Miracle-dz/UniFAR-FTUs huggingface dataset:
Lymph Node Cellular and Viral Dynamics in Natural Hosts and Impact for HIV Cure Strategies

Combined antiretroviral therapies (cARTs) efficiently control HIV replication leading to undetectable viremia and drastic increases in lifespan of people living with HIV. However, cART does not cure HIV infection as virus persists in cellular and anatomical reservoirs, from which the virus generally rebounds soon after cART cessation. One major anatomical reservoir are lymph node (LN) follicles, where HIV persists through replication in follicular helper T cells and is also trapped by follicular dendritic cells. Natural hosts of SIV, such as African green monkeys and sooty mangabeys, generally do not progress to disease although displaying persistently high viremia. Strikingly, these hosts mount a strong control of viral replication in LN follicles shortly after peak viremia that lasts throughout infection. Herein, we discuss the potential interplay between viral control in LNs and the resolution of inflammation, which is characteristic for natural hosts. We furthermore detail the differences that exist between non-pathogenic SIV infection in natural hosts and pathogenic HIV/SIV infection in humans and macaques regarding virus target cells and replication dynamics in LNs. Several mechanisms have been proposed to be implicated in the strong control of viral replication in natural host’s LNs, such as NK cell-mediated control, that will be reviewed here, together with lessons and limitations of in vivo cell depletion studies that have been performed in natural hosts. Finally, we discuss the impact that these insights on viral dynamics and host responses in LNs of natural hosts have for the development of strategies toward HIV cure.
Using Spatial Reinforcement Learning to Build Forest Wildfire Dynamics Models From Satellite Images

Machine learning algorithms have increased tremendously in power in recent years but have yet to be fully utilized in many ecology and sustainable resource management domains such as wildlife reserve design, forest fire management and invasive species spread. One thing these domains have in common is that they contain dynamics that can be characterized as a Spatially Spreading Process (SSP) which requires many parameters to be set precisely to model the dynamics, spread rates and directional biases of the elements which are spreading. We present related work in Artificial Intelligence and Machine Learning for SSP sustainability domains including forest wildfire prediction. We then introduce a novel approach for learning in SSP domains using Reinforcement Learning (RL) where fire is the agent at any cell in the landscape and the set of actions the fire can take from a location at any point in time includes spreading North, South, East, West or not spreading. This approach inverts the usual RL setup since the dynamics of the corresponding Markov Decision Process (MDP) is a known function for immediate wildfire spread. Meanwhile, we learn an agent policy for a predictive model of the dynamics of a complex spatially-spreading process. Rewards are provided for correctly classifying which cells are on fire or not compared to satellite and other related data. We examine the behaviour of five RL algorithms on this problem: Value Iteration, Policy Iteration, Q-Learning, Monte Carlo Tree Search and Asynchronous Advantage Actor-Critic (A3C). We compare to a Gaussian process based supervised learning approach and discuss the relation of our approach to manually constructed, state-of-the-art methods from forest wildfire modelling. We also discuss the relation of our approach to manually constructed, state-of-the-art methods from forest wildfire modelling. We validate our approach with satellite image data of two massive wildfire events in Northern Alberta, Canada; the Fort McMurray fire of 2016 and the Richardson fire of 2011. The results show that we can learn predictive, agent-based policies as models of spatial dynamics using RL on readily available satellite images that other methods and have many additional advantages in terms of generalizability and interpretability.
A 50‐year high‐resolution atmospheric reanalysis over France with the Safran system

