bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic biases in DNA copy number originate from isolation procedures
Authors: van Heesch Sebastiaan , Mokry Michal , Boskova Veronika , Junker Wade , Mehon Rajdeep , Toonen Pim , de Bruijn Ewart , Shull James D , Aitman Timothy J , Cuppen Edwin , Guryev Victor 
Published: April 2013

Abstract
Background
The ability to accurately detect DNA copy number variation in both a sensitive and quantitative manner is important in many research areas. However, genome-wide DNA copy number analyses are complicated by variations in detection signal.

Results
While GC content has been used to correct for this, here we show that coverage biases are tissue-specific and independent of the detection method as demonstrated by next-generation sequencing and array CGH. Moreover, we show that DNA isolation stringency affects the degree of equimolar coverage and that the observed biases coincide with chromatin characteristics like gene expression, genomic isochores, and replication timing.

Conclusion
These results indicate that chromatin organization is a main determinant for differential DNA retrieval. These findings are highly relevant for germline and somatic DNA copy number variation analyses.
Provoking progress: a new chapter
Authors: Siegel Vivian 
Published: April 2013

Summary
Journals do more than publish collections of research articles and reviews; they also create community, influence standards for community behavior and ‘provoke progress’ in a particular field. In this Editorial, founding Editor-in-Chief Vivian Siegel compares launching a journal to raising a child, and reflects on the choices and successes of her tenure at DMM as she passes the leadership of the journal to new editors.
Organization and modulation of nuclear lamina structure
Authors: Gerace Larry , Comeau Claudette , Benson Mary 
Published: April 2013

ABSTRACT
The nuclear lamina is a protein meshwork associated with the nucleoplasmic surface of the inner nuclear membrane, that is suggested to be important for organizing nuclear envelope and interphase chromosome architecture. To investigate the structural organization of the lamina, we have analysed rat liver nuclear envelopes by various chemical extraction procedures. From these studies, we have defined conditions that yield a nuclear envelope subfraction that is both highly enriched in the lamina and devoid of pore complexes. This fraction contains mostly lamins A, B and C, the three major lamina polypeptides that are apparently arranged in a polymeric assembly. Our chemical extraction studies also indicate that lamin B has a stronger interaction with nuclear membranes than the other two lamins, and support the possibility that lamin B is important for attaching the lamina to the inner nuclear membrane.
We have examined the synthesis and assembly of the lamins during interphase in tissue-culture cells to investigate lamina structure by a second approach. We found that all three lamins are synthesized at similar rates throughout the cell cycle in synchronized Chinese hamster ovary cells, and that their biosynthesis is not temporally coupled to DNA replication. Our studies indicate that newly synthesized lamins are rapidly assembled into an insoluble lamina structure but that the apparent half-time for lamina insertion differs for individual lamins. We have also observed that lamin A is synthesized as an apparent precursor molecule that is converted to mature lamin A only after integration into the lamina structure.
The lamina is reversibly depolymerized during cell division, a process that may be mediated by enzymic phosphorylation of the lamins. To investigate this possibility further, we have analysed charge-altering modifications of the lamins on two-dimensional gels, and have found that phosphorylation is the only detectable modification of these proteins that occurs specifically during mitosis. Furthermore, we have determined that when the lamins are disassembled during metaphase, each lamin has approximately 2 moles of associated phosphate/mole lamin, a value that is four to sevenfold higher than the average interphase level. Considering this information, we discuss a model by which depolymerization and reassembly of the lamina can regulate the reversible disassembly of the nuclear envelope during mitosis.
Efficacy and Safety Evaluation of a Large Niacin Therapeutic Interchange Program
Authors: Chaffman Michael O , Webster William B , Winiecki John T 
Published: April 2013

