Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasticity of Cyanobacterial Thylakoid Microdomains Under Variable Light Conditions

Photosynthetic light reactions proceed in thylakoid membranes (TMs) due to the activity of pigment–protein complexes. These complexes are heterogeneously organized into granal/stromal thylakoids (in plants) or into recently identified cyanobacterial microdomains (MDs). MDs are characterized by specific ratios of photosystem I (PSI), photosystem II (PSII), and phycobilisomes (PBS) and they are visible as sub-micrometer sized areas with different fluorescence ratios. In this report, the process of long-term plasticity in cyanobacterial thylakoid MDs has been explored under variable growth light conditions using Synechocystis sp. PCC6803 expressing YFP tagged PSI. TM organization into MDs has been observed for all categorized shapes of cells independently of their stage in cell cycle. The heterogeneous PSI, PSII, and PBS thylakoid areas were also identified under two types of growth conditions: at continuous light (CL) and at light-dark (L-D) cycle. The acclimation from CL to L-D cycle changed spatial distribution of photosystems, in particular PSI became more evenly distributed in thylakoids under L-D cycle. The process of the spatial PSI (and partially also PSII) redistribution required 1 week and was accompanied by temporal appearance of PBS decoupling probably caused by the re-organization of photosystems. The overall acclimation we observed was defined as TM plasticity as it resembles higher plants grana/stroma reorganization at variable growth light conditions. In addition, we observed large cell to cell variability in the actual MDs organization. It leads us to suggest that the plasticity, and cell to cell variability in MDs could be a manifestation of phenotypic heterogeneity, a recently broadly discussed phenomenon for prokaryotes.
Predictive Factor for COVID-19 Worsening: Insights for High-Sensitivity Troponin and D-Dimer and Correlation With Right Ventricular Afterload

Background: Coronavirus disease 2019 (COVID-19) has been associated with cardiovascular complications and coagulation disorders. Objectives: To explore clinical and biological parameters of COVID-19 patients with hospitalization criteria that could predict referral to intensive care unit (ICU). Methods: Analyzing the clinical and biological profiles of COVID-19 patients at admission. Results: Among 99 consecutive patients that fulfilled criteria for hospitalization, 48 were hospitalized in the medicine department, 21 were first admitted to the medicine ward department and referred later to ICU, and 30 were directly admitted to ICU from the emergency department. At admission, patients requiring ICU were more likely to have lymphopenia, decreased SpO2, a D-dimer level above 1,000 ng/mL, and a higher high-sensitivity cardiac troponin (Hs-cTnI) level. A receiver operating characteristic curve analysis identified Hs-cTnI above 9.75 pg/mL as the best predictive criteria for ICU referral [area under the curve (AUC), 86.4; 95% CI, 76.6–96.2]. This cutoff for Hs-cTnI was confirmed in univariate [odds ratio (OR), 22.8; 95% CI, 6.0–116.2] and multivariate analysis after adjustment for D-dimer level (adjusted OR, 20.85; 95% CI, 4.76–128.4). Transthoracic echocardiography parameters subsequently measured in 72 patients showed an increased right ventricular (RV) afterload correlated with Hs-cTnI (r = 0.42, p = 0.010) and D-dimer (r = 0.18, p = 0.047). Conclusion: Hs-cTnI appears to be the best relevant predictive factor for referring COVID-19 patients to ICU. This result associated with the correlation of D-dimer with RV dilatation probably reflects a myocardial injury due to an increased RV wall tension. This reinforces the hypothesis of a COVID-19-associated microvascular thrombosis inducing a higher RV afterload.
Safety and Efficacy of Adjunctive Therapy With Artesunate in the Treatment of Severe Malaria: A Systematic Review and Meta-Analysis