The assessment of regional climate change requires the development of reference long‐term retrospective meteorological datasets. This article presents an 8‐km‐resolution atmospheric reanalysis over France performed with the the Safran‐gauge‐based analysis system for the period 1958–2008. Climatological features of the Safran 50‐year analysis—long‐term mean values, inter‐annual and seasonal variability—are first presented for all computed variables: rainfall, snowfall, mean air temperature, specific humidity, wind speed and solar and infrared radiation. The spatial patterns of precipitation, minimum and maximum temperature are compared with another spatialization method, and the temporal consistency of the reanalysis is assessed through various validation experiments with both dependent and independent data. These experiments demonstrate the overall robustness of the Safran reanalysis and the improvement of its quality with time, in connection with the sharp increase in the observation network density that occurred in the 1990s. They also show the differentiated sensitivity of variables to the number of available ground observations, with precipitation and air temperature being the more robust ones. The comparison of trends from the reanalysis with those from homogenized series finally shows that if spatial patterns are globally consistent with both approaches, care must be taken when using literal values from the reanalysis and corresponding statistical significance in climate change detection studies. The Safran 50‐year atmospheric reanalysis constitutes a long‐term forcing datasets for land surface schemes and thus enables the simulation of the past 50 years of water resources over France. Copyright © 2009 Royal Meteorological Society
Optimus: an efficient dynamic resource scheduler for deep learning clusters

Deep learning workloads are common in today's production clusters due to the proliferation of deep learning driven AI services (e.g., speech recognition, machine translation). A deep learning training job is resource-intensive and time-consuming. Efficient resource scheduling is the key to the maximal performance of a deep learning cluster. Existing cluster schedulers are largely not tailored to deep learning jobs, and typically specifying a fixed amount of resources for each job, prohibiting high resource efficiency and job performance. This paper proposes Optimus, a customized job scheduler for deep learning clusters, which minimizes job training time based on online resource-performance models. Optimus uses online fitting to predict model convergence during training, and sets up performance models to accurately estimate training speed as a function of allocated resources in each job. Based on the models, a simple yet effective method is designed and used for dynamically allocating resources and placing deep learning tasks to minimize job completion time. We implement Optimus on top of Kubernetes, a cluster manager for container orchestration, and experiment on a deep learning cluster with 7 CPU servers and 6 GPU servers, running 9 training jobs using the MXNet framework. Results show that Optimus outperforms representative cluster schedulers by about 139% and 63% in terms of job completion time and makespan, respectively.
Effects of inspiratory muscle training in COPD patients: A systematic review and meta‐analysis

In chronic obstructive pulmonary disease (COPD), quality of life and exercise capacity are altered in relationship to dyspnea. Benefits of inspiratory muscle training (IMT) on quality of life, dyspnea, and exercise capacity were demonstrated, but when it is associated to pulmonary rehabilitation (PR), its efficacy on dyspnea is not demonstrated. The aim of this systematic review with meta‐analysis was to verify the effect of IMT using threshold devices in COPD patients on dyspnea, quality of life, exercise capacity, and inspiratory muscles strength, and the added effect on dyspnea of IMT associated with PR (vs. PR alone).
Influence of different fillers and SBS modified bituminous blends on fatigue, self-healing and thixotropic performance of mastics

The prediction of asphalt pavement performance is closely linked to the behaviour of mastic, consisting of filler and bitumen, which can be modelled as viscoelastic material. The purpose of this study is to investigate the effect of different fillers and bituminous blends on mastic fatigue response, considering recoverable phenomena in viscoelastic materials (thixotropy and self-healing) that concurrently occur. Three fillers (limestone, basalt and Portland cement) and three aged polymer modified bitumen contents (0%, 45% and 100%) were blended with a virgin polymer modified bitumen obtaining nine mastics characterised in terms of fatigue, self-healing and thixotropy using a Dynamic Shear Rheometer. Data obtained are analysed through a model previously adopted for polymer modified bitumens and mastics, allowing the determination of the fatigue endurance limit. Results show that the presence of filler with increasing particle density and/or Rigden voids causes a higher mastic stiffness without a clear trend on fatigue performance. In fact, great attention should be put on filler-bitumen interactions based on the physicochemical nature of filler. Moreover, whatever the filler considered, an enhancement in the fatigue endurance limit is detected in the mastics blended with a percentage of aged polymer modified bitumen (up to 45%), promoting the addition of Reclaimed Asphalt to obtain more performing and sustainable recycled mixtures.
Phase-based features for motor imagery brain-computer interfaces

