Probability Models for Degree Distributions of Protein Interaction Networks

The degree distribution of many biological and technological networks has been described as a power-law distribution. While the degree distribution does not capture all aspects of a network, it has often been suggested that its functional form contains important clues as to underlying evolutionary processes that have shaped the network. Generally, the functional form for the degree distribution has been determined in an ad-hoc fashion, with clear power-law like behaviour often only extending over a limited range of connectivities. Here we apply formal model selection techniques to decide which probability distribution best describes the degree distributions of protein interaction networks. Contrary to previous studies this well defined approach suggests that the degree distribution of many molecular networks is often better described by distributions other than the popular power-law distribution. This, in turn, suggests that simple, if elegant, models may not necessarily help in the quantitative understanding of complex biological processes.

Continental-scale patterns of pathogen prevalence: a case study on the corncrake

Pathogen infections can represent a substantial threat to wild populations, especially those already limited in size. To determine how much variation in the pathogens observed among fragmented populations is caused by ecological factors, one needs to examine systems where host genetic diversity is consistent among the populations, thus controlling for any potentially confounding genetic effects. Here, we report geographic variation in haemosporidian infection among European populations of corncrake. This species now occurs in fragmented populations, but there is little genetic structure and equally high levels of genetic diversity among these populations. We observed a longitudinal gradient of prevalence from western to Eastern Europe negatively correlated with national agricultural yield, but positively correlated with corncrake census population sizes when only the most widespread lineage is considered. This likely reveals a possible impact of local agriculture intensity, which reduced host population densities in Western Europe and, potentially, insect vector abundance, thus reducing the transmission of pathogens. We conclude that in the corncrake system, where metapopulation dynamics resulted in variations in local census population sizes, but not in the genetic impoverishment of these populations, anthropogenic activity has led to a reduction in host populations and pathogen prevalence

Validity of Various Approaches to Global Kinetic Modeling of Material Lifetimes

Chemical kinetic modeling has been used for many years in process optimization, estimating real-time material performance, and lifetime prediction. Chemists have tended towards developing detailed mechanistic models, while engineers have tended towards global or lumped models. Many, if not most, applications use global models by necessity, since it is impractical or impossible to develop a rigorous mechanistic model. Model fitting acquired a bad connotation in the thermal analysis community after that community realized a decade after other disciplines that deriving kinetic parameters for an assumed model from a single heating rate produced unreliable and sometimes nonsensical results. In its place, advanced isoconversional methods, which have their roots in the Friedman and Ozawa-Flynn-Wall methods of the 1960s, have become increasingly popular. In fact, as pointed out by the ICTAC kinetics project in 2000, valid kinetic parameters can be derived by both isoconversional and model fitting methods as long as a diverse set of thermal histories are used to derive the kinetic parameters. The current paper extends the understanding from that project to give a better appreciation of the strengths and weaknesses of isoconversional and model-fitting approaches. Examples are given from a variety of data sets

The Impact of Thermal Degradation on Properties of Electrical Machine Winding Insulation Material

Inter-turn stator short circuits can develop quickly leading to serious damage of an electric machine. However, degradation mechanisms of winding insulation material are not yet fully understood. Therefore, the main contribution of this article is analysis of the impact of thermal ageing on the electrical properties of the thin film winding insulation. The insulation samples have been aged thermally at 200–275 °C and for 100–1600 hours. After ageing, impedance spectroscopy measurements were undertaken on the samples and equivalent circuit model (ECM) parameters fitted for each measurement. This allows the impact of thermal ageing on ECM parameters to be analysed, giving insight into the changes of the electrical properties of the insulation. Finally, high voltage was applied to the samples aiming to identify the breakdown voltage characteristics of the insulation material

Intention of preserving forest remnants among landowners in the Atlantic Forest: The role of the ecological context via ecosystem services

Unravelling the psychological processes determining landowners' support towards forest conservation is crucial, particularly in rural areas of the tropics, where most forest remnants are within private lands. As human–nature connections are known to shape pro‐environmental behaviours, the intention of preserving forest remnants should ultimately be determined by the ecological context people live in. Here, we investigate the pathways through which the ecological context (forest cover), via direct contact with forests and ecosystem services and disservices, influence the psychological antecedents of conservation behaviour (beliefs, attitude and intention of preserving forest remnants). We conceptualized a model based on the Reasoned Action Approach, using the ecological context and these three forest experiences as background factors, and tested the model using Piecewise Structural Equation Modelling. Data were collected through an interview‐based protocol applied to 106 landowners across 13 landscapes varying in forest cover in a consolidated rural region in the Brazilian Atlantic Forest. Our results indicate that: (a) ecosystem services are more important than disservices for shaping intention of preserving forests, particularly non‐provisioning services; (b) contact with forest has an indirect effect on intention, by positively influencing the frequency of receiving ecosystem services; (c) people living in more forested ecological contexts have more contact with forests, receive ecosystem services more frequently and, ultimately, have stronger intention of preserving forests. Hence, our study suggests a dangerous positive feedback loop between deforestation, the extinction of forest experiences and impairment of human–nature connections. Local demands across the full range of ecosystem services, the balance between services and disservices and the ecological context people live in should be considered when developing conservation initiatives in tropical rural areas