Objective: The purpose of this meta-analysis of longitudinal studies is to determine the safety and efficacy of artesunate combined with other forms of adjunctive therapies for severe malaria. Methods: Following the PRISMA guidelines, we searched multiple databases with the search terms “artesunate” and “adjunctive therapy” and “severe malaria” in July 2020. If the search showed a randomized controlled trial, the study was included in this meta-analysis. The random-effects model was used to calculate the combined incidence rate and relative risk or risk difference. Results: This meta-analysis included nine longitudinal studies with 724 participants. We found that the mortality rates in the artesunate monotherapy group and the artesunate + adjuvant therapy group are similar (RD = −0.02, 95% confidence interval: −0.06–0.02). The incidence of adverse reactions in the artesunate monotherapy group and the artesunate + adjuvant therapy group was also similar. Conclusion: No significant differences in safety and efficacy were observed between the artesunate monotherapy group and the artesunate + adjuvant therapy group. Higher quality and rigorously designed randomized controlled studies are needed to validate our findings.
The Neurobehavioral Mechanisms Underlying Attitudes Toward People With Mental or Physical Illness

Social factors play a significant role in the health outcomes of those struggling with mental or physical health issues. People with mental illness experience more social stigmatization and receive less concern for their welfare than do those with physical illness. However, the cognitive and neural mechanisms by which such a bias in attitude arises remain unclear. This functional MRI study examined whether a lack of self-other similarity during mental state attribution affects perceivers’ theory of mind and, subsequently, how they value a patient’s welfare. During scanning, participants were asked to respond to an expression of caring and sympathetic concern from either their own perspective or while adopting the perspective of patients labeled physically ill or mentally ill. Participants reported that physically ill patients would share their affective responses to the situations, but mentally ill patients would not. Furthermore, mentalizing about physically ill patients was associated with increased activity in the ventromedial prefrontal cortex (vmPFC), a critical region for empathic concern and value-based decisions. In contrast, mentalizing about mentally ill patients preferentially engaged the dorsal anterior cingulate cortex (dACC) and anterior insula, regions previously implicated in empathic distress, in which activity correlated with individual differences in prejudice control. The findings indicate that a lack of perceived self-other similarity poses a challenge to the theory of mind and thus requires greater cognitive resources and neural computations. This might give rise to stereotyped beliefs about and prejudice against the mentally ill and failure to respond with appropriate empathy and care.
Suppression of Pitch Labeling: No Evidence for an Impact of Absolute Pitch on Behavioral and Neurophysiological Measures of Cognitive Inhibition in an Auditory Go/Nogo Task

Pitch labeling in absolute pitch (AP), the ability to recognize the pitch class of a sound without an external reference, is effortless, fast, and presumably automatic. Previous studies have shown that pitch labeling in AP can interfere with task demands. In the current study, we used a cued auditory Go/Nogo task requiring same/different decisions to investigate both behavioral and electrophysiological correlates of increased inhibitory demands related to automatic pitch labeling. The task comprised two Nogo conditions: a Nogo condition with pitch differences larger than one semitone, and a second Nogo condition with pitch differences of only a quarter semitone. The first Nogo condition tested if auditory-related inhibition processes are generally altered in AP musicians. The second Nogo condition tested the suppressibility of the pitch labeling using a Stroop-like effect: the two tones belonged to the same pitch class but were not identical in terms of tone frequency. If pitch labeling cannot be suppressed, the conflicting information would be expected to increase the inhibitory load in AP musicians. Our data provided no evidence for an increased difficulty to inhibit a prepotent response or to suppress conflicting pitch-labeling information in AP: AP musicians showed similar commission error rates as non-AP musicians in both Nogo conditions. N2d and P3d amplitudes of AP musicians were also comparable to those of non-AP musicians. The event-related potentials (ERPs) were, however, modulated by the Nogo condition, probably indicating an effect of stimulus similarity. It is possible that, depending on the context, pitch labeling in AP musicians is not entirely automatic and can be suppressed.
Fusion of Bacterial Flagellin to a Dendritic Cell-Targeting αCD40 Antibody Construct Coupled With Viral or Leukemia-Specific Antigens Enhances Dendritic Cell Maturation and Activates Peptide-Responsive T Cells

