Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecosystem valuation: some principles and a partial application

Understanding the economic value of nature and the services it provides to humanity has become increasingly important for local, national and global policy, and decision‐making. However, problems arise in that it is difficult to obtain meaningful values for goods and services that ecosystems provide which have no formal market, or are characteristically intangible. Additional problems occur when economic methods are applied inappropriately and when the importance of ecosystem maintenance for human welfare is underestimated. In this article, we provide clarification to practitioners on important considerations in ecosystem services valuation. We first review and adapt definitions of ecosystem services in order to make an operational link to valuation methods. We make a distinction between intermediate and final ecosystem services and also identify non‐monetary ways to incorporate regulatory and support services into decision‐making. We then discuss the spatially explicit nature of ecosystem service provision and benefits capture, and highlight the issues surrounding the valuing of marginal changes, nonlinearities in service benefits, and the significance of non‐convexities (threshold effects). Finally, we argue for a sequential decision support system that can lead to a more integrated and rigorous approach to ecosystem valuation and illustrate some of its features in a coastal ecosystem management context. Copyright © 2011 John Wiley & Sons, Ltd.
Effects of Subchronic Exposures to Concentrated Ambient Particles in Mice: VI. Gene Expression in Heart and Lung Tissue

Abstract The purpose of this exploratory study within the integrated subchronic inhalation exposure study () was to identify genes in heart and lung tissue that changed in expression level as a result of subchronic exposure to concentrated ambient particles (CAPs). Identification of CAPs exposure-related changes in gene expression could serve in the formulation of mechanistic hypotheses and/or to suggest possible biomarkers of exposure. In the exploratory study undertaken here, tissues from multiple replicates of ApoE/low-density-lipoprotein double knockout (DK) mice were examined for relative exposure-related changes in gene expression. Due to limited resources, the number of replicates was three for each tissue (lung and heart) of each exposure condition (CAPs or air control). A rigorous comparison of exposure versus control data using the“significance analysis of microarrays” (SAM) method indicated that only one gene was differentially expressed at a significant level. However, when using a less restrictive, nonstatistical analytical treatment of the data, several genes that might be involved in PM-related heart or lung pathology, and/or the circadian rhythm of physiological processes, were identified. A more comprehensive study is required to more definitively assess differences in gene expression in heart and lung resulting from exposure to CAPs.
Automated Classification of Glaucoma Images by Wavelet Energy Features

Glaucoma is the second leading cause of blindness worldwide. As glaucoma progresses, more optic nerve tissue is lost and the optic cup grows which leads to vision loss. This paper compiles a system that could be used by non-experts to filtrate cases of patients not affected by the disease. This work proposes glaucomatous image classification using texture features within images and efficient glaucoma classification based on Probabilistic Neural Network (PNN). Energy distribution over wavelet sub bands is applied to compute these texture features. Wavelet features were obtained from the daubechies (db3), symlets (sym3), and biorthogonal (bio3.3, bio3.5, and bio3.7) wavelet filters. It uses a technique to extract energy signatures obtained using 2-D discrete wavelet transform and the energy obtained from the detailed coefficients can be used to distinguish between normal and glaucomatous images. We observed an accuracy of around 95%, this demonstrates the effectiveness of these methods. Keywords- Wavelet transform, Glaucoma, Image texture, Feature extraction, PNN.
Using causal paths to improve performance and correctness in distributed systems

