurite extensions; presence of P/Q, N and T-type voltage-gated Ca2+ channels; and expression of neuron specific enolase (NSE), synaptosomal-associated protein 25 (SNAP-25), nicotinic acetylcholine receptor α7 (nAChR-α7) and other neuronal markers. Moreover, retinoic acid treated cells had a significant increase in evoked Ca2+-dependent neurotransmitter release capacity. In toxicity studies of the toxic gas, phosgene (CG), that differentiation of M17 cells with RA was required to see the changes in intracellular free Ca2+ concentrations following exposure to CG.

Conclusion
Taken together, retinoic acid treated cells had improved morphological features as well as neuronal characteristics and functions; thus, these retinoic acid differentiated BE(2)-M17 cells may serve as a better neuronal model to study neurobiology and/or neurotoxicity.
Active microscope stabilization in three dimensions using image correlation
Authors: McGorty Ryan , Kamiyama Daichi , Huang Bo 
Published: April 2013

Abstract

Background
Super-resolution microscopy techniques are often extremely susceptible to sample drift due to their high spatial resolution and the long time needed for data acquisition. While several techniques for stabilizing against drift exist, many require complicated additional hardware or intrusive sample preparations. We introduce a method that requires no additional sample preparation, is simple to implement and simultaneously corrects for x, y and z drift.

Results
We use bright-field images of the specimen itself to calculate drift in all three dimensions: x, y and z. Bright-field images are acquired on an inexpensive CCD. By correlating each acquired bright-field image with an in-focus and two out-of-focus reference images we determine and actively correct for drift at rates of a few Hertz. This method can maintain stability to within 10 nm for x and y and 20 nm for z over several minutes.

Conclusion
Our active drift stabilization system is capable of simultaneously compensating x, y and z drift through an image-based correlation method that requires no special sample treatment or extensive microscope modifications. While other techniques may provide better stability, especially for higher frequency drift, our method is easy to implement and widely applicable in terms of both sample type and microscopy technique.
Efficacy of SPI-1865, a novel gamma-secretase modulator, in multiple rodent models
Authors: Loureiro Robyn M , Dumin Jo Ann , McKee Timothy D , Austin Wesley F , Fuller Nathan O , Hubbs Jed L , Shen Ruichao , Jonker Jeff , Ives Jeff , Bronk Brian S , Tate Barbara 
Published: April 2013

Abstract
Introduction
Modulation of the gamma-secretase enzyme, which reduces the production of the amyloidogenic Aβ42 peptide while sparing the production of other Aβ species, is a promising therapeutic approach for the treatment of Alzheimer's disease. Satori has identified a unique class of small molecule gamma-secretase modulators (GSMs) capable of decreasing Aβ42 levels in cellular and rodent model systems. The compound class exhibits potency in the nM range in vitro and is selective for lowering Aβ42 and Aβ38 while sparing Aβ40 and total Aβ levels. In vivo, a compound from the series, SPI-1865, demonstrates similar pharmacology in wild-type CD1 mice, Tg2576 mice and Sprague Dawley rats.

Methods
Animals were orally administered either a single dose of SPI-1865 or dosed for multiple days. Aβ levels were measured using a sensitive plate-based ELISA system (MSD) and brain and plasma exposure of drug were assessed by LC/MS/MS.

Results
In wild-type mice using either dosing regimen, brain Aβ42 and Aβ38 levels were decreased upon treatment with SPI-1865 and little to no statistically meaningful effect on Aβ40 was observed, reflecting the changes observed in vitro. In rats, brain Aβ levels were examined and similar to the mouse studies, brain Aβ42 and Aβ38 were lowered. Comparable changes were also observed in the Tg2576 mice, where Aβ levels were measured in brain as well as plasma and CSF.