Motor imagery (MI) brain-computer interfaces (BCIs) translate a subject's motor intention to a command signal. Most MI BCIs use power features in the mu or beta rhythms, while several results have been reported using a measure of phase synchrony, the phase-locking value (PLV). In this study, we investigated the performance of various phase-based features, including instantaneous phase difference (IPD) and PLV, for control of a MI BCI. Patterns of phase synchrony differentially appear over the motor cortices and between the primary motor cortex (M1) and supplementary motor area (SMA) during MI. Offline results, along with preliminary online sessions, indicate that IPD serves as a robust control signal for differentiating between MI classes, and that the phase relations between channels are relatively stable over several months. Offline and online trial-level classification accuracies based on IPD ranged from 84% to 99%, whereas the performance for the corresponding amplitude features ranged from 70% to 100%.
Voltage-driven, local, and efficient excitation of nitrogen-vacancy centers in diamond

Leveraging magnetoelastic coupling, we show a power efficient mechanism for exciting nitrogen-vacancy centers in diamond. Magnetic sensing technology has found widespread application in a diverse set of industries including transportation, medicine, and resource exploration. These uses often require highly sensitive instruments to measure the extremely small magnetic fields involved, relying on difficult-to-integrate superconducting quantum interference devices and spin-exchange relaxation-free magnetometers. A potential alternative, nitrogen-vacancy (NV) centers in diamond, has shown great potential as a high-sensitivity and high-resolution magnetic sensor capable of operating in an unshielded, room-temperature environment. Transitioning NV center–based sensors into practical devices, however, is impeded by the need for high-power radio frequency (RF) excitation to manipulate them. We report an advance that combines two different physical phenomena to enable a highly efficient excitation of the NV centers: magnetoelastic drive of ferromagnetic resonance and NV-magnon coupling. Our work demonstrates a new pathway that combine acoustics and magnonics that enables highly energy-efficient and local excitation of NV centers without the need for any external RF excitation and, thus, could lead to completely integrated, on-chip, atomic sensors.
Web-based Validation for Contextual Targeted Paraphrasing

In this work, we present a scenario where contextual targeted paraphrasing of sub-sentential phrases is performed automatically to support the task of text revision. Candidate paraphrases are obtained from a preexisting repertoire and validated in the context of the original sentence using information derived from the Web. We report on experiments on French, where the original sentences to be rewritten are taken from a rewriting memory automatically extracted from the edit history of Wikipedia.
ACL reconstruction with hamstring tendon autograft and accelerated brace-free rehabilitation: a systematic review of clinical outcomes

Objective To investigate the clinical outcomes after hamstring tendon autograft ACL reconstruction (ACLR) with accelerated, brace-free rehabilitation. Design Systematic review according to Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines. Data sources Embase, MEDLINE Ovid, Web of Science, Cochrane CENTRAL and Google scholar from 1 January 1974 to 31 January 2017. Eligibility criteria for selecting studies Study designs reporting outcomes in adults after arthroscopic, primary ACLR with hamstring autograft and accelerated, brace-free rehabilitation. Results Twenty-four studies were included in the review. The clinical outcomes after hamstring tendon autograft ACLR with accelerated brace-free rehabilitation were the following: (1) early start of open kinetic exercises at 4 weeks in a limited range of motion (ROM, 90°−45°) and progressive concentric and eccentric exercises from 12 weeks did not alter outcomes, (2) gender and age did not influence clinical outcomes, (3) anatomical reconstructions showed better results than non-anatomical reconstructions, (4) there was no difference between single-bundle and double-bundle reconstructions, (5) femoral and tibial tunnel widening occurred, (6) hamstring tendons regenerated after harvest and (7) biological knowledge did not support return to sports at 4–6 months. Conclusions After hamstring tendon autograft ACLR with accelerated brace-free rehabilitation, clinical outcome is similar after single-bundle and double-bundle ACLR. Early start of open kinetic exercises at 4 weeks in a limited ROM (90°−45°) and progressive concentric and eccentric exercises from 12 weeks postsurgery do not alter clinical outcome. Further research should focus on achievement of best balance between graft loading and graft healing in the various rehabilitation phases after ACLR as well as on validated, criterion-based assessments for safe return to sports. Level of evidence Level 2b; therapeutic outcome studies.
Neonatal Diabetes Mellitus : Clinical and Genetic Approach

