Global gene expression profile in myelodysplastic syndromes using SAGE

The molecular pathogenesis of myelodysplastic syndromes (MDS) is poorly understood. In order to expand our knowledge of genetic defects in MDS, we determined the overall profile of genes expressed in bone marrow from patients with refractory anemia with excess blasts ( RAEB) by serial analysis of gene expression ( SAGE). The present report describes a partial transcriptome of RAEB bone marrow derived from 56,694 sequenced tags that provides information about expressed gene products. This is the first attempt to determine an overall profile of gene expression specifically in RAEB at diagnosis using SAGE, which should be useful in the understanding of the physiopathology of MDS and in identifying the genes involved.

Differential expression of E-cadherin gene in human neuroepithelial tumors

Cadherins are cell-to-cell adhesion molecules that play an important role in the establishment of adherent-type junctions by mediating calcium-dependent cellular interactions. The CDH1 gene encodes the transmembrane glycoprotein E-cadherin which is important in maintaining homophilic cell-cell adhesion in epithelial tissues. E-cadherin interacts with catenin proteins to maintain tissue architecture. Structural defects or loss of expression of E-cadherin have been reported as a common feature in several human cancer types. This study aimed to evaluate the expression of E-cadherin and their correlation with clinical features in microdissected brain tumor samples from 81 patients, divided into 62 astrocytic tumors grades I to IV and 19 medulloblastomas, and from 5 white matter non-neoplasic brain tissue samples. E-cadherin (CDH1) gene expression was analyzed by quantitative real-time polymerase chain reaction. Mann-Whitney, Kruskal-Wallis, Kaplan-Meir, and log-rank tests were performed for statistical analyses. We observed a decrease in expression among pathological grades of neuroepithelial tumors. Non-neoplasic brain tissue showed a higher expression level of CDH1 gene than did neuroepithelial tumors. Expression of E-cadherin gene was higher in astrocytic than embryonal tumors (P = 0.0168). Low-grade malignancy astrocytomas (grades I-II) showed higher CDH1 expression than did high-grade malignancy astrocytomas (grades III-IV) and medulloblastomas (P < 0.0001). Non-neoplasic brain tissue showed a higher expression level of CDH1 gene than grade I malignancy astrocytomas, considered as benign tumors (P = 0.0473). These results suggest that a decrease in E-cadherin gene expression level in high-grade neuroepithelial tumors may be a hallmark of malignancy in dedifferentiated tumors and that it may be possibly correlated with their progression and dissemination.

New Source of Muscle-Derived Stem Cells with Potential for Alveolar Bone Reconstruction in Cleft Lip and/or Palate Patients

Cleft lip and palate (CLP), one of the most frequent congenital malformations, affects the alveolar bone in the great majority of the cases, and the reconstruction of this defect still represents a challenge in the rehabilitation of these patients. One of the current most promising strategy to achieve this goal is the use of bone marrow stem cells (BMSC); however, isolation of BMSC or iliac bone, which is still the mostly used graft in the surgical repair of these patients, confers site morbidity to the donor. Therefore, in order to identify a new alternative source of stem cells with osteogenic potential without conferring morbidity to the donor, we have used orbicular oris muscle (OOM) fragments, which are regularly discarded during surgery repair (cheiloplasty) of CLP patients. We obtained cells from OOM fragments of four unrelated CLP patients (CLPMDSC) using previously described preplating technique. These cells, through flow cytometry analysis, were mainly positively marked for five mesenchymal stem cell antigens (CD29, CD90, CD105, SH3, and SH4), while negative for hematopoietic cell markers, CD14, CD34, CD45, and CD117, and for endothelial cell marker, CD31. After induction under appropriate cell culture conditions, these cells were capable to undergo chondrogenic, adipogenic, osteogenic, and skeletal muscle cell differentiation, as evidenced by immunohistochemistry. We also demonstrated that these cells together with a collagen membrane lead to bone tissue reconstruction in a critical-size cranial defects previously induced in non-immunocompromised rats. The presence of human DNA in the new bone was confirmed by PCR with human-specific primers and immunohistochemistry with human nuclei antibodies. In conclusion, we showed that cells from OOM have phenotypic and behavior characteristics similar to other adult stem cells, both in vitro and in vivo. Our findings suggest that these cells represent a promising source of stem cells for alveolar bone grafting treatment, particularly in young CLP patients.

