Miracle-dz/UniFAR-FTUs huggingface dataset:
Mathematical Modeling of Streptococcus pneumoniae Colonization, Invasive Infection and Treatment

Streptococcus pneumoniae (Sp) is a commensal bacterium that normally resides on the upper airway epithelium without causing infection. However, factors such as co-infection with influenza virus can impair the complex Sp-host interactions and the subsequent development of many life-threatening infectious and inflammatory diseases, including pneumonia, meningitis or even sepsis. With the increased threat of Sp infection due to the emergence of new antibiotic resistant Sp strains, there is an urgent need for better treatment strategies that effectively prevent progression of disease triggered by Sp infection, minimizing the use of antibiotics. The complexity of the host-pathogen interactions has left the full understanding of underlying mechanisms of Sp-triggered pathogenesis as a challenge, despite its critical importance in the identification of effective treatments. To achieve a systems-level and quantitative understanding of the complex and dynamically-changing host-Sp interactions, here we developed a mechanistic mathematical model describing dynamic interplays between Sp, immune cells, and epithelial tissues, where the host-pathogen interactions initiate. The model serves as a mathematical framework that coherently explains various in vitro and in vitro studies, to which the model parameters were fitted. Our model simulations reproduced the robust homeostatic Sp-host interaction, as well as three qualitatively different pathogenic behaviors: immunological scarring, invasive infection and their combination. Parameter sensitivity and bifurcation analyses of the model identified the processes that are responsible for qualitative transitions from healthy to such pathological behaviors. Our model also predicted that the onset of invasive infection occurs within less than 2 days from transient Sp challenges. This prediction provides arguments in favor of the use of vaccinations, since adaptive immune responses cannot be developed de novo in such a short time. We further designed optimal treatment strategies, with minimal strengths and minimal durations of antibiotics, for each of the three pathogenic behaviors distinguished by our model. The proposed mathematical framework will help to design better disease management strategies and new diagnostic markers that can be used to inform the most appropriate patient-specific treatment options.
International Macroeconomic Dynamics

For a long time, the study of macroeconomics has focused almost exclusively on a closed economy and downplayed the role of international transactions. Today, however, researchers recognize that one cannot fully understand domestic macroeconomic relationships without considering the global economy within which each country operates. Increasingly, economists are treating international transactions as an integral part of the macroeconomic system, and international macroeconomics has become an area of intensive research activity. International Macroeconomic Dynamics provides extensive applications of important macroeconomic dynamic models to the international economy. It adopts the main contemporary macroeconomic framework, the representative agent model, and develops a series of models of increasing complexity. The author considers both small and large economies and analyzes them in both deterministic and stochastic contexts. The emphasis is very much on the development of the analytical models; a novel feature is the extensive use of continuous-time stochastic methods. While the author applies the models to a range of important policy issues, particularly issues of fiscal policy, the reader is invited to view the analyses as blueprints for other applications.
Listening to the patients: using participatory design in the development of a cardiac telerehabilitation web portal.

Background Cardiovascular disease is the leading cause of all deaths worldwide. Cardiac rehabilitation is an effective approach for preventing secondary complications, but it remains a complex intervention because of the need for lifestyle changes. One solution is to employ interactive telerehabilitation or eHealth web portals. However, these have not been implemented as intended by developers. The aim of this study was to evaluate the design and usability of a cardiac telerehabilitation web portal, called the 'HeartPortal', for use among heart failure (HF) patients. Methods The HeartPortal was designed using participatory design (PD). The design process involved HF patients, their relatives, healthcare professionals (HCP), healthcare company specialists and researchers. Self-determination theory (SDT) was used to enable the design to elicit intrinsic motivation within the patients. With eHealth literacy skills in mind, the goal of the HeartPortal was to successfully target the end-users. The PD process and data collection techniques included cultural probes, workshops, participant-observation, questionnaires, and problem-solving tasks. Results The PD process helped us design an interactive web portal, the HeartPortal. Based on participants' feedback, the design incorporated features such as being able to make notes and to communicate with HCP, view data from self-tracking devices in a graphic form, and to obtain information on rehabilitation in the form of text, audio, and video. More than half of those testing the HeartPortal found that it was easy to navigate, and most of the users stated that it had an excellent structure and that using it could possibly improve their condition. Conclusions Overall, the HeartPortal was found to be logical and easy to navigate and will now be tested in a clinical trial within the Future Patient Telerehabilitation Program.
Phonation Contrast in Two Register Contrast Languages and Its Influence on Vowel Quality and Tone

This study aims to provide a better understanding of the phonetic realization of phonation contrast in register contrast languages and its interaction with vowels and tones by comparing the production of two Yi languages: Southern Yi and Bo. Results show that 1) Electroglottographic contact quotient is the essential mechanism of the phonation contrast in both languages; 2) Phonation mainly influences the vowel space in Yi with tense vowels lower in tongue position; 3) by contrast, the Bo phonation contrast leads to significant F0 differences within each tonal category.
Advanced Nonlinear Control of Three Phase Shunt Active Power Filter

