Scaffold topologies. 1. Exhaustive enumeration up to eight rings

Mapping the chemical space of small organic molecules is approached from a theoretical graph theory viewpoint, in an effort to begin the systematic exploration of molecular topologies. We present an algorithm for exhaustive generation of scaffold topologies with up to eight rings and an efficient comparison method for graphs within this class. This method uses the return index, a topological invariant derived from the adjacency matrix of the graph. Furthermore, we describe an algorithm that verifies the adequacy of the comparison method. Applications of this method for chemical space exploration in the context of drug discovery are discussed. The key result is a unique characterization of scaffold topologies, which may lead to more efficient ways to query large chemical databases.     

Determination of diethylhexyladipate and acetyltributylcitrate in aqueous extracts after cloud point extraction coupled with microwave assisted back extraction and gas chromatographic separation

The determination of commercial plasticizers (di-(2-ethylhexyl)adipate (DEHA) and acetyl tributyl citrate (ATBC)) in aqueous solutions is described. The newly proposed technique of applying microwaves to cloud point extracts in order to enable combination with gas chromatographic analysis has been used for this purpose. Both plasticizers were entrapped in the micelles of the non-ionic surfactant Triton X-114 and removed from the bulk phase by centrifugation. Micellization was enhanced by increasing the ionic strength of the solution with concentrated NaCl. Extraction recoveries of the proposed method were over 95% for water and 3% (w/v) aqueous acetic acid and over 85% for 10% (v/v) aqueous ethanol, respectively. The calibration curves obtained, following the proposed methodology have a linear range between 50 and 2000 microg/L for each analyte while the detection limits were as low as 15 and 19 microg/L for DEHA and ATBC, respectively, with an RSD below 5% even for low concentrations. As an analytical demonstration the proposed methodology was applied for the determination of the migration levels of the selected plasticizers from a PVC food packaging film into aqueous simulants.     

Ultrafast transport of laser-excited spin-polarized carriers in Au/Fe/MgO(001)

Hot carrier-induced spin dynamics is analyzed in epitaxial Au/Fe/MgO(001) by a time domain approach. We excite a spin current pulse in Fe by 35 fs laser pulses. The transient spin polarization, which is probed at the Au surface by optical second harmonic generation, changes its sign after a few hundred femtoseconds. This is explained by a competition of ballistic and diffusive propagation considering energy-dependent hot carrier relaxation rates. In addition, we observe the decay of the spin polarization within 1 ps, which is associated with the hot carrier spin relaxation time in Au.     

Active stereo sound localization

Estimating the direction of arrival of sound in three-dimensional space is typically performed by generalized time-delay processing on a set of signals from a fixed array of omnidirectional microphones. This requires specialized multichannel A/D hardware, and careful arrangement of the microphones into an array. This work is motivated by the desire to instead only use standard two-channel audio A/D hardware and portable equipment. To estimate direction of arrival of persistent sound, the position of the microphones is made variable by mounting them on one or more computer-controlled pan-and-tilt units. In this paper, we describe the signal processing and control algorithm of a device with two omnidirectional microphones on a fixed baseline and two rotational degrees of freedom. Experimental results with real data are reported with both impulsive and speech sounds in an untreated, normally reverberant indoor environment.     

In Silico Investigation of the Biological Implications of Complex DNA Damage with Emphasis in Cancer Radiotherapy through a Systems Biology Approach

Different types of DNA lesions forming in close vicinity, create clusters of damaged sites termed as “clustered/complex DNA damage” and they are considered to be a major challenge for DNA repair mechanisms resulting in significant repair delays and induction of genomic instability. Upon detection of DNA damage, the corresponding DNA damage response and repair (DDR/R) mechanisms are activated. The inability of cells to process clustered DNA lesions efficiently has a great impact on the normal function and survival of cells. If complex lesions are left unrepaired or misrepaired, they can lead to mutations and if persistent, they may lead to apoptotic cell death. In this in silico study, and through rigorous data mining, we have identified human genes that are activated upon complex DNA damage induction like in the case of ionizing radiation (IR) and beyond the standard DNA repair pathways, and are also involved in cancer pathways, by employing stringent bioinformatics and systems biology methodologies. Given that IR can cause repair resistant lesions within a short DNA segment (a few nm), thereby augmenting the hazardous and toxic effects of radiation, we also investigated the possible implication of the most biologically important of those genes in comorbid non-neoplastic diseases through network integration, as well as their potential for predicting survival in cancer patients.     

Monitoring of Polycyclic Aromatic Hydrocarbon Levels in Mussels (Mytilus galloprovincialis) from Aquaculture Farms in Central Macedonia Region,Greece, Using Gas Chromatography–Tandem Mass Spectrometry Method

A new sensitive and selective gas chromatography tandem mass spectrometry (GC-MS/MS) method was developed for the analysis of 26 polycyclic aromatic hydrocarbons (PAHs), including 16 Environmental Protection Agency (EPA) and 15 + 1 European Union (EU) PAHs, in mussel samples from aquaculture farms in Thermaikos and Strymonian Gulf, Central Macedonia Region, in three sampling periods. Concentrations were found at moderate to low values at all sampling sites, without exceeding maximum levels set by EU. Low molecular weight PAHs were predominant in all samples. Seasonal variation of the concentrations was observed; values were slightly higher in the winter period. Use of diagnostic ratios for potential sources of PAHs showed both petrogenic and pyrolitic origin. In comparison to other related studies of mussels from the Mediterranean Sea, Greek mussels cultivated in the studied gulfs are low in contaminants due to minimal environmental pollution effects. Low concentrations of PAHs are in compliance with the low values of other POPs which were found in the mussels.     

The assessment of user-perceived web quality: Application of a satisfaction benchmarking approach

The assessment of website quality is considered as a problem of measuring user satisfaction, in order to analyse user perceptions and preferences. The presented pilot user satisfaction survey concerns the major cellular phone service providers in Greece. The analysis is based on a multicriteria preference disaggregation approach for satisfaction benchmarking analysis and consists of the following parts: (1) the user satisfaction analysis, which concerns the identification of customer preferences and includes the estimation of the relative importance and the demanding level of the different user satisfaction dimensions, and (2) the satisfaction benchmarking analysis, which is mainly focused on the performance evaluation of the competitive organisations against the satisfaction criteria, as well as the identification of the competitive advantages of each company. The results presented in this paper demonstrate how business organisations may locate their position against competition, pinpoint their weak points and determine which website characteristics will improve their global performance.     

Are Real-Time Displays of Benefit in the Singing Studio? An Exploratory Study

This article reports on an exploratory research project to evaluate the usefulness or otherwise of real-time visual feedback in the singing studio. The primary purpose of the work was not to optimize the technology for this application, but to work alongside teachers and students to study the impact of real-time visual feedback technology use on the students' learning experiences. An action research methodology was used to explore the benefit of real-time displays over an extended period. The experimental phase of the work was guided by a Liaison Panel of teachers and academics in the areas of singing, pedagogy, voice science, speech therapy, and linguistic science. Qualitative data were collected from eight students working with two professional singing teachers. The teachers and students acted as co-researchers under the action research paradigm. Teachers and students alike kept journals of their teaching and learning experiences. Singing lessons were observed regularly by the research team, coded for teacher and student behaviors, and all co-researchers were interviewed at the mid- and endpoint of the project. The use of technology had a positive impact on the learning process, and this is evidenced through case study data.