Conclusions
Taken together, these data indicate that SPI-1865 is orally bioavailable, brain penetrant, and effective at lowering Aβ42 in a dose responsive manner. With this unique profile, the class of compounds represented by SPI-1865 may be a promising new therapy for Alzheimer's disease.
Gene-environment interaction between body mass index and transforming growth factor beta 1 (TGFβ1) gene in knee and hip osteoarthritis
Authors: Muthuri Stella G , Doherty Sally , Zhang Weiya , Maciewicz Rose A , Muir Kenneth R , Doherty Michael 
Published: April 2013

Abstract
Introduction
The objective was to investigate potential gene-environment interaction between body mass index (BMI) and each of eight TGFβ1 polymorphisms in knee and hip osteoarthritis (OA).

Methods
We conducted a case-control study of Caucasian men and women aged 45 to 86 years from Nottingham, United Kingdom (Genetics of OA and Lifestyle (GOAL) study). Cases had clinically severe symptoms and radiographic knee or hip OA; controls had no symptoms and no radiographic knee/hip OA. We used logistic regression to investigate the association of TGFβ1 polymorphisms and OA when stratifying by BMI. Knee and hip OA were analyzed separately with adjustment for potential confounders. Additive and multiplicative interactions were examined.

Results
2,048 cases (1,042 knee OA, 1,006 hip OA) and 967 controls were studied. For hip OA, the highest risk was in overweight (BMI ≥25 kg/m2) individuals with the variant allele of single-nucleotide polymorphism (SNP) rs1800468 (odds ratio (OR) 2.21, 95% confidence interval (CI) 1.55, 3.15). Evaluation of gene-environment interaction indicated significant synergetic interaction (relative excess risk due to interaction (RERI) = 0.93, synergy index (SI) = 4.33) with an attributable proportion due to interaction (AP) of 42% (AP = 0.42; 95% CI 0.16, 0.68). Multiplicative interaction was also significant (OR for interaction (ORINT) = 2.27, P = 0.015). For knee OA, the highest risk was in overweight individuals with homozygous genotype 11 of SNP rs2278422 (OR = 6.95, P <0.001). In contrast, the variant allele indicated slightly lower risks (OR = 4.72, P <0.001), a significant antagonistic interaction (RERI = -2.66, SI = 0.59), AP = -0.56 (95%CI -0.94, -0.17) and a significant multiplicative interaction (ORINT = 0.47, P = 0.013).

Conclusion
TGFβ1 gene polymorphisms interact with being overweight to influence the risk of large joint OA.
Shear stress modulates macrophage-induced urokinase plasminogen activator expression in human chondrocytes
Authors: Yeh Chih-Chang , Chang Shun-Fu , Huang Ting-Ying , Chang Hsin-I , Kuo Hsing-Chun , Wu Yi-Chien , Hsieh Ching-Hsiang , Shi Chung-Sheng , Chen Cheng-Nan 
Published: April 2013

Abstract
Introduction
Synovial macrophages, which can release proinflammatory factors, are responsible for the upregulation of cartilage-breakdown proteases and play critical roles in cartilage degradation during the progression of osteoarthritis (OA). In addition, shear stress exerts multifunctional effects on chondrocytes by inducing the synthesis of catabolic or anabolic genes. However, the interplay of macrophages, chondrocytes, and shear stress during the regulation of cartilage function remains poorly understood. We investigated the mechanisms underlying the modulation of human chondrocyte urokinase plasminogen activator (uPA) expression by macrophages and shear stress.

Methods
Human chondrocytes were stimulated by peripheral blood-macrophage- conditioned medium (PB-MCM), or exposure of chondrocytes cultured in PB-MCM to different levels of shear stress (2 to 20 dyn/cm2). Real-time polymerase chain reaction was used to analyze uPA gene expression. Inhibitors and small interfering RNA were used to investigate the mechanism for the effects of PB-MCM and shear stress in chondrocytes.

