bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis
Authors: Nagalla Srikanth , Chou Jeff W , Willingham Mark C , Ruiz Jimmy , Vaughn James P , Dubey Purnima , Lash Timothy L , Hamilton-Dutoit Stephen J , Bergh Jonas , Sotiriou Christos , Black Michael A , Miller Lance D 
Published: April 2013

Abstract
Background
Gene expression signatures indicative of tumor proliferative capacity and tumor-immune cell interactions have emerged as principal biology-driven predictors of breast cancer outcomes. How these signatures relate to one another in biological and prognostic contexts remains to be clarified.

Results
To investigate the relationship between proliferation and immune gene signatures, we analyzed an integrated dataset of 1,954 clinically annotated breast tumor expression profiles randomized into training and test sets to allow two-way discovery and validation of gene-survival associations. Hierarchical clustering revealed a large cluster of distant metastasis-free survival-associated genes with known immunological functions that further partitioned into three distinct immune metagenes likely reflecting B cells and/or plasma cells; T cells and natural killer cells; and monocytes and/or dendritic cells. A proliferation metagene allowed stratification of cases into proliferation tertiles. The prognostic strength of these metagenes was largely restricted to tumors within the highest proliferation tertile, though intrinsic subtype-specific differences were observed in the intermediate and low proliferation tertiles. In highly proliferative tumors, high tertile immune metagene expression equated with markedly reduced risk of metastasis whereas tumors with low tertile expression of any one of the three immune metagenes were associated with poor outcome despite higher expression of the other two metagenes.

Conclusions
These findings suggest that a productive interplay among multiple immune cell types at the tumor site promotes long-term anti-metastatic immunity in a proliferation-dependent manner. The emergence of a subset of effective immune responders among highly proliferative tumors has novel prognostic ramifications.
DNA binding specificities of the long zinc-finger recombination protein PRDM9
Authors: Billings Timothy , Parvanov Emil D , Baker Christopher L , Walker Michael , Paigen Kenneth , Petkov Petko M 
Published: April 2013

Abstract
Background
Meiotic recombination ensures proper segregation of homologous chromosomes and creates genetic variation. In many organisms, recombination occurs at limited sites, termed 'hotspots', whose positions in mammals are determined by PR domain member 9 (PRDM9), a long-array zinc-finger and chromatin-modifier protein. Determining the rules governing the DNA binding of PRDM9 is a major issue in understanding how it functions.

Results
Mouse PRDM9 protein variants bind to hotspot DNA sequences in a manner that is specific for both PRDM9 and DNA haplotypes, and that in vitro binding parallels its in vivo biological activity. Examining four hotspots, three activated by Prdm9
Cst
and one activated by Prdm9
Dom2
, we found that all binding sites required the full array of 11 or 12 contiguous fingers, depending on the allele, and that there was little sequence similarity between the binding sites of the three Prdm9
Cst
activated hotspots. The binding specificity of each position in the Hlx1 binding site, activated by Prdm9
Cst
, was tested by mutating each nucleotide to its three alternatives. The 31 positions along the binding site varied considerably in the ability of alternative bases to support binding, which also implicates a role for additional binding to the DNA phosphate backbone.

Conclusions
These results, which provide the first detailed mapping of PRDM9 binding to DNA and, to our knowledge, the most detailed analysis yet of DNA binding by a long zinc-finger array, make clear that the binding specificities of PRDM9, and possibly other long-array zinc-finger proteins, are unusually complex.
Epigenetic changes associated with disease progression in a mouse model of childhood allergic asthma
Authors: Collison Adam , Siegle Jessica S. , Hansbro Nicole G. , Kwok Chau-To , Herbert Cristan , Mattes Joerg , Hitchins Megan , Foster Paul S. , Kumar Rakesh K. 
Published: April 2013