Conventional dendritic cell (DC) vaccine strategies, in which DCs are loaded with antigens ex vivo, suffer biological issues such as impaired DC migration capacity and laborious GMP production procedures. In a promising alternative, antigens are targeted to DC-associated endocytic receptors in vivo with antibody–antigen conjugates co-administered with toll-like receptor (TLR) agonists as adjuvants. To combine the potential advantages of in vivo targeting of DCs with those of conjugated TLR agonists, we generated a multifunctional antibody construct integrating the DC-specific delivery of viral- or tumor-associated antigens and DC activation by TLR ligation in one molecule. We validated its functionality in vitro and determined if TLR ligation might improve the efficacy of such a molecule. In proof-of-principle studies, an αCD40 antibody containing a CMV pp65-derived peptide as an antigen domain (αCD40CMV) was genetically fused to the TLR5-binding D0/D1 domain of bacterial flagellin (αCD40.FlgCMV). The analysis of surface maturation markers on immature DCs revealed that fusion of flagellin to αCD40CMV highly increased DC maturation (3.4-fold elevation of CD80 expression compared to αCD40CMV alone) by specifically interacting with TLR5. Immature DCs loaded with αCD40. FlgCMV induced significantly higher CMVNLV-specific T cell activation and proliferation compared to αCD40CMV in co-culture experiments with allogeneic and autologous T cells (1.8-fold increase in % IFN-γ/TNF-α+ CD8+ T cells and 3.9-fold increase in % CMVNLV-specific dextramer+ CD8+ T cells). More importantly, we confirmed the beneficial effects of flagellin-dependent DC stimulation using a tumor-specific neoantigen as the antigen domain. Specifically, the acute myeloid leukemia (AML)-specific mutated NPM1 (mNPM1)-derived neoantigen CLAVEEVSL was delivered to DCs in the form of αCD40mNPM1 and αCD40. FlgmNPM1 antibody constructs, making this study the first to investigate mNPM1 in a DC vaccination context. Again, αCD40. FlgmNPM1-loaded DCs more potently activated allogeneic mNPM1CLA-specific T cells compared to αCD40mNPM1. These in vitro results confirmed the functionality of our multifunctional antibody construct and demonstrated that TLR5 ligation improved the efficacy of the molecule. Future mouse studies are required to examine the T cell-activating potential of αCD40. FlgmNPM1 after targeting of dendritic cells in vivo using AML xenograft models.
Can Mobile Technology Help Prevent the Burden of Dementia in Low- and Mid-Income Countries?

According to the World Health Organization (WHO), the global population aged above 60 years will double in size by 2050, with an estimated total of about 2 billion people. The increase in life expectancy, combined with unhealthy behaviors and physical inactivity (1), is linked to an increase in non-communicable diseases (NCDs). Additionally, related to aging but not yet considered to be an NCD is cognitive decline, which is an important medical condition resulting in a significant loss of autonomy. Globally, the current number of people living with dementia is estimated to be 50 million, with nearly 10 million new cases every year, and representing a serious public health problem (2). Identified as one of the major challenges of the twenty-first century, the WHO proclaimed that cognitive decline and dementia are a mental health global priority. The burden of cognitive diseases for patients, relatives, and nations is thus a major public health problem that must be addressed (3–5). In addition, there is a significant impact on well-being for both patients and their relatives (6, 7). These concerns in developed countries regarding the increased incidence of NCDs are now also of significant importance for midand low-income countries (8). In this paper we aim to summarize the current level of evidence supporting the use of mobile technology to prevent dementia in lowand mid-income countries by undertaken a narrative review. Obstacles and future directions are also discussed.
Membrane Dynamics and Organization of the Phagocyte NADPH Oxidase in PLB-985 Cells