BACKGROUND An extended-release niacin product (Niaspan, Abbott Laboratories) was identified as a product with a less costly therapeutic alternative; a therapeutic product interchange was implemented. OBJECTIVE To evaluate the efficacy and safety of a product therapeutic interchange from Niaspan to a controlled-release niacin product (Slo-Niacin, Upsher-Smith Laboratories) among patients at a large US Department of Veterans Affairs health care facility. METHODS Patients with active prescriptions for Niaspan underwent a therapeutic product interchange to Slo-Niacin; following conversion of the product, the medical record for each patient was reviewed and pre- and postconversion clinical information and conversion details were transcribed into a database for subsequent analysis and study. The primary efficacy end point was pre- and postconversion level of low-density lipoprotein cholesterol; secondary efficacy end points were levels of serum total cholesterol, high-density lipoprotein cholesterol, and triglycerides. Abnormal serum liver enzyme levels greater than 3 times the upper limits of normal was the primary safety end point; blood hemoglobin A1c was assessed as a secondary safety end point. RESULTS A total of 5321 patients' medical records were reviewed; for the efficacy evaluation, 539 patients were maintained on a daily dose of Slo-Niacin that was the same as the previous Niaspan dose. The dosage of any other concurrently prescribed dyslipidemia medication was unchanged. Analysis of these cases indicated that the conversion of Niaspan to Slo-Niacin was not associated with a difference in serum lipids over a mean (SD) of 503.9 (98.0) postconversion observation days with the exception of a decrease in mean serum triglyceride concentration of 19.8 mg/dL (p = 0.0003). Evaluation of all 5321 patients given Slo-Niacin for up to 724 days did not detect any safety differences between Slo-Niacin and Niaspan. Local facility cost avoidance exceeded $800,000 in the first postconversion year. CONCLUSIONS Data from a medication use evaluation of modified-release niacin products therapeutic interchange in a large US Department of Veterans Affairs health care facility show that the switch from Niaspan to Slo-Niacin had no negative effects on lipid-altering efficacy or safety but generated significant cost avoidance.
Prediction of hot flow curves of construction steels by physically-based constitutive equations
Authors: Varela-Castro G. , Cabrera J.M. 
Published: April 2013

ABSTRACTThe development of accurate constitutive equations is important for the success of computer simulations of high temperature forming operations. Often, these simulations must be made on alloys that have not been completely characterized. For that reason physically-based constitutive equations taking the chemical composition into consideration, involving deformation mechanisms and characteristic properties of the material are necessary. The influence that exerts the solute elements to an alloy on the mechanisms of diffusion on deformation processes at high temperatures is not an easy subject and the available information in literature is scarce.This study examines that influence working on the basis of eight structural plain carbon steels with the chemical composition ranging between 0.15-0.45%C, 0.2-0.4%Si and 0.6-1.6%Mn produced by Electro-Slag Remelting ESR process and tested by isothermal uniaxial compression technique. The studied deformation conditions include strain rates ranging between 5·10−4 to 1·10−1 s−1 and temperatures between 0.6-0.75Tm, with Tm the melting temperature.A constitutive expression for the hot working behavior is proposed, it includes the variation of the diffusion parameters with the chemical composition. To such aim the effect of the chemical composition of the alloy on the pre-exponential factor D0 of the gamma iron self-diffusion coefficient Dsd is included. Finally, a comparison of the experimental and predicted results shows the good agreement of the model with experimental flow data.
Enhanced Performance of Symmetric Double Layer Capacitor by Flexible Binder-free SWCNT Membrane Electrodes
Authors: Ma Danhao , Kalupson James , Shetty Pralav , Adu Kofi , Rajagopalan Ramakrishnan 
Published: April 2013

ABSTRACTWe present results on an aqueous symmetric double layer electrochemical capacitor (EDLC) constructed with a flexible binder-free single wall carbon (SWCNTs) membrane as electrodes. The capacitors were cycled from 0 to 1V @ 10 A/g for 10,000 cycles with 99.9% coulombic efficiency and 94% energy efficiency, and 100% depth of discharge. The power performance of the aqueous symmetric SWCNTs membrane capacitor is almost 100 –1000 times better than commercial non-aqueous EDLC capacitors.
Mechanical Properties of Pillared-Graphene Nanostructures under Shear Loads
Authors: Sasaki H. , Hagi T. , Shintani K. 
Published: April 2013

ABSTRACTThe shear deformations of pillared-graphene nanostructures are investigated using molecular dynamics simulation. Slight anisotropy regarding the direction of a shear load is detected. Changing the loading area in graphene and the radius of a single-walled carbon nanotube (SWNT) as a pillar, the deformations near the joints of graphene and a SWNT are examined in detail. It is concluded the anisotropy of the shear deformation of the nanostructure is due to the atomic structures at the joints of graphene and a SWNT as a pillar, and the out-of-plane deformations of graphene near the joints dominantly affect the overall shear deformation of the nanostructure.
Biaxially Stretchable Transparent Conductors That Use Metallic Single-Walled Carbon Nanotube Films
Authors: Ho Xinning , Tey Ju Nie , Liu Wenjun , Cheng Chek Kweng , Wei Jun 
Published: April 2013

