Spatial distribution of upland beetles in relation to landform, vegetation and grazing management

Dennis, P., Aspinall, R. J., Gordon, I. J. (2002). Spatial distribution of upland beetles in relation to landform vegetation and grazing management. Basic and Applied Ecology, 3 (2), 183?193. Sponsorship: SEERAD RAE2008

DIP: Density Inference Protocol for wireless sensor networks and its application to density-unbiased statistics

Wireless sensor networks have recently emerged as enablers of important applications such as environmental, chemical and nuclear sensing systems. Such applications have sophisticated spatial-temporal semantics that set them aside from traditional wireless networks. For example, the computation of temperature averaged over the sensor field must take into account local densities. This is crucial since otherwise the estimated average temperature can be biased by over-sampling areas where a lot more sensors exist. Thus, we envision that a fundamental service that a wireless sensor network should provide is that of estimating local densities. In this paper, we propose a lightweight probabilistic density inference protocol, we call DIP, which allows each sensor node to implicitly estimate its neighborhood size without the explicit exchange of node identifiers as in existing density discovery schemes. The theoretical basis of DIP is a probabilistic analysis which gives the relationship between the number of sensor nodes contending in the neighborhood of a node and the level of contention measured by that node. Extensive simulations confirm the premise of DIP: it can provide statistically reliable and accurate estimates of local density at a very low energy cost and constant running time. We demonstrate how applications could be built on top of our DIP-based service by computing density-unbiased statistics from estimated local densities.

An Information Theoretic Framework for Field Monitoring Using Autonomously Mobile Sensors

We consider a mobile sensor network monitoring a spatio-temporal field. Given limited cache sizes at the sensor nodes, the goal is to develop a distributed cache management algorithm to efficiently answer queries with a known probability distribution over the spatial dimension. First, we propose a novel distributed information theoretic approach in which the nodes locally update their caches based on full knowledge of the space-time distribution of the monitored phenomenon. At each time instant, local decisions are made at the mobile nodes concerning which samples to keep and whether or not a new sample should be acquired at the current location. These decisions account for minimizing an entropic utility function that captures the average amount of uncertainty in queries given the probability distribution of query locations. Second, we propose a different correlation-based technique, which only requires knowledge of the second-order statistics, thus relaxing the stringent constraint of having a priori knowledge of the query distribution, while significantly reducing the computational overhead. It is shown that the proposed approaches considerably improve the average field estimation error by maintaining efficient cache content. It is further shown that the correlation-based technique is robust to model mismatch in case of imperfect knowledge of the underlying generative correlation structure.

On the Interaction between TCP and the Wireless Channel in CDMA2000 Networks

In this work, we conducted extensive active measurements on a large nationwide CDMA2000 1xRTT network in order to characterize the impact of both the Radio Link Protocol and more importantly, the wireless scheduler, on TCP. Our measurements include standard TCP/UDP logs, as well as detailed RF layer statistics that allow observability into RF dynamics. With the help of a robust correlation measure, normalized mutual information, we were able to quantify the impact of these two RF factors on TCP performance metrics such as the round trip time, packet loss rate, instantaneous throughput etc. We show that the variable channel rate has the larger impact on TCP behavior when compared to the Radio Link Protocol. Furthermore, we expose and rank the factors that influence the assigned channel rate itself and in particular, demonstrate the sensitivity of the wireless scheduler to the data sending rate. Thus, TCP is adapting its rate to match the available network capacity, while the rate allocated by the wireless scheduler is influenced by the sender's behavior. Such a system is best described as a closed loop system with two feedback controllers, the TCP controller and the wireless scheduler, each one affecting the other's decisions. In this work, we take the first steps in characterizing such a system in a realistic environment.

Fixational Instability and Natural Image Statistics: Implications for Early Visual Representations

Under natural viewing conditions small movements of the eye, head, and body prevent the maintenance of a steady direction of gaze. It is known that stimuli tend to fade when they a restabilized on the retina for several seconds. However; it is unclear whether the physiological motion of the retinal image serves a visual purpose during the brief periods of natural visual fixation. This study examines the impact of fixational instability on the statistics of the visua1 input to the retina and on the structure of neural activity in the early visual system. We show that fixational instability introduces a component in the retinal input signals that in the presence of natural images, lacks spatial correlations. This component strongly influences neural activity in a model of the LGN. It decorrelates cell responses even if the contrast sensitivity functions of simulated cells arc not perfectly tuned to counterbalance the power-law spectrum of natural images. A decorrelation of neural activity at the early stages of the visual system has been proposed to be beneficial for discarding statistical redundancies in the input signals. The results of this study suggest that fixational instability might contribute to establishing efficient representations of natural stimuli.