With the rise of the Internet has come a rise in the importance of distributed systems. Distributed systems-groups of networked computers cooperating to run a single application or service-power modern web sites and communication services, infrastructure services like content-distribution networks and overlay networks, and parallel computations. With the complexity of distributed systems comes bugs: errors that affect a system's correctness, performance, or both. Traditional debugging tools and methods do not apply well to distributed systems. Thus, new tools are needed that will enable programmers to find and fix bugs in distributed systems. These improvements will in turn improve the performance and reliability that end users experience. Many bugs reflect discrepancies between a system's behavior and the programmer's assumptions about that behavior. In this thesis, we show that expressing distributed system behavior as a set of causal paths and helping programmers separate those paths into expected and unexpected behavior is a powerful technique for improving the performance and correctness of distributed systems. This dissertation presents three distinct debugging tools, representing several approaches to tracing, analyzing, checking, and displaying system behavior. We applied our debugging tools to several distributed systems of varying size and complexity, accurately discovering the behavior of each system. We found and fixed bugs in several of the systems. Our experiences using the tools with real systems demonstrate a trade-off between the disruptiveness of a debugging methodology and the accuracy of its results. Namely, Project 5 can be applied without changing the target application, but its accuracy is limited. Wide-area Project 5 requires interposition and results in more accurate and more detailed analyses. Pip requires changes to application source code and generates a behavior model detailed enough for automatic extraction of errors. It is difficult to quantify the benefits of debugging tools. However, a number of different programmers were able to use these tools to rapidly locate and diagnose subtle and previously unknown bugs, validating the utility of these techniques for improving the reliability and performance of distributed systems.
Exploring the electrocardiogram as a potential tool to screen for premotor Parkinson's disease

The aim of this study was to test the hypothesis that patients with REM sleep behavior disorder, many of whom will develop Parkinson's disease (PD) or a related synucleinopathy, will demonstrate decreased heart rate variability (HRV) compared with a group of age‐matched controls as measured by an electrocardiogram during wakefulness. We compared HRV in 11 untreated idiopathic REM sleep behavior disorder patients (9 men and 2 women; mean age, 63.3 years; SD, 7.5 years) and 11 control subjects with idiopathic insomnia without REM sleep behavior disorder (7 men and 4 women; mean age, 59.5 years; SD, 8.7 years). Subjects with other causes of reduced HRV were excluded. HRV was determined from 5‐minute presleep segments of a single channel electrocardiogram recorded during polysomnographic evaluations, using R‐R intervals during wakefulness. Time domain, geometric measures, and spectral analysis of the R‐R intervals were significantly different between cases and controls. A discriminant function analysis correctly classified 95.5% of subjects (overall model fit, P = 0.016). Leave‐one‐out cross‐validation correctly classified 77.3% of subjects. HRV during wakefulness is significantly decreased in patients with idiopathic REM sleep behavior disorder compared with control subjects, suggesting abnormalities of both sympathetic and parasympathetic function. Patients with RBD may later develop motor and cognitive features of a Lewy body disorder, such as PD. Cardiac autonomic dysfunction is also impaired in PD, suggesting that impaired HRV may be an early sign of PD. HRV measured by routine electrocardiograms could be used to screen for Lewy body disorders such as PD. © 2010 Movement Disorder Society.
Exploration of optimal orbits in the strongly perturbed environment of the 2001 SN263 triple asteroid system

