Miracle-dz/UniFAR-FTUs huggingface dataset:
A Stochastic Model for Early HIV-1 Population Dynamics

A simple stochastic mathematical model is developed and investigated for early human immunodeficiency virus type-1 (HIV-1) population dynamics. The model, which is a multi-dimensional diffusion process, includes activated uninfected CD4 T cells, latently and actively infected CD4 T cells and free virions occurring in plasma. Stochastic effects are assumed to arise in the process of infection of CD4 T cells and transitions may occur from uninfected to latently or actively infected cells by chance mechanisms. Using the best currently available parameter values, the intrinsic variability in response to a given initial infection is examined by solving the stochastic system numerically. We estimate the statistical distributions of the time of occurrence and the magnitude of the early peak in viral concentration. The maximum of the viral load has a value in the experimental range and its time of occurrence has a 95% confidence interval from 19.4 to 25.1 days. The stochastic nature of the growth of viral density is extremely pronounced in the first few days after initial infection. Threshold effects are noted at virion levels of about 3–5×10 mm. In addition to modeling the intrinsic variability in HIV-1 growth, we have explored the effects of perturbations in the parameter values in order to assess the additional stochastic effects of between-patient variability. We found that changes in the initial number of virions or dose size, the rate at which latently infected CD4 T cells are converted to the actively infected form and the fraction of latent cells had only minor effects on the size, speed and variability of the response. In contrast, decreased speed and magnitude but greater variability in response were obtained when the death rate of uninfected CD4 T cells, the death rate of actively infected cells and the clearance rate of the virus were increased or when the appearance rate of uninfected CD4 T cells, the number of virions produced by infected cells, the infection rate of CD4 T cells and the initial number of uninfected activated CD4 T cells were decreased. We also determined the distribution of the time to reach a given virion density. From this distribution the probability of detection of the virus as a function of time can be estimated. The numerical results obtained are in the range of experimental values and are discussed in relation to recently proposed detection and testing procedures. 7 1998 Academic Press
Urans simulations of static drift and dynamic manoeuvres of the KVLCC2 tanker

Computational Fluid Dynamics is used to investigate the global forces and moments acting on the KVLCC2 hull form under going straight line, drift and pure sway planar motion mechanism tests. Simulated results are compared with experimental results for the unappended hull in shallow water and a fully appended hull with a propeller acting at the ship self propulsion point. A body fitted mesh undergoes transverse motion within an overall fixed mesh to capture planar motion mechanism tests. A blade element momentum code is coupled with the RANS solver for the self propulsion case. A workstation is used for the calculations with mesh sizes up to 2x106 elements. Computational uncertainty is typically 2-3% for side force and yaw moment but greater than 15% for resistance. With this mesh motion strategy manoeuvres can be well represented within a practical computational time scale.
Smart Regulation: Designing Environmental Policy

PART 1: PRACTICE AND POTENTIAL IN ENVIRONMENTAL REGULATION 1. Introduction:- Regulation, deregulation and beyond Building on what we've got Towards a successful policy mix The structure of this book How we approached our task: assumptions, evaluation criteria and methodology 2. Instruments for Environmental Protection:- Introduction Varieties of Regulatory Instruments 3. Parties, Roles and Interactions:- Third parties: public interest groups Third parties: commercial Governing at a distance Instrument and institutional interactions Conclusion PART 2: REDESIGNING REGULATION: A SECTOR SPECIFIC ANALYSIS 4. The Chemical Industry:- Introduction The chemical industry and its environmental impact The regulatory environment and its shortcomings Redesigning regulation: towards efficient and effective policy instruments Towards a broader policy mix Broader lessons Conclusion 5. The Agriculture Industry:- The agriculture industry and its environmental impact Characteristics of the agriculture industry The regulatory environment and its shortcomings Assessing instrument options: towards efficient and effective agricultural policy Institutional influences: the role of third parties Design considerations Conclusions 6. Designing Integrative Environmental Policy:- Introduction Regulatory design processes Regulatory design principles Instrument Mixes Conclusion Index
Monetary Policy and Asymmetric Volatility in Stock Returns: Evidence from Taiwan