Pyramidal quantum dots: single and entangled photon sources and correlation studies

Practical realisation of quantum information science is a challenge being addressed by researchers employing various technologies. One of them is based on quantum dots (QD), usually referred to as artificial atoms. Being capable to emit single and polarization entangled photons, they are attractive as sources of quantum bits (qubits) which can be relatively easily integrated into photonic circuits using conventional semiconductor technologies. However, the dominant self-assembled QD systems suffer from asymmetry related problems which modify the energetic structure. The main issue is the degeneracy lifting (the fine-structure splitting, FSS) of an optically allowed neutral exciton state which participates in a polarization-entanglement realisation scheme. The FSS complicates polarization-entanglement detection unless a particular FSS manipulation technique is utilized to reduce it to vanishing values, or a careful selection of intrinsically good candidates from the vast number of QDs is carried out, preventing the possibility of constructing vast arrays of emitters on the same sample. In this work, site-controlled InGaAs QDs grown on (111)B oriented GaAs substrates prepatterned with 7.5 μm pitch tetrahedrons were studied in order to overcome QD asymmetry related problems. By exploiting an intrinsically high rotational symmetry, pyramidal QDs were shown as polarization-entangled photon sources emitting photons with the fidelity of the expected maximally entangled state as high as 0.721. It is the first site-controlled QD system of entangled photon emitters. Moreover, the density of such emitters was found to be as high as 15% in some areas: the density much higher than in any other QD system. The associated physical phenomena (e.g., carrier dynamic, QD energetic structure) were studied, as well, by different techniques: photon correlation spectroscopy, polarization-resolved microphotoluminescence and magneto-photoluminescence.

The development of new methods for high resolution radio astronomy imaging

Very Long Baseline Interferometry (VLBI) polarisation observations of the relativistic jets from Active Galactic Nuclei (AGN) allow the magnetic field environment around the jet to be probed. In particular, multi-wavelength observations of AGN jets allow the creation of Faraday rotation measure maps which can be used to gain an insight into the magnetic field component of the jet along the line of sight. Recent polarisation and Faraday rotation measure maps of many AGN show possible evidence for the presence of helical magnetic fields. The detection of such evidence is highly dependent both on the resolution of the images and the quality of the error analysis and statistics used in the detection. This thesis focuses on the development of new methods for high resolution radio astronomy imaging in both of these areas. An implementation of the Maximum Entropy Method (MEM) suitable for multi-wavelength VLBI polarisation observations is presented and the advantage in resolution it possesses over the CLEAN algorithm is discussed and demonstrated using Monte Carlo simulations. This new polarisation MEM code has been applied to multi-wavelength imaging of the Active Galactic Nuclei 0716+714, Mrk 501 and 1633+382, in each case providing improved polarisation imaging compared to the case of deconvolution using the standard CLEAN algorithm. The first MEM-based fractional polarisation and Faraday-rotation VLBI images are presented, using these sources as examples. Recent detections of gradients in Faraday rotation measure are presented, including an observation of a reversal in the direction of a gradient further along a jet. Simulated observations confirming the observability of such a phenomenon are conducted, and possible explanations for a reversal in the direction of the Faraday rotation measure gradient are discussed. These results were originally published in Mahmud et al. (2013). Finally, a new error model for the CLEAN algorithm is developed which takes into account correlation between neighbouring pixels. Comparison of error maps calculated using this new model and Monte Carlo maps show striking similarities when the sources considered are well resolved, indicating that the method is correctly reproducing at least some component of the overall uncertainty in the images. The calculation of many useful quantities using this model is demonstrated and the advantages it poses over traditional single pixel calculations is illustrated. The limitations of the model as revealed by Monte Carlo simulations are also discussed; unfortunately, the error model does not work well when applied to compact regions of emission.

