Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Expression Signatures Associated With Immune and Virological Responses to Therapeutic Vaccination With Dendritic Cells in HIV-Infected Individuals

The goal of HIV therapeutic vaccination is to induce HIV-specific immune response able to control HIV replication. We previously reported that vaccination with ex vivo generated Dendritic Cells (DC) loaded with HIV-lipopeptides in HIV-infected patients (n = 19) on antiretroviral therapy (ART) was well-tolerated and immunogenic. Vaccine-elicited HIV-specific T cell responses were associated with improved control of viral replication following antiretroviral interruption (ATI from w24 to w48). We show an inverse relationship between HIV-specific responses (production of IL-2, IL-13, IL-21, IFN-g, CD4 polyfunctionality, i.e., production of at least two cytokines) and the peak of viral load during ATI. Here we have performed an integrative systems vaccinology analysis including: (i) post vaccination (w16) immune responses assessed by cytometry, cytokine secretion, and Interferon-γ ELISPOT assays; (ii) whole blood and cellular gene expression measured during vaccination; and (iii) viral parameters following ATI, with the objective to disentangle the relationships between these markers and to identify vaccine signatures. During vaccination, 69 gene expression modules out of 260 varied significantly including (by order of significance) modules related to inflammation (Chaussabel Modules M3.2, M4.13, M4.6, M5.7, M7.1, M4.2), plasma cells (M4.11) and T cells (M4.1, 4.15). Cellular immune responses were positively correlated to genes belonging to T cell functional modules (M4.1, M4.15) at w16 and negatively correlated to genes belonging to inflammation modules (M7.1, M5.7, M3.2, M4.13, M4.2). More specifically, we show that prolonged increased abundance of inflammatory gene pathways related to toll-like receptor signaling (especially TLR4) are associated with both lower vaccine immune responses and control of viral replication post ATI. Further comparison of DC vaccine gene signatures with previously reported non-HIV vaccine signatures, such as flu and pneumococcal vaccines, revealed common pathways across vaccines. Overall, these results show that too long duration and too high intensity of vaccine inflammatory responses hamper the magnitude of effector responses.
How robust are Holocene treeline simulations? A model–data comparison in the European Arctic treeline region

Treeline encroachments and retractions can provide global‐scale feedbacks to the climate system, and treeline dynamics are therefore of great relevance for understanding global climate variability. To assess the accuracy of long‐term treeline simulations based on the generalized dynamic vegetation model LPJ‐GUESS, we simulate European Arctic treeline dynamics over the past 9000 years and compare the results with fossil‐based reconstructions. The results show that while LPJ‐GUESS is limited in its ability to capture species‐level current treeline patterns and past dynamics, it is generally able to realistically simulate the Holocene coniferous treeline changes with a cutoff biomass carbon of 2 C kg m−2. The model captures the northward expansion of the boreal forest during the mid Holocene and correctly simulates a treeline retreat in response to climate cooling during the last 3000 years. However, there are data–simulation disagreements particularly during the early Holocene, which mainly result from the differences between the two palaeoclimate model scenarios used to drive the simulations. We suggest that the spatial accuracy of the model could be improved by incorporating the influence of topographic features, the extent of the Arctic peatlands, the tree species life‐history characteristics, microclimate and other ecological factors. Copyright © 2013 John Wiley & Sons, Ltd.
Influence of Eurasian spring snow cover on Asian summer rainfall

The Eurasian snow cover anomaly in spring has been considered as one of the important factors affecting Asian summer monsoon variability. Using the long time series (1922–98) of Eurasian spring (March–April) snow cover (ESSC) reconstructed by Brown (2000. Journal of Climate 13: 2339) and snow cover (1973–98) and depth (1979–87) data from satellite observation, the influences of ESSC on the all‐India monsoon (June–September) rainfall (AIMR) and the summer rainfall over all parts of Asia are examined. It is found that the statistical relation between AIMR and ESSC changes over a multi‐decadal time scale. The negative correlation between them has increased markedly since the mid 1970s. The region where the summer rainfall has the strongest and most stable negative correlation with the preceding ESSC is located in northern Mongolia, south of Lake Baikal. The correlation between the summer rainfall and ESSC increases after the data are treated with a low‐pass filter, showing that the impact of snow cover may be seen more clearly with the removal of the effect of El Niño–southern oscillation. Comparative analyses for contrasting years with excessive and deficient snow cover show that the anomalies of ESSC occur mainly in northwestern Eurasia. In the years of excessive ESSC anomalies, cooling and a cyclonic circulation anomaly in the lower troposphere appear over the northern part of Eurasia, leading to a Rossby‐wave‐train‐like circulation response, then a weakened East Asia summer monsoon and deficient rainfall with an anticyclonic circulation anomaly south of Lake Baikal. Anomalies with opposite signs occur in the years of deficient snow cover. Copyright © 2002 Royal Meteorological Society.
Co‐location of the Downdip End of Seismic Coupling and the Continental Shelf Break

