Miracle-dz/UniFAR-FTUs huggingface dataset:
COCARDE Study–Cardiac Imaging Phenotype in Patients With COVID-19: Protocol for a Prospective Observational Study

Background: The effects of SARS-CoV-2 (COVID-19) on the myocardium and their role in the clinical course of infected patients are still unknown. The severity of SARS-CoV-2 is driven by hyperinflammation, and the effects of SARS-CoV-2 on the myocardium may be significant. This study proposes to use bedside observations and biomarkers to characterize the association of COVID-19 with myocardial injury. Objective: The aim of the study is to describe the myocardial function and its evolution over time in patients infected with SARS-CoV-2 and to investigate the link between inflammation and cardiac injury. Methods: This prospective, monocentric, observational study enrolled 150 patients with suspected or confirmed SARS-CoV-2 infection at Toulouse University Hospital, Toulouse, France. Patients admitted to the intensive care unit (ICU), regular cardiologic ward, and geriatric ward of our tertiary university hospital were included during the pandemic period. Blood sampling, electrocardiography, echocardiography, and morphometric and demographic data were prospectively collected. Results: A total of 100 patients were included. The final enrolment day was March 31, 2020, with first report of results at the end of the first quarter of 2021. The first echocardiographic results at admission of 31 patients of the COCARDE-ICU substudy population show that biological myocardial injury in COVID-19 has low functional impact on left ventricular systolic function. Conclusions: A better understanding of the effects of COVID-19 on myocardial function and its link with inflammation would improve patient follow-up and care. Trial Registration: Clinicaltrials.gov NCT04358952; https://clinicaltrials.gov/ct2/show/NCT04358952 International Registered Report Identifier (IRRID): DERR1-10.2196/24931 (JMIR Res Protoc 2022;11(1):e24931) doi: 10.2196/24931
Recurrent FOXK1::GRHL and GPS2::GRHL fusions in trichogerminoma

We report 21 cases of trichogerminoma harbouring previously undescribed FOXK1::GRHL1/2 or GPS2::GRHL1/2/3 in‐frame fusion transcripts. Microscopic examination of a preliminary set of five cases revealed well‐delimitated tumours located in the dermis with frequent extension to the subcutaneous tissue. Tumours presented a massive and nodular architecture and consisted of a proliferation of basaloid cells. A biphasic pattern sometime resulting in tumour cell nests (‘cell balls’) was present. Immunohistochemistry demonstrated the expression of cytokeratins (CKs) 15, 17, and PHLDA1. In addition, numerous CK20‐positive Merkel cells were detected. RNA sequencing (RNA‐seq) revealed a FOXK1::GRHL1 chimeric transcript in three cases and a FOXK1::GRHL2 fusion in two cases. In a second series for validation (n = 88), FOXK1::GRHL1/2 fusion transcripts were detected by RT‐qPCR or FISH in an additional 12 trichogerminomas and not in any other follicular tumour entities or basal cell carcinoma cases (n = 66). Additional RNA‐seq analysis in trichogerminoma cases without detected FOXK1::GRHL1/2 rearrangements revealed GPS2::GRHL1 fusion transcripts in two cases, GPS2::GRHL2 in one case, and GPS2::GRHL3 fusion transcript in one case. Therefore, our study strongly suggests that GRHL1/2/3 gene rearrangements might represent the oncogenic driver in trichogerminoma, a subset of follicular tumours characterized by immature features and numerous Merkel cells. © 2022 The Pathological Society of Great Britain and Ireland.
Estrogens in wastewaters: Can different operating conditions improve their removal in anaerobic conditions?

The removal of estrone (E1) and 17α‐ethinylestradiol (EE2) from synthetic wastewater under anaerobic conditions, at environmental relevant concentrations (80 and 4 μg L−1, for E1 and EE2, respectively), was here assessed. Results indicated that the increase in temperature favoured E1 removal (complete removal at 25°C, and 34°C after 25 h), while EE2 does not seem to be affected. The lowest mixed liquor suspended solid (MLSS) concentrations promoted a higher removal of E1 and EE2 (with a complete removal for E1 after 25 h and of 74% after 265 h for EE2 with a MLSS of 2 g L−1). Moreover, the presence of nitrate does not seem to have influence on E1 and EE2 removal. These studies represent a step forward in the knowledge of the influence of different conditions on the estrogens' removal under anaerobic conditions.
Application of Neuromorphic Olfactory Approach for High-Accuracy Classification of Malts

