On the glog-normal distribution and its application to the gene expression problem

In this article, we characterized the glog-normal distribution and present a comprehensive treatment of the properties of this model. Specifically, we present the probability density function as well as a graphical analysis of this density, the cumulative distribution function and the moments for this statistical distribution. Additionally, by using likelihood methods, we estimate the parameters, carry out asymptotic inference and discuss influence diagnostics of this model. Finally, we show the usefulness of the glog-normal distribution for modeling gene expression microarray intensity data by means of a real numerical example.     

Impact of human activity on NO soil fluxes

Changes in land use driven by the increasing demand of food are affecting the fluxes of trace gases to the atmosphere. The more important human activities that affect NO soil fluxes are: deforestation, intensification of agricultural practices, and biomass burning. In this review emphasis is given to identifying the physicochemical and biological processes involved in the changes, and no attempt to quantify their contribution to global or regional NO budgets is made.Conversion of tropical forest to pasture is occurring very rapidly. An increase of the NO emission is observed immediately after deforestation (1–5 years) followed by a significant decrease (below forest levels) in old pastures and secondary successional forests. It seems that deforested tropical areas produce, in the long term, less NO than primary forests. The observed changes are not completely understood, but are most likely driven by the availability of exchangeable nitrogen and the bacteria' population.Soil plowing and fertilization are important factors that affect NO fluxes in agricultural soils. Plowing increases soil porosity and aeration, as well increasing the surface area that is exposed to the atmosphere. These physical changes increase the production of soil nitrate, and the escape efficiency of NO from the soil, enhancing NO fluxes. The emission of NO from fertilized soils depends on many variables: type of fertilizer (i.e. ammonium, nitrate), the structure of the soil microbial community (e.g., populations of nitrifiers and denitrifiers), meteorogical conditions (e.g. soil moisture and temperature), and soil management (e.g. plowing). A combination of these factors should explain the large range reported for the fraction of N-fertilizer that is emitted as NO to the atmosphere. Measurements made in diverse ecosystems show that vegetation burning enhances NO soil emissions. However, it seems that different processes, which are not well understood, occur at the various sites; e.g., in the tropical savannah, enhanced emissions, from dry soils, are observed immediately after burning, whereas in Californian chaparral burned dry soils emit on average less than the unburned plots, and the fluxes only increase after soil wetting. Changes in the physical conditions of the soil surface and N availability are the most likely factors that explain the increased fluxes.     

Tracking the Interplay between Bound Peptide and the Lid Domain of DnaK,Using Molecular Dynamics

Hsp70 chaperones consist of two functional domains: the 44 kDa Nucleotide Binding Domain (NBD), that binds and hydrolyses ATP, and the 26 kDa Substrate Binding Domain (SBD), which binds unfolded proteins and reactivates them, utilizing energy obtained from nucleotide hydrolysis. The structure of the SBD of the bacterial Hsp70, DnaK, consists of two sub-domains: A β-sandwich part containing the hydrophobic cavity to which the hepta-peptide NRLLLTG (NR) is bound, and a segment made of 5 α-helices, called the “lid” that caps the top of the β-sandwich domain. In the present study we used the Escherichia coli Hsp70, DnaK, as a model for Hsp70 proteins, focusing on its SBD domain, examining the changes in the lid conformation. We deliberately decoupled the NBD from the SBD, limiting the study to the structure of the SBD section, with an emphasis on the interaction between the charges of the peptide with the residues located in the lid. Molecular dynamics simulations of the complex revealed significant mobility within the lid structure; as the structure was released from the forces operating during the crystallization process, the two terminal helices established a contact with the positive charge at the tip of the peptide. This contact is manifested only in the presence of electrostatic attraction. The observed internal motions within the lid provide a molecular role for the function of this sub-domain during the reaction cycle of Hsp 70 chaperones.     

Measurement and Characterization of “Resonance Friction” at High Sliding Speeds in a Model Automotive Wet Clutch

The friction forces between various lubricated “friction materials” and sapphire disks were measured using a new “high-speed” rotating disk attachment to the surface forces apparatus (SFA). Two different clutch lubricants and two different friction materials were tested at sliding speeds and normal loads from 5 to 25 m/s, and 0.2 to 1 N (nominal pressures ~1 MPa), respectively. The results show that “resonance friction”—characterized by large amplitude oscillatory (i.e., sinusoidal) vibrations, also known as shudder or chatter—dominates dynamical considerations at high sliding speed, replacing the smooth sliding or low-amplitude stick–slip that is characteristic of low speed/low load sliding. The characteristic (rotational) speeds or frequencies at which resonance friction occurs depend only on the coupled/uncoupled mechanical resonance frequencies of the loading and friction-sensing mechanisms. In contrast, the intensity of and time to enter/exit shudder depends strongly on the lubricating oil and, to a lesser extent, on the friction material. Physical–chemical analyses of the friction materials before and after testing showed that the samples undergo primarily structural rather than chemical changes. Our results provide new fundamental insights into the resonance friction phenomenon and suggest means for its control.     