The issue of monetary neutrality has long been debated by monetary economists and financial economists. However, most studies address this question by examining the equity return with symmetric volatility respond to monetary shock in developed economies, such as in the United States stock markets. This paper employs empirical models to examine the asymmetric conditional volatilities of equity returns to monetary policy rules in the 21 industries indices of Taiwanese stock exchange market. The regular meetings of the Board of Directors (hence forth, BOD) at the Central Bank of China (Taiwan) are used for monetary policy announcements. Not only the regular BOD meetings but the BOD meetings with surprise shocks (unanticipated announcements) are considered for testing the announcement effects (see, Balduzzi, Elton and Green [1]; de Goeij and Marquering [10]). The generalized autoregressive conditional heteroskedasticity extended by Glosten, Jagannathan and Runkle [14] (hereafter, GJR-GARCH) is used to measure our asymmetric conditional volatilities. Finally, the out-of-sample forecasting performance and likelihood ration test are also adopted in the study. We conclude that the asymmetric volatilities of equity prices can be identified based on the changes of monetary policy announcements that occurs around the dates of BOD meetings. More interestingly, the asymmetric effects of conditional volatilities in unanticipated shocks dates are lightly lower than that in regular meetings. The results present that monetary policy has real and quantitatively essential effect on the asymmetric conditional variance in equity returns in Taiwan.
Stock Market Mean Reversion and Portfolio Choice over the Life Cycle

We solve for optimal consumption and portfolio choice in a life-cycle model with short-sales and borrowing constraints; undiversifiable labor income risk; and a predictable, time-varying, equity premium and show that the investor pursues aggressive market timing strategies. Importantly, in the presence of stock market predictability, the model suggests that the conventional financial advice of reducing stock market exposure as retirement approaches is correct on average, but ignoring changing market information can lead to substantial welfare losses. Therefore, enhanced target-date funds (ETDFs) that condition on expected equity premia increase welfare relative to target-date funds (TDFs). Out-of-sample analysis supports these conclusions.
Developing a Global Data Record of Daily Landscape Freeze/Thaw Status Using Satellite Passive Microwave Remote Sensing

The landscape freeze-thaw (F/T) state parameter derived from satellite microwave remote sensing is closely linked to the surface energy budget, hydrological activity, vegetation growing season dynamics, terrestrial carbon budgets, and land-atmosphere trace gas exchange. Satellite microwave remote sensing is well suited for global F/T monitoring due to its insensitivity to atmospheric contamination and solar illumination effects, and its strong sensitivity to the relationship between landscape dielectric properties and predominantly frozen and thawed conditions. We investigated the utility of multifrequency and dual polarization brightness temperature (Tb) measurements from the Special Sensor Microwave Imager (SSM/I) to map global patterns and daily variations in terrestrial F/T cycles. We defined a global F/T classification domain by examining biophysical cold temperature constraints to vegetation growing seasons. We applied a temporal change classification algorithm based on a seasonal thresholding scheme to classify daily F/T states from time series Tb measurements. The SSM/I F/T classification accuracy was assessed using in situ air temperature measurements from the global WMO weather station network. A single-channel classification of 37 GHz, V-polarization Tb time series provided generally improved performance over other SSM/I frequencies, polarizations and channel combinations. Mean annual F/T classification accuracies were 92.2 ±0.8 [SD] % and 85.0 ±0.7 [SD] % for respective SSM/I time series of P.M. and A.M. orbital nodes over the global domain and a 20-year (1988-2007) satellite record. The resulting database provides a continuous and relatively long-term record of daily F/T dynamics for the global biosphere with well-defined accuracy.
Genetic Reconstruction of One Hereditary Nonpolyposis Colorectal Cancer History with Multiple Initiations of the Disease