Current developments in artificial olfactory systems, also known as electronic nose (e-nose) systems, have benefited from advanced machine learning techniques that have significantly improved the conditioning and processing of multivariate feature-rich sensor data. These advancements are complemented by the application of bioinspired algorithms and architectures based on findings from neurophysiological studies focusing on the biological olfactory pathway. The application of spiking neural networks (SNNs), and concepts from neuromorphic engineering in general, are one of the key factors that has led to the design and development of efficient bioinspired e-nose systems. However, only a limited number of studies have focused on deploying these models on a natively event-driven hardware platform that exploits the benefits of neuromorphic implementation, such as ultra-low-power consumption and real-time processing, for simplified integration in a portable e-nose system. In this paper, we extend our previously reported neuromorphic encoding and classification approach to a real-world dataset that consists of sensor responses from a commercial e-nose system when exposed to eight different types of malts. We show that the proposed SNN-based classifier was able to deliver 97% accurate classification results at a maximum latency of 0.4 ms per inference with a power consumption of less than 1 mW when deployed on neuromorphic hardware. One of the key advantages of the proposed neuromorphic architecture is that the entire functionality, including pre-processing, event encoding, and classification, can be mapped on the neuromorphic system-on-a-chip (NSoC) to develop power-efficient and highly-accurate real-time e-nose systems.
Availability and Suitability of Digital Health Tools in Africa for Pandemic Control: Scoping Review and Cluster Analysis

Background Gaining oversight into the rapidly growing number of mobile health tools for surveillance or outbreak management in Africa has become a challenge. Objective The aim of this study is to map the functional portfolio of mobile health tools used for surveillance or outbreak management of communicable diseases in Africa. Methods We conducted a scoping review by combining data from a systematic review of the literature and a telephone survey of experts. We applied the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines by searching for articles published between January 2010 and December 2020. In addition, we used the respondent-driven sampling method and conducted a telephone survey from October 2019 to February 2020 among representatives from national public health institutes from all African countries. We combined the findings and used a hierarchical clustering method to group the tools based on their functionalities (attributes). Results We identified 30 tools from 1914 publications and 45 responses from 52% (28/54) of African countries. Approximately 13% of the tools (4/30; Surveillance Outbreak Response Management and Analysis System, Go.Data, CommCare, and District Health Information Software 2) covered 93% (14/15) of the identified attributes. Of the 30 tools, 17 (59%) tools managed health event data, 20 (67%) managed case-based data, and 28 (97%) offered a dashboard. Clustering identified 2 exceptional attributes for outbreak management, namely contact follow-up (offered by 8/30, 27%, of the tools) and transmission network visualization (offered by Surveillance Outbreak Response Management and Analysis System and Go.Data). Conclusions There is a large range of tools in use; however, most of them do not offer a comprehensive set of attributes, resulting in the need for public health workers having to use multiple tools in parallel. Only 13% (4/30) of the tools cover most of the attributes, including those most relevant for response to the COVID-19 pandemic, such as laboratory interface, contact follow-up, and transmission network visualization.
Environmental drivers of dynamic soil erosion change in a Mediterranean fluvial landscape

Background Rainfall and other climatic agents are the main triggers of soil erosion in the Mediterranean region, where they have the potential to increase discharge and sediment transport and cause long-term changes in the river system. For the Magra River Basin (MRB), located in the upper Tyrrhenian coast of Italy, we estimated changes in net erosion as a function of the geographical characteristics of the basin, the seasonal distribution of precipitation, and the vegetation cover. Methods and findings Based on rainfall erosivity and surface flow and transport sub-models, we developed a simplified model to assess basin-wide sediment yields on a monthly basis by upscaling the point rainfall input. Our calibration dataset of monthly data (Mg km-2 month-1, available for the years 1961 and 1963–1969) revealed that our model satisfactorily reproduces the net soil erosion in the study area (R2 = 0.81). For the period 1950–2020, the reconstruction of an annually aggregated time-series of monthly net erosion data (297 Mg km-2 yr-1 on average) indicated a moderate decline in sediment yield after 1999. This is part of a long-term downward trend, which highlights the role played by land-use changes and reforestation of the mountainous areas of the basin. Conclusion This study shows the environmental history and dynamics of the basin, and thus the varying sensitivity of hydrological processes and their perturbations. Relying on a few climatic variables as reported from a single representative basin location, it provides an interpretation of empirically determined factors that shape active erosional landscapes. In particular, we showed that the most recent extreme storms associated with sediment yield have been characterised by lower cumulative rainfall, indicating a greater propensity for the basin to produce sediment more discontinuously over time.
Thiol-Ene Coupling of High Oleic Sunflower Oil towards Application in the Modification of Flexible Polyurethane Foams