Along subduction margins, the morphology of the near shore domain records the combined action of erosion from ocean waves and permanent tectonic deformation from the convergence of plates. We observe that at subduction margins around the globe, the edge of continental shelves tends to be located above the downdip end of seismic coupling on the megathrust. Coastlines lie farther landward at variable distances. This observation stems from a compilation of well‐resolved coseismic and interseismic coupling data sets. The permanent interseismic uplift component of the total tectonic deformation can explain the localization of the shelf break. It contributes a short wave‐length gradient in vertical deformation on top of the structural and isostatic deformation of the margin. This places a hinge line between seaward subsidence and landward uplift above the downdip end of high coupling. Landward of the hinge line, rocks are uplifted in the domain of wave‐base erosion and a shelf is maintained by the competition of rock uplift and wave erosion. Wave erosion then sets the coastline back from the tectonically meaningful shelf break. We combine a wave erosion model with an elastic deformation model to illustrate how the downdip end of high coupling pins the location of the shelf break. In areas where the shelf is wide, onshore geodetic constraints on seismic coupling are limited and could be advantageously complemented by considering the location of the shelf break. Subduction margin morphology integrates hundreds of seismic cycles and could inform the persistence of seismic coupling patterns through time.
Evaluation of a Web-Based E-Learning Platform for Brief Motivational Interviewing by Nurses in Cardiovascular Care: A Pilot Study

Background Brief motivational interviewing (MI) can contribute to reductions in morbidity and mortality related to coronary artery disease, through health behavior change. Brief MI, unlike more intensive interventions, was proposed to meet the needs of clinicians with little spare time. While the provision of face-to-face brief MI training on a large scale is complicated, Web-based e-learning is promising because of the flexibility it offers. Objective The primary objective of this pilot study was to examine the feasibility and acceptability of a Web-based e-learning platform for brief MI (MOTIV@CŒUR), which was evaluated by nurses in cardiovascular care. The secondary objective was to assess the preliminary effect of the training on nurses’ perceived brief MI skills and self-reported clinical use of brief MI. Methods We conducted a single-group, pre-post pilot study involving nurses working in a coronary care unit to evaluate MOTIV@CŒUR, which is a Web-based e-learning platform for brief MI, consisting of two sessions lasting 30 and 20 minutes. MOTIV@CŒUR covers 4 real-life clinical situations through role-modeling videos showing nurse-client interactions. A brief introduction to MI is followed by role playing, during which a nurse practitioner evaluates clients’ motivation to change and intervenes according to the principles of brief MI. The clinical situations target smoking, medication adherence, physical activity, and diet. Nurses were asked to complete both Web-based training sessions asynchronously within 20 days, which allowed assessment of the feasibility of the intervention. Data regarding acceptability and preliminary effects (perceived skills in brief MI, and self-reported clinical use of conviction and confidence interventions) were self-assessed through Web-based questionnaires 30 days (±5 days) after the first session. Results We enrolled 27 women and 4 men (mean age 37, SD 9 years) in March 2016. Of the 31 participants, 24 (77%, 95% CI 63%–91%) completed both sessions in ≤20 days. At 30 days, 28 of the 31 participants (90%) had completed at least one session. The training was rated as highly acceptable, with the highest scores observed for information quality (mean 6.26, SD 0.60; scale 0–7), perceived ease of use (mean 6.16, SD 0.78; scale 0–7), and system quality (mean 6.15, SD 0.58; scale 0–7). Posttraining scores for self-reported clinical use of confidence interventions were higher than pretraining scores (mean 34.72, SD 6.29 vs mean 31.48, SD 6.75, respectively; P=.03; scale 10–50). Other results were nonsignificant. Conclusions Brief MI training using a Web-based e-learning platform including role-modeling videos is both feasible and acceptable according to cardiovascular care nurses. Further research is required to evaluate the e-learning platform in a randomized controlled trial. Trial Registration International Standard Randomized Controlled Trial Number (ISRCTN): 16510888; http://www.isrctn. com/ISRCTN16510888 (Archived by WebCite at http://www.webcitation.org/6jf7dr7bx)
FECUNDITY OF NORTHERN SHRIMp, PANDALUS BOREALIS, (CRUSTACEA, DECAPODA) IN AREAS OF THE NORTHWEST ATLANTIC