The scheme of accumulation of genetic alterations in a long-term case of hereditary nonpolyposis colorectal cancer (HNPCC) was reconstructed by the retrospective analysis of postoperative tissue materials. This unique case re- sulted from a primary lesion in MLH1 gene and revealed two genetic pathways of carcinogenesis in tumors separated by lifetime and localization.
Feature Vector Selection and Use With Hidden Markov Models to Identify Frequency-Modulated Bioacoustic Signals Amidst Noise

This paper describes an effective process for automated detection and classification of frequency-modulated sounds from birds, crickets, and frogs that have a narrow short-time frequency bandwidth. An algorithm is provided for extracting these signals from background noise using a frequency band threshold filter on spectrograms. Feature vectors are introduced and demonstrated to accurately model the resultant bioacoustic signals with hidden Markov models. Additionally, sequences of sounds are successfully modeled with composite hidden Markov models, allowing for a wider range of automated species recognition.
Psychophysiomatics: A new perspective in computational life science

Technologies in engineering, information and life sciences are being introduced at a more rapid rate than has been seen for several decades. The interplay of these scientific technologies are unlocking doors to novel interdisciplinary research avenues. This paper presents the concept of psychophysiomatics as a new perspective in the combination of the diverse knowledge of psychiatry, psychology, physiology, computational science and engineering. With this combination it is hoped to discover new findings at systems level of the life science.
Stellar Pollution in the Solar Neighborhood

We study spectroscopically determined iron abundances of 640 solar-type stars to search for the signature of accreted iron-rich material. We find that the metallicity [Fe/H] of a subset of 466 main-sequence stars, when plotted as a function of stellar mass, mimics the pattern seen in lithium abundances in open clusters. Using Monte Carlo models, we find that, on average, these stars appear to have accreted ~0.5 M⊕ of iron while on the main-sequence. A consistency check is provided by a much smaller sample of 19 stars in the Hertzsprung gap, which are slightly evolved and the convection zones of which are significantly more massive; they have lower average [Fe/H], and their metallicity shows no clear variation with stellar mass. We argue that our Sun is likely to have accreted a similar amount of iron; in this respect, most systems resemble ours rather than the currently known extrasolar planetary systems. These findings suggest that terrestrial-type material is common around solar-type stars.
Towards a UML profile for QoS: a contribution in the reliability domain

Non-functional attributes of software/hardware systems are aspects of interest to embed in modeling notations. In the last few years, extensions of UML in this direction have been proposed, and some of them have been recently adopted as final specifications, such as the UML Profile for Schedulability, Performance, and Time. In this paper we intend to further contribute to the integration of UML with non-functional aspects, and we devise a lightweight extension of UML (i.e., stereotypes, tagged values and constraints) to represent issues related to the reliability modeling of component-based systems. To a certain extent we lay on other profiles to make easier the embedding of such issues and to work toward a unifying UML profile for Quality of Service and Fault Tolerance. Our extensions mostly concern the fault forecasting task, which enables the specification of models describing the failure rates of components and combines them to obtain a reliability factor for the whole system. Example diagrams from an elevator system help to show how the concepts introduced here can be used to design reliability-integrated UML models of component-based systems. In order to demonstrate the practical benefits of our approach we also show how to fit the proposed tagged values into a reliability model.
Quality of Experience in Communications Ecosystem

Communications ecosystem covers a huge area from technical issues to business models and human behaviour. Due to this extreme diversity various societies need to discuss with each other, each of them using their own language. Engineers talk about network performance and quality of service, business people talk about average revenue per user and customer churn while behavioural scientists talk about happiness and experiences. Thus, everyone who wants to understand, or even analyze, the whole ecosystem, has to deal with all these diverse issues. In addition to the apparent communication problems, the main challenges of ecosystem analysis are to realistically model human behaviour, and to efficiently combine the models developed for different domains. A central concept when solving these problems is quality of experience (QoE). This paper sheds light on the role of QoE by means of a common framework that covers the whole communications ecosystem. Additionally, a research agenda for a holistic ecosystem analysis is outlined.
Discovering Genes Involved in Alcohol Dependence and Other Alcohol Responses

