Multiple heat pulses during PCR extension enabling amplification of GC-rich sequences and reducing amplification bias

PCR amplification over GC-rich and/or long repetitive sequences is challenging because of thermo-stable structures resulting from incomplete denaturation, reannealing, and self-annealing of target sequences. These structures block the DNA polymerase during the extension step, leading to formation of incomplete extension products and favoring amplification of nonspecific products rather than specific ones. We have introduced multiple heat pulses in the extension step of a PCR cycling protocol to temporarily destabilize such blocking structures, in order to enhance DNA polymerase extension over GC-rich sequences. With this novel type of protocol, we were able to amplify all expansions of CGG repeats in five Fragile X cell lines, as well as extremely GC-rich nonrepetitive segments of the GNAQ and GP1BB genes. The longest Fragile X expansion contained 940 CGG repeats, corresponding to about 2.8 kilo bases of 100% GC content. For the GNAQ and GP1BB genes, different length PCR products in the range of 700 bases to 2 kilobases could be amplified without addition of cosolvents. As this technique improves the balance of amplification efficiencies between GC-rich target sequences of different length, we were able to amplify all of the allelic expansions even in the presence of the unexpanded allele.     

Michromatic scope for enhancement of color difference

A michromatic (microscope plus chromatic) scope is a device that enhances the color discrimination between two spectral color datasets. Three spectral filters are required, instead of the conventional red, green, and blue filters, for the implementation of a michromatic camera. In this study, we describe two approaches to the design of these filters: in the first case, the design is based on the direct optimization of the filter characteristics (transmittance), whereas in the second case, the design is based on the nonnegative tensor factorization (NTF) of the spectral datasets. A michromatic camera can be implemented using these filters along with compatible postprocessing in‐camera firmware. Here, we performed experiments with two color datasets: one comprising skin and vein colors, and one comprising skin and cosmetics colors. These were further divided into a training set and a test set. The filters were defined using the training set, and the operation of the filters was tested and magnified using the test set. Our experiments demonstrated that the proposed approaches are suitable for color discrimination. For the first color dataset, the enhancement produced using the optimized filters was up to 252% of the original value, and the average color difference ΔE was increased from 2.82 to 9.93. NTF and preprocessing further enhanced the ΔE up to 21.84. For the second color dataset, NTF and postprocessing enhanced the ΔE from 4.33 to 29.19. The proposed discrimination enhancement could be physically implemented in a designated digital charge‐coupled device camera with proper filter installation and compatible postprocessing. © 2010 Wiley Periodicals, Inc. Col Res Appl, 2010     

Urgent need for new approach to energy policy: The case of Finland

The process of climate change is already under way and is a serious threat facing the planet. Our response to this threat will irrevocably transform the energy sector and the priorities within it. The trend in emissions over the next decade will largely determine whether the process of climate change can be kept at a moderate level. This literature-based study focuses on Finland as an example case. Oil price fluctuations, economic development and changes in consumer values and attitudes are key forces that will drive change in the energy sector. A greater diversity of energy sources is vital if we are to avoid a catastrophic warming of the climate. The use of renewable energy sources must be increased, and the efficiency of producing, transmitting and distributing energy must be improved. The energy sector must also exploit the potential of nuclear energy, wind, solar and hydro power, afforestation measures, biomass resources, carbon capture and storage (CCS) technology and the nano-bio sector. National policies and measures must be set out in detail and global cooperation enhanced. The presence and impact of factors that impede the work to curb climate change must also be taken into account in energy strategies if these strategies are to be successful.     

Criteria for the matrix equivalence of words

This paper investigates the criteria for deciding whether two words are matrix equivalent. Certain upper diagonal matrices, generally referred to as the Parikh matrices, have been widely investigated because of their usefulness in computing the numbers of subword occurrences and thereby characterizing words by numbers. However, apart from the binary alphabet, not much is known about the properties of the matrix equivalent words, that is, words possessing the same matrix. The paper investigates both the general criteria, as well as the criteria valid in natural special cases. An exhaustive solution is obtained for ternary alphabets.     

Transposition invariant words

We define an operation called transposition on words of fixed length. This operation arises naturally when the letters of a word are considered as entries of a matrix. Words that are invariant with respect to transposition are of special interest. It turns out that transposition invariant words have a simple interpretation by means of elementary group theory. This leads us to investigate some properties of the ring of integers modulo n$n$ and primitive roots. In particular, we show that there are infinitely many prime numbers p$p$ with a primitive root dividing p+1$p+1$ and infinitely many prime numbers p$p$ without a primitive root dividing p+1$p+1$. We also consider the orbit of a word under transposition.     

