Data analysis tool for comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry

Data processing and identification of unknown compounds in comprehensive two-dimensional gas chromatography combined with time-of-flight mass spectrometry (GC×GC/TOFMS) analysis is a major challenge, particularly when large sample sets are analyzed. Herein, we present a method for efficient treatment of large data sets produced by GC×GC/TOFMS implemented as a freely available open source software package, Guineu. To handle large data sets and to efficiently utilize all the features available in the vendor software (baseline correction, mass spectral deconvolution, peak picking, integration, library search, and signal-to-noise filtering), data preprocessed by instrument software are used as a starting point for further processing. Our software affords alignment of the data, normalization, data filtering, and utilization of retention indexes in the verification of identification as well as a novel tool for automated group-type identification of the compounds. Herein, different features of the software are studied in detail and the performance of the system is verified by the analysis of a large set of standard samples as well as of a large set of authentic biological samples, including the control samples. The quantitative features of our GC×GC/TOFMS methodology are also studied to further demonstrate the method performance and the experimental results confirm the reliability of the developed procedure. The methodology has already been successfully used for the analysis of several thousand samples in the field of metabolomics.     

Functional magnetic resonance imaging of swine brain during change in thiopental anesthesia into EEG burst-suppression level--a preliminary study

Deepening anesthesia produces well known changes in electroencephalogram (EEG) and evoked potentials, differing in pathological and normal brain. Yet, it is not known how the T2*-weighted signal changes in the healthy brain during deepening anesthesia. We studied the effect of thiopental bolus on functional magnetic resonance imaging (fMRI) in the healthy brain using porcine model. In five pigs (2–3 months, 20–25 kg), the control bolus prior to fMRI resulted in a change into burst-suppression. After the recovery of continuous EEG, fMRI (4 min) was performed with a single bolus of thiopental (11.4-17.1 mg/kg) administered 1 min after the onset of imaging. This was repeated in four of five pigs. Positive (6-8%) or negative (-3 to -8%) signal intensity changes correlated to the thiopental bolus injection were seen in the group average fMRI response. Positive response was 1.6% and negative response 2.3% of the total brain region of interest (ROI) voxels. Responding voxels were distributed more prominently in the thalamic ROI (4.5%) than in the cortical ROI (2.2%). The group average of unthresholded voxel time courses showed that the net effect of thiopental bolus was a small (0.5%) but a clear positive change in the thalamic region, while variance changed in the global level. In conclusion, this study is the first to show that significant signal intensity changes occur in fMRI response during the sudden deepening of thiopental anesthesia. However, these responses are neither anatomically constant nor global in the healthy swine brain.     

Configurable parallel memory architecture for multimedia computers

This paper presents a novel parallel memory architecture for multimedia computers. Applying a configurable or programmable addressing circuitry capable of parallel memory accesses, the memory management of multimedia applications can be enhanced. Necessary computer architecture changes to virtual address representation, paging, virtual memory, address computation circuitry and data permutation are discussed. These changes allow the memory to be partitioned for different access functions. In addition, the same memory area can be accessed by multiple access patterns. Therefore, a general-purpose computing system that is capable of exploiting the repeating memory access patterns in its applications can be built. Performance of the configurable parallel memory architecture (CPMA) is analyzed in the case of a selection of algorithms from a video encoder. These motion estimation algorithms and zigzag scanning benefit from the multiple memory access functions, which is apparent from the comparisons to the traditional sequential memory accesses.     

Simulation on wavelength-dependent complex refractive index of liquids obtained by phase retrieval from reflectance dip due to surface plasmon resonance

A method for the calculation of the wavelength-dependent complex refractive index of absorbing liquid from reflectance in the vicinity of surface plasmon resonance (SPR) is presented. The calculation is based on the maximum entropy method (MEM). As an example, phase retrieval from a simulated SPR reflectance of a red colored liquid solution is carried out. It is proposed that MEM can be applied to wavelength-dependent complex refractive index assessment from reflectance of absorbing liquids in SPR measurement in wavelength scanning mode.     

Best compromise solution for a new multiobjective scheduling problem

In future wireless networks, a mobile terminal will be able to communicate with a service provider using several network connections. These connections to networks will have different properties and they will be priced separately. In order to minimize the total communication time and the total transmission costs, an automatic method for selecting the network connections is needed. Here, we describe the network connection selection problem and formulate it mathematically. We discuss solving the problem and analyse different multiobjective optimization approaches for it.     

