Squalene epoxidase, located on chromosome 8q24.1, is upregulated in 8q+ breast cancer and indicates poor clinical outcome in stage I and II disease

Gains of chromosomes 7p and 8q are associated with poor prognosis among oestrogen receptor-positive (ER+) stage I/II breast cancer. To identify transcriptional changes associated with this breast cancer subtype, we applied suppression subtractive hybridisation method to analyse differentially expressed genes among six breast tumours with and without chromosomal 7p and 8q gains. Identified mRNAs were validated by real-time RT–PCR in tissue samples obtained from 186 patients with stage I/II breast cancer. Advanced statistical methods were applied to identify associations of mRNA expression with distant metastasis-free survival (DMFS). mRNA expression of the key enzyme of cholesterol biosynthesis, squalene epoxidase (SQLE, chromosomal location 8q24.1), was associated with ER+ 7p+/8q+ breast cancer. Distant metastasis-free survival in stage I/II breast cancer cases was significantly inversely related to SQLE mRNA in multivariate Cox analysis (P<0.001) in two independent patient cohorts of 160 patients each. The clinically favourable group associated with a low SQLE mRNA expression could be further divided by mRNA expression levels of the oestrogen-regulated zinc transporter LIV-1. The data strongly support that SQLE mRNA expression might indicate high-risk ER+ stage I/II breast cancers. Further studies on tumour tissue from standardised treated patients, for example with tamoxifen, may validate the role of SQLE as a novel diagnostic parameter for ER+ early stage breast cancers

Preventive Antibacterial Therapy in Acute Ischemic Stroke: A Randomized Controlled Trial

BACKGROUND: Pneumonia is a major risk factor of death after acute stroke. In a mouse model, preventive antibacterial therapy with moxifloxacin not only prevents the development of post-stroke infections, it also reduces mortality, and improves neurological outcome significantly. In this study we investigate whether this approach is effective in stroke patients. METHODS: Preventive ANtibacterial THERapy in acute Ischemic Stroke (PANTHERIS) is a randomized, double-blind, placebo-controlled trial in 80 patients with severe, non-lacunar, ischemic stroke (NIHSS>11) in the middle cerebral artery (MCA) territory. Patients received either intravenous moxifloxacin (400 mg daily) or placebo for 5 days starting within 36 hours after stroke onset. Primary endpoint was infection within 11 days. Secondary endpoints included neurological outcome, survival, development of stroke-induced immunodepression, and induction of bacterial resistance. FINDINGS: On intention-to treat analysis (79 patients), the infection rate at day 11 in the moxifloxacin treated group was 15.4% compared to 32.5% in the placebo treated group (p = 0.114). On per protocol analysis (n = 66), moxifloxacin significantly reduced infection rate from 41.9% to 17.1% (p = 0.032). Stroke associated infections were associated with a lower survival rate. In this study, neurological outcome and survival were not significantly influenced by treatment with moxifloxacin. Frequency of fluoroquinolone resistance in both treatment groups did not differ. On logistic regression analysis, treatment arm as well as the interaction between treatment arm and monocytic HLA-DR expression (a marker for immunodepression) at day 1 after stroke onset was independently and highly predictive for post-stroke infections. INTERPRETATION: PANTHERIS suggests that preventive administration of moxifloxacin is superior in reducing infections after severe non-lacunar ischemic stroke compared to placebo. In addition, the results emphasize the pivotal role of immunodepression in developing post-stroke infections. TRIAL REGISTRATION: Controlled-Trials.com ISRCTN74386719

Genome Features of “Dark-Fly”, a Drosophila Line Reared Long-Term in a Dark Environment

Organisms are remarkably adapted to diverse environments by specialized metabolisms, morphology, or behaviors. To address the molecular mechanisms underlying environmental adaptation, we have utilized a Drosophila melanogaster line, termed “Dark-fly”, which has been maintained in constant dark conditions for 57 years (1400 generations). We found that Dark-fly exhibited higher fecundity in dark than in light conditions, indicating that Dark-fly possesses some traits advantageous in darkness. Using next-generation sequencing technology, we determined the whole genome sequence of Dark-fly and identified approximately 220,000 single nucleotide polymorphisms (SNPs) and 4,700 insertions or deletions (InDels) in the Dark-fly genome compared to the genome of the Oregon-R-S strain, a control strain. 1.8% of SNPs were classified as non-synonymous SNPs (nsSNPs: i.e., they alter the amino acid sequence of gene products). Among them, we detected 28 nonsense mutations (i.e., they produce a stop codon in the protein sequence) in the Dark-fly genome. These included genes encoding an olfactory receptor and a light receptor. We also searched runs of homozygosity (ROH) regions as putative regions selected during the population history, and found 21 ROH regions in the Dark-fly genome. We identified 241 genes carrying nsSNPs or InDels in the ROH regions. These include a cluster of alpha-esterase genes that are involved in detoxification processes. Furthermore, analysis of structural variants in the Dark-fly genome showed the deletion of a gene related to fatty acid metabolism. Our results revealed unique features of the Dark-fly genome and provided a list of potential candidate genes involved in environmental adaptation