Results
Stimulation of human chondrocytes with PB-MCM was found to induce uPA expression. We demonstrated that activation of the JNK and Akt pathways and NF-κB are critical for PB-MCM-induced uPA expression. Blocking assays by using IL-1ra further demonstrated that IL-1β in PB-MCM is the major mediator of uPA expression in chondrocytes. PB-MCM-treated chondrocytes subjected to a lower level of shear stress showed inhibition of MCM-induced JNK and Akt phosphorylation, NF-κB activation, and uPA expression. The PB-MCM-induced uPA expression was suppressed by AMP-activated protein kinase (AMPK) agonist. The inhibitor or siRNA for AMPK abolished the shear-mediated inhibition of uPA expression.

Conclusions
These data support the hypothesis that uPA upregulation stimulated by macrophages may play an active role in the onset of OA and in the shear-stress protection against this induction.
Association between digital dermatoglyphics and handedness among Sinhalese in Sri Lanka
Authors: Wijerathne Buddhika TB , Rathnayake Geetha K 
Published: April 2013

BackgroundThe relationship between handedness and digital dermatoglyphic patterns has never been investigated in the Sinhalese population. The goal of this study is to establish the above mentioned relationship, which would positively aid personal identification. FindingsOne hundred Sinhalese students (50 right-handed and 50 left-handed) were studied for their digital dermatoglyphic pattern distribution. The results show that a statistically significant correlation exists for digit 3 (P=0.002, Fisher’s exact test) of the right hand and digit 1 (P=0.002, Fisher’s exact test) and digit 2 (P=0.021, Fisher’s exact test) of the left hand. Further, whorl patterns are more common in right-handed than left-handed Sinhalese students.Conclusions Statistically significant differences in handedness and digital dermatoglyphic patterns were evident among Sinhalese people. Further study with a larger sample size is recommended.
Giant aneurysm of the basilar artery in an 86 year old woman
Authors: Yu Yong peng , Zhao Hong qin , Ren Wei feng , Chi Xiang lin 
Published: April 2013

In this article we present an 80 year old female patient with an unruptured giant aneurysm of the basilar artery presenting with posterior circulation ischemic symptoms. Angiography and CT revealed giant basilar aneurysmal dilatation with severe and wide intracranial arteriosclerosis. We described the uniqueness of this case. Giant basilar aneurysm is associated with various complications particularly brain stem infarction. It is emphasized that arteriosclerosis plays an important role in the formation of giant basilar aneurysms.
Thermally Stable Two-Dimensional Photonic Crystal for Selective Emitters
Authors: Lee Heon J. , Bathurst Stephen P. , Kim Sang-Gook 
Published: April 2013

ABSTRACTA fundamental challenge in solar-thermal-electrical energy conversion is the thermal stability of materials and devices at high operational temperatures. This study focuses on the thermal stability of selective emitters for solar thermophotovoltaic (STPV) systems to enhance the conversion efficiency. 2-D photonic crystals are periodic micro/nano-scale structures that are designed to affect the motion of photons at certain wavelengths. The structured patterns, however, lose their structural integrity at high temperature, which disrupts the tight tolerances required for spectral control of the thermal emitters. Through analytical studies and experimental observations, the four major mechanisms of thermal degradation of 2-D photonic crystal are identified: oxidation, grain growth and re-crystallization, surface diffusion, and evaporation and re-condensation. In this work, the design of a flat surface photonic crystal (FSPC) is proposed and experimental validations are performed.
Facile Synthesis and Effect of Eu, Tb Co-doping On the Tunable Luminescent Properties of YBO3
Authors: Zhang Xianwen , Marathe Archis , Sohal Sandeep , Holtz Mark , Davis Marauo , Hope-Weeks Louisa J. , Chaudhuri Jharna 
Published: April 2013