— The problem of controlling three-phase shunt active power filter (TPSAPF) is addressed in this paper in presence of nonlinear loads of rectifier type. The control objective is twofold: (i) compensation of harmonic currents and the reactive power absorbed by the nonlinear load; (ii) regulation the DC bus voltage of the converter. A nonlinear controller which has a cascade structure comprises two loops, an inner-loop which is formed by two non-linear regulators is designed, using the Backstepping technique, to provide the harmonic compensation and an outer-loop is designed to regulate the DC bus voltage of the converter. Controller performances are illustrated by numerical simulation in Matlab/Simulink environment.
IEPC-2002-030 Interactions within a Cluster of Low Power Hall

This work examines a long duration Hall thruster start transient caused by the vacuum chamber environment. During operation of a cluster of four Hall thrusters, large anode discharge fluctuations, visible as increased anode current and a more diffuse plume structure, occur in an apparently random manner. For single thrusters, the transient appears as a smoothly decaying elevated anode current with a diffuse plume which persists for less than 500 seconds. The start transient is characterized by severe 18 kHz oscillations which dominate the anode discharge. This contrasts with typical steady state behavior of a strong DC component overlaid with a low amplitude 25 kHz component. The main discharge chamber has been previously determined to be the source of this behavior. The work shows that transient appears to be a result of the release of water previously hydrated on to on the surface layer of the boron nitride acceleration channel insulator. This material is a declared work of the U.S. Government and is not subject to copyright protection in the United States. 2 thrust and impulse from an initial short duration firing. For this reason, understanding the characteristics of this anode current start transient may also be important for missions with short duration initial firings.
Is negative mass media news always associated with outgroup prejudice? The buffering role of direct contact

We examined the association of the combination of direct intergroup contact and mass media news with attitudes toward immigrants and gay people in Italy, hypothesizing that direct intergroup contact would buffer the negative association between media news and attitudes, but only when contact was intimate or positive. Measuring contact variables and attitudes toward immigrants (Study 1, N = 428; Study 2, N = 426) and gay men and women (Study 3, N = 220), we found that intimate and positive direct intergroup contact was associated with more positive attitudes toward outgroup members, whereas exposure to negative news was related to more negative attitudes. Moreover, our results supported the buffering hypothesis, as the negative association between negative news and intergroup attitudes was significantly weaker amongst respondents with higher levels of intimate and positive intergroup contact.
A Method of Detecting Code Cloning in Open Source Software

In this paper, we discuss an approach to detect code copying in open source software. This approach generates a small fingerprint that includes the main features of the class files contained in a Java Archive (Jar) file. By comparing the intrinsic and extrinsic features of the class files, the approach can find the cloned code in anonymous Jar files. This approach provides a tool to detect cloned code correctly and effectively
Phase-Lead Stabilization of Force-Projecting Master-Slave Systems With a New Sliding Mode Filter

The force-projecting master-slave (MS) control scheme is the reversed implementation of the conventional force-reflecting scheme. This paper presents a method to stabilize force projecting MS systems using a linear phase-lead compensator and a new nonlinear filter. The nonlinear filter is a modified version of Jin et al.'s parabolic sliding mode filter, which produces a relatively small phase lag. Some numerical properties of the new filter are presented. The filter is then applied to an experimental MS system composed of two industrial manipulators. A force scaling factor of 25 was achieved with maintaining the stability.
Genomic Instability Within Centromeres of Interspecific Marsupial Hybrids

Several lines of evidence suggest that, within a lineage, particular genomic regions are subject to instability that can lead to specific types of chromosome rearrangements important in species incompatibility. Within family Macropodidae (kangaroos, wallabies, bettongs, and potoroos), which exhibit recent and extensive karyotypic evolution, rearrangements involve chiefly the centromere. We propose that centromeres are the primary target for destabilization in cases of genomic instability, such as interspecific hybridization, and participate in the formation of novel chromosome rearrangements. Here we use standard cytological staining, cross-species chromosome painting, DNA probe analyses, and scanning electron microscopy to examine four interspecific macropodid hybrids (Macropus rufogriseus × Macropus agilis). The parental complements share the same centric fusions relative to the presumed macropodid ancestral karyotype, but can be differentiated on the basis of heterochromatic content, M. rufogriseus having larger centromeres with large C-banding positive regions. All hybrids exhibited the same pattern of chromosomal instability and remodeling specifically within the centromeres derived from the maternal (M. rufogriseus) complement. This instability included amplification of a satellite repeat and a transposable element, changes in chromatin structure, and de novo whole-arm rearrangements. We discuss possible reasons and mechanisms for the centromeric instability and remodeling observed in all four macropodid hybrids.
AEROSOL EFFECTS ON SATELLITE RETRIEVALS OF CLOUD OPTICAL PROPERTIES IN THE