Coefficient of normal restitution of viscous particles and cooling rate of granular gases

We investigate the cooling rate of a gas of inelastically interacting particles. When we assume velocity dependent coefficients of restitution the material cools down slower than with constant restitution. This behavior might have large influence to clustering and structure formation processes.Comment: 3 figures, Phys. Rev. E (in press

Intense physical activity is associated with cognitive performance in the elderly

Numerous studies have reported positive impacts of physical activity on cognitive function. However, the majority of these studies have utilised physical activity questionnaires or surveys, thus results may have been influenced by reporting biases. Through the objective measurement of routine levels of physical activity via actigraphy, we report a significant association between intensity, but not volume, of physical activity and cognitive functioning. A cohort of 217 participants (aged 60–89 years) wore an actigraphy unit for 7 consecutive days and underwent comprehensive neuropsychological assessment. The cohort was stratified into tertiles based on physical activity intensity. Compared with individuals in the lowest tertile of physical activity intensity, those in the highest tertile scored 9%, 9%, 6% and 21% higher on the digit span, digit symbol, Rey Complex Figure Test (RCFT) copy and Rey Figure Test 30-min recall test, respectively. Statistically, participants in the highest tertile of physical activity intensity performed significantly better on the following cognitive tasks: digit symbol, RCFT copy and verbal fluency test (all P<0.05). The results indicate that intensity rather than quantity of physical activity may be more important in the association between physical activity and cognitive function

Phenotypic and genomic profiling of Staphylococcus argenteus in Canada and the United States and recommendations for clinical result reporting

Staphylococcus argenteus is a newly described species, formerly known as S. aureus clonal complex 75 (CC75). Here, we describe the largest collection of S. argenteus isolates in North America, highlighting identification challenges. We present phenotypic and genomic characteristics and provide recommendations for clinical reporting. Between 2017 and 2019, 22 isolates of S. argenteus were received at 2 large reference laboratories for identification. Identification with routine methods (biochemical, matrix-assisted laser desorption ionization–time of flight mass spectrometry [MALDI-TOF MS], 16S rRNA gene analysis) proved challenging to confidently distinguish these isolates from S. aureus. Whole-genome sequencing analysis was employed to confirm identifications. Using several different sequence-based analyses, all clinical isolates under investigation were confirmed to be S. argenteus with clear differentiation from S. aureus. Seven of 22 isolates were recovered from sterile sites, 11 from nonsterile sites, and 4 from surveillance screens. While sequence types ST1223/coa type XV, ST2198/coa type XIV, and ST2793/coa type XId were identified among the Canadian isolates, the majority of isolates (73%) belonged to multilocus sequence types (MLST) ST2250/coa type XId and exhibited a high degree of homology at the genomic level. Despite this similarity, 5 spa types were identified among ST2250 isolates, demonstrating some diversity between strains. Several isolates carried mecA, as well as other resistance and virulence determinants (e.g., PVL, TSST-1) commonly associated with S. aureus. Based on our findings, the growing body of literature on S. argenteus, the potential severity of infections, and possible confusion associated with reporting, including use of incorrect breakpoints for susceptibility results, we make recommendations for clinical laboratories regarding this organism

Fitting Ranked English and Spanish Letter Frequency Distribution in U.S. and Mexican Presidential Speeches

The limited range in its abscissa of ranked letter frequency distributions causes multiple functions to fit the observed distribution reasonably well. In order to critically compare various functions, we apply the statistical model selections on ten functions, using the texts of U.S. and Mexican presidential speeches in the last 1-2 centuries. Dispite minor switching of ranking order of certain letters during the temporal evolution for both datasets, the letter usage is generally stable. The best fitting function, judged by either least-square-error or by AIC/BIC model selection, is the Cocho/Beta function. We also use a novel method to discover clusters of letters by their observed-over-expected frequency ratios.Comment: 7 figure

Dynamic Behavior in Piezoresponse Force Microscopy

Frequency dependent dynamic behavior in Piezoresponse Force Microscopy (PFM) implemented on a beam-deflection atomic force microscope (AFM) is analyzed using a combination of modeling and experimental measurements. The PFM signal comprises contributions from local electrostatic forces acting on the tip, distributed forces acting on the cantilever, and three components of the electromechanical response vector. These interactions result in the bending and torsion of the cantilever, detected as vertical and lateral PFM signals. The relative magnitudes of these contributions depend on geometric parameters of the system, the stiffness and frictional forces of tip-surface junction, and operation frequencies. The dynamic signal formation mechanism in PFM is analyzed and conditions for optimal PFM imaging are formulated. The experimental approach for probing cantilever dynamics using frequency-bias spectroscopy and deconvolution of electromechanical and electrostatic contrast is implemented.Comment: 65 pages, 15 figures, high quality version available upon reques