ABSTRACTEu3+/Tb3+co-doped YBO3 three-dimensional (3D) microstructures have been hydrothermally prepared by adjusting solvent and the molar ratio of Y3+ to B (Y/B) at 180 °C. The whole process was carried out under alkaline conditions without the use of any surfactant or catalyst. Characterizations of the samples are carried out using X-ray powder diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and high-resolution TEM (HRTEM). The photoluminescence (PL) colors of YBO3 sample co-doped with Eu3+ and Tb3+ under ultraviolet excitation can be tuned from red, through yellow and green-yellow, to green by changing the relative doping concentrations of the two activator ions. These phosphors with multicolor emissions in the visible region be potentially used as labels for light-display systems, optoelectronic devices and biological molecules.
Plasmonic Enhancement of Optical Absorption of UV Radiation in ZnO Thin Film Based Ultraviolet Photodetectors
Authors: Rajan Akshta , Paliwal Ayushi , Gupta Vinay , Tomar Monika 
Published: April 2013

ABSTRACTUltraviolet (UV) photoconductivity in pure ZnO thin films and metal (Ag, Au, Pt) nanoparticles (NPs) dispersed on ZnO thin films based UV photodetectors biased at 5 V for ultra violet radiation of λ = 365 nm and intensity = 24 µwatt/cm2 has been studied. All the three metal (Ag, Au, Pt) NPs synthesized by Polyol process when dispersed on the surface of 100 nm thin ZnO film results in enhanced photoconductive gain (K) in comparison to pure ZnO (3.1×103). An increase of about an order in K has been obtained in the case of Ag NPs/ZnO and Au NPs/ZnO UV photodetectors ( K = 6.9×104 and 5.3×104 respectively). On the other hand, Pt NPs enhance K by about two orders (5.0×105). Such an enhanced photoconductive gain has been achieved due to the lowering of dark current after dispersing the metal NPs on the surface of ZnO and increased photocurrent upon UV illumination. This may be attributed to the plasmon propagating property in metal NPs which enhances the light trapping through optical absorption in ZnO thin film surface (high photo current).
Surface Sensitive Spectroscopy Study of Ion Beam Irradiation Induced Structural Modifications in Borosilicate Glasses
Authors: Gandy Amy S. , Stennett Martin C. , Hyatt Neil C. 
Published: April 2013

ABSTRACTFe K edge X-ray absorption (XAS) and Fourier Transform Infra-Red (FT-IR) spectroscopies have been used to study potential structural modifications in sodium borosilicate glasses as a consequence of Kr+ irradiation. Glasses were doped with simulant waste elements and irradiated at room temperature with 450 keV Kr+ ions to a fluence of 2x1015 Kr+ ions cm-1. According to SRIM calculations, a damaged surface region approximately 400nm wide was produced. In order to probe only the damaged surface layer, XAS measurements were taken in total electron yield mode and FT-IR spectroscopy was conducted in reflectance off the glass surface. No change in Fe valence state was detected by XAS following irradiation. Reflectance FT-IR data revealed a shift to higher wavenumbers in the absorption bands located between 850 and 1100 cm-1 in the doped glasses, corresponding to bond stretching in the silicate network. Deconvolution of FT-IR spectra revealed the shift was due to polymerisation of the silicate network. Network connectivity was found to decrease in the un-doped glass, following irradiation. The results suggest an increase in silicate network connectivity by a cation mediated process, and demonstrates the successful application of surface sensitive XAS and FT-IR to the investigation of ion beam induced damage in amorphous materials.
Group III-Nitride Based Electronic and Optoelectronic Integrated Circuits for Smart Lighting Applications
Authors: Justice J. , Kadiyala A. , Dawson J. , Korakakis D. 
Published: April 2013