Essays on Vietnam’s Financial Reforms: Foreign Exchange Statistics and Evidence of Long-Run Equilibrium

In this paper, we examine exchange rates in Vietnam’s transitional economy. Evidence of long-run equilibrium are established in most cases through a single co-integrating vector among endogenous variables that determine the real exchange rates. This supports relative PPP in which ECT of the system can be combined linearly into a stationary process, reducing deviation from PPP in the long run. Restricted coefficient vectors ß’ = (1, 1, -1) for real exchange rates of currencies in question are not rejected. This empirics of relative PPP adds to found evidences by many researchers, including Flre et al. (1999), Lee (1999), Johnson (1990), Culver and Papell (1999), Cuddington and Liang (2001). Instead of testing for different time series on a common base currency, we use different base currencies (USD, GBP, JPY and EUR). By doing so we want to know the whether theory may posit significant differences against one currency? We have found consensus, given inevitable technical differences, even with smallerdata sample for EUR. Speeds of convergence to PPP and adjustment are faster compared to results from other researches for developed economies, using both observed and bootstrapped HL measures. Perhaps, a better explanation is the adjustment from hyperinflation period, after which the theory indicates that adjusting process actually accelerates. We observe that deviation appears to have been large in early stages of the reform, mostly overvaluation. Over time, its correction took place leading significant deviations to gradually disappear.

Sensitivity of HER-2/neu antibodies in archival tissue samples of invasive breast carcinomas. Correlation with oncogene amplification in 160 cases.

Overexpression and amplification of the HER-2 oncogene in patients with breast cancer has correlated with early onset of metastasis, resistance to hormonal therapy and some forms of chemotherapy, and shortened survival. Therefore, evaluation of this putative prognostic or predictive factor seems critical. Because different antibodies are used for the detection of the 185-kd HER-2 oncoprotein, we studied the sensitivity of 3 frequently used antibodies. Immunohistochemistry results were correlated with gene amplification level as assessed by fluorescence in situ hybridization. Protein overexpression was found in 17.2% and 12.5% of cases using antibodies against the external (TAB250) and internal (CB11) domains of the protein, respectively, and in 38.0% of cases using a rabbit polyclonal antibody. Fluorescence in situ hybridization was successful in all 160 tumors, and amplification was found in 37 tumors (23.1%). The monoclonal antibody TAB250 had the lowest misclassification rate, 9.6% (sensitivity, 67%; specificity, 97.5%).

Low demographic variability in wild primate populations: fitness impacts of variation, covariation, and serial correlation in vital rates.

In a stochastic environment, long-term fitness can be influenced by variation, covariation, and serial correlation in vital rates (survival and fertility). Yet no study of an animal population has parsed the contributions of these three aspects of variability to long-term fitness. We do so using a unique database that includes complete life-history information for wild-living individuals of seven primate species that have been the subjects of long-term (22-45 years) behavioral studies. Overall, the estimated levels of vital rate variation had only minor effects on long-term fitness, and the effects of vital rate covariation and serial correlation were even weaker. To explore why, we compared estimated variances of adult survival in primates with values for other vertebrates in the literature and found that adult survival is significantly less variable in primates than it is in the other vertebrates. Finally, we tested the prediction that adult survival, because it more strongly influences fitness in a constant environment, will be less variable than newborn survival, and we found only mixed support for the prediction. Our results suggest that wild primates may be buffered against detrimental fitness effects of environmental stochasticity by their highly developed cognitive abilities, social networks, and broad, flexible diets.

Assessment of LD matrix measures for the analysis of biological pathway association.

Complex diseases will have multiple functional sites, and it will be invaluable to understand the cross-locus interaction in terms of linkage disequilibrium (LD) between those sites (epistasis) in addition to the haplotype-LD effects. We investigated the statistical properties of a class of matrix-based statistics to assess this epistasis. These statistical methods include two LD contrast tests (Zaykin et al., 2006) and partial least squares regression (Wang et al., 2008). To estimate Type 1 error rates and power, we simulated multiple two-variant disease models using the SIMLA software package. SIMLA allows for the joint action of up to two disease genes in the simulated data with all possible multiplicative interaction effects between them. Our goal was to detect an interaction between multiple disease-causing variants by means of their linkage disequilibrium (LD) patterns with other markers. We measured the effects of marginal disease effect size, haplotype LD, disease prevalence and minor allele frequency have on cross-locus interaction (epistasis). In the setting of strong allele effects and strong interaction, the correlation between the two disease genes was weak (r=0.2). In a complex system with multiple correlations (both marginal and interaction), it was difficult to determine the source of a significant result. Despite these complications, the partial least squares and modified LD contrast methods maintained adequate power to detect the epistatic effects; however, for many of the analyses we often could not separate interaction from a strong marginal effect. While we did not exhaust the entire parameter space of possible models, we do provide guidance on the effects that population parameters have on cross-locus interaction.

