Miracle-dz/UniFAR-FTUs huggingface dataset:
In vivo kinetics of SARS-CoV-2 infection and its relationship with a person’s infectiousness

Significance Quantifying the kinetics of SARS-CoV-2 infection and individual infectiousness is important for understanding SARS-CoV-2 transmission and evaluating intervention strategies. Here, we developed within-host models of SARS-CoV-2 infection, and by fitting them to clinical data, we estimated key within-host viral dynamic parameters. We also developed a mechanistic model for viral transmission and show that the logarithm of the viral load in the upper respiratory tract serves as an appropriate surrogate for a person’s infectiousness. Using data on how viral load changes during infection, we further evaluated the effectiveness of PCR and antigen-based testing strategies for averting transmission and identifying infected individuals. The within-host viral kinetics of SARS-CoV-2 infection and how they relate to a person’s infectiousness are not well understood. This limits our ability to quantify the impact of interventions on viral transmission. Here, we develop viral dynamic models of SARS-CoV-2 infection and fit them to data to estimate key within-host parameters such as the infected cell half-life and the within-host reproductive number. We then develop a model linking viral load (VL) to infectiousness and show a person’s infectiousness increases sublinearly with VL and that the logarithm of the VL in the upper respiratory tract is a better surrogate of infectiousness than the VL itself. Using data on VL and the predicted infectiousness, we further incorporated data on antigen and RT-PCR tests and compared their usefulness in detecting infection and preventing transmission. We found that RT-PCR tests perform better than antigen tests assuming equal testing frequency; however, more frequent antigen testing may perform equally well with RT-PCR tests at a lower cost but with many more false-negative tests. Overall, our models provide a quantitative framework for inferring the impact of therapeutics and vaccines that lower VL on the infectiousness of individuals and for evaluating rapid testing strategies.
Novelty-induced frontal-STN networks in Parkinson's disease

Evaluating and responding to new information requires cognitive control. Here, we studied novelty-response mechanisms in Parkinson's disease (PD). In PD patient-volunteers, we recorded from cortical circuits with scalp-based electroencephalography (EEG) and from subcortical circuits using intraoperative neurophysiology during surgeries for implantation of deep-brain stimulation (DBS) electrodes. We report three major results. First, novel auditory stimuli triggered midfrontal ~4-Hz rhythms, which were attenuated in PD patients but were not linked with cognitive function or novelty-associated slowing. Second, 32% of subthalamic nucleus (STN) neurons were response-modulated; nearly all (94%) of these were also modulated by novel stimuli. Finally, response-modulated STN neurons were coherent with midfrontal low-frequency activity. These findings link scalp-based measurements of neural activity with neuronal activity in the STN. Our results provide insight into midfrontal cognitive control mechanisms and how hyperdirect circuits evaluate new information.
Different features of the cortical sensorimotor rhythms are uniquely linked to the severity of specific symptoms in Parkinson's disease

Parkinson's disease (PD) is associated with functional changes in the neural activity within the brain's sensorimotor network, which in turn are related to the characteristic motor symptoms in PD. The functional changes in PD are particularly prominent in terms of oscillatory neuronal activity in the characteristic sensorimotor alpha and beta rhythms. However, summaries in terms of alpha or beta power do not capture the full range of the complex dynamic nature of the signals from the somatosensory cortex. This raises the question of how to quantify and summarise the functional changes in such oscillatory features in a manner that captures the relevant disease- and symptom-related neural activity. We investigated the role of spontaneous cortical somatosensory activity in the electrophysiological alpha and beta bands among a cohort of early- to mid-stage PD patients (N=78) and age- and gender-matched healthy controls (N=60) using source reconstructed resting-state magnetoencephalography (MEG) recordings. We quantified the oscillatory features of the neural time series by its oscillatory alpha power, beta power, and 1/f broadband characteristics using power spectral density, and additionally by characterising "burst" properties in the signals. We examined the relationship between the signal features and disease state, age, sex, and cortical thickness. Using multiple regression, we examined the relative contribution of the oscillatory features on the clinical manifestation of motor symptoms in the PD group. Our results show that PD patients differ from healthy controls on several of the oscillatory features, showing higher beta-band power, higher burst amplitude, and steeper 1/f broadband characteristics compared to healthy controls, as well as a steeper age-related decrease in the bursts rate. While there was a high degree of correlation between some of the oscillatory features, several features also appeared functionally separated, showing independent feature-to-symptom relationships. For instance, oscillatory beta power increased with the severity of midline function symptoms, while burst rate decreased with the severity of bradykinesia. Our study shows that quantification of distinct features within the oscillatory sensorimotor neural time series in PD captures different underlying mechanisms related to disease progression and symptom severity, which in turn has a potential for a more individualised and precision-based approach to assessing functional neural changes in PD.
Bactericidal and Virucidal Activities of Biogenic Metal-Based Nanoparticles: Advances and Perspectives