Satellite retrievals of cloud optical depth and effective radius are shown to be underestimated in the South Atlantic Ocean, where biomass-burning aerosols typically reside above low-level, liquid water stratocumulus clouds. A radiative transfer model is used to calculate top of the atmosphere (TOA) reflectances for a case where an aerosol layer is elevated above a liquid cloud in the South Atlantic Ocean. Both absorbing and scattering aerosols are modeled at varying aerosol optical depths (AOD) at 0.86 μm and 2.10 μm. Optimal estimation methods are used to convert reflectance pairs into a retrieved cloud optical depth and effective radius, similar to the Moderate Resolution Imaging Spectroradiometer (MODIS, aboard Aqua satellite) algorithm. Absorbing aerosols lead to an underestimation of the retrieved cloud optical depth by up to 60 – 80%, while scattering aerosols can lead to an overor underestimate of the optical depth by up to 10%, depending on the cloud thickness. Effective radius retrievals can be overand underestimated if absorbing aerosols are present, depending on the AOD. Scattering aerosols result in an overestimation of effective radius by up to 0 – 10%. A-Train satellite observations from August 2006 – December 2010 in the South Atlantic Ocean also show that the MODIS biases in cloud optical depth and effective radius are likely affecting retrieved properties and hence retrieved cloud droplet number concentrations when the aerosol layer is vertically separated from the cloud.
Recovering 3 D Shape and Motion from Image Streams using Non-Linear Least Squares

The simultaneous recovery of 3D shape and motion from image sequences is one of the more difficult problems in computer vision. Classical approaches to the problem rely on using algebraic techniques to solve for these unknowns given two or more images. More recently, a batch analysis of image streams (the temporal tracks of distinguishable image features) under orthography has resulted in highly accurate reconstructions. We generalize this approach to perspective projection and partial or uncertain tracks by using a non-linear least squares technique. While our approach requires iteration, it quickly converges to the desired solution, even in the absence of a pri ri knowledge about the shape or motion. Important features of the algorithm include its ability to handle partial point tracks, to use line segment matches and point matches simultaneously, and to use an object-centered representation for faster and more accurate structure and motion recovery. We also show how a projective (as opposed to scaled rigid) structure can be recovered when the camera calibration parameters are unknown.
Reviewing the Reviewers: Characterizing Biases and Competencies using Socially Meaningful Attributes

We propose augmenting collaborative reviewing systems with an automatic annotation capability that helps users interpret reviews. Given an item and its review by a certain author, our approach is to find a reference set of similar items that is both easy to describe and meaningful to users. Depending on the number of available same-author reviews of items in the reference set, an annotation produced by our system may consist of similar items that the author has reviewed, the rank of the reviewed item among items in this set, a comparison of the author’s scores to averages, and other similar information that indicate the biases and competencies of the reviewer. We validate our approach in the context of movie reviews and describe an algorithm that, for example, presented with a review of a Woody Allen comedy, is able to derive annotations of the form: “This reviewer rates this movie better than 4 out of 6 other Woody Allen comedies that he rated” or ”This is the only Woody Allen comedy among the 29 movies rated by this reviewer” or “This reviewer rated 85 comedies. He likes this movie more than 60% of them. He likes comedies less than the average reviewer. ”
Adp-Ribosylation Factor 6 and Endocytosis at the Apical Surface of Madin-Darby Canine Kidney Cells

We report that the small GTPase, ADP-ribosylation factor 6 (ARF6), is present only on the apical surface of polarized MDCK epithelial cells. Overexpression of a mutant of ARF6, ARF6–Q67L, which is predicted to be in the GTP-bound form, stimulates endocytosis exclusively at this surface. Surprisingly, overexpression of the mutant ARF6–T27N, which is predicted to be in the GDP-bound form, also stimulated apical endocytosis, though to a lesser extent. ARF6-stimulated endocytosis is inhibited by a dominant-negative form of dynamin, or a dominant-negative hub fragment of clathrin heavy chain, indicating that it is mediated by clathrin. Correspondingly, overexpression of either mutant of ARF6 leads to an increase in the number of clathrin-coated pits at the apical plasma membrane. When ARF6–Q67L is overexpressed in the presence of the dominant-negative dynamin, the ARF6–Q67L colocalizes with clathrin and with IgA bound to its receptor. We conclude that ARF6 is an important modulator of clathrin-mediated endocytosis at the apical surface of epithelial cells.
Capture fields: modularity in a stream-relational event processing langauge