Application of Low-Level Laser Irradiation (LLLI) and rhBMP-2 in Critical Bone Defect of Ovariectomized Rats: Histomorphometric Evaluation

Objectives: The aim of this study was to evaluate the osteogenic potential of recombinant human bone morphogenetic protein-2 (rhBMP-2) and low-level laser irradiation (LLLI), isolated or combined in critical bone defects (5mm) in parietal bone using ovariectomized female rats as an experimental animal model. Materials and Methods: Forty-nine female Wistar rats, bilaterally ovariectomized (OVX), were divided into seven treatment groups of seven animals each: (I) laser in a single application, (II) 7 mu g of pure rhBMP-2, (III) laser and 7 mu g of pure rhBMP-2, (IV) 7 mu g of rhBMP-2/monoolein gel, (V) laser and 7 mu g of rhBMP-2/monoolein gel, (VI) laser and pure monoolein gel, and (VII) critical bone defect controls. The low-level laser source used was a gallium aluminum arsenide semiconductor diode laser device (lambda = 780 nm, D = 120 J/cm(2)). Results: Groups II and III presented higher levels of newly formed bone than all other groups with levels of 40.57% and 40.39%, respectively (p < 0.05). The levels of newly formed bone of groups I, IV, V, and VI were similar with levels of 29.67%, 25.75%, 27.75%, and 30.64%, respectively (p > 0.05). The area of new bone formation in group VII was 20.96%, which is significantly lower than groups I, II, III, and VI. Conclusions: It was concluded that pure rhBMP-2 and a single dose of laser application stimulated new bone formation, but the new bone formation area was significantly increased when only rhBMP-2 was used. Additionally, the laser application in combination with other treatments did not influence the bone formation area.

A SEARCH FOR UNRECOGNIZED CARBON-ENHANCED METAL-POOR STARS IN THE GALAXY

We have developed a new procedure to search for carbon-enhanced metal-poor (CEMP) stars from the Hamburg/ESO (HES) prism-survey plates. This method employs an extended line index for the CH G band, which we demonstrate to have superior performance when compared to the narrower G-band index formerly employed to estimate G-band strengths for these spectra. Although CEMP stars have been found previously among candidate metal-poor stars selected from the HES, the selection on metallicity undersamples the population of intermediate-metallicity CEMP stars (-2.5 <= [Fe/H] <= -1.0); such stars are of importance for constraining the onset of the s-process in metal-deficient asymptotic giant branch stars (thought to be associated with the origin of carbon for roughly 80% of CEMP stars). The new candidates also include substantial numbers of warmer carbon-enhanced stars, which were missed in previous HES searches for carbon stars due to selection criteria that emphasized cooler stars. A first subsample, biased toward brighter stars (B < 15.5), has been extracted from the scanned HES plates. After visual inspection (to eliminate spectra compromised by plate defects, overlapping spectra, etc., and to carry out rough spectral classifications), a list of 669 previously unidentified candidate CEMP stars was compiled. Follow-up spectroscopy for a pilot sample of 132 candidates was obtained with the Goodman spectrograph on the SOAR 4.1 m telescope. Our results show that most of the observed stars lie in the targeted metallicity range, and possess prominent carbon absorption features at 4300 angstrom. The success rate for the identification of new CEMP stars is 43% (13 out of 30) for [Fe/H] < -2.0. For stars with [Fe/H] < -2.5, the ratio increases to 80% (four out of five objects), including one star with [Fe/H] < -3.0.

Bilayer graphene dual-gate nanodevice: An ab initio simulation

We study the electronic transport properties of a dual-gated bilayer graphene nanodevice via first-principles calculations. We investigate the electric current as a function of gate length and temperature. Under the action of an external electrical field we show that even for gate lengths up 100 angstrom, a nonzero current is exhibited. The results can be explained by the presence of a tunneling regime due the remanescent states in the gap. We also discuss the conditions to reach the charge neutrality point in a system free of defects and extrinsic carrier doping.