Fecundity of the northern shrimp, Pandalus borealis, and relationships between number of eggs and carapace length were determined from 15 samples taken in 9 areas of the Northwest Atlantic. The sam­ pling area extended from Davis Strait to the south coast of Newfoundland. Comparisons of samples suggested that fecundity levels can vary between seasons, years, and areas. A relationship between egg production and environmental temperature was not evident from available samples. The northern or pink shrimp, Pandalus borealis, is a protandric hermaphrodite with a circumboreal distribution. In the Northwest Atlantic, it occurs from about lat. 75°N at West Greenland to about lat. 42°N at Georges Bank (Squires 1970). Fecun­ dity of this species in the North Atlantic has been studied in southern Norway (Rasmussen 1953), northern Norway (Thomassen 1977), the North Sea (Allen 1959), Iceland (Skt1lad6ttir et al. 1978), West Greenland (Horsted and Smidt 1956), Barents Sea (Teigsmark 1983), and Gulf of Maine (Haynes and Wigley 1969). Bottom water temperatures recorded at depths where shrimp samples were collected dur­ ing these studies varied considerably between areas but were within the range of tolerance for survival of adults as reported by Allen in 1959 (-1.68" to 11.13°C). This paper provides information on the fecundity of P. borealis in the Northwest Atlantic. Samples were collected in areas of known shrimp concentra­ tion off Baffin Island, in the eastern Hudson Strait and Labrador Sea, and off the south coast of New­ foundland. Bottom temperatures at sampling sites also varied between these areas but were confined to the lower half of the tolerance range «7°C). Com­ parisons are made between selected combinations of the data sets presented. The possible effects of ambient temperature on fecundity levels also are considered.
New Algal Records from the Arabian Gulf Coast of Saudi Arabia

The marine algal flora of the Arabian (Persian) Gulf received little attention than other marine water bodies. In this paper a total of 26 species are reported for the first time as occurring in the Arabian Gulf coast of Saudi Arabia, including 13 species as new records for the Gulf. These species related to Chlorophyceae (8), Bacillariophyceae (6), Phaeophyceae (4) and Rhodophyceae (8). Description of these newly reported species were provided in the text.
Re-weighting EUROMOD for demographic change: an application on Slovenian and Lithuanian data

This paper discusses an application of re-weighting to account for demographic change within a comparative micro-simulation setting. We use the Slovenian and Lithuanian components of the EUROMOD micro-simulation model with data referring to demographic characteristics of the population in 2010 to test the proposed procedures. The data are re-weighted to reflect demographic change up to 2012 and 2020 as indicated in the Eurostat Population Projections (Europop).
Treatment of wastewater from rubber industry in Malaysia

Presently, Malaysia is the third largest rubber producer in the world, whereby the rubber industry is an economically and socially significant industry. Rubber industry consumes large volumes of water, uses chemicals and other utilities and produces enormous amounts of wastes and effluent. Discharge of untreated rubber effluent to waterways resulted in water pollution that affected the human health. With a new global trend towards a sustainable development, the industry needs to focus on cleaner production technology, waste minimization, utilization of waste, resource recovery and recycling of water. The present work aims at highlighting various technologies that currently have been used for treatment of rubber effluent in Malaysia. The work introduces the basis of these processes including their benefits and also problems. It also adheres to the future trends of rubber effluent treatment in Malaysia by reviewing various treatment technologies for natural rubber industry implemented by Thailand, the world largest rubber producer. These new and effective effluent treatment methods would minimize environmental pollution of rubber industry and bring it to become sustainable and environmental friendly.
A secure design of WoT services for smart cities. (Conception sécurisée de services IoT pour les villes connectées)