For the past 20 years, the small bodies of the solar system, such as asteroids and comets, have been increasingly gathering the interest of scientists and space agencies. The latter have been multiplying the number of space missions to study them. Brazil does not want to be left out and has been working on its own mission, ASTER, which has the particularity of having as a target a triple asteroid system. Although adding great scientific interest to the mission, this characteristic considerably complicates the mission design, by making the space probe move in a complex gravitational field and submitting it to very strong perturbations forces. Following the past researches on the ASTER mission, which mostly dealt with the characterisation of the 2001 SN263 asteroid system, this work focuses on the preliminary design of mission orbits suitable for the exploration of the asteroids. Two phases of the mission are considered: the arrival in the system, which requires a parking orbit; and the exploration phase. For the latter, two scenarios are studied: a parallel and a sequential observations of the system. To find the optimal orbits for each of these cases, a computer tool has been designed, which comprises an orbit integrator able to propagate the trajectory of a spacecraft within the asteroid system, and an optimiser which uses evolutionary algorithms to find optima from a 5-dimensional search space in a single- or multi-dimensional objective space, according to objective functions that can be chosen and adapted to match the case considered. The computer tool performs well for all cases, and allows to draw general conclusions on which kind of orbits to consider for the ASTER mission. The results show that the solar radiation pressure is by far the most problematic perturbation and is hence driving the properties of the solutions. Among all cases, many optima are terminator orbits, which are by nature strong against solar radiation perturbations. Moreover, orbits closer to the bodies are more stable, and any trajectory too distant from the bodies will be blown away. This work concludes on the suitability of the optimisation methods selected to the orbit design for this mission, although it is advised to still improve the software to model the dynamics of the system in a more detailed manner, and on recommendations for the ASTER mission. No satisfying parking orbit has been found and the relative strength of the solar radiation pressure implies that there does not exist orbits sufficiently remote from the bodies to serve as parking orbits. It is recommended to investigate other solutions with active orbit maintenance. As for the exploration phase, the sequential observation scheme shows its superiority. Satisfying observation orbits can be found about all three bodies, which is not the case for the parallel observation because of the zones of instability present in-between the bodies.
Working Notes for the InFile Campaign : Online Document Filtering Using 1 Nearest Neighbor

This paper has been written as a part of the InFile (IN- Formation, FILtering, Evaluation) campaign. This project is a cross- language adaptive filtering evaluation campaign, sponsored by the French national research agency, and it is a pilot track of the CLEF (Cross Lan- guage Evaluation Forum) 2008 campaigns. We propose in this paper an online algorithm to learn category specific thresholds in a multiclass en- vironment where a document can belong to more than one class. Our method uses 1 Nearest Neighbor (1NN) algorithm for classification. It uses simulated user feedback to fine tune the threshold and in turn the classification performance over time. The experiments were run on En- glish language corpus containing 100,000 documents. The best results have a precision of 0.366 and the recall is 0.260.
Breaking Immune Tolerance to the Prion Protein Using Prion Protein Peptides Plus Oligodeoxynucleotide-CpG in Mice1

The absence of a detectable immune response during transmissible spongiform encephalopathies is likely due to the fact that the essential component of infectious agents, the prion protein (PrP), is a self Ag expressed on the surface of many cells of the host. To overcome self-tolerance to PrP, we used 30-mer PrP peptides previously shown to be immunogenic in Prnp−/− mice, together with CFA or CpG-oligodeoxynucleotides (CpG) in IFA. Generation of anti-PrP T and B cell responses was analyzed in the spleen, lymph nodes, and serum of immunized C57BL/6 wild-type mice. Immunization with PrP peptides emulsified in CFA did not trigger an immune response to PrP. When CpG were used, vaccination with peptides P143–172 and P158–187 generated IFN-γ-secreting splenic T cells, and only P158–187 significantly stimulated IL-4-secreting T cells. Both peptides induced few Ab-producing B cells, and low and variable serum Ab titers. In contrast, immunization with peptide P98–127 did not induce significant levels of T cell responses but elicited specific peptide Abs. T cell epitope mapping, performed using 15-mer peptides covering PrP segment 142–182, revealed that an immunogenic motif lies between positions 156 and 172. These results demonstrate that T and B cell repertoires against PrP can be stimulated in C57BL/6 when adjuvant of the innate immunity such as CpG, but not CFA, is added to PrP peptides, and that the pattern of immune responses varies according to the epitope.
The Legionella pneumophila iraAB Locus Is Required for Iron Assimilation, Intracellular Infection, and Virulence