Formation of atomic carbon chains from graphene nanoribbons

The formation of one-dimensional carbon chains from graphene nanoribbons is investigated using ab initio molecular dynamics. We show under what conditions it is possible to obtain a linear atomic chain via pulling of the graphene nanoribbons. The presence of dimers composed of two-coordinated carbon atoms at the edge of the ribbons is necessary for the formation of the linear chains, otherwise there is simply the full rupture of the structure. The presence of Stone-Wales defects close to these dimers may lead to the formation of longer chains. The local atomic configuration of the suspended atoms indicates the formation of single and triple bonds, which is a characteristic of polyynes.

Spin filtering and disorder-induced magnetoresistance in carbon nanotubes: Ab initio calculations

Nitrogen-doped carbon nanotubes can provide reactive sites on the porphyrin-like defects. It is well known that many porphyrins have transition-metal atoms, and we have explored transition-metal atoms bonded to those porphyrin-like defects inN-doped carbon nanotubes. The electronic structure and transport are analyzed by means of a combination of density functional theory and recursive Green's function methods. The results determined the heme B-like defect (an iron atom bonded to four nitrogens) is the most stable and has a higher polarization current for a single defect. With randomly positioned heme B defects in nanotubes a few hundred nanometers long, the polarization reaches near 100%, meaning they are effective spin filters. A disorder-induced magnetoresistance effect is also observed in those long nanotubes, and values as high as 20 000% are calculated with nonmagnectic eletrodes.

Electronic, structural, and transport properties of Ni-doped graphene nanoribbons

We have investigated the electronic and transport properties of zigzag Ni-adsorbed graphene nanoribbons (Ni/GNRs) using ab initio calculations. We find that the Ni adatoms lying along the edge of zigzag GNRs represent the energetically most stable configuration, with an energy difference of approximately 0.3 eV when compared to the adsorption in the middle of the ribbon. The carbon atoms at the ribbon edges still present nonzero magnetic moments as in the pristine GNR even though there is a quenching by a factor of almost five in the value of the local magnetic moments at the C atoms bonded to the Ni. This quenching decays relatively fast and at approximately 9 A from the Ni adsorption site the magnetic moments have already values close to the pristine ribbon. At the opposite edge and at the central carbon atoms the changes in the magnetic moments are negligible. The energetic preference for the antiparallel alignment between the magnetization at the opposite edges of the ribbon is still maintained upon Ni adsorption. We find many Ni d-related states within an energy window of 1 eV above and below the Fermi energy, which gives rise to a spin-dependent charge transport. These results suggest the possibility of manufacturing spin devices based on GNRs doped with Ni atoms.

Defect-induced effects on carrier migration through one-dimensional poly(para-phenylenevinylene) chains

Defects in one-dimensional (1D) systems can be intrinsically distinct from its three-dimensional counterparts, and polymer films are good candidates for showing both extremes that are difficult to individuate in the experimental data. We study theoretically the impact of simple hydrogen and oxygen defects on the electron transport properties of one-dimensional poly(para-phenylenevinylene) chains through a multiscale technique, starting from classical structural simulations for crystalline films to extensive ab initio calculations within density functional theory for the defects in single crystalline-constrained chains. The most disruptive effect on carrier transport comes from conjugation breaking imposed by the overcoordination of a carbon atom in the vinyl group independently from the chemical nature of the defect. The particular case of the [C=O] (keto-defect) shows in addition unexpected electron-hole separation, suggesting that the experimentally detected photoluminescence bleaching and photoconductivity enhancement could be due to exciton dissociation caused by the 1D characteristics of the defect.

Designing real nanotube-based gas sensors

Using a combination of density functional theory and recursive Green's functions techniques, we present a full description of a large scale sensor, accounting for disorder and different coverages. Here, we use this method to demonstrate the functionality of nitrogen-rich carbon nanotubes as ammonia sensors as an example. We show how the molecules one wishes to detect bind to the most relevant defects on the nanotube, describe how these interactions lead to changes in the electronic transport properties of each isolated defect, and demonstrate that there are significative resistance changes even in the presence of disorder, elucidating how a realistic nanosensor works.

Transport properties of single vacancies in nanotubes

We present density of states and electronic transport calculations of single vacancies in carbon nanotubes. We confirm that the defect reconstructs into a pentagon and a nonagon, following the removal of a single carbon atom. This leads to the formation of a dangling bond. Finally, we demonstrate that care must be taken when calculating the density of states of impurities in one-dimensional systems in general. Traditional treatments of these systems using periodic boundary conditions leads to the formation of minigaps even in the limit of large unit cells.