WebRTC est une technologie recente de communication qui permet d’etablir des echanges multimedia conversationnels directement entre navigateurs. Nous nous interessons dans cette these a des locuteurs dans un Smart Space (SS) defini comme un environnement centre-utilisateur instrumente par unensemble de capteurs et d’actionneurs connectes. Nous analysons les capacites necessaires pour permettre a un participant d’une session WebRTC d’impliquer dans cette meme session, les flux induits par les objets connectes appartenant au SS d’un utilisateur quelconque de la session. Cette approche recele un gisement de nombreux nouveaux usages. Nous limitons notre analyse a ceux concernant l’exercice distant d’une expertise et d’un savoir-faire. Techniquement, il s’agit d’articuler de facon controlee WebRTC et IoT/WoT. Nous procedons a une extension de WebRTC par WoT pour fournir a tout utilisateur d’une session WebRTC, un acces aux objets connectes du SS de tout autre participant a la session, en mettant l’accent sur la securisation de cet acces ainsi que sur sa conformite aux exigences de respect de la vie privee (RGPD) de l’utilisateur concerne. Le positionnement de notre approche dans le contexte des services de communication operant dans les villes connectees, impose la prise en compte de SSs multiples et varies induisant chacun ses propres politiques de routage et de securite. Pour repondre a nos objectifs, il devient necessaire au cours d’une session WebRTC, d’identifier, selectionner, deployer et appliquer les regles de routage et de securite de facon a garantir un acces rapide et securise aux differents SSs concernes et distribues sur tout le reseau. Nous developpons une architecture originale repondant a ces besoins et integrant un controleur SDN du fait de l’etroite imbrication entre les problematiques de routage et de securite. Un prototype illustrant notre approche a ete mis en oeuvre et teste afin d’evaluer la performance et la securite du systeme. Nous illustrons finalement notre approche dans le domaine de la sante en demontrant son apport pour gerer une infrastructure de grande taille telle qu’un hopital.
Statistical Genomics: Linkage, Mapping, and QTL Analysis

Introduction Forward Introducing Genomics Statistical Genomics Related Books Biology in Genomics Introduction Mendelian Genetics and Cytogenetics Population Genetics Quantitative Genetics Molecular Genetics Exercises Introduction to Genomics Genome Genomics Genetic Markers Exercises Statistics in Genomics Introduction Distribution Likelihood Hypothesis Test Estimation Sample Size Determination Summary Exercises Single-Locus Models Introduction Expected Segregation Ratio Marker Screening Natural Population Exercises Two-Locus Models I: Controlled Cross Introduction Linkage Detection Recombination Frequency Estimation Statistical Properties Sample Size Consideration Dominant Markers in F2 Progeny Violation of Assumptions Summary Exercises Two-Locus Model II: Natural Population Introduction Linkage Phase Problem Mixture of Self and Random Mating Exercises Two-Locus Model III: Using Disequilibrium Introduction Linkage Disequilibrium Transmission Disequilibrium Test Other Disequilibrium Based Analysis Estimation of Recombination Frequency Exercises Linkage Grouping and Locus Ordering Introduction Linkage Grouping Three-Locus Ordering Multiple-Locus Ordering Probability of Estimated Locus Orders Exercise Multi-Locus Model Introduction Three-Locus Model Map Function Multi-Locus Map Distance Marker Coverage and Map Density Exercises Linkage Map Merging Introduction Factors Related to Linkage Map Merging Hypothesis on Gene Orders Linkage Map Pooling Exercises QTL Mapping I: Introduction History Quantitative Genetics Models Example Data Exercise QTL Mapping II: Single-Marker Analysis Rationale Single-Marker Analysis in Backcross Progeny Single Marker Analysis Using F2 Progeny Summary Exercises QTL Mapping III: Interval Mapping Introduction Interval Mapping Using Backcross Progeny Interval Mapping Using F2 Progeny Composite Interval Mapping Summary Exercises QTL Mapping IV: Natural Population Introduction Open-Pollinated Populations Sib-Pair Method Exercises QTL Mapping V: Power Introduction Single QTL Detection Power Multiple QTL Exercises QTL Mapping VI: Future Considerations Problems with QTL Mapping QTL Resolution Mapping Strategies What are QTL Future QTL Mapping Exercises Computer Tools Computer Tools for Genomic Data Analysis Future Considerations PGRI (Plant Genome Research Initiative Resampling and Simulation in Genomics Introduction Resampling Computer Simulation Mapping Population Simulation Exercises Bibliography Author Index Subject Index
Protecting data confidentiality combining data fragmentation, encryption, and dispersal over a distributed environment. (Protection de la confidentialité des données par un ensemble de méthodes de fragmentation, chiffrement, et dispersion dans un environnement distribué)