ABSTRACT Legionella pneumophila, a facultative intracellular parasite of human alveolar macrophages and protozoa, causes Legionnaires' disease. Using mini-Tn10 mutagenesis, we previously isolated a L. pneumophila mutant that was hypersensitive to iron chelators. This mutant, NU216, and its allelic equivalent, NU216R, were also defective for intracellular infection, particularly in iron-deficient host cells. To determine whether NU216R was attenuated for virulence, we assessed its ability to cause disease in guinea pigs following intratracheal inoculation. NU216R-infected animals yielded 1,000-fold fewer bacteria from their lungs and spleen compared to wild-type-130b-infected animals that had received a 50-fold-lower dose. Moreover, NU216R-infected animals subsequently cleared the bacteria from these sites. While infection with 130b resulted in high fever, weight loss, and ruffled fur, inoculation with NU216R did not elicit any signs of disease. DNA sequence analysis revealed that the transposon insertion in NU216R lies in the first open reading frame of a two-gene operon. This open reading frame (iraA) encodes a 272-amino-acid protein that shows sequence similarity to methyltransferases. The second open reading frame (iraB) encodes a 501-amino-acid protein that is highly similar to di- and tripeptide transporters from both prokaryotes and eukaryotes. Southern hybridization analyses determined that theiraAB locus was largely limited to strains of L. pneumophila, the most pathogenic of the Legionellaspecies. A newly derived mutant containing a targeted disruption ofiraB showed reduced ability to grow under iron-depleted extracellular conditions, but it did not have an infectivity defect in the macrophage-like U937 cells. These data suggest thatiraA is critical for virulence of L. pneumophila while iraB is involved in a novel method of iron acquisition which may utilize iron-loaded peptides.
Small and Even Smaller Circles: The Size of Mobile Phone-Based Core Social Networks in Scandinavia and South Asia

Previous research in developed countries has shown that mobile phone users call and text to a relatively small circle of people. Research from the Global South indicates that core network size is often larger than in the developed world since the logistics of daily life require extended informal logistics. This suggests that the core social network, as seen in the use of mobile voice and texting, will be larger in developing countries than in developed countries. This is tested using mobile phone log data from Norway, Malaysia, Thailand and Pakistan. A total of 4000 subscribers and their “one hop” social networks (approx. 80,000 links) were examined. The results show that the core mobile phone-based networks are not larger in developing countries. This indicates that cost, literacy and other cultural issues are significant when considering the question of core network size as seen in the use of mobile telephony.
Interactive Verification of Concurrent Systems using Symbolic Execution

This paper presents an interactive proof method for the verification of temporal properties of concurrent systems based on symbolic execution. Symbolic execution is a well known and very intuitive strategy for the verification of sequential programs. We have carried over this approach to the interactive verification of arbitrary linear temporal logic properties of (infinite state) parallel programs. The resulting proof method is very intuitive to apply and can be automated to a large extent. It smoothly combines first-order reasoning with reasoning in temporal logic. The proof method has been implemented in the interactive verification environment KIV and has been used in several case studies.
IIS: A Marriage of Computational Linguistics, Psychology, and Educational Technologies

There are numerous projects at the University of Memphis Institute for Intelligent Systems (IIS) that involve a marriage of natural language processing, computational linguistics, psychology, and educational technologies. We use natural language and computational linguistic technologies to accomplish a variety of goals related to psychology and educational practice, including text analysis and the development of interactive tutoring systems. This paper describes these technologies and some of our computational methods.
FAQ-Learning in Matrix Games: Demonstrating Convergence Near Nash Equilibria, and Bifurcation of Attractors in the Battle of Sexes

This article studies Frequency Adjusted Q-learning (FAQ-learning), a variation of Q-learning that simulates simultaneous value function updates. The main contributions are empirical and theoretical support for the convergence of FAQ-learning to attractors near Nash equilibria in two-agent two-action matrix games. The games can be divided into three types: Matching pennies, Prisoners' Dilemma and Battle of Sexes. This article shows that the Matching pennies and Prisoners' Dilemma yield one attractor of the learning dynamics, while the Battle of Sexes exhibits a supercritical pitchfork bifurcation at a critical temperature of τ, where one attractor splits into two attractors and one repellent fixed point. Experiments illustrate that the distance between fixed points of the FAQ-learning dynamics and Nash equilibria tends to zero as the exploration parameter τ of FAQ-learning approaches zero.
Movements and Inferred Foraging by Bowhead Whales in the Canadian Beaufort Sea during August and September, 2006–12