ABSTRACTWith general lighting applications being responsible for over 20% of the energy consumption in the United States, advances in solid-state lighting have the potential for considerable energy and cost savings. The United States Department of Energy predicts that the increased use of solid state lighting will result in a 46% lighting consumption energy savings by the year 2030. Smart lighting systems have the potential for reducing energy costs while also providing a means for short distance data transmission via free space optics. The group III-nitride (III-N) family of materials, including aluminum nitride (AlN), gallium nitride (GaN), indium nitride (InN), their binary and ternary alloys, are uniquely situated to provide light emitting diodes (LEDs) across the full visible spectrum, photodetectors (PDs) and high power, high speed transistors. In this work, aluminum gallium nitride (AlGaN) / GaN high electron mobility transistors (HEMTs) and indium gallium nitride (InGaN) photodiodes (PDs) are fabricated and characterized. HEMTs and LEDs (or PDs) are grown on the same substrate for the purpose of creating electronic and optoelectronic integrated circuits.
Influence of Momentary Annealing on the Nanoscale Surface Morphology of Room Temperature Pulsed Laser Deposited NiO(111) Epitaxial Thin Films on Atomically Stepped Sapphire (0001) Substrates
Authors: Yamauchi Ryosuke , Tan Geng , Shiojiri Daishi , Tsuchimine Nobuo , Koyama Koji , Kaneko Satoru , Matsuda Akifumi , Yoshimoto Mamoru 
Published: April 2013

ABSTRACTWe examined the influence of momentary annealing on the nanoscale surface morphology of NiO(111) epitaxial thin films deposited on atomically stepped sapphire (0001) substrates at room temperature in O2 at 1.3 × 10−3 and 1.3 × 10−6 Pa using a pulsed laser deposition (PLD) technique. The NiO films have atomically flat surfaces (RMS roughness: approximately 0.1–0.2 nm) reflecting the step-and-terrace structures of the substrates, regardless of the O2 deposition pressure. After rapid thermal annealing (RTA) of the NiO(111) epitaxial film deposited at 1.3 × 10−3 Pa O2, a periodic straight nanogroove array related to the atomic steps of the substrate was formed on the film surface for 60 s. In contrast, the fabrication of a transient state in the nanogroove array formation was achieved with RTA of less than 1 s. However, when the O2 atmosphere during PLD was 1.3 × 10−6 Pa, random crystal growth was observed and resulted in a disordered rough surface nanostructure after RTA.
Surface States Influence in Al Schottky Barrier of Ge Nanowires
Authors: Kamimura Hanay , Simon Ricardo A. , Berengue Olivia M. , Amorim Cleber A. , Chiquito Adenilson J. , Leite Edson R. 
Published: April 2013

ABSTRACTAiming the understanding of how the application to devices is affected by the presence of oxygen in semiconductor nanostructures, Al/Ge-nanowires Schottky devices were fabricated without any previous treatment to remove the native oxide from nanowires' surface, originated during the growth process. Electronic transport properties of these devices were investigated and it was observed that interface states originated from the disordered oxide layer effectively pinned the Fermi level at the Ge surface, affecting Schottky barriers. Numerical calculations were made to complement this study agreeing with experiments.
Ultrafast Photostriction in Thin Film Bismuth Ferrite and its Correlation to Electronic Dynamics
Authors: Li Yuelin , Wen Haidan , Chen Pice , Cosgriff Margaret P. , Walko Donald , Lee June Hyuk , Adamo Carolina , Schaller Richard , Rowland Clare , Schlepuetz Christian , Dufresne Eric , Zhang Qingteng , Giles Carlos , Schlom Darrell , Freeland John , Evans Paul 
Published: April 2013

ABSTRACTA series of laser pump, x-ray probe experiments show that above band gap photoexcitation can generate a large out-of-plane strain in multiferroic BiFeO3 thin films. The strain decays in a time scale that is the same as the photo-induced carriers measured in an optical transient absorption spectroscopy experiment. We attribute the strain to the piezoelectric effect due to screening of the depolarization field by laser induced carriers. A strong film thickness dependence of strain and carrier relaxation is also observed, revealing the role of the carrier transport in determining the structural and carrier dynamics in complex oxide thin films.