Ro-vibrational averaging of the isotropic hyperfine coupling constant for the methyl radical

© 2015 AIP Publishing LLC. We present the first variational calculation of the isotropic hyperfine coupling constant of the carbon-13 atom in the CH3 radical for temperatures T = 0, 96, and 300 K. It is based on a newly calculated high level ab initio potential energy surface and hyperfine coupling constant surface of CH3 in the ground electronic state. The ro-vibrational energy levels, expectation values for the coupling constant, and its temperature dependence were calculated variationally by using the methods implemented in the computer program TROVE. Vibrational energies and vibrational and temperature effects for coupling constant are found to be in very good agreement with the available experimental data. We found, in agreement with previous studies, that the vibrational effects constitute about 44% of the constant's equilibrium value, originating mainly from the large amplitude out-of-plane bending motion and that the temperature effects play a minor role

Nonresonant Raman spectra of the methyl radical ¹²CH₃ simulated in variational calculations

We report first-principles variational simulation of the non-resonant Raman spectrum for the methyl radical (¹²CH₃) in the electronic ground state. Calculations are based on a high level ab initio potential energy and dipole moment surfaces of CH₃ and employ the accurate variational treatment of the ro-vibrational dynamics implemented in the general code TROVE [S. N. Yurchenko, W. Thiel, and P. Jensen, J. Mol. Spectrosc. 245, 126–140 (2007); A. Yachmenev and S. N. Yurchenko, J. Chem. Phys. 143, 014105 (2015)]. TROVE can be applied to arbitrary molecules of moderate size and we extend here its capabilities towards simulations of Raman spectra. The simulations for CH₃ are found to be in a good agreement with the available experimental data

Gene expression relationship between prostate cancer cells of Gleason 3, 4 and normal epithelial cells as revealed by cell type-specific transcriptomes

Background: Prostate cancer cells in primary tumors have been typed CD10(-)/CD13(-)/CD24(hi)/CD26(+)/CD38(lo)/CD44(-)/CD104(-). This CD phenotype suggests a lineage relationship between cancer cells and luminal cells. The Gleason grade of tumors is a descriptive of tumor glandular differentiation. Higher Gleason scores are associated with treatment failure. Methods: CD26(+) cancer cells were isolated from Gleason 3+3 (G3) and Gleason 4+4 (G4) tumors by cell sorting, and their gene expression or transcriptome was determined by Affymetrix DNA array analysis. Dataset analysis was used to determine gene expression similarities and differences between G3 and G4 as well as to prostate cancer cell lines and histologically normal prostate luminal cells. Results: The G3 and G4 transcriptomes were compared to those of prostatic cell types of non-cancer, which included luminal, basal, stromal fibromuscular, and endothelial. A principal components analysis of the various transcriptome datasets indicated a closer relationship between luminal and G3 than luminal and G4. Dataset comparison also showed that the cancer transcriptomes differed substantially from those of prostate cancer cell lines. Conclusions: Genes differentially expressed in cancer are potential biomarkers for cancer detection, and those differentially expressed between G3 and G4 are potential biomarkers for disease stratification given that G4 cancer is associated with poor outcomes. Differentially expressed genes likely contribute to the prostate cancer phenotype and constitute the signatures of these particular cancer cell types.National Institutes of Health (NIH)[CA111244]National Institutes of Health (NIH)[CA98699]National Institutes of Health (NIH)[CA85859]National Institutes of Health (NIH)[DK63630][P50-GMO-76547

ExoMol line lists - XLIV. IR and UV line list for silicon monoxide (SiO)

A new silicon monoxide (28Si16O) line list covering infrared, visible and ultraviolet regions called SiOUVenIR is presented. This line list extends the infrared EBJT ExoMol line list by including vibronic transitions to the A 1Π and E 1Σ+ electronic states. Strong perturbations to the A 1Π band system are accurately modelled through the treatment of 6 dark electronic states: C 1Σ−, D 1Δ, a 3Σ+, b 3Π, e 3Σ− and d 3Δ. Along with the X 1Σ+ ground state, these 9 electronic states were used to build a comprehensive spectroscopic model of SiO using a combination of empirical and ab initio curves, including the potential energy (PE), spin-orbit (SO), electronic angular momentum (EAM) and (transition) dipole moment curves. The ab initio PE and coupling curves, computed at the multireference configuration interaction (MRCI) level of theory, were refined by fitting their analytical representations to 2617 experimentally derived SiO energy levels determined from 97 vibronic bands belonging to the X–X, E–X and A–X electronic systems through the MARVEL procedure. 112 observed forbidden transitions from the C–X, D–X, e–X, and d–X bands were assigned using our predictions, and these could be fed back into the MARVEL procedure. The SiOUVenIR line list was computed using published ab initio transition dipole moments for the E–X and A–X bands; the line list is suitable for temperatures up to 10 000 K and for wavelengths longer than 140 nm. SiOUVenIR is available from www.exomol.com and the CDS database

ExoMol line lists - XLIV. IR and UV line list for silicon monoxide (SiO)