Calculation of sliding power loss in spur gear contacts

An engineering-level calculation model for sliding power loss in spur gear contacts is presented. Teeth contact through the line of action is modelled as a constantly changing roller contact whose radius, speed, and load can be calculated from the gear geometry under the given operating conditions. The gear mesh cycle is approximated by a large number of elastohydrodynamic contacts. A constant film thickness and a Hertzian pressure distribution are assumed in each contact. The model includes non-Newtonian lubricant behaviour together with temperature and mixed lubrication effects in contact. The numerical solver is reasonably fast in evaluating effectively the sliding power loss dependence on the essential gear and lubricant parameters. The features and behaviour trends of the calculated sliding power losses have a close similarity with published results obtained from measurements and experiment-based power loss models with mineral oil. The limiting shear stress of the lubricant is observed to have an essential role in the power loss behaviour especially at high loads.     

Morphological,mechanical, tribological,and thermal expansion properties of organoclay reinforced polyethylene composites

The morphological, mechanical, thermal, and tribological properties of high‐density polyethylene (HDPE) composites reinforced with organo‐modified nanoclay (3 and 6 wt%) were studied. A commercial maleic anhydride‐based polymeric compatibilizer (PEgMA) was used to improve the adhesion between the polyethylene and clay. Transmission electron microscopy (TEM) characterization of composites revealed that nanoclay exists mainly in a multilayered structure in the HDPE matrix. Mechanical testing of composites showed that Young's modulus and tensile strength increased with nanoclay content. Coefficients of the linear thermal expansion (CLTE) of HDPE–PEgMA–clay composites were slightly lower in the flow direction than those of HDPE–PEgMA. The tribological properties were measured in dry conditions against a steel counterface. The friction coefficient of the matrix was decreased by the addition of clay. Electron microscopic results suggested that the wear mechanism for HDPE and HDPE composites was mainly adhesive. Clay agglomerates were observed on the worn surfaces of the composites, which may partly explain decreased friction. POLYM. ENG. SCI., 2013. © 2012 Society of Plastics Engineers     

Modeling of helical gear contact with tooth deflection

The majority of gear tribological studies are made on spur gears. However, helical gears are generally used in industry, and their contact behavior deserves more attention to establish a realistic base for detailed friction, wear and life studies. This study focuses on the modeling of helical gear contact with tooth deflection. A calculation model for helical gear contact analysis is introduced. Helical gear surface profiles are constructed from gear tool geometry by simulating the hobbing process. The model uses three-dimensional finite elements for the calculation of tooth deflection including tooth bending, shearing and tooth foundation flexibility. The model combines contact analysis with structural analysis to avoid large meshes. Tooth foundation flexibility was found to have an essential role in contact load sharing between the meshing teeth, whereas contact flexibility plays only a minor role. The capability of different local contact calculation methods was also studied.     

A DLL clock generator for a high speed A/D-converter with 1 ps jitter and skew calibrator with 1 ps precision in 0.35 μm CMOS

This paper presents a clock generator circuit for a high-speed analog-to-digital converter (ADC). A time-interleaved ADC requires accurate clocking for the converter fingers. The target ADC has 12 interleaved fingers each running at a speed of 166 MS/s, which corresponds to an equivalent sampling frequency of 2 GS/s. A delay-locked loop (DLL) based clock generator has been proposed to provide multiple clock signals for the converter. The DLL clock generator has been implemented with a 0.35 μm SiGe BiCMOS process (only MOS-transistor were used in DLL) by Austria Micro Systems and it occupies a 0.6 mm² silicon area. The measured jitter of the DLL is around 1 ps and the delay between phases can be adjusted using 1 ps precision.     

Enhanced magnetooptical response in dumbbell-like Ag-CoFe2O4 nanoparticle pairs

We study magnetooptical Faraday rotation in a colloidal solution of "dumbbell-like", physically conjoined nanoparticle pairs composed of a ferromagnetic (CoFe2O4) and a noble metal (Ag). We show that outside the CoFe2O4 interband dominated spectral regime, the coupled dumbbells show significantly enhanced magnetooptic response relative to single CoFe2O4 nanoparticles, derived from plasmonic contribution by the Ag nanoparticles.