Neonatal diabetes mellitus (NDM) is monogenic diabetes occurs in the first 6 month of age with an incidence of one in 20,000 to 500,000 newborn. This form of diabetes can be either transient (TNDM) resolves within a few months to relapse mainly at pubertal age or permanent (PNDM) stays for life.Abnormalities in the chromosome 6q24 region is present in approximately 70% of TNDM cases, mutations in the KCNJ11 genes, encoding the Kir6.2 subunit of the pancreatic KATP channel is the main case of PNDM, while mutations in the ABCC8 genes encoding the SUR1 subunit of the pancreatic KATP channel can be present in both TNDM and PNDM. Patients with TNDM usually presented earlier and have lower birth weight than PNDM, but there is a considerable overlapping in clinical features between the two groups necessitate molecular genetic tests for accurate diagnosis which has important therapeutic impacts on patients leading to transfer most of PNDM patients with activating mutations in KCNJ11 and ABCC8 genes, from insulin therapy to oral sulfonylurea. This review about NDM focuses on clinical presentation, genetic etiologies,diagnosis, acute treatment and long-term management. We describe a diagnostic algorithms for assessment of suspected neonatal diabetes to increase the yield of positive tests (Figure 2,3).
Diachronic Usage Relatedness (DURel): A Framework for the Annotation of Lexical Semantic Change

We propose a framework that extends synchronic polysemy annotation to diachronic changes in lexical meaning, to counteract the lack of resources for evaluating computational models of lexical semantic change. Our framework exploits an intuitive notion of semantic relatedness, and distinguishes between innovative and reductive meaning changes with high inter-annotator agreement. The resulting test set for German comprises ratings from five annotators for the relatedness of 1,320 use pairs across 22 target words.
Frailty phenotypes and mortality after lung transplantation: A prospective cohort study

Frailty is associated with increased mortality among lung transplant candidates. We sought to determine the association between frailty, as measured by the Short Physical Performance Battery (SPPB), and mortality after lung transplantation. In a multicenter prospective cohort study of adults who underwent lung transplantation, preoperative frailty was assessed with the SPPB (n = 318) and, in a secondary analysis, the Fried Frailty Phenotype (FFP; n = 299). We tested the association between preoperative frailty and mortality following lung transplantation with propensity score–adjusted Cox models. We calculated postestimation marginalized standardized risks for 1‐year mortality by frailty status using multivariate logistic regression. SPPB frailty was associated with an increased risk of both 1‐ and 4‐year mortality (adjusted hazard ratio [aHR]: 7.5; 95% confidence interval [CI]: 1.6‐36.0 and aHR 3.8; 95%CI: 1.8‐8.0, respectively). Each 1‐point worsening in SPPB was associated with a 20% increased risk of death (aHR: 1.20; 95%CI: 1.08‐1.33). Frail subjects had an absolute increased risk of death within the first year after transplantation of 12.2% (95%CI: 3.1%‐21%). In secondary analyses, FFP frailty was associated with increased risk of death within the first postoperative year (aHR: 3.8; 95%CI: 1.1‐13.2) but not over longer follow‐up. Preoperative frailty is associated with an increased risk of death after lung transplantation.
EURADOS work on internal dosimetry