Neutrophils are the first cells recruited at the site of infections, where they phagocytose the pathogens. Inside the phagosome, pathogens are killed by proteolytic enzymes that are delivered to the phagosome following granule fusion, and by reactive oxygen species (ROS) produced by the NADPH oxidase. The NADPH oxidase complex comprises membrane proteins (NOX2 and p22phox), cytoplasmic subunits (p67phox, p47phox, and p40phox) and the small GTPase Rac. These subunits assemble at the phagosomal membrane upon phagocytosis. In resting neutrophils the catalytic subunit NOX2 is mainly present at the plasma membrane and in the specific granules. We show here that NOX2 is also present in early and recycling endosomes in human neutrophils and in the neutrophil-like cell line PLB-985 expressing GFP-NOX2. In the latter cells, an increase in NOX2 at the phagosomal membrane was detected by live-imaging after phagosome closure, probably due to fusion of endosomes with the phagosome. Using super-resolution microscopy in PLB-985 WT cells, we observed that NOX2 forms discrete clusters in the plasma membrane. The number of clusters increased during frustrated phagocytosis. In PLB-985NCF1ΔGT cells that lack p47phox and do not assemble a functional NADPH oxidase, the number of clusters remained stable during phagocytosis. Our data suggest a role for p47phox and possibly ROS production in NOX2 recruitment at the phagosome.
A Multi-Source Data Fusion Framework for Revealing the Regulatory Mechanism of Breast Cancer Immune Evasion

For precision medicine, there is an enormous need to understand the immune evasion mechanism of tumor development, especially when tumor heterogeneity significantly affects the effect of immunotherapy. Recognizing the subtypes of breast cancer based on the immune-related genes helps to understand the immune escape pathways dominated by different subtypes, so as to implement effective treatment measures for different subtypes. For that, we used non-negative matrix factorization and consistent clustering algorithm on The Cancer Genome Atlas RNA-seq breast cancer data and recognized 4 subtypes according to the curated immune-related genes. Then, we conducted differential expression analysis between each subtype of breast cancer and normal tissue of RNA-seq data from non-cancer individuals collected by the Genotype-Tissue Expression to find out subtype-related immune genes. After that, we carried out correlation analysis between copy number variants (CNV) and mRNA of immune genes and investigated the regulatory mechanism of the immune genes, which cannot be explained by CNV based on ATAC-seq data. The experimental results reveal that CDH1 and PVRL2 are potential for immune evasion in all 4 subgroups. The expression variations of CDH1 can be mainly explained by its CNV, while the expression variation of PVRL2 is more likely regulated by transcript factors.
A Methodology and Tool for Mapping the Risk of Cumulative Effects on Benthic Habitats

The implementation of the European integrated marine policy poses many scientific challenges. Among them, the knowledge and understanding of interactions between anthropogenic pressures and ecological components is an important issue, particularly to help define Good Environmental Status, environmental targets and monitoring programs of the Marine Strategy Framework Directive (2008, MSFD). Assessment of cumulative effects of different pressures is a particularly complex issue requiring modeling tools and methods, as well as accurate data sets on human activities, anthropogenic pressures and ecological components. The results of these assessments are also uncertain and highly dependent on the calculation methods and assumptions, as well as on the data sets used. Within this context, we developed a technical and methodological approach to map the risk of cumulative effects of different pressures on benthic habitats. These developments were initiated as part of the implementation of the MSFD in France to contribute to the diagnosis of the marine environment. Here we provide a demonstrator to illustrate the feasibility for mapping the risk of cumulative effects of different pressures on benthic habitats, as well as the confidence index and the variability associated with this analysis. The method is based on a spatial analysis using a mapping of benthic habitats and their sensitivity to pressures, as well as the distribution and intensity of human activities and associated pressures. We collected and prepared relatively accurate and consistent data sets to describe human activities and benthic habitats. Data sets are embedded into a grid that facilitates the management and analysis of the data and exploitation of the results. The demonstrator consists of a relational database using the Spatial Query Language (SQL) language as well as data analysis scripts using the R language. The first demonstrator operations validated the main methodological and technical choices and helped to identify future developments needed to facilitate the appropriation and integration of these approaches in the implementation of public policies for the management of the marine environment.
Réseaux de neurones pour la résolution d’analogies entre phrases en traduction automatique par l’exemple (Neural networks for the resolution of analogies between sentences in EBMT )

