Automatic data recording of circadian rhythms

This paper illustrates a method for automatic data recording using the printer port of personal computer and software designed ad hoc. The system was tested by measuring circadian rhythms of activity in the subterranean rodent Ctenomys talarum. Data is recorded in a text-only comma-delimited file, and displayed on screen.     

Spotlight surveys for white-tailed deer: Monitoring panacea or exercise in futility?

Many monitoring programs for white-tailed deer (Odocoileus virginianus) on both private and public lands across the United States have long relied on the use of road-based spotlight surveys for monitoring population size and trends. Research has suggested spotlight surveys are ineffective and that road-based surveys for deer are biased because of highly variable detection rates. To evaluate variability in detection rates relative to the assumption that repeated surveys along roads will provide reliable trend data for use in calculating deer density estimates, we collected 5 years of thermal-imager and spotlight survey data using a multiple-observer, closed-capture approach. Using a Huggin's closed capture model, data bootstrapping, and variance components analyses, our results suggest that density estimates for white-tailed deer generated from data collected during road-based spotlight surveys are likely not reflective of the standing deer population. Detection probabilities during individual spotlight surveys ranged from 0.00 to 0.80 (median = 0.45) across all surveys, and differed by observer, survey, management unit, and survey transect replicate. Mean spotlight detection probability (0.41) and process standard deviation (0.12) estimates indicated considerable variability across surveys, observers, transects, and years, which precludes the generation of a correction factor or use of spotlight data to evaluate long-term trends at any scale. Although recommended by many state, federal, and non-governmental agencies, our results suggest that the benefit of spotlight survey data for monitoring deer populations is limited and likely represents a waste of resources with no appreciable management information gained. © 2012 The Wildlife Society.     

Zero‐modified Poisson model: Bayesian approach,influence diagnostics,and an application to a Brazilian leptospirosis notification data

In this paper, a Bayesian method for inference is developed for the zero‐modified Poisson (ZMP) regression model. This model is very flexible for analyzing count data without requiring any information about inflation or deflation of zeros in the sample. A general class of prior densities based on an information matrix is considered for the model parameters. A sensitivity study to detect influential cases that can change the results is performed based on the Kullback–Leibler divergence. Simulation studies are presented in order to illustrate the performance of the developed methodology. Two real datasets on leptospirosis notification in Bahia State (Brazil) are analyzed using the proposed methodology for the ZMP model.     

Data acquisition in thermal physiology: Measurements of shivering

1. 1.|Simple electronics for measurement of shivering, which include direct and mean rectified EMG (U_mrv), are suggested.

2. 2.|A software system (LabGraph) for measurement and analysis is described.

3. 3.|Three different electrode designs were tested with the system by recording electromyography (EMG) from m. iliotibialis with subdermal, intramuscular and safety pin electrodes in bantam hens exposed to cold eggs. The signal characteristics of EMG are discussed in relation to electrode design and signal processing.

4. 4.|A method for normalizing EMG activity within an experiment to units of heat production is presented and was tested successfully in bantam hens.

Optimisation of data locality in energy calculations for large-scale molecular dynamics simulations

The main bottleneck of molecular dynamic simulations is the estimation of nonbonded pairwise interaction, which often employs neighbour search algorithms to find out interacting atom pairs. These methods have some drawbacks in fulfilling data locality principle, which is unable to take full advantage of modern computer architecture. In this article, we developed a new method by introducing a temporary list to reduce the sparsity in data access. This list permits to obtain a compact and sequential data structure which benefits to efficiently fulfil the data locality principle. We tested and compared the performance of the new method with that of the extensively used reordering method. The new method based on linked cell list is shown to increase 13% of computation speed and have better parallelism in comparison with reordering method. The increase in parallel efficiency makes the new method a promising option for large-scale molecular simulations.     

Regression Models for Clinical Trials with Correlated Categorical Responses

Regression models for correlated categorical data are presented in which the covariance is a function of measured effects. The regression and covariance parameters are estimated by extended least square methods. A numerical example of a clinical trial comparing two antiemetic treatment regimes for patients receiving chemotherapy is given to illustrate the approach.     

Quantifying the relationship between urban development intensity and carbon dioxide emissions using a panel data analysis

As a factor associated with urban management and planning, urban development intensity (UDI) could in fact form the basis for a new rationale in coordinating urban sustainable development and reducing CO₂ emissions. However, existing literature engaging in the task of quantifying the impacts of urban development intensity on CO₂ emissions is limited. Therefore, the goal of this study is to quantify the relationship between urban development intensity and CO₂ emissions for a panel made up of the five major cities in China (Beijing, Shanghai, Tianjin, Chongqing and Guangzhou) using time series data from 1995 to 2011. Firstly, this study calculated CO₂ emissions for the five selected cities and presented a comprehensive index system for the assessment of the level of urban development intensity based on six aspects (land-use intensity, economic intensity, population intensity, infrastructure intensity, public service intensity and eco-environmental intensity) using locally important socioeconomic variables. Panel data analysis was subsequently utilised in order to quantify the relationships between urban development intensity and CO₂ emissions. The empirical results of the study indicate that factors such as land-use intensity, economic intensity, population intensity, infrastructure intensity and public service intensity exert a positive influence on CO₂ emissions. Further, the estimated coefficients suggest that land-use intensity is the most important factor in relation to CO₂ emissions. Conversely, eco-environmental intensity was identified as having a major inhibitory effect on CO₂ emission levels. The findings of this study hold important implications for both academics and practitioners, indicating that, on the path towards developing low-carbon cities in China, the effects of urban development intensity must be taken into consideration.     

PseqIP: a nonredundant and exhaustive protein sequence data bank generated from 4 major existing collections

Four major protein sequence data collections (NBRF-PIR, PSD-Kyoto, PGtrans, and NEWAT) have been merged into a single nonredundant data bank called PseqIP. The data bank entries were automatically matched by a heuristic computer program relying on the fast computation of the number of tetrapeptides shared by two sequences. PseqIP 1.0 includes 6,068 different protein sequences for a total of 1,357,067 residues, representing most of the available sequence information to date. During the course of this work, we found about 600 occurrences of a protein sequence recorded with a one-amino-acid variation in at least two different data banks. A flat file (ASCII computer-readable format) version of PseqIP 1.0, well-suited for exhaustive homology searches and statistical sequence analysis, is available from our laboratory.