European Radiation Dosimetry Group (EURADOS) Working Group 7 is a network on internal dosimetry that brings together researchers from more than 60 institutions in 21 countries. The work of the group is organised into task groups that focus on different aspects, such as development and implementation of biokinetic models (e.g. for diethylenetriamine penta-acetic acid decorporation therapy), individual monitoring and the dose assessment process, Monte Carlo simulations for internal dosimetry, uncertainties in internal dosimetry, and internal microdosimetry. Several intercomparison exercises and training courses have been organised. The IDEAS guidelines, which describe – based on the International Commission on Radiological Protection’s (ICRP) biokinetic models and dose coefficients – a structured approach to the assessment of internal doses from monitoring data, are maintained and updated by the group. In addition, Technical Recommendations for Monitoring Individuals for Occupational Intakes of Radionuclides have been elaborated on behalf of the European Commission, DG-ENER (TECHREC Project, 2014–2016, coordinated by EURADOS). Quality assurance of the ICRP biokinetic models by calculation of retention and excretion functions for different scenarios has been performed and feedback was provided to ICRP. An uncertainty study of the recent caesium biokinetic model quantified the overall uncertainties, and identified the sensitive parameters of the model. A report with guidance on the application of ICRP biokinetic models and dose coefficients is being drafted at present. These and other examples of the group’s activities, which complement the work of ICRP, are presented.
SpoIIQ Anchors Membrane Proteins on Both Sides of the Sporulation Septum in Bacillus subtilis*

During the process of spore formation in Bacillus subtilis, many membrane proteins localize to the polar septum where they participate in morphogenesis and signal transduction. The forespore membrane protein SpoIIQ plays a central role in anchoring several mother-cell membrane proteins in the septal membrane. Here, we report that SpoIIQ is also responsible for anchoring a membrane protein on the forespore side of the sporulation septum. Co-immunoprecipitation experiments reveal that SpoIIQ resides in a complex with the polytopic membrane protein SpoIIE. During the early stages of sporulation, SpoIIE participates in the switch from medial to polar division and co-localizes with FtsZ at the polar septum. We show that after cytokinesis, SpoIIE is released from the septum and transiently localizes to all membranes in the forespore compartment. Upon the initiation of engulfment, it specifically re-localizes to the septal membrane on the forespore side. Importantly, the re-localization of SpoIIE to the engulfing septum requires SpoIIQ. These results indicate that SpoIIQ is required to anchor membrane proteins on both sides of the division septum. Moreover, our data suggest that forespore membrane proteins can localize to the septal membrane by diffusion-and-capture as has been described for membrane proteins in the mother cell. Finally, our results raise the intriguing possibility that SpoIIE has an uncharacterized function at a late stage of sporulation.
Electronic and vibrational properties of V 2 C -based MXenes: From experiments to first-principles modeling

In the present work, the electronic and vibrational properties of both pristine ${\mathrm{V}}_{2}\mathrm{C}$ and fully terminated ${\mathrm{V}}_{2}\mathrm{C}{T}_{2}$ (where $T=\mathrm{F},$ O, OH) two-dimensional monolayers are investigated using density functional theory. First, the atomic structures of ${\mathrm{V}}_{2}\mathrm{C}$-based MXene phases are optimized, and their respective dynamical stabilities are discussed. Second, electronic band structures are computed indicating that ${\mathrm{V}}_{2}\mathrm{C}$ is metallic as well as all the corresponding functionalized systems. Third, the vibrational properties (phonon frequencies and spectra) of ${\mathrm{V}}_{2}\mathrm{C}$-based MXenes are computed with the density functional perturbation theory and reported. Both Raman-active (${E}_{g}$, ${A}_{1g}$) and infrared-active (${E}_{u}$, ${A}_{2u}$) vibrational modes are predicted ab initio with the aim to correlate the experimental Raman peaks with the calculated vibrational modes and to assign them to specific atomic motions. The effect of the terminal groups on the vibrational properties is emphasized, along with the effect on the presence and position of the corresponding Raman peaks. Our results provide insights for the identification and characterization of ${\mathrm{V}}_{2}\mathrm{C}$-based samples using Raman spectroscopy.