Endotoxins associated with cyanobacteria and their removal during drinking water treatment

The aim of this study was to investigate endotoxin concentrations in cyanobacterial water blooms and strains, and to assess the removal of endotoxins during drinking water treatment. Endotoxin concentrations were measured from 151 hepatotoxic, neurotoxic and non-toxic cyanobacterial water blooms by using Limulus amebocyte lysate (LAL) assay, and the results were compared to bacterial data. Endotoxin activities ranged from 20 to 3.8 x 10(4) endotoxin units (EU) per ml. Endotoxicity of the samples correlated with phycobiliprotein concentration that was used to assess cyanobacterial abundance, heterotrophic plate count, and Aeromonas spp. but it did not correlate with the number of coliforms or streptococci. The high endotoxin concentrations occasionally detected in the water bloom samples were probably due to Gram negative bacteria that existed together with cyanobacteria since the 26 axenic cyanobacterial strains from different genera that were studied showed very low endotoxin activity. No differences in endotoxin activity were detected between hepatotoxic, neurotoxic and non-toxic strains. Removal of endotoxins during drinking water treatment was studied at nine waterworks that previously had been associated with high numbers of cyanobacteria and that used different processes for water purification. Endotoxin concentration in raw waters ranged from 18 to 356 EU ml(-1). The treatment processes reduced 59-97% of the endotoxin activity; in the treated water the concentration ranged from 3 to 15 EU ml(-1). The most significant reduction occurred at the early stages of water treatment, during coagulation, settling and sand filtration. Activated carbon filtration either increased or had no effect on endotoxin concentration. Ozonation and chlorination had little effect on the endotoxin concentrations.     

Machine Learning Identifies Robust Matrisome Markers and Regulatory Mechanisms in Cancer

The expression and regulation of matrisome genes—the ensemble of extracellular matrix, ECM, ECM-associated proteins and regulators as well as cytokines, chemokines and growth factors—is of paramount importance for many biological processes and signals within the tumor microenvironment. The availability of large and diverse multi-omics data enables mapping and understanding of the regulatory circuitry governing the tumor matrisome to an unprecedented level, though such a volume of information requires robust approaches to data analysis and integration. In this study, we show that combining Pan-Cancer expression data from The Cancer Genome Atlas (TCGA) with genomics, epigenomics and microenvironmental features from TCGA and other sources enables the identification of “landmark” matrisome genes and machine learning-based reconstruction of their regulatory networks in 74 clinical and molecular subtypes of human cancers and approx. 6700 patients. These results, enriched for prognostic genes and cross-validated markers at the protein level, unravel the role of genetic and epigenetic programs in governing the tumor matrisome and allow the prioritization of tumor-specific matrisome genes (and their regulators) for the development of novel therapeutic approaches.     

Carcass and meat quality traits of four different pig crosses

The study compared properties of Finnish Landrace × Yorkshire crossbred sows mated with Finnish Landrace (FL), Norwegian Landrace (NL), Norwegian Duroc × Norwegian Landrace (NDL), or Swedish Hampshire (SH) boars. The focus was to study the cross-sectional area of loin, cross-sectional area and number of muscle fibres, loin colour and pH value as well as the ratio of water to protein in the loin.The four studied crosses were quite similar having only small differences in carcass and meat quality. The carcass lean content was the lowest in NDL. The loins of FL and NL were longer than the loins of NDL and of SH. The cross-sectional area of loin was the largest in SH. The loin of FL was lighter in colour and the loin of SH was redder than the loins of the other crosses studied. The protein content was lower and the ratio of water to protein higher in loin of SH than in the other crosses.     

Manoeuvring between regulations to achieve locally accepted results: analysis of school meals in Latvia and Finland

Rather than having a consistent food policy, countries often tend to regulate food from the margins of other policy domains such as agricultural, environmental, welfare or educational policies. Regulatory interventions perceive food as an instrument rather than a domain with its own specific set of policy issues and view food provision as an activity to achieve certain economic, social and environmental objectives. This fragments the food policy into disintegrated points of interventions from various policy areas and leaves unregulated voids that can be exploited either to improve or to reduce the effectiveness of the interventions. This article explores interlinkages between fragmented policies and regulations to offer a conceptual model linking regulated elements of the food system. The research is a multiple case study consisting of three cases: one Finnish and two Latvian. The aim of the study is 1) to expose the variety of perspectives used to set regulations for school meals and 2) to analyse how these regulations are aligned by the actors implementing them. The empirical data is composed of literature, regulatory documents, interviews, scenario workshops and media data. The results indicate that the key perspectives used to set regulatory interventions in both countries are entitlements, health and environment. However, actors implementing regulations have remarkable space for interpretation and manoeuvring.     

Complexation of Ni(II) by Dimethylglyoxime for Rapid Removal and Monitoring of Ni(II) in Water

The complexation of Ni(II) with dimethylglyoxime (DMG) entrapped within a Nafion membrane and a DMG–sol–gel matrix was studied and compared for different solutions. First and pseudo-second order kinetic models, Elovich, intra-particle, and liquid film diffusion models were applied to evaluate sorption kinetics. Complexation of Ni(II) by DMG entrapped in the polymeric materials followed a pseudo-second order kinetic model; moreover, DMG in Nafion also allowed diffusion-controlled uptake. The pseudo-second order rate constant was significantly higher for the free ligand in solution than for Ni(II) accumulation in the surface-attached DMG-Nafion. The DMG–sol–gel removal ability of Ni(II) was tested using actual mine water. The presence of interferences only insignificantly decreased the removal percentage of Ni(II), thus confirming the high selectivity of DMG towards Ni(II). Also, an electrochemical sensor modified with DMG in Nafion was investigated further for direct electrochemical determination of Ni(II) in untreated mine water. Determination errors and interference effects were low. Thus, this approach represents an effective potential solution for selective Ni(II) removal from mine water as well as a rapid and cheap sensor for on-site monitoring of Ni(II) in mine and environmental waters.