Anti-beta(1)-adrenergic receptor antibodies and heart failure: causation, not just correlation.

Antibodies specific for the beta(1)-adrenergic receptor are found in patients with chronic heart failure of various etiologies. From work presented in this issue of the JCI, we can now infer that these antibodies actually contribute to the pathogenesis of chronic heart failure. This commentary discusses mechanisms by which these antibodies may engender cardiomyopathy.

Measurement of intracellular strain on deformable substrates with texture correlation.

Mechanical stimuli are important factors that regulate cell proliferation, survival, metabolism and motility in a variety of cell types. The relationship between mechanical deformation of the extracellular matrix and intracellular deformation of cellular sub-regions and organelles has not been fully elucidated, but may provide new insight into the mechanisms involved in transducing mechanical stimuli to biological responses. In this study, a novel fluorescence microscopy and image analysis method was applied to examine the hypothesis that mechanical strains are fully transferred from a planar, deformable substrate to cytoplasmic and intranuclear regions within attached cells. Intracellular strains were measured in cells derived from the anulus fibrosus of the intervertebral disc when attached to an elastic silicone membrane that was subjected to tensile stretch. Measurements indicated cytoplasmic strains were similar to those of the underlying substrate, with a strain transfer ratio (STR) of 0.79. In contrast, nuclear strains were much smaller than those of the substrate, with an STR of 0.17. These findings are consistent with previous studies indicating nuclear stiffness is significantly greater than cytoplasmic stiffness, as measured using other methods. This study provides a novel method for the study of cellular mechanics, including a new technique for measuring intranuclear deformations, with evidence of differential magnitudes and patterns of strain transferred from the substrate to cell cytoplasm and nucleus.

R Markdown: Integrating A Reproducible Analysis Tool into Introductory Statistics

Nolan and Temple Lang argue that “the ability to express statistical computations is an es- sential skill.” A key related capacity is the ability to conduct and present data analysis in a way that another person can understand and replicate. The copy-and-paste workflow that is an artifact of antiquated user-interface design makes reproducibility of statistical analysis more difficult, especially as data become increasingly complex and statistical methods become increasingly sophisticated. R Markdown is a new technology that makes creating fully-reproducible statistical analysis simple and painless. It provides a solution suitable not only for cutting edge research, but also for use in an introductory statistics course. We present experiential and statistical evidence that R Markdown can be used effectively in introductory statistics courses, and discuss its role in the rapidly-changing world of statistical computation.

Spatial and temporal scales of neuronal correlation in visual area V4.

The spiking activity of nearby cortical neurons is correlated on both short and long time scales. Understanding this shared variability in firing patterns is critical for appreciating the representation of sensory stimuli in ensembles of neurons, the coincident influences of neurons on common targets, and the functional implications of microcircuitry. Our knowledge about neuronal correlations, however, derives largely from experiments that used different recording methods, analysis techniques, and cortical regions. Here we studied the structure of neuronal correlation in area V4 of alert macaques using recording and analysis procedures designed to match those used previously in primary visual cortex (V1), the major input to V4. We found that the spatial and temporal properties of correlations in V4 were remarkably similar to those of V1, with two notable differences: correlated variability in V4 was approximately one-third the magnitude of that in V1 and synchrony in V4 was less temporally precise than in V1. In both areas, spontaneous activity (measured during fixation while viewing a blank screen) was approximately twice as correlated as visual-evoked activity. The results provide a foundation for understanding how the structure of neuronal correlation differs among brain regions and stages in cortical processing and suggest that it is likely governed by features of neuronal circuits that are shared across the visual cortex.