ABSTRACTTransparent electronic devices that retain their electrical properties upon stretching and twisting are envisioned to be used in transparent wearable electronics and stretchable displays. An integral part of stretchable transparent electronic devices is the stretchable transparent conductor. In this work, we demonstrate biaxially stretchable transparent conductors that use metallic single-walled carbon nanotube films. Two dimensionally buckled metallic single-walled carbon nanotube films are realized. The “wavy” film “flattens out” when stretched and its electrical resistance hardly changes up to 3% applied strain. A similar film without any buckled structures suffers a severe degradation in electrical conductivity. Besides exhibiting stretchability, these transparent conductors display good sheet resistance (down to 3 kΩ/□) and transmittance (∼ 80% at a wavelength of 550 nm).
Concentrated Solutions of Highly Conductive Pyrene-Functionalized Carbon Nanotubes Suitable for Printing
Authors: Landorf Christopher William , Lamb James , Shih Wu-Sheng , Kayastha Vijaya , Bledsoe John , Garrison Jacqueline , Nelson Marriana 
Published: April 2013

ABSTRACTAs produced, raw carbon nanotubes are not soluble in many solvents necessary for printing applications. Standard methods for circumventing this problem involve sidewall functionalization and surfactants. Sidewall functionalization invariably destroys the π-network that gives carbon nanotubes their useful electronic properties, while surfactants deposit an insulating layer onto the carbon nanotube surface that must be washed off to regain the desired properties. Non-covalent functionalization offers the possibility to achieve solubility without destroying the π-network, but published methods have resulted in relatively low concentrations or substandard electronic performance. We have developed a scalable method to non-covalently functionalize long (> 3 μm) carbon nanotubes with simple pyrene derivatives. This method produces highly dispersed solutions with concentrations as high as 2.5 g/l that can be used to produce conductive coatings with sheet resistance as low as 350 Ω/sq with 85% transmittance at 550 nm without post-deposition washing or doping treatments. The functionalized carbon nanotubes can be formulated into solutions that can be printed by ink-jet deposition, Aerosol-Jet® deposition, screen printing, and spray coating for printed electronics fabrication, and the solutions are stable for months without signs of bundling.
The effects of Pulsed Green Laser Annealing for Carbon NanoWalls (CNWs)
Authors: Kawaguchi Norihito , Yoshimura Akihiko 
Published: April 2013

ABSTRACTThe effects of the pulsed green laser annealing at ambient nitrogen for two different heights-CNWs grown on silicon substrate were investigated on the crystallinity and morphology using Raman spectroscopy, SEM, TEM and XPS. For the 1μm height-CNWs, the peak intensity of D-band spectra decreased as the laser energy density increased up to 1.3Jcm-2, ID/IG ratio decreased from 2.5 to 0.7. The crystallinity of CNWs was improved by the laser irradiation. For the 1μm height-CNWs irradiated above 1.5Jcm-2, the height of CNWs decreased gradually as the laser energy density increased, it was clarified that the surfaces of CNWs were vaporized by the laser irradiation. For the 20μm height-CNWs, the peak intensity of D band spectra also decreased until the laser energy density increased up to 0.8Jcm-2, ID/IG ratio decreased from 1.6 to 0.5. From the TEM observation of CNWs irradiated at 0.8 Jcm-2, it was confirmed that the laser irradiation changed CNWs to be highly oriented crystal structure. However above 0.8Jcm-2, the crystallinity was deteriorated due to the vaporization of CNWs as the same as the 1μm height-CNWs. The pulsed green laser annealing is effective to improve the crystallinity of CNWs on optimal laser energy density for both height-CNWs, the higher laser energy densities vaporized the CNWs and changed the morphology and crystallinity of CNWs.
Solubility of Carbon in Nanocrystalline α-Iron
Authors: Kirchner Alexander , Eymann Konrad , Quadbeck Peter , Strauß Alexander , Kieback Bernd 
Published: April 2013