A new silicon monoxide (28Si16O) line list covering infrared, visible and ultraviolet regions called SiOUVenIR is presented. This line list extends the infrared EBJT ExoMol line list by including vibronic transitions to the A 1Π and E 1Σ+ electronic states. Strong perturbations to the A 1Π band system are accurately modelled through the treatment of 6 dark electronic states: C 1Σ−, D 1Δ, a 3Σ+, b 3Π, e 3Σ− and d 3Δ. Along with the X 1Σ+ ground state, these 9 electronic states were used to build a comprehensive spectroscopic model of SiO using a combination of empirical and ab initio curves, including the potential energy (PE), spin-orbit (SO), electronic angular momentum (EAM) and (transition) dipole moment curves. The ab initio PE and coupling curves, computed at the multireference configuration interaction (MRCI) level of theory, were refined by fitting their analytical representations to 2617 experimentally derived SiO energy levels determined from 97 vibronic bands belonging to the X–X, E–X and A–X electronic systems through the MARVEL procedure. 112 observed forbidden transitions from the C–X, D–X, e–X, and d–X bands were assigned using our predictions, and these could be fed back into the MARVEL procedure. The SiOUVenIR line list was computed using published ab initio transition dipole moments for the E–X and A–X bands; the line list is suitable for temperatures up to 10 000 K and for wavelengths longer than 140 nm. SiOUVenIR is available from www.exomol.com and the CDS database

Gene expression down-regulation in CD90+ prostate tumor-associated stromal cells involves potential organ-specific genes

<p>Abstract</p> <p>Background</p> <p>The prostate stroma is a key mediator of epithelial differentiation and development, and potentially plays a role in the initiation and progression of prostate cancer. The tumor-associated stroma is marked by increased expression of CD90/THY1. Isolation and characterization of these stromal cells could provide valuable insight into the biology of the tumor microenvironment.</p> <p>Methods</p> <p>Prostate CD90⁺stromal fibromuscular cells from tumor specimens were isolated by cell-sorting and analyzed by DNA microarray. Dataset analysis was used to compare gene expression between histologically normal and tumor-associated stromal cells. For comparison, stromal cells were also isolated and analyzed from the urinary bladder.</p> <p>Results</p> <p>The tumor-associated stromal cells were found to have decreased expression of genes involved in smooth muscle differentiation, and those detected in prostate but not bladder. Other differential expression between the stromal cell types included that of the CXC-chemokine genes.</p> <p>Conclusion</p> <p>CD90⁺prostate tumor-associated stromal cells differed from their normal counterpart in expression of multiple genes, some of which are potentially involved in organ development.</p

Genomic analysis of the function of the transcription factor gata3 during development of the Mammalian inner ear

We have studied the function of the zinc finger transcription factor gata3 in auditory system development by analysing temporal profiles of gene expression during differentiation of conditionally immortal cell lines derived to model specific auditory cell types and developmental stages. We tested and applied a novel probabilistic method called the gamma Model for Oligonucleotide Signals to analyse hybridization signals from Affymetrix oligonucleotide arrays. Expression levels estimated by this method correlated closely (p<0.0001) across a 10-fold range with those measured by quantitative RT-PCR for a sample of 61 different genes. In an unbiased list of 26 genes whose temporal profiles clustered most closely with that of gata3 in all cell lines, 10 were linked to Insulin-like Growth Factor signalling, including the serine/threonine kinase Akt/PKB. Knock-down of gata3 in vitro was associated with a decrease in expression of genes linked to IGF-signalling, including IGF1, IGF2 and several IGF-binding proteins. It also led to a small decrease in protein levels of the serine-threonine kinase Akt2/PKB beta, a dramatic increase in Akt1/PKB alpha protein and relocation of Akt1/PKB alpha from the nucleus to the cytoplasm. The cyclin-dependent kinase inhibitor p27(kip1), a known target of PKB/Akt, simultaneously decreased. In heterozygous gata3 null mice the expression of gata3 correlated with high levels of activated Akt/PKB. This functional relationship could explain the diverse function of gata3 during development, the hearing loss associated with gata3 heterozygous null mice and the broader symptoms of human patients with Hearing-Deafness-Renal anomaly syndrome

The deuteron: structure and form factors

A brief review of the history of the discovery of the deuteron in provided. The current status of both experiment and theory for the elastic electron scattering is then presented.Comment: 80 pages, 33 figures, submited to Advances in Nuclear Physic

The role of the family in attributing meaning to living with HIV and its stigma in Turkey

Stigma attached to HIV/AIDS remains a global problem, with severe negative consequences for people living with HIV (PLHIV). Family support is fundamental for PLHIV’s psychological and physical well-being. HIV-related stigma is high in Turkey, where HIV/AIDS prevalence is low and the epidemic is not considered a priority. Based on qualitative data generated with HIV-positive women and men, this article explores the process of stigmatization, as experienced and perceived by PLHIV in Turkey, focusing on the institution of the family. Results indicated that enacted stigma from family members is lower than anticipated. While most participants’ narratives showed patterns of support rather than rejection from families, the strong expectations around the cultural value attributed to “the family” are found to be the main facilitators of internalized stigma. The article critically discusses the meaning and implications of family support, addressing the role of patriarchal values attributed to womanhood, manhood, and sexuality in Turkey

Integrability of Green-Schwarz Sigma Models with Boundaries

We construct integrability preserving boundary conditions for Green-Schwarz sigma-models on semi-symmetric spaces. The boundary conditions are expressed as gluing conditions of the flat-connection, using an involutive metric preserving automorphism. We show that the boundary conditions preserve half of the space-time supersymmetry and an infinite set of conserved charges. We find integrable D-brane configurations for AdS_5 x S^5 and AdS_4 x CP^3 backgrounds.Comment: 24 pages. v2 references added. v3 typos fixed, sec. 3 improved, references added, published versio