Much progress has been achieved in the preparation and application of engineered nanoparticles (NPs) in the field of medicine, mainly for antibacterial and antiviral applications. In the war against bacteria and viruses, besides traditional antibiotics and antiviral drugs, metal-based nanoparticles, such as silver (AgNPs), copper (CuNPs), copper oxides (CuO-NPs), iron oxide (FeO-NPs), zinc oxide (ZnO-NPs), and titanium oxide (TiO2-NPs) have been used as potent antimicrobial agents. These nanoparticles can be synthesized by traditional methods, such as chemical and physical routes, or more recently by biogenic processes. A great variety of macro and microorganisms can be successfully used as reducing agents of metal salt precursors in the biogenic synthesis of metal-based NPs for antimicrobial activity. Depending on the nature of the biological agent, NPs with different sizes, aggregation states, morphology, surface coatings and charges can be obtained, leading to different antimicrobial effects. Considering the drug resistance to traditional therapies, the development of versatile nanomaterials with potent antimicrobial effects is under intensive investigation. In this sense, this review presents and discusses the recent progress in the preparation and application of metal-based nanoparticles biogenically synthesized for antibacterial and antivirus applications. The strength and limitations are critically discussed.
Millimetre-Wave Dual-Polarized Differentially-Fed 2D Multibeam Patch Antenna Array

In this paper, a novel millimetre-wave dual-polarized 2D multibeam antenna array incorporating differentially-fed antenna elements is proposed to achieve high cross-polarization discrimination (XPD) when the beams scan to the maximal pointing angles. The antenna element is composed of a SIW cavity with four shorted patches placed inside, and it is differentially excited for dual-polarization by a pair of feeding strips and transverse slots beneath the patches. Differential excitation is realized by a power divider designed on two laminate layers. Two Butler Matrices placed perpendicularly with each other in different laminates are employed to generate four tilted beams with dual-polarization. A 2× 2 dual-polarized 2D multibeam antenna array working at 28 GHz is designed, fabricated, and measured. The operation bandwidth of the antenna is 26.8 GHz – 29.2 GHz. The improvement in the XPD is experimentally demonstrated by far-field measurement. When the beams scan to 30◦ off the boresight, the measured XPDs are 28 dB at the centre frequency and higher than 25 dB over the operation bandwidth, which confirms that the cross-polarized radiation in the 2D multibeam antenna array is suppressed by using the differential-feeding technique. The measured gain is in the range from 7.6 dBi to 10.5 dBi.
Kalεido: Real-Time Privacy Control for Eye-Tracking Systems

Recent advances in sensing and computing technologies have led to the rise of eye-tracking platforms. Ranging from mo-biles to high-end mixed reality headsets, a wide spectrum of interactive systems now employs eye-tracking. However, eye gaze data is a rich source of sensitive information that can reveal an individual’s physiological and psychological traits. Prior approaches to protecting eye-tracking data suffer from two major drawbacks: they are either incompatible with the current eye-tracking ecosystem or provide no formal privacy guarantee. In this paper, we propose Kal e ido , an eye-tracking data processing system that (1) provides a formal privacy guarantee, (2) integrates seamlessly with existing eye-tracking ecosystems, and (3) operates in real-time. Kal e ido acts as an intermediary protection layer in the software stack of eye-tracking systems. We conduct a comprehensive user study and trace-based analysis to evaluate Kal e ido . Our user study shows that the users enjoy a satisfactory level of utility from Kal e ido . Additionally, we present empirical evidence of Kal e ido ’s effectiveness in thwarting real-world attacks on eye-tracking data.
Revisiting Knowledge Distillation: An Inheritance and Exploration Framework

Knowledge Distillation (KD) is a popular technique to transfer knowledge from a teacher model or ensemble to a student model. Its success is generally attributed to the privileged information on similarities/consistency between the class distributions or intermediate feature representations of the teacher model and the student model. However, directly pushing the student model to mimic the probabilities/features of the teacher model to a large extent limits the student model in learning undiscovered knowledge/features. In this paper, we propose a novel inheritance and exploration knowledge distillation framework (IE-KD), in which a student model is split into two parts - inheritance and exploration. The inheritance part is learned with a similarity loss to transfer the existing learned knowledge from the teacher model to the student model, while the exploration part is encouraged to learn representations different from the inherited ones with a dis-similarity loss. Our IE-KD framework is generic and can be easily combined with existing distillation or mutual learning methods for training deep neural networks. Extensive experiments demonstrate that these two parts can jointly push the student model to learn more diversified and effective representations, and our IE-KD can be a general technique to improve the student network to achieve SOTA performance. Furthermore, by applying our IE-KD to the training of two networks, the performance of both can be improved w.r. t. deep mutual learning.
Layered Paxos: A Hierarchical Approach to Consensus