The genetic determinants of alcoholism still are largely unknown, hindering effective treatment and prevention. Systematic approaches to gene discovery are critical if novel genes and mechanisms involved in alcohol dependence are to be identified. Although no animal model can duplicate all aspects of alcoholism in humans, robust animal models for specific alcohol-related traits, including physiological alcohol dependence and associated withdrawal, have been invaluable resources. Using a variety of genetic animal models, the identification of regions of chromosomal DNA that contain a gene or genes which affect a complex phenotype (i.e., quantitative trait loci [QTLs]) has allowed unbiased searches for candidate genes. Several QTLs with large effects on alcohol withdrawal severity in mice have been detected, and fine mapping of these QTLs has placed them in small intervals on mouse chromosomes 1 and 4 (which correspond to certain regions on human chromosomes 1 and 9). Subsequent work led to the identification of underlying quantitative trait genes (QTGs) (e.g., Mpdz) and high-quality QTG candidates (e.g., Kcnj9 and genes involved in mitochondrial respiration and oxidative stress) and their plausible mechanisms of action. Human association studies provide supporting evidence that these QTLs and QTGs may be directly relevant to alcohol risk factors in clinical populations.
Extending the 5S Framework of Digital Libraries to support Complex Objects, Superimposed Information, and Content-Based Image Retrieval Services

Advanced services in digital libraries (DLs) have been developed and widely used to address the required capabilities of an assortment of systems as DLs expand into diverse application domains. These systems may require support for images (e.g., Content-Based Image Retrieval), Complex (information) Objects, and use of content at fine grain (e.g., Superimposed Information). Due to the lack of consensus on precise theoretical definitions for those services, implementation efforts often involve ad hoc development, leading to duplication and interoperability problems. This article presents a methodology to address those problems by extending a precisely specified minimal digital library (in the 5S framework) with formal definitions of aforementioned services. The theoretical extensions of digital library functionality presented here are reinforced with practical case studies as well as scenarios for the individual and integrative use of services to balance theory and practice. This methodology has implications that other advanced services can be continuously integrated into our current extended framework whenever they are identified. The theoretical definitions and case study we present may impact future development efforts and a wide range of digital library researchers, designers, and developers.
Making the invisible visible: A new diagnostic tool in endodontics

Development of an endodontic diagnostic tool that is objective and does not elicit any pain will improve chairside diagnosis and ensure patient comfort. This study utilized Red-Green-Blue (RGB) color analysis and Eulerian Video Magnification (EVM) to assess periapical tissues by revealing hidden data in videos of the intraoral tissues. The goal of this hypothesis generating pilot study was to determine whether these technologies detect changes in blood flow and aid in diagnosis of periapical inflammation (disease). We obtained videos of the oral mucosa overlying the periapical tissues of teeth with clinical signs of apical periodontitis (n=20). Controls (n=20) were the oral mucosa overlying periapical tissues of normal contralateral teeth. Videos were analyzed using RGB analysis and EVM via a high level computing language, MATLAB. Data were analyzed using Wilcoxon matched pairs signed rank test and significance set at p<0.05. RGB/EVM analysis were not able to detect a difference in blood flow in the intra-oral videos of both the diseased and control tissues. iv ACKNOWLEDGEMENTS
Circadian Rhythms of Oxidative Stress Markers and Melatonin Metabolite in Patients with Xeroderma Pigmentosum Group A