ABSTRACTBy using a thermodynamic model of nanocrystalline alloys the grain size effect on the solubility of carbon in α-iron is calculated. More specifically the enrichment at grain boundaries is predicted to result in a solubility enhancement. An experimental setup is devised to measure carbon solubility in nanocrystalline iron powder in equilibrium with graphite. At 390 °C a solubility of 0.514 at% is determined for nanocrystalline iron with a grain size of 23 nm.
Fracture Patterns of Boron Nitride Nanotubes
Authors: Perim Eric , Santos Ricardo Paupitz , Autreto Pedro Alves da Silva , Galvao Douglas S. 
Published: April 2013

ABSTRACTDuring the last years carbon-based nanostructures (such as, fullerenes, carbon nanotubes and graphene) have been object of intense investigations. The great interest in these nanostructures can be attributed to their remarkable electrical and mechanical properties. Their inorganic equivalent structures do exist and are based on boron nitride (BN) motifs. BN fullerenes, nanotubes and single layers have been already synthesized. Recently, the fracture patterns of single layer graphene and multi-walled carbon nanotubes under stress have been studied by theoretical and experimental methods. In this work we investigated the fracturing process of defective carbon and boron nitride nanotubes under similar stress conditions. We have carried out fully atomistic molecular reactive molecular dynamics simulations using the ReaxFF force field. The similarities and differences between carbon and boron nitride fracture patterns are addressed.
Effects of Processing Parameters and Nanofillers on Mechanical and Thermal Properties and Morphology of Impact Modified Poly (lactic acid)
Authors: Acik Eda , Yilmazer Ulku 
Published: April 2013

ABSTRACTTernary nanocomposites of poly (lactic acid) (PLA) were produced by melt blending with two types of elastomers and five types of organoclays to obtain improved mechanical properties such as tensile strength, modulus and impact strength. One of the elastomers is a random copolymer of ethylene and glycidyl methacrylate (E-GMA) and the other one is a random terpolymer of ethylene-butyl acrylate-maleic anhydride (E-BA-MAH). Organically modified montmorillonites (OMMT) were utilized as nanofillers. XRD, DSC, tensile and impact tests were done on the injection molded samples. FTIR, SEM and TEM analyses are still in progress. As preliminary results, thermal analysis showed that the addition of compatibilizers and organoclays does not have a distinct effect on the thermal properties of the composites, and no evidence of nucleation activity of compatibilizers or organoclays was found. For all types of organoclays, the nanocomposites produced with E-GMA exhibited better mechanical properties in comparison to nanocomposites containing E-BA-MAH, especially for the impact strength.
Microstructural Behavior of Energetic Crystalline Aggregates
Authors: LABARBERA D. , ZIKRY M.A. 
Published: April 2013

ABSTRACTA dislocation-density based crystalline plasticity and specialized finite-element formulations were used to study the behavior of energetic crystalline aggregates. The energetic crystalline material studied was RDX (cyclotrimethylene trinitramine) with a polymer binder and different void porosities. The aggregate was subjected to different dynamic pressures, and the analyses indicate that maximum temperature increases, constrained dislocation densities, and plastic strain accumulations occurred around the void peripheries, which affected overall deformation behavior. These regions of extreme temperature rise and thermal decomposition can result in hot spot formation.
Physical properties of La0.8Sr0.2MnO3nanotubes and fibers
Authors: Simião Daniel Felipe , Zenatti Alessandra , Escote Marcia T. 
Published: April 2013

ABSTRACTThis work describes the study of synthesis and physical characterization of nanostructured manganite oxides. The La0.8Sr0.2MnO3 (LSM) nanotubes and fibers have been prepared by electrospinning and pore wetting technique. The samples were characterized by Xray diffraction (XRD), scanning electron microscopy (SEM) and magnetization as a function of temperature (M(T)). XRD results of LSM fibers and nanotubes revealed that both samples crystallize in a rhombohedra-distorted perovskite structure. SEM pictures of these samples revealed ultrafine grains assembled in fibers and nanotubes samples. Analysis of these images revealed samples with external diameter ranging from 300 to 1.4 mm, and 7 μm to hundreds of mm in length. The M(T) measurements of samples La0.8Sr0.2MnO3 revealed a paramagnetic/ferromagnetic transition with decreasing temperature. Such transition occurs at temperatures of Tc ≈ 337 K and Tc ≈ 360 K for the nanotubes and fibers, respectively. Furthermore, this variation of the Tc values is also reported in literature for other manganite nanostructures. Such variation can be related to the microstructural characteristics observed for both LSM samples produced in this work. In general, it is believed that both methodologies allowed the production of nanostructures LSM. Also, these results suggest that the dimensionality of the samples seems to interfere in the physical properties of LSM manganite.
Control of Volume Fraction of Non-180° Domains by Thermal Strain in Epitaxial Rhombohedral Pb(Zr, Ti)O3 Thick Films
Authors: Ehara Yoshitaka , Utsugi Satoru , Oikawa Takahiro , Yamada Tomoaki , Funakubo Hiroshi 
Published: April 2013