Complex Event Processing Platforms are a popular technology for developing real-time responsive information processing systems. Because these systems are domain specific, the programming languages used to develop them are consumed by many different users, from domain experts to systems programmers, who want to build applications quickly and change them often. In many application domains, such as trading and system monitoring, data volumes and application constraints make performance critical. This leads to competing priorities between developer productivity and application performance. Support for modular components and component reuse is one area where this tradeoff is apparent. The preexisting module system in the StreamBase StreamSQL programming language was developed for performance, enabling whole program analysis and static typing. It suffered from limitations in error reporting and module reusability. We present newly developed extensions to the StreamSQL module system which allow modules to be used in a variety of environments, hygienically preserving any information that must pass through unchanged. This approach preserves application performance and type-safety while im- proving reusability of modules and increasing error transparency, as measured by the average time taken to find and fix certain kinds of errors. We conclude that a stream-relational language like StreamSQL can have flexible and performant type-safe modules, and that programmers of all abilities benefit from this functionality.
Mining Scholarly Communication and Interaction on the Social Web

The explosion of Web 2.0 platforms including social networking sites such as Twitter, blogs and wikis affects all web users: scholars included. As a result, there is a need for a comprehensive approach to gain a broader understanding and timely signals of scientific communication as well as how researchers interact on the social web. Most current work in this area deals with either a low number of researchers and heavily relies on manual annotation or large-scale analysis without deep understanding of the underlying researcher population. In this proposal, we present a holistic approach to solve these problems. This research proposes novel methods to collect, filter, analyze and make sense of scholars and scholarly communication by integrating heterogeneous data sources from fast social media streams as well as the academic web. Applying reproducible research, contributing applications and data sets, the thesis proposal strives to add value by mining the social web for social good.
Parsing-based automatic Chinese term extraction

Term extraction is to automatically extract domain specific terms from a given corpus. Previous works of term extraction only focus on the termhood measurement, rather than the nested candidates. Different from previous methods which identify the nested candidates using the surface lexical information, such as word form characteristics, or the grammatical analysis described as the part-of-speech(POS) sequence patterns, this paper proposes a parsing-based approach to extract noun phrases as nested candidates, therefore, can fully explore the syntactic structure information. Experiments show that the proposed approach performs equally well as the conventional POS sequence patterns approach in the recall of candidates, but with fewer impossible ones. Combined with C-value as the termhood measure, the proposed approach obtains consistent improvements in the rank list of terms.
Data inversion for hyperspectral objects in astronomy

We present an original method for reconstruction of hyperspectral objects (two spatial and one spectral dimensions) from data provided by the infrared slit spectrograph on board the Spitzer Space Telescope. The originality of the work lies in the fact that bothmeasurementmodel and inversionmethod are tackled in continuous (spatial and spectral) variables. The method is built in a deterministic regularization framework and enable to achieve both deconvolution and over-resolution. Results show that the method is able to evidence spatial structures not detectable by means of conventional methods. The spatial resolution is shown to be improved by a factor 1.5. We discuss our data processing approach for the new generation of infrared to millimeter space observatories launched in 2009 (Herschel and Planck).
Possible Usage of Sentiment Analysis for Calculating Vectors of Felific Calculus

In this paper we introduce an algorithm for affective reasoning based on Bent ham's Felific Calculus known also as the hedonic calculus. Knowledge recquired for the task is retrived from a blog corpus by means of sentiment analysis on sentences containing an action or state input. This approach allows a machine to gather information on how usually other people feel when something happens, why people did it and what could happen after the act. Such knowledge is important for understanding actions of others, and for acquiring emphatic skills by a machine. In addition to emotion categorization of Nakamura, we introduce two lexicons based on McDougall's instinct classification and Kohlbergian stages of moral development, then show some basic efficiency of the retrieved knowledge.
Analysis of the MSVMO method - the probabilistic SVM outputs

Number of experiments has shown that for classification problems, if SVM models trained over the same data set have similar SVM outputs with respect to a given input vector x, the values of the corresponding MSVMO probabilities [3] have small differences. This means that the information from the MSVMO method from different SVM models trained over the same data set is essentially the same.
Best-Response Learning of Team Behaviour in Quake III

This paper proposes a mechanism for learning a best-response strategy to improve opponent intelligence in team-oriented commercial computer games. The mechanism, called TEAM2, is an extension of the TEAM mechanism for team-oriented adaptive behaviour explored in [Bakkes et al. , 2004] and focusses on the exploitation of relevant gameplay experience. We compare the performance of the TEAM2 mechanism with that of the original TEAM mechanism in simulation studies. The results show the TEAM2 mechanism to be better able to learn team behaviour. We argue that the application as an online learning mechanism is hampered by occasional very long learning times due to an improper balance between exploitation and exploration. We conclude that TEAM2 improves opponent behaviour in team-oriented games and that for online learning the balance between exploitation and exploration is of main importance.