Xeroderma pigmentosum group A (XPA) is a genetic disorder in DNA nucleotide excision repair (NER) with severe neurological disorders, in which oxidative stress and disturbed melatonin metabolism may be involved. Herein we confirmed the diurnal variation of melatonin metabolites, oxidative stress markers, and antioxidant power in urine of patients with XPA and age-matched controls, using enzyme-linked immunosorbent assay (ELISA). The peak of 6-sulfatoxymelatonin, a metabolite of melatonin, was seen at 6:00 in both the XPA patients and controls, though the peak value is lower, specifically in the younger age group of XPA patients. The older XPA patients demonstrated an increase in the urinary levels of 8-hydroxy-2′-deoxyguanosine and hexanoyl-lysine, a marker of oxidative DNA damage and lipid peroxidation, having a robust peak at 6:00 and 18:00, respectively. In addition, the urinary level of total antioxidant power was decreased in the older XPA patients. Recently, it is speculated that oxidative stress and antioxidant properties may have a diurnal variation, and the circadian rhythm is likely to influence the NER itself. We believe that the administration of melatonin has the possibility of ameliorating the augmented oxidative stress in neurodegeneration, especially in the older XPA patients, modulating the melatonin metabolism and the circadian rhythm.
Environment, Area, and Diversification in the Species‐Rich Flowering Plant Family Iridaceae

Phylogenetic analyses provide a means to explore evolutionary explanations for regional variation in species richness. The environment might also explain much of the previously unexplained imbalance of phylogenetic trees. We use data on geographic distribution and phylogenetic affinity to examine correlates of species richness among genera of irises (family: Iridaceae). Irises display strong phylogenetic imbalance, with a few clades containing a disproportionate number of species, most notably those found in the dry Mediterranean climate of the Cape of South Africa. The abiotic environment and area are strong predictors of iris species richness, but environment alone is insufficient to explain the high diversity of Cape clades. One possible explanation is that the interaction between biological traits and environment resulted in the unusually high diversification rates in the region.
Does Internet Connectivity Affect Export Performance? Evidence from the Transition Economies

Over the past few years, many commentators have suggested that the Internet is one of the forces driving globalization. This paper tries to assess one aspect of these claims, looking at whether Internet access appears to affect the export performance of enterprises in low- and middle-income economies in Eastern Europe and Central Asia. The papers finds that even after controlling for self-selectivity bias and for factors that might affect both exports and Internet connectivity, enterprises with Internet access appear to export more than similar enterprises without access. Further, Internet access appears to affect industrial and service enterprises to similar degrees.
Bandwidth dimensioning in packet-based aggregation networks

Dimensioning of link capacities in packet networks in most cases is based on average traffic and some degree of over-provisioning. While mean traffic load is well understood and measurable, the appropriate degree of over-provisioning is a matter of guess and sometimes controversial disputes among experts. We show that traffic fluctuations around the mean value— and in consequence the required over-provisioning— are decisively influenced by the end user access capacity. A theoretical analysis of flow inter-arrival time and flow length probability distributions is used to derive a practical dimensioning rule for packet links in aggregation networks (LAN as well as WAN). The theory has been cross checked by real life experiments with real network equipment.
A New Method to Predict the Epidemiology of Fungal Keratitis by Monitoring the Sales Distribution of Antifungal Eye Drops in Brazil

Purpose Fungi are a major cause of keratitis, although few medications are licensed for their treatment. The aim of this study is to observe the variation in commercialisation of antifungal eye drops, and to predict the seasonal distribution of fungal keratitis in Brazil. Methods Data from a retrospective study of antifungal eye drops sales from the only pharmaceutical ophthalmologic laboratory, authorized to dispense them in Brazil (Opthalmos) were gathered. These data were correlated with geographic and seasonal distribution of fungal keratitis in Brazil between July 2002 and June 2008. Results A total of 26,087 antifungal eye drop units were sold, with a mean of 2.3 per patient. There was significant variation in antifungal sales during the year (p<0.01). A linear regression model displayed a significant association between reduced relative humidity and antifungal drug sales (R2 = 0.17,p<0.01). Conclusions Antifungal eye drops sales suggest that there is a seasonal distribution of fungal keratitis. A possible interpretation is that the third quarter of the year (a period when the climate is drier), when agricultural activity is more intense in Brazil, suggests a correlation with a higher incidence of fungal keratitis. A similar model could be applied to other diseases, that are managed with unique, or few, and monitorable medications to predict epidemiological aspects.