Summary
Development of asthma in childhood is linked to viral infections of the lower respiratory tract in early life, with subsequent chronic exposure to allergens. Progression to persistent asthma is associated with a Th2-biased immunological response and structural remodelling of the airways. The underlying mechanisms are unclear, but could involve epigenetic changes. To investigate this, we employed a recently developed mouse model in which self-limited neonatal infection with a pneumovirus, followed by sensitisation to ovalbumin via the respiratory tract and low-level chronic challenge with aerosolised antigen, leads to development of an asthmatic phenotype. We assessed expression of microRNA by cells in the proximal airways, comparing changes over the period of disease progression, and used target prediction databases to identify genes likely to be up- or downregulated as a consequence of altered regulation of microRNA. In parallel, we assessed DNA methylation in pulmonary CD4+ T cells. We found that a limited number of microRNAs exhibited marked up- or downregulation following early-life infection and sensitisation, for many of which the levels of expression were further changed following chronic challenge with the sensitizing antigen. Targets of these microRNAs included genes involved in immune or inflammatory responses (e.g. Gata3, Kitl) and in tissue remodelling (e.g. Igf1, Tgfbr1), as well as genes for various transcription factors and signalling proteins. In pulmonary CD4+ T cells, there was significant demethylation at promoter sites for interleukin-4 and interferon-γ, the latter increasing following chronic challenge. We conclude that, in this model, progression to an asthmatic phenotype is linked to epigenetic regulation of genes associated with inflammation and structural remodelling, and with T-cell commitment to a Th2 immunological response. Epigenetic changes associated with this pattern of gene activation might play a role in the development of childhood asthma.
Structural and functional analysis of a yeast centromere (cen3)
Authors: Carbon John , Clarke Louise 
Published: April 2013

ABSTRACT
Structure-function analysis of a yeast (Saccharomyces cerevisiae) centromere (CEN3) has been carried out by altering the nucleotide sequence of the DNA within and surrounding the centromere of yeast chromosome III, and observing the behaviour of the resulting altered chromosomes during mitotic and meiotic cell divisions. A centromere substitution vector (pJC3-13) was constructed, which contains in the proper orientation: the DNA sequences that normally flank the chromosome III centromere, a wild-type URA3 gene for selection, and a unique BawzHI restriction site for insertion of various DNA sequences to be assayed for centromere activity. Cleavage of the plasmid DNA with EcoRI generates a linear DNA fragment whose ends are homologous with the regions flanking the centromere. Transformation of the appropriate homozygous ura3 diploid yeast strain with this linear DNA results in URA3+ transformants in which the CEN3 region on one copy of chromosome III has been replaced by the URA3 gene and the DNA sequence previously inserted into the vector. These studies identify a 289 base-pair (bp) DNA fragment from the CEN3 region that retains full centromere function when used to replace the normal CEN3 sequence. Centromeres function equally well in either orientation, and the chromosome XI centromere (CENIT) can be used to replace CEN3, with no observable effect on mitotic or meiotic chromosome segregation. Various DNA restriction fragments occurring within the CEN3 region were used alone or in combinations to replace the normal CEN3 sequence. Yeast centromeres contain a high A+T region about 82-89 bp in length (element II) flanked by a highly conserved 11 bp sequence (III) and a less-conserved 14bp sequence (I). The experiments demonstrate that both regions II and III are necessary for normal centromere function, although centromeres containing III plus truncated or rearranged portions of the high A+T region II retain partial activity. Chromosomes of the latter type often give abnormal segregation patterns through meiosis, including separation and random segregation of sister chromatids during the first meiotic division.
Black Sheep
Authors: Coluzzi Seth J. 
Published: April 2013

Modal theory has been fraught with shortcomings and inconsistencies from the Renaissance to the present, but the Phrygian mode has proven especially problematic, earning a reputation as the unruly black sheep of the modal family. Much of the difficulty stems from the inadequacy of the clausula in mi to serve as an effective terminal cadence, the threat of mi contra fa between scale degrees 5 and 2 (B and F), and the tendency of Phrygian works to prefer the fourth and sixth degrees (A and C) as cadential goals. Although recent studies have attempted to provide nonmodal explanations for the melodic and cadential peculiarities of the Phrygian mode, these efforts have for the most part fallen short of serving as effective, normative theories, leaving instead a gap between music, mode, and model.
The present study examines how the Phrygian mode functions both on the musical surface and on the larger scale in music of the late sixteenth century, showing how a new form of terminal cadence came into widespread practice after 1550 that proved utterly devoid of theoretical grounding. This overview leads to the exposition of a structural model for the Phrygian mode that is both normative within this repertory and accountable to contemporary modal theory. Although analyses of works by Rore, Palestrina, and Wert are used in support of this theoretical model, the main analytical focus is devoted to the madrigals “Tirsi morir volea” (1580) and “Cruda Amarilli, che col nome ancora” (1595) of Luca Marenzio. Based on these examples of Marenzio’s handling of the Phrygian mode, I question the modal designation of one work from Marenzio’s Seventh Book (1595), offering a new explanation for the book’s enigmatic departure from an ordering based on its principal textual source, Guarini’s Il pastor fido.
Incorporation of Luminescent Zinc Oxide Nanoparticles into Polystyrene
Authors: Li Rui , Fern George R. , Withnall Robert , Silver Jack , Bishop Peter , Thiebaut Benedicte 
Published: April 2013

