Effects of three-body interactions on the structure and thermodynamics of liquid krypton

Large-scale molecular dynamics simulations are performed to predict the structural and thermodynamic properties of liquid krypton using a potential energy function based on the two-body potential of Aziz and Slaman plus the triple-dipole Axilrod-Teller (AT) potential. By varying the strength of the AT potential we study the influence of three-body contribution beyond the triple-dipole dispersion. It is seen that the AT potential gives an overall good description of liquid Kr, though other contributions such as higher order three-body dispersion and exchange terms cannot be ignored.Comment: 11 pages, 3 figures, LaTeX, to appear in J. Chem. Phy

Pooled RNAi Screens - Technical and Biological Aspects

RNA interference (RNAi) screens have recently emerged as an exciting new tool for studying gene function in mammalian cells. In order to facilitate those studies, short hairpin RNA (shRNA) expression libraries covering the entire human transcriptome have become commercially available. To make use of the full potential of such large-scale shRNA libraries, microarray-based methods have been developed to analyze complex pooled RNAi screens. In terms of microarray analysis, different strategies have been pursued by different research groups, largely influenced by the employed shRNA library. In this review, we compare the three major shRNA expression libraries with a focus on their suitability for a microarray-based analysis of pooled screens. We analyze and compare approaches previously used to perform pooled RNAi screens and point out their advantages as well as limitations

DNA Methylation of the ABO Promoter Underlies Loss of ABO Allelic Expression in a Significant Proportion of Leukemic Patients

Background: Loss of A, B and H antigens from the red blood cells of patients with myeloid malignancies is a frequent occurrence. Previously, we have reported alterations in ABH antigens on the red blood cells of 55% of patients with myeloid malignancies. Methodology/Principal Findings: To determine the underlying molecular mechanisms of this loss, we assessed ABO allelic expression in 21 patients with ABH antigen loss previously identified by flow cytometric analysis as well as an additional 7 patients detected with ABH antigen changes by serology. When assessing ABO mRNA allelic expression, 6/12 (50%) patients with ABH antigen loss detected by flow cytometry and 5/7 (71%) of the patients with ABH antigen loss detected by serology had a corresponding ABO mRNA allelic loss of expression. We examined the ABO locus for copy number and DNA methylation alterations in 21 patients, 11 with loss of expression of one or both ABO alleles, and 10 patients with no detectable allelic loss of ABO mRNA expression. No loss of heterozygosity (LOH) at the ABO locus was observed in these patients. However in 8/11 (73%) patients with loss of ABO allelic expression, the ABO promoter was methylated compared with 2/10 (20%) of patients with no ABO allelic expression loss (P = 0.03). Conclusions/Significance: We have found that loss of ABH antigens in patients with hematological malignancies is associated with a corresponding loss of ABO allelic expression in a significant proportion of patients. Loss of ABO allelic expression was strongly associated with DNA methylation of the ABO promoter.Tina Bianco-Miotto, Damian J. Hussey, Tanya K. Day, Denise S. O'Keefe and Alexander Dobrovi

The effects of trauma on intimate relationships: A qualitative study with clinical couples

Research has traditionally focused on the development of symptoms in those who experienced trauma directly but has overlooked the impact of trauma on victims' families. In recent years, researchers and clinicians have begun to examine how individual exposure to traumatic events affects the spouses or partners, children, and professional helpers of trauma survivors. The current study examines qualitative interview data from 17 individuals, analyzed using a retroductive methodology to identify how intimate relationships are affected when there is a history of trauma exposure. The following primary themes were identified: increased communication, decreased communication, increased cohesion/connection, decreased cohesion/connection, increased understanding, decreased understanding, sexual intimacy problems, symptoms of relationship distress, support from partner, and relationship resources. Areas for future research and clinical implications are identified

Single-Step Selection of Bivalent Aptamers Validated by Comparison with SELEX Using High-Throughput Sequencing

The identification of nucleic acid aptamers would be advanced if they could be obtained after fewer rounds of selection and amplification. In this paper the identification of bivalent aptamers for thrombin by SELEX and single-step selection are compared using next generation sequencing and motif finding informatics. Results show that similar aptamers are identified by both methods. This is significant because it shows that next generation sequencing and motif finding informatics have the potential to simplify the selection of aptamers by avoiding multiple rounds of enzymatic transcription and amplification

Heat transfer in separated flows on the pressure side of turbine blades

Heat transfer in separated flows on the pressure side of a typical high lift turbine profile is numerically investigated by means of an in-house CFD code. The numerical code was first validated on attached flows in turbine blades. To obtain flow separation cases, the profile is subject to large negative incidences so that a separation bubble is obtained at the pressure side. The numerical results are compared to available experimental data for code validation. It is shown how local minima and maxima values of the heat transfer coefficient are related to the separation and reattachment points, where the velocity component perpendicular to the wall is shown to have a significant effect on the heat transfe

Test of structural models for the (4 4) phase formed by oxygen adsorption on the Pt3Sn(1 1 1) surface

Exposure of the Pt3Sn(1 1 1) surface to oxygen at a pressure in the 10-6 mbar range at 800 K leads to the formation of a chemisorbed phase with a (4 × 4) periodicity. In previous works we investigated the structure of the (4 × 4) phase by means of scanning tunneling microscopy (STM) and XPD. STM images show that the (4 × 4) periodicity results from an array of protrusions and holes. XPD data suggest that oxygen adsorption induces the reconstruction of the substrate with the formation of a Sn-O overlayer. In the present work, several structural models compatible with the STM and XPD results were tested by tensor LEED analysis. The best agreement with the experimental I-V curves was obtained for a model similar to that proposed to interpret the STM images of the Ag(1 1 1)(4 × 4)-O phase. According to this structure, the protrusions observed in STM would correspond to tin atoms occupying on-top positions