Each spring, most bowhead whales of the Bering-Chukchi-Beaufort (BCB) population migrate to the southeast Beaufort Sea and summer in Canadian waters. In August and September, they form aggregations, which are known to occur mainly in the shallow, shelf waters when oceanographic conditions promote concentration of their zooplankton prey. The movements of individual bowheads while they occupy these late summer habitats are less well known; our knowledge is based on photographic evidence and limited tagging studies conducted from 1982 to 2000. In this study, 85% (17) of the 20 satellite-tagged whales that could have spent some time in the Canadian portion of the Beaufort Sea during late summer 2006 to 2012 spent all or part of August and September there. We analyzed location data for 16 whales, using a two-state switching correlated random walk (CRW) behavioural model, and classified locations in the Canadian waters as associated with lingering behaviour (inferred foraging) or directed travel. We found that these whales spent the greatest proportion of their time lingering (59%), followed by traveling (22%), and transitioning between lingering and traveling (19%). Using only lingering locations for these tagged whales in all study years pooled, we calculated kernel densities and defined five areas within the 75% density contour as aggregation areas. Together, the five aggregation areas we defined comprised 25 341 km2, 14.1% of the total area used by these tagged whales in Canadian waters during August and September of the deployment years. Three aggregation areas were located in shallow waters of the Beaufort Sea Shelf and were used almost exclusively by immature tagged whales in our sample. Two other aggregation areas were observed, one in Darnley Bay and one in Viscount Melville Sound in the Canadian Arctic Archipelago. Each of these was used by one mature whale. Tagged whales were observed to use one or two aggregation areas in a single season, and rarely more. The proportion of lingering time spent in each aggregation area was highly variable among individuals. The largest aggregation area (10 877 km2), located over the Beaufort Shelf north of the Tuktoyaktuk Peninsula (5 – 52 m depth), was used by 13 of the 16 tagged whales, almost exclusively by the immature whales, including three of four that were tracked in two consecutive summers. The Beaufort Shelf overall (and possibly the Tuktoyaktuk Shelf, including the Outer Shelf, in particular) was especially important for immature bowhead whales, while mature whales used habitats beyond the Beaufort Shelf during late summer. Findings may be important to inform both decisions on management and mitigative actions relating to bowhead whale use of the Beaufort Shelf and studies that aim to improve our understanding of the prey base of BCB bowhead whales in the Canadian Beaufort Sea region.
Stochastic thermodynamics, fluctuation theorems and molecular machines

Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics such as work, heat and entropy production to the level of individual trajectories of well-defined non-equilibrium ensembles. It applies whenever a non-equilibrium process is still coupled to one (or several) heat bath(s) of constant temperature. Paradigmatic systems are single colloidal particles in time-dependent laser traps, polymers in external flow, enzymes and molecular motors in single molecule assays, small biochemical networks and thermoelectric devices involving single electron transport. For such systems, a first-law like energy balance can be identified along fluctuating trajectories. For a basic Markovian dynamics implemented either on the continuum level with Langevin equations or on a discrete set of states as a master equation, thermodynamic consistency imposes a local-detailed balance constraint on noise and rates, respectively. Various integral and detailed fluctuation theorems, which are derived here in a unifying approach from one master theorem, constrain the probability distributions for work, heat and entropy production depending on the nature of the system and the choice of non-equilibrium conditions. For non-equilibrium steady states, particularly strong results hold like a generalized fluctuation–dissipation theorem involving entropy production. Ramifications and applications of these concepts include optimal driving between specified states in finite time, the role of measurement-based feedback processes and the relation between dissipation and irreversibility. Efficiency and, in particular, efficiency at maximum power can be discussed systematically beyond the linear response regime for two classes of molecular machines, isothermal ones such as molecular motors, and heat engines such as thermoelectric devices, using a common framework based on a cycle decomposition of entropy production.