—We present a new consensus algorithm for use in distributed systems. The algorithm, Layered Paxos, is designed for hierarchical systems where processes can be grouped into disjoint components. The underlying communication network is assumed to be two-fold with quick communication between processes in the same component and high-latency communication between processes in different components. Layered Paxos uses the Paxos algorithm as a building block with the addition of a few mechanisms to achieve hierarchical consensus and aims to increase the overall consensus throughput of a system that follows this two-fold communication paradigm. We present a theoretical proof that Layered Paxos satisﬁes the basic safety and liveness properties of Paxos in addition to some related to the hierarchical nature of the system. Finally, we present the experimental results of the comparison between Layered Paxos and Paxos in a hierarchical system, in which Layered Paxos was able to achieve up to 5x the throughput of Paxos.
Simultaneous Localization and Mapping with Moving Object Tracking for Drones

—This thesis addresses the problem of simultaneous localization and mapping with moving object tracking (SLAM-MOT) with application to unmanned aerial vehicles in uncertain and dynamic environments. The ﬁrst part of the thesis presents the formulation and design of an inertial-based ﬁlter for the SLAMMOT problem. The proposed solution includes the implementation of a modiﬁed version of the multiple hypothesis tracking method for data association of the environment’s objects, the use of the interacting multiple model algorithm for detection and tracking of moving objects (MO), and data fusion is performed using an extended Kalman ﬁlter, as a result of the nonlinear kinematics of the system. The consistency and performance of the devised SLAMMOT ﬁlter are successfully conﬁrmed with both simulation and experimental results, using an instrumented quadrotor equipped with an RGB-D camera. The second part of the thesis presents the formulation and design of a novel sensor-based ﬁlter for the SLAMMOT problem, that builds on the same methods for data association, detection, and tracking of MO. However, due to the sensor-based approach, the system dynamics are formulated in such a way that can be regarded as linear for ﬁlter design purposes, from which a Kalman ﬁlter is applied for data fusion. The convergence and effectiveness of the devised SLAMMOT ﬁlter are successfully conﬁrmed with simulation results.
Direct Reprogramming of Cardiac Fibroblasts to Repair the Injured Heart

Coronary heart disease is a leading cause of mortality and morbidity. Those that survive acute myocardial infarction are at significant risk of subsequent heart failure due to fibrotic remodelling of the infarcted myocardium. By applying knowledge from the study of embryonic cardiovascular development, modern medicine offers hope for treatment of this condition through regeneration of the myocardium by direct reprogramming of fibrotic scar tissue. Here, we will review mechanisms of cell fate specification leading to the generation of cardiovascular cell types in the embryo and use this as a framework in which to understand direct reprogramming. Driving expression of a network of transcription factors, micro RNA or small molecule epigenetic modifiers can reverse epigenetic silencing, reverting differentiated cells to a state of induced pluripotency. The pluripotent state can be bypassed by direct reprogramming in which one differentiated cell type can be transdifferentiated into another. Transdifferentiating cardiac fibroblasts to cardiomyocytes requires a network of transcription factors similar to that observed in embryonic multipotent cardiac progenitors. There is some flexibility in the composition of this network. These studies raise the possibility that the failing heart could one day be regenerated by directly reprogramming cardiac fibroblasts within post-infarct scar tissue.
ROLE OF BIOLOGICAL PROCESSES DURING MANGANESE REMOVAL FROM UNDERGROUND WATER

This article briefly presents the results of the effect of oxidants during filtration of groundwater with high level of manganese compounds. Significant role of biological processes along with physico-chemical at demanganation of groundwater has been noticed. It has been studied that biological processes are dominated in low concentrations of oxidants. At high concentration of disinfectant the role of physico-chemical processes begin to dominate. Thus, there is a significant role of microorganisms in physico-chemical process of manganese removal. Obtained results showed that the oxygen is more efficient oxidizer than sodium hypochlorite for compounds of manganese presented in groundwater.
An exploration of how gender stereotypes influence how practitioners identify and respond to victims (or those at risk) of child sexual exploitation