High oleic sunflower oil-based polyol was obtained by thiol-ene coupling and applied in the preparation of flexible polyurethane foams. The photochemically initiated thiol-ene click reaction was carried out under UV irradiation using 2-mercaptoethanol. Bio-based polyol with hydroxyl value of 201.4 mg KOH/g was used as 30 wt% substituent of petrochemical polyether polyol in the formulations of flexible foams. Both reference foams, as well as foams modified with bio-based polyol, were formulated to have various isocyanate indices (0.85, 0.95, 1.05). Flexible foams were compared in terms of their thermomechanical properties and analyzed using FT-IR and SEM microscopy. Modification with bio-based polyol resulted in foams with superior compression properties, higher support factor, and lower resilience than reference foams. TGA and FT-IR curves confirmed the presence of urethane/urea and ether linkages in the polyurethane matrix. Moreover, double glass transition temperature corresponding to soft and hard segments of polyurethane was observed by DSC proving the phase-separated morphology.
Genotyping for HLA Risk Alleles to Prevent Drug Hypersensitivity Reactions: Impact Analysis

Human Leukocyte Antigen (HLA) variants can be a risk factor for developing potentially fatal drug hypersensitivity reactions. Our aim was to estimate the potential impact of genotyping for the HLA risk alleles incorporated in the Dutch Pharmacogenetics Working Group (DPWG) guidelines in The Netherlands. We estimated the number of hypersensitivity reactions and associated deaths that can be avoided annually by genotyping for these HLA risk alleles. Additionally, the cost-effectiveness was estimated. Nationwide implementation of genotyping HLA risk alleles before initiating drugs with an actionable drug–gene interaction can potentially save the life of seven allopurinol initiators and two flucloxacillin initiators each year in The Netherlands. Besides these deaths, 28 cases of abacavir hypersensitivity, 24 cases of allopurinol induced SCARs, 6 cases of carbamazepine induced DRESS and 22 cases of flucloxacillin induced DILI can be prevented. Genotyping HLA-B*5701 in abacavir initiators has a number needed to genotype of 31 to prevent one case of abacavir hypersensitivity and is cost-saving. Genotyping HLA-B*5801 in allopurinol initiators has a number needed to genotype of 1149 to prevent one case of SCAR but is still cost-effective. Genotyping before initiating antiepileptic drugs or flucloxacillin is not cost-effective. Our results confirm the need for mandatory testing of HLA-B*5701 in abacavir initiators, as indicated in the drug label, and show genotyping of HLA-B*5801 in allopurinol initiators should be considered.
Higher-level phylogeny of Chrysomelidae based on expanded sampling of mitogenomes

Chrysomelidae is one of the most diverse lineages of beetles. The classification and phylogeny of Chrysomelidae have been contentious. In this study, we obtained 16 new mitogenome sequences by using next-generation sequencing. Combined with the published mitogenomes, we inferred the phylogenetic relationships of Chrysomelidae. Different data recoding strategies and substitution models were applied to phylogenetic reconstruction. In the Maximum likelihood analyses under the homogeneous model, Dayhoff recoding allowed for the improved phylogenetic resolution due to the decreased level of heterogeneous sequence divergence. Bayesian inference under the heterogeneous model yielded generally well resolved subfamily relationships. The present mitogenome data strongly supported Chrysomelidae as a monophyletic group. Consistent with previous work, we found three major subfamily clades within Chrysomelidae. However, the pattern of the “sagrine” clade plus the “eumolpine” clade being sister to the “chrysomeline” clade contrasted with the prior study. The placement of the genus Syneta with regards to these three clades was ambiguous. Relationships recovered suggested several major chrysomelid lineages, including: (1) Bruchinae in the “sagrine” clade; (2) Donaciinae + Criocerinae; (3) Spilopyrinae + (Cassidinae + (Eumolpinae + (Lamprosomatinae + Cryptocephalinae))); (4) Chrysomelinae + (Alticinae + Galerucinae). Results also suggested the placement of Timarcha outside the major Chrysomelinae.
Genomic Characterization of Parengyodontium torokii sp. nov., a Biofilm-Forming Fungus Isolated from Mars 2020 Assembly Facility