ABSTRACTEpitaxial rhombohedral Pb(Zr0.65Ti0.35)O3films with (100) and (110)/(10-1) and (111)/(11-1) orientations were grown on various kinds of singlecrystal substrates having different thermal expansion coefficient. Volume fractions of (110) and (111) orientations in respective (110)/(10-1) and (111)/(11-1)-oriented films were almost linearly increased with increasing thermal strain, εthermal, applied to the films that wasgenerated under the cooling process after the deposition from the growth temperature to the Curie temperature.Observed saturationpolarization (Psat)was changed linearly with the volume fractions of (110) and (111) orientations, in the same manner asthe volume fractions of (001) and (101) orientations in (001)/(100) and (101)/(110) oriented tetragonal Pb(Zr,Ti)O3 filmsreported previously. These results showed that the volume fraction of the non-180o domains Pb(Zr,Ti)O3films of both tetragonal and rhombohedral symmetriescan be manipulated by εthermal, which brings possibly to control the Psat value.
Carrier Transport Mechanisms in Metal-Insulator–Metal Au/Ba0.8Sr0.2TiO3/ ZrO2/ Ba0.8Sr0.2TiO3/Pt Thin Film Heterostructures
Authors: Sahoo Santosh K. , Bakhru H. , Kumar Sumit , Misra D. , Wolden Colin A. , Mohapatra Y. N. , Agrawal D. C. 
Published: April 2013

ABSTRACTBa0.8Sr0.2TiO3/ZrO2 heterostructured thin films are deposited on Pt/Ti/SiO2/Si substrates by a sol-gel process. The current versus voltage (I-V) measurements of metal-insulator-metal (MIM) devices using the above multilayered thin film as the dielectric have been taken in the temperature range of 310 to 410K. The electrical conduction mechanisms contributing to the leakage current at different field regions have been studied in this work. Various models are used to know the different leakage mechanisms contributing to the conduction current in these devices. It is observed that Poole-Frenkel mechanism is the dominant conduction process in the high field region with a deep trap level energy (φt) of 1.31 eV whereas space charge limited current (SCLC) mechanism and Ohmic conduction process are contributing to the leakage current in the medium and low field regions respectively. The estimated shallow trap level (Et) for SCLC mechanism is 0.26 eV whereas the activation energy (Ea) for the electrons in the Ohmic conduction process is about 0.07 eV. An energy band diagram is given to explain the various leakage mechanisms in different field regions for these heterostructured thin films.
Silver Decorated Carbon Nanospheres as Effective Visible Light Photocatalyst
Authors: Armstrong W. , Sapkota B. , Mishra S. R. 
Published: April 2013

AbstractThe objective of this study was to assess usability of silver nanoparticles loaded on amorphous carbon (Ag-C) hollow nanospheres for the removal of Methylene Blue (MB) molecules from aqueous solutions. Using microwave technique, silver nanoparticles of different weight ratio was deposited onto amorphous carbon templates. The carbon hollow spheres were derived from glucose using hydrothermal technique. Interestingly crystallite size of Ag decreased with the silver loading on carbon nanospheres. Using UV-vis spectroscopy, the kinetics of MB removal from the solution was assessed. The degradation of MB followed pseudo-first-order kinetics. The obtained results showed that Ag-C particles are efficient MB degradation agent with the rate constant as high as 0.19 m-1 under visible light and 0.041 m -1 under UV light. Thus Ag-C particles are good alternative as low-cost scavenger of dye molecules in wastewater treatments.