ABSTRACTZinc oxide (ZnO) nanoparticles and nanoparticles of luminescent zinc oxide (ZnO:Zn) phosphor were successfully synthesised and well characterised. A transparent polystyrene composite sheet containing ZnO:Zn nanoparticles was prepared by a solvent casting method. The sheet manifested comparable transmission to a virgin polystyrene film due to very uniform dispersion of the ZnO:Zn nanoparticles into the polystyrene. Evidence for uniform dispersion was evident in both its luminescent properties and in a SEM image. The photoluminescent characteristics of the ZnO:Zn, both as a pure powder and embedded in a polystyrene matrix, are reported. The uniformity of the photoluminescence of the composite sheet under near ultraviolet excitation is demonstrated. The luminescent ZnO:Zn nanoparticles are shown to have applications for use not only as an inhibitor of the ultraviolet degradation of polymers, but also for providing polymers with light emitting functionality.
First-Principles Calculation of the Electronic Properties of Single-Walled Carbon Nanotubes under Torsions
Authors: Mihara K. , Shintani K. 
Published: April 2013

ABSTRACTThe structures and electronic properties of single-walled carbon nanotubes (SWNTs) under torsions are investigated using first-principles calculation based on the density functional theory. A SWNT of the chiral indices (5,0) is equilibrated under a torsion, and its equilibrium energy is obtained. It is revealed there is a structure having the minimum energy at a torsion of a specific angle of twist between 0 deg/Å and 1.88 deg/Å. Next, shear deformations corresponding to torsions imposed on the SWNTs of the chiral indices (5,0) and (5,1) are given to graphene sheets, and their energy band structures are calculated. It is concluded their band gaps decrease with the increase of the specific angle of twist.
Highly-Tunable Polymer/CNTs Nanostructures: A Rapid and Facile Approach for Controlled Architecture and Composition
Authors: Mechrez Guy , Suckeveriene Ran Y. , Narkis Moshe , Segal Ester 
Published: April 2013

ABSTRACTThis research presents a new fabrication method for tailoring polymer/carbon nanotubes (CNTs) nanostructures with controlled architecture and composition. The CNTs are finely dispersed in a polymeric latex i.e. polyacrylate, via ultrasonication, followed by a microfiltration process. The later step allows preserving the homogeneous dispersion structure in the resulting solid nanocomposite. The combination of microfiltration and proper choice of the polymer latex allows for the design of complex nanostructures with tunable properties e.g., porosity, mechanical properties. An important attribute of this methodology is the ability to tailor any desired composition of polymer-CNTs systems, i.e., nanotubes content can practically vary anywhere between 0 to 100 wt%. Thus, for the first time a given polymer/CNTs system is studied over the entire CNTs composition, resembling immiscible binary polymer blends. The polymer in these systems exhibits a structural transition from a continuous matrix (nanocomposite) to segregated domains dispersed within a porous CNTs network. An analogy of this structural transition to phase inversion phenomena in immiscible polymer blends is suggested.
Electronic Transport and Doping Effects in Reduced Graphene Oxide Measured by Scanning Probe Microscopy
Authors: Kehayias Christopher E. , MacNaughton Samuel , Sonkusale Sameer , Staii Cristian 
Published: April 2013