Flavonoids as stabilizers of fish oil: An alternative to synthetic antioxidants

The antioxidant activities against fish oil oxidation of six commercially available flavonoids and of five flavonoids purified from two Chilean native plants were compared to those ofdl-α-tocopherol and of two synthetic antioxidants, butylated hydroxytoluene and butylated hydroxyanisole. Among the commercial flavonoids, catechin, morin and quercetin showed a higher activity when fish oil oxidation (either spontaneous or Fe²⁺-induced) was assessed from the formation of peroxides or thiobarbituric acid-reactive substances. Among the native flavonoids, the 5,3′,4′-trihydroxy-7-methoxy flavanone (designated as Pt-2) showed the highest antioxidant activity. Mixtures of quercetin or of Pt-2 withdl-α-tocopherol produced better inhibitory effects when compared to that of each substance assayed by itself. Also, when Pt-2 and quercetin were assayed in combination (0.3 g/kg oil and 0.7 g/kg oil, respectively), a synergistic antioxidant effect was observed. Results indicate that several flavonoids could be used as natural antioxidants as a means to replace those synthetic antioxidants, the use of which has been questioned.     

Validation of the rancimat test for the assessment of the relative stability of fish oils

The induction periods for the peroxidation of various fish oils at 55–90°C were studied by the Rancimat test. The natural logarithms of the induction periods varied linearly with respect to temperature, with a mean coefficient of −7.5×10⁻²°C⁻¹, which was significantly different from that reported for vegetable oils. The activation energy for the formation of volatile acids had a mean value of 38.9 kJ/mol and was independent of the fish oil source. Peroxide formation under Rancimat test conditions followed first-order kinetics. The same kinetics were followed under Schaal Oven test conditions (forced-air oven, 60°C). On the basis of the results obtained, the Rancimat test appears to be useful in determining the relative stabilities of fish oils without the change in peroxide decomposition kinetics that may occur at elevated temperatures.     

Comparison of rancimat evaluation modes to assess oxidative stability of fish oils

Two Rancimat evaluation modes, the induction period (IP), and the time needed to achieve a selected difference in conductivity (tΔK) were compared for assessing relative stability of anchovy, sardine, and hake liver oils. Mean coefficients of variation were 2.5 and 2.4% for IP and tΔK values, respectively, for oils oxidized in the range 55–90°C. Natural logarithms of IP and tΔK values varied linearly with temperature (P<0.001). A linear relationship (r=0.999) was established between the IP and tΔK values (P<0.001). Relative oxidative stability of fish oils was determined with the same degree of confidence by either IP or tΔK values.     

Fatty acid composition, extraction, fractionation, and stabilization of bullfrog (Rana catesbeiana) oil

The oil extracted from the fat-storage organ (fat body) of the bullfrog (Rana catesbeiana) was characterized for its fatty acid composition. The main fatty acids were palmitic (18.1%), stearic (4.1%), myristic (2.7%), oleic (31.7%), and linoleic (12.9%) acids. Long-chain polyunsaturated fatty acids were also present in significant amounts, i.e., eicosapentaenoic (1.5%) and docosahexaenoic (4.7%), and were probably derived from the fish meal content of the diet. A partially fractionated oil was extracted from the homogenized and frozen fat body with an oleic acid content of 43.2%. The natural alkaloid boldine, added at 0.5 mg/g oil level, improved the oxidative stability by a factor ranging from 1.7 to 2.4, as assessed by the Oil Stability Index method between 90 and 110°C. The stabilization effect of boldine was higher than that of naringenin, morin, and quercitin and for the synthetic antioxidant butylated hydroxytoluene at the same concentration level.     

High resolution quantitative piezoresponse force microscopy of BiFeO3 nanofibers with dramatically enhanced sensitivity

Piezoresponse force microscopy (PFM) has emerged as the tool of choice for characterizing piezoelectricity and ferroelectricity of low-dimensional nanostructures, yet quantitative analysis of such low-dimensional ferroelectrics is extremely challenging. In this communication, we report a dual frequency resonance tracking technique to probe nanocrystalline BiFeO(3) nanofibers with substantially enhanced piezoresponse sensitivity, while simultaneously determining its piezoelectric coefficient quantitatively and correlating quality factor mappings with dissipative domain switching processes. This technique can be applied to probe the piezoelectricity and ferroelectricity of a wide range of low-dimensional nanostructures or materials with extremely small piezoelectric effects.