Abstract Child sexual exploitation (CSE) has been found to have a detrimental and long‐lasting impact upon a victim's physical and emotional well‐being. A large body of research has raised concerns about how practitioners identify and respond to CSE. In particular, research has indicated that male victims of CSE are commonly being overlooked by practitioners. It has been suggested that this may occur as a result of gender stereotypes. However, this has not been specifically explored by existing research. Therefore, this research project explored how gender stereotypes may influence how practitioners identify and respond to children and young people who are victims (or at risk) of CSE. Semi‐structured interviews were conducted with eight practitioners from one Youth Offending Service in the South West of England. Three key themes emerged from the interviews. These themes highlight that as a result of gender stereotypes, practitioners may be less likely and/or slower to identify males as victims and may be less likely to provide males with supportive multi‐agency responses. This paper makes recommendations about how this issue can be addressed to ensure that all victims of CSE are adequately safeguarded.
Application of Polyaluminium Chloride Coagulant in Urban River Water Treatment Influenced the Microbial Community in River Sediment

Polyaluminium chloride (PAC) has been widely used as a chemical coagulant in water treatment. However, little is known about the impact of PAC performance on the microbial community in sediments. In this study, the archaeal, bacterial, and fungal communities in urban river sediments with and without PAC treatment were investigated. Prokaryotic diversity decreased at the PAC addition site (A2) and increased along with the river flow (from A3 to A4), while eukaryotic diversity was the opposite. The abundance of core microbiota showed a similar trend. For example, the dominant Proteobacteria presented the highest relative abundance in A1 (26.8%) and the lowest in A2 (15.3%), followed by A3 (17.5%) and A4 (23.0%). In contrast, Rozellomycota was more dominant in A2 (56.6%) and A3 (58.1%) than in A1 (6.2%) and A4 (16.3%). Salinity, total dissolved solids, and metal contents were identified as the key physicochemical factors affecting the assembly of core microorganisms. The predicted functions of archaea and fungi were mainly divided into methane cycling and saprotrophic nutrition, respectively, while bacterial function was more diversified. The above findings are helpful to enhance our understanding of microorganism response to PAC and have significance for water treatment within the framework of microecology.
The effects of a strength exercise intervention on the gait biomechanics and gastrocnemius muscle-tendon unit behavior in the elderly

The interaction between the medial gastrocnemius (MG) muscle and the Achilles tendon (AT), i.e. muscle-tendon unit (MTU) interaction, is crucial to minimize the energy cost of walking. The fascicles follow a different length-change pattern from those of MTU and tendon during walking, leading to beneficial contractile conditions for MG. Aging is associated with a decreased AT stiffness, which impacts walking performance. Older adults tend to decrease their preferred walking speed, adapting muscle fascicle behavior as a strategy to decrease the energy cost of walking. Nonetheless, aged-AT can increase its stiffness through training interventions, which has been related to more optimal muscle fascicle lengths during walking. To our knowledge, the impact of a training-induced increase in AT stiffness in the interaction of MG MTU during walking in the elderly was not assessed. Thus, we investigated the effect of a 12-week strength exercise on the walking kinetics and kinematics and MG MTU behavior in older adults. MG muscle fascicles of 11 older male adults were tracked using dynamic ultrasonography during treadmill walking trials. Kinetic and kinematic data were collected, and musculoskeletal models used to determine joint angles and moments and to estimate MTU lengths. No length and velocity changes in MG MTU, fascicle and tendinous tissues were observed after training. Additionally, a similar walking pattern before and after training was found, with no joint kinematics and kinetics significant differences. Questions remain regarding the MTU training-induced adaptations of the aged MG during walking and further research is warranted to draw more conclusions.
Hydroxychloroquine for Pre-Exposure Prophylaxis for Sars-Cov-2

Jaime López de la Iglesia1, Naiara Cubelos Fernández2*, Roi Naveiro Flores3, Marina Montoro Gómez2, Francisco Javier González de Haro2, María Lamuedra Gil de Gómez2, María Ajenjo González5, Estefanía Tobal Vicente2, María Teresa Nuevo Guisado2, Isabel Torío Gómez2, Ana Peñalver Andrada2, Nuria Martínez Cao2, Paula González Figaredo2, Carlos Robles García2, Lidia Anastasia Alvarado Machón2, Ángeles Lafont Alcalde2, Michael Daws Gómez-Landero2 and José Cesáreo Naveiro Rilo4
N A ] 2 2 Fe b 20 21 Accurate and efficient splitting methods for dissipative particle dynamics

We study numerical methods for dissipative particle dynamics (DPD), which is a system of stochastic differential equations and a popular stochastic momentum-conserving thermostat for simulating complex hydrodynamic behavior at mesoscales. We propose a new splitting method that is able to substantially improve the accuracy and efficiency of DPD simulations in a wide range of the friction coefficients, particularly in the extremely large friction limit that corresponds to a fluid-like Schmidt number, a key issue in DPD. Various numerical experiments on both equilibrium and transport properties are performed to demonstrate the superiority of the newly proposed method over popular alternative schemes in the literature.