Structural and optical properties of rare earth-doped (Ba(0.77)Ca(0.23))(1-x)(Sm, Nd, Pr, Yb)(x)TiO(3)

The structural, dielectric, and vibrational properties of pure and rare earth (RE)-doped Ba(0.77) Ca(0.23)TiO(3) (BCT23; RE = Nd, Sm, Pr, Yb) ceramics obtained via solid-state reaction were investigated. The pure and RE-doped BCT23 ceramics sintered at 1450 degrees C in air for 4 h showed a dense microstructure in all ceramics. The use of RE ions as dopants introduced lattice-parameter changes that manifested in the reduction of the volume of the unit cell. RE-doped BCT23 samples exhibit a more homogenous microstructure due to the absence of a Ti-rich phase in the grain boundaries as demonstrated by scanning electron microscopy imaging. The incorporation of REs led to perturbations of the local symmetry of TiO(6) octahedra and the creation of a new Raman mode. The results of Raman scattering measurements indicated that the Curie temperature of the ferroelectric phase transition depends on the RE ion and ion content, with the Curie temperature shifting toward lower values as the RE content increases, with the exception of Yb(3+) doping, which did not affect the ferroelectric phase transition temperature. The phase transition behavior is explained using the standard soft mode model. Electronic paramagnetic resonance measurements showed the existence of Ti vacancies in the structure of RE-doped BCT23. Defects are created via charge compensation mechanisms due to the incorporation of elements with a different valence state relative to the ions of the pure BCT23 host. It is concluded that the Ti vacancies are responsible for the activation of the Raman mode at 840 cm(-1), which is in agreement with lattice dynamics calculations. (c) 2011 American Institute of Physics. [doi:10.1063/1.3594710]

Substrate/semiconductor interface effects on the emission efficiency of luminescent polymers

The importance of interface effects for organic devices has long been recognized, but getting detailed knowledge of the extent of such effects remains a major challenge because of the difficulty in distinguishing from bulk effects. This paper addresses the interface effects on the emission efficiency of poly(p-phenylene vinylene) (PPV), by producing layer-by-layer (LBL) films of PPV alternated with dodecylbenzenesulfonate. Films with thickness varying from similar to 15 to 225 nm had the structural defects controlled empirically by converting the films at two temperatures, 110 and 230 degrees C, while the optical properties were characterized by using optical absorption, photoluminescence (PL), and photoluminescence excitation spectra. Blueshifts in the absorption and PL spectra for LBL films with less than 25 bilayers (<40-50 nm) pointed to a larger number of PPV segments with low conjugation degree, regardless of the conversion temperature. For these thin films, the mean free-path for diffusion of photoexcited carriers decreased, and energy transfer may have been hampered owing to the low mobility of the excited carriers. The emission efficiency was then found to depend on the concentration of structural defects, i.e., on the conversion temperature. For thick films with more than 25 bilayers, on the other hand, the PL signal did not depend on the PPV conversion temperature. We also checked that the interface effects were not caused by waveguiding properties of the excited light. Overall, the electronic states at the interface were more localized, and this applied to film thickness of up to 40-50 nm. Because this is a typical film thickness in devices, the implication from the findings here is that interface phenomena should be a primary concern for the design of any organic device. (C) 2011 American Institute of Physics. [doi:10.1063/1.3622143]

Microstructuration induced differences in the thermo-optical and luminescence properties of Nd:YAG fine grain ceramics and crystals

The temperature and compositional dependences of thermo- optical properties of neodymium doped yttrium aluminum garnet (YAG) crystals and fine grain ceramics have been systematically investigated by means of time- resolved thermal lens spectrometry. We have found that Nd:YAG ceramics show a reduced thermal diffusivity compared to Nd:YAG single crystals in the complete temperature range investigated (80-300 K). The analysis of the time- resolved luminescent properties of Nd(3+) has revealed that the reduction in the phonon mean free path taking place in Nd:YAG ceramics cannot be associated with an increment in the density of lattice defects, indicating that phonon scattering at grain boundaries is the origin of the observed reduction in the thermal diffusivity of Nd: YAG ceramics. Finally, our results showed the ability of the time- resolved thermal lens to determine and optimize the thermo- optical properties of Nd: YAG ceramic based lasers. (C) 2008 American Institute of Physics. [DOI: 10.1063/1.2975335]