ABSTRACTWe present a Scanning Probe Microscopy study of doping and sensing properties of reduced graphene oxide (rGO)-based nanosensors. rGO devices are created by dielectrophoretic assembly of rGO platelets onto interdigitated electrode arrays, which are lithographically pre-patterned on top of SiO2/Si wafers. The availability of several types of oxygen functional groups allows rGO to interact with a wide range of organic dopants, including methanol, ethanol, acetone, and ammonia. We perform sensitive Scanning Kelvin Probe Microscopy (SKPM) measurements on patterned rGO electronic circuits and show that the local electrical potential and charge distribution are significantly changed when the device is exposed to organic dopants. We also demonstrate that SKPM experiments allow us to quantify the amount of charge transferred to the sensor during chemical doping, and to spatially resolve the active sites of the sensor where the doping process takes place.
Impact of photoinduced processes on the plasmonic enhancement of colloidal quantum dot emission
Authors: Sadeghi S. M. , West R. G. , Patty Kira D. 
Published: April 2013

ABSTRACTWe study the mutual effects of photoinduced processes (irradiation effects) and plasmonic emission enhancement in close-packed CdSe/ZnS colloidal quantum dots in the vicinity of gold metallic nanoparticles with two significantly different size distributions. For this we examine the impact of the heat generated by the metallic nanoparticles, the strength of plasmonic field enhancement, and the rate of energy transfer from the quantum dots to metallic nanoparticles in the presence of a laser field with low and moderate intensities. Our results show that the interplay between the photophysics of the quantum dots and their plasmonic emission enhancement is significantly pronounced when the metallic nanoparticles are large. In such a case we observed large suppression of photoinduced fluorescence enhancement (PFE). For smaller metallic nanoparticles the results suggest mostly an overall time-independent suppression of the quantum dots’ emission with no significant impact on PFE.
Disclination Shape Analysis for Nematic Liquid Crystals under Micron-range Capillary Confinement
Authors: Shams Alireza , Yao Xuxia , Park Jung Ok , Srinivasarao Mohan , Rey Alejandro D. 
Published: April 2013

ABSTRACTNematic liquid crystals (NLCs) under micron-range confinement exhibit a rich defect phenomenology that can be used to extract elastic (Frank moduli) material parameters of critical importance for next generation electro-optical devices. In this work we develop a model to predict defect-driven textural transformations that arise when a NLC is confined to a circular capillary. In the initial transformation stage an unstable disclination defect of strength +1 nucleates in the axis of the capillary and quickly branches into two stable +1/2 disclination defects. The model includes: (1) the Kirchhoff branch balance equation which predicts the splitting of a +1 into two +1/2 wedge disclinations; (2) the curvature of the +1/2 disclination lines as a function of elastic properties. This model shows that by increasing the ratio of tension strength to bending stiffness, the branch point angle increases, but the final defect distance decreases; and (3) the aperture branching angle of the +1/2 lines as a function of the elastic properties and the magnitude of the curvature at the branch point. These three predictions form the basis for the evaluation of the Frank elastic moduli on NLCs. The key advantage of the implemented methodology is to use time-dependent textural transformations under micron-range capillary confinement to extract elastic parametric data needed to further develop NLCs in functional and structural application.
Thermo-responsive metallo-supramolecular gels based on terpyridine end-functionalized amphiphilic diblock copolymers
Authors: Brassinne Jérémy , Fustin Charles-André , Gohy Jean-François 
Published: April 2013

ABSTRACTA thermo-responsive hydrogel was prepared on the basis of terpyridine endfunctionalized polystyrene-block-poly(N-isopropylacrylamide) diblock copolymer. As a first level of assembly, the copolymer was dissolved in a selective solvent to yield micelles bearing terpyridine ligands at the extremity of the coronal chains. The second level of self-assembly was triggered upon addition of metal ions to the micellar solution. Mechanical properties of the accordingly obtained micellar gel were finally characterized by rotational rheometry, below and above the lower critical solution temperature.
Pulsed Electron Beam Deposition of Nanocrystalline Diamond
Authors: Henda Redhouane , Alshekhli Omar 
Published: April 2013