Cet article propose un modèle de réseau de neurones pour la résolution d’équations analogiques au niveau sémantique et entre phrases dans le cadre de la traduction automatique par l’exemple. Son originalité réside dans le fait qu’il fusionne les deux approches, directe et indirecte, de la traduction par l’exemple.
Design optimisation of multiplier-free parallel pipelined FFT on field programmable gate array

Fast Fourier transform (FFT) is utilised to minimise the complexity of discrete Fourier transform by converting signals from frequency domain to time domain and conversely. Digital signal processing systems like image processing, general filtering, sonar, spread-spectrum communications and convolutions use this FFT operations. Radix-2 decimation in frequency (R2DIF) method is designed to execute an efficient FFT architecture in this study. Each and every state of the FFT stores the input and output the data using the R2DIF method. Also, the complex twiddle factors in FFT are replaced by the proposed uniform Montgomery algorithm. This technique simply performs the shift-add method instead of the multiplication process which also enhances the convergence of the calculation. So, the FFT implementation is done with the help of the proposed method which reduces the usage of chips in the process. Based on this approach, it performs the operation of FFT from 16 points to 1024 points and the performance of this proposed method is compared with existing approaches. Moreover, it does not require expensive dedicated functional blocks and uses only distributed logic resources. The simulation is carried out by the Xilinx platform using Verilog coding. The proposed design outperforms conventional methods in terms of less usage power and high speed.
Open-circuit voltage decay: moving to a flexible method of characterisation

: Open-Circuit Voltage Decay is a method to characterize minority carrier effective lifetime ( τ eff ). It is non-destructive, simple and low-cost. It has been mainly used in silicon p-n junctions. τ eff is a very important parameter to optimize device design but also to supervise process steps. Actually, it is not the only parameter we can obtain by OCVD. Due to the intrinsic space charge region (SCR) capacitance of a p-n junction, doping level of the lowest-doped region ( N l ) and built-in potential ( V bi ) are extractable. Moreover, it is also possible to obtain the shunt resistance ( R sh ) value when it has a signiﬁcant effect on the p-n junction behaviour. We ﬁrst applied the well-established one-diode model in transient regime to simulate OCVD signal. In a second step, we used an optimization algorithm to ﬁt the experimental curve of a silicon diode in order to extract τ eff , N l , V bi and R sh . These values were compared to those obtained from C-V and I-V. Results are promising and demonstrates for the ﬁrst time, the ﬂexibility of the OCVD method. It opens up the perspective for development of add-on features of the method and for measuring short lifetime.
Hybrid mapped optical-OFDM using non-linear companding technique for indoor visible light communication application

In this study, the authors have developed an analytical model for reducing the peak-to-average-power ratio (PAPR) using non-linear companding transform (NCT) based on inverse hyperbolic sine function. As a consequence of non-linear transform, this study compensates the system bit error rate (BER) degradation with the help of an error efficient hybrid modulation. By means of an inflexion point and companding parameter, more design flexibility is achieved; as a result, a trade-off between PAPR and BER has reasonably been more precise. To the best of the authors’ awareness, no findings have yet been reported on the performance evaluation of the optical orthogonal frequency division multiplexing (OOFDM) system using a hybrid modulation technique. To find out the advantages of hybrid modulation with NCT, the authors inspect the nature of PAPR reduction, and BER improvement through numerical simulations. The numerical BER results exhibit roughly 3 dBm decay in the power efficiency of hybrid modulation with NCT over discrete Fourier transform (DFT) precoding technique. On the other hand, the NCT technique with hybrid modulation has 6 dB less PAPR than the DFT precoding technique.