This thesis dissertation revisits state-of-the-art fragmentation techniques making them faster and cost-efficient. The main focus is put on increasing data confidentiality without deteriorating the processing performance. The ultimate goal is to provide a user with a set of fast fragmentation methods that could be directly applied inside an industrial context to reinforce the confidentiality of the stored data and/or accelerate the fragmentation processing. First, a rich survey on fragmentation as a way of preserving data confidentiality is presented. Second, the family of all-or-nothing transforms is extended with three new proposals. They all aim at protecting encrypted and fragmented data against the exposure of the encryption key but are designed to be employed in three different contexts: for data fragmentation in a multi-cloud environment, a distributed storage system, and an environment composed of one storage provider and one private device. Third, a way of accelerating fragmentation is presented that achieves better performance than data encryption using the most common symmetric-key encryption algorithm. Fourth, a lightweight fragmentation scheme based on data encoding, permuting, and dispersing is introduced. It totally gets rid of data encryption allowing the fragmentation to be performed even faster; up to twice as fast as data encryption. Finally, fragmentation inside sensor networks is revisited, particularly in the Unattended Wireless Sensor Networks. The main focus in this case is put not solely on the fragmentation performance, but also on the reduction of storage and transmission costs by using data aggregation.
Safe Assets

A safe asset’s real value is insulated from shocks, including declines in GDP from rare macroeconomic disasters. However, in a Lucas-tree world, the aggregate risk is given by the process for GDP and cannot be altered by the creation of safe assets. Therefore, in the equilibrium of a representative-agent version of this economy, the quantity of safe assets will be nil. With heterogeneity in coefficients of relative risk aversion, safe assets can take the form of private bond issues from low-risk-aversion to high-risk-aversion agents. The model assumes Epstein-Zin/Weil preferences with common values of the intertemporal elasticity of substitution and the rate of time preference. The model achieves stationarity by allowing for random shifts in coefficients of relative risk aversion. We derive the equilibrium values of the ratio of safe to total assets, the shares of each agent in equity ownership and wealth, and the rates of return on safe and risky assets. In a baseline case, the steady-state risk-free rate is 1.0% per year, the unlevered equity premium is 4.2%, and the quantity of safe assets ranges up to 15% of economy-wide assets (comprising the capitalized value of GDP). A disaster shock leads to an extended period in which the share of wealth held by the low-risk-averse agent and the risk-free rate are low but rising, and the ratio of safe to total assets is high but falling. In the baseline model, Ricardian Equivalence holds in that added government bonds have no effect on rates of return and the net quantity of safe assets. Surprisingly, the crowding-out coefficient for private bonds with respect to public bonds is not 0 or -1 but around -0.5, a value found in some existing empirical studies.
EFF-FAS: enhanced fruit fly optimisation based search and tracking by flying ad hoc swarm

Flying ad hoc swarms are networks formed by autonomously operated aerial nodes. These nodes can be simple high altitude platforms or specifically configured unmanned aircraft (UA). Such networks are autonomous, temporary and mission dependent. One of the major applications of this ad hoc swarm formations is the efficient search and tracking of an area without any redundancy and overlapping. Non-redundant cell tracking is a computationally expensive task, which requires optimisation strategies to be adopted during a search process. Incorporating fruit fly optimisation (FOA) algorithm to a strategic search and track operation simplifies the complexity of the overall system. In this paper, FOA is extended in terms of its applicability by modifying the procedures of the algorithm to allow its applicability to an aerial swarm for non-redundant search over a predefined area with lower complexity. Network simulations demonstrate the effectiveness of the proposed approach towards search and track operations.