ABSTRACTPulsed electron beam ablation (15 keV, 1 kA, 100 ns) has been used to grow thin films of nanocrystalline diamond on silicon substrates. The films have been grown at room temperature and 150°C, and under argon as the working background gas at a pressure of about 4 mTorr. Visible reflectance spectroscopic analysis has shown films thickness to range between about 55 nm and 115 nm. Visible-Raman spectroscopic measurements have confirmed the presence of sp3 carbon bonds with a substantial fraction in the deposited films, and surrounded by a graphitic phase. The morphological features of the films have been assessed by atomic force microscopy (AFM) and scanning electron microscopy (SEM). The films surface is relatively smooth at room temperature and for low thickness, and becomes rougher at high temperature and for thicker films.
Al-SiC Nanocomposites Produced by Ball Milling and Spark Plasma Sintering
Authors: Picu R.C. , Gracio J.J. , Vincze G.T. , Mathew N. , Schubert T. , Lopez A.B. , Buchheim C. 
Published: April 2013

ABSTRACTIn this work Al-SiC nanocomposites were prepared by high energy ball milling followed by spark plasma sintering of the powder. For this purpose Al micro-powder was mixed with 50 nm diameter SiC nanoparticles. The final composites had grains of approximately 100 nm dimensions, with SiC particles located mostly at grain boundaries. To characterize their mechanical behavior, uniaxial compression, micro- and nano-indentation were performed. Materials with 1vol% SiC as well as nanocrystalline Al produced by the same means with the composite were processed, tested and compared. AA1050 was also considered for reference. It was concluded that the yield stress of the nanocomposite with 1 vol% SiC is 10 times larger than that of regular pure Al (AA1050). Nanocrystalline Al without SiC and processed by the same method has a yield stress 7 times larger than AA1050. Therefore, the largest increase is due to the formation of nanograins, with the SiC particles’ role being primarily that of stabilizing the grains. This was demonstrated by performing annealing experiments at 150°C and 250°C for 2h, in separate experiments.
Study on the photo-transfer thermoluminescence in Eu doped potassium chloride
Authors: Duran-Munoz Hector , Perez-Salas Raul , Piters Thomas 
Published: April 2013

ABSTRACTIn this work a survey of possible optical stimulation processes in irradiated KCl:Eu with a focusing on photo-transfer thermoluminescence (PTTL) effects are shown. For different wavelengths in the range from 180 to 800 nm a cycle of measurements was performed, each comprising of a TL measurement after light irradiation, a TL measurement after beta irradiation for reference purposes and a PTTL measurement. The latter was obtained by applying first a beta irradiation, then a partial readout up to a certain end temperature followed by a monochromatic light irradiation of a specific wavelength and finally a TL measurement. This procedure was repeated for different partial readout end temperatures. From the results the existence of at least four different photo-transfer processes, induced by 310, 245 and 550 nm light are deduced. The photo transfer process induced by an approximate value of 245 nm produced a TL glow peak not seen before in beta or light induced TL. Furthermore it was observed that some of the TL peaks created by light of 240 and 260 nm were strongly sensitized after a beta irradiation and a partial readout.
Single-Mode Superconductivity in LaAlO3/SrTiO3 Nanostructures
Authors: Veazey Joshua P. , Cheng Guanglei , Irvin Patrick , Lu Shicheng , Huang Mengchen , Bi Feng , Bark Chung-Wung , Ryu Sangwoo , Cho Kwang-Hwan , Eom Chang-Beom , Levy Jeremy 
Published: April 2013

ABSTRACTThe properties of superconductors at the extreme limits of dimensionality are of fundamental interest. The interface of LaAlO3 and SrTiO3 hosts a quasi-two-dimensional superconductor below Tc≈200 mK. Here we report superconductivity in nanowire-shaped structures created at the LaAlO3/SrTiO3 interface using conductive atomic force microscope lithography. Nanowire cross-sections are small compared to the superconducting coherence length in LaAlO3/SrTiO3 (w <<ξSC∼100 nm), placing them in the quasi-1D regime. The ability to “write” fully superconducting nanostructures on an insulating LaAlO3/SrTiO3 “canvas” opens possibilities for the development of new families of superconducting nanoelectronics. Four-terminal transport measurements suggest that in some devices both the normal and superconducting states are confined to a single quantum channel.