Investigating the effect of artists’ paint formulation on degradation rates of TiO2-based oil paints

This study reports on the effect of artists’ paint formulation on degradation rates of TiO2-based oil paints. Titanium white oil paint exists in a multitude of different recipes, and the effect of the formulation on photocatalytic binder degradation kinetics is unknown. These formulations contain, among others, one or both titanium dioxide polymorphs, zinc oxide, the extenders barium sulfate or calcium carbonate and various additives. Most research performed on the photocatalytic degradation process focusses on pure titanium white-binder mixtures and thus does not take into account the complete paint system. Since photocatalytic oil degradation is a process initiated by the absorption of UV light, any ingredient or combination of ingredients influencing the light scattering and absorption properties of the paint films may affect the degradation rate. In this study three sets of experiments are conducted, designed using the design of experiments (DoE) approach, to screen for the most important formulation factors influencing the degradation rate. The benefits of using DoE, compared to a more traditional ‘one factor at a time approach’ are robustness, sample efficiency, the ability of evaluate mixtures of multiple components as well as the ability to evaluate factor interactions. The three sets of experiments investigate (1) the influence of the TiO2 type, (2) the impact of different mixtures of two types of TiO2, ZnO and the additive aluminum stearate and (3) the influence of common extenders in combination with photocatalytic TiO2, on the photocatalytic degradation of the oil binder. The impact of the formulation on the degradation rate became apparent, indicating the shortcoming of oversimplified studies. The protective effect of photostable TiO2 pigments, even in a mixture with photocatalytic TiO2 pigments, as well as the negative effect of extenders was demonstrated. Furthermore, the ambiguous role of ZnO (photocatalytic or not) and aluminum stearate is highlighted. Neither can be ignored in a study of degradation behavior of modern oil paints and require further investigation

How reproducible are surface areas calculated from the BET equation?

Porosity and surface area analysis play a prominent role in modern materials science. At the heart of this sits the Brunauer-Emmett-Teller (BET) theory, which has been a remarkably successful contribution to the field of materials science. The BET method was developed in the 1930s for open surfaces but is now the most widely used metric for the estimation of surface areas of micro- and mesoporous materials. Despite its widespread use, the calculation of BET surface areas causes a spread in reported areas, resulting in reproducibility problems in both academia and industry. To prove this, for this analysis, 18 already-measured raw adsorption isotherms were provided to sixty-one labs, who were asked to calculate the corresponding BET areas. This round-robin exercise resulted in a wide range of values. Here, the reproducibility of BET area determination from identical isotherms is demonstrated to be a largely ignored issue, raising critical concerns over the reliability of reported BET areas. To solve this major issue, a new computational approach to accurately and systematically determine the BET area of nanoporous materials is developed. The software, called "BET surface identification" (BETSI), expands on the well-known Rouquerol criteria and makes an unambiguous BET area assignment possible

Spatially resolving valley quantum interference of a donor in silicon

Electron and nuclear spins of donor ensembles in isotopically pure silicon experience a vacuum-like environment, giving them extraordinary coherence. However, in contrast to a real vacuum, electrons in silicon occupy quantum superpositions of valleys in momentum space. Addressable single-qubit and two-qubit operations in silicon require that qubits are placed near interfaces, modifying the valley degrees of freedom associated with these quantum superpositions and strongly influencing qubit relaxation and exchange processes. Yet to date, spectroscopic measurements have only probed wavefunctions indirectly, preventing direct experimental access to valley population, donor position and environment. Here we directly probe the probability density of single quantum states of individual subsurface donors, in real space and reciprocal space, using scanning tunnelling spectroscopy. We directly observe quantum mechanical valley interference patterns associated with linear superpositions of valleys in the donor ground state. The valley population is found to be within 5% of a bulk donor when 2.85 ± 0.45 nm from the interface, indicating that valley-perturbation-induced enhancement of spin relaxation will be negligible for depths greater than 3 nm. The observed valley interference will render two-qubit exchange gates sensitive to atomic-scale variations in positions of subsurface donors. Moreover, these results will also be of interest for emerging schemes proposing to encode information directly in valley polarization. © 2014 Macmillan Publishers Limited