A fungal strain (FJII-L10-SW-P1) was isolated from the Mars 2020 spacecraft assembly facility and exhibited biofilm formation on spacecraft-qualified Teflon surfaces. The reconstruction of a six-loci gene tree (ITS, LSU, SSU, RPB1 and RPB2, and TEF1) using multi-locus sequence typing (MLST) analyses of the strain FJII-L10-SW-P1 supported a close relationship to other known Parengyodontium album subclade 3 isolates while being phylogenetically distinct from subclade 1 strains. The zig-zag rachides morphology of the conidiogenous cells and spindle-shaped conidia were the distinct morphological characteristics of the P. album subclade 3 strains. The MLST data and morphological analysis supported the conclusion that the P. album subclade 3 strains could be classified as a new species of the genus Parengyodontium and placed in the family Cordycipitaceae. The name Parengyodontium torokii sp. nov. is proposed to accommodate the strain, with FJII-L10-SW-P1 as the holotype. The genome of the FJII-L10-SW-P1 strain was sequenced, annotated, and the secondary metabolite clusters were identified. Genes predicted to be responsible for biofilm formation and adhesion to surfaces were identified. Homology-based assignment of gene ontologies to the predicted proteome of P. torokii revealed the presence of gene clusters responsible for synthesizing several metabolic compounds, including a cytochalasin that was also verified using traditional metabolomic analysis.
Chitosan/poly(lactic-co-glycolic)acid Nanoparticle Formulations with Finely-Tuned Size Distributions for Enhanced Mucoadhesion

Non-parenteral drug delivery systems using biomaterials have advantages over traditional parenteral strategies. For ocular and intranasal delivery, nanoparticulate systems must bind to and permeate through mucosal epithelium and other biological barriers. The incorporation of mucoadhesive and permeation-enhancing biomaterials such as chitosan facilitate this, but tend to increase the size and polydispersity of the nanoparticles, making practical optimization and implementation of mucoadhesive nanoparticle formulations a challenge. In this study, we adjusted key poly(lactic-co-glycolic) acid (PLGA) nanoparticle formulation parameters including the organic solvent and co-solvent, the concentration of polymer in the organic phase, the composition of the aqueous phase, the sonication amplitude, and the inclusion of chitosan in the aqueous phase. By doing so, we prepared four statistically unique size groups of PLGA NPs and equally-sized chitosan-PLGA NP counterparts. We loaded simvastatin, a candidate for novel ocular and intranasal delivery systems, into the nanoparticles to investigate the effects of size and surface modification on drug loading and release, and we quantified size- and surface-dependent changes in mucoadhesion in vitro. These methods and findings will contribute to the advancement of mucoadhesive nanoformulations for ocular and nose-to-brain drug delivery.
A Laser-Based Multipass Absorption Sensor for Sub-ppm Detection of Methane, Acetylene and Ammonia

A compact, sensitive laser-based absorption sensor for multispecies monitoring of methane (CH4), acetylene (C2H2) and ammonia (NH3) was developed using a compact multipass gas cell. The gas cell is 8.8 cm long and has an effective optical path length of 3.0 m with a sampling volume of 75 mL. The sensor is composed of three fiber-coupled distributed feedback lasers operating near 1512 nm, 1532 nm and 1654 nm, an InGaAs photodetector and a custom-designed software for data acquisition, signal processing and display. The lasers were scanned over the target absorption features at 1 Hz. First-harmonic-normalized wavelength modulation spectroscopy (f = 3 kHz) with the second harmonic detection (WMS-2f/1f) is employed to eliminate the unwanted power fluctuations of the transmitted laser caused by aerosol/particles scattering, absorption and beam-steering. The multispecies sensor has excellent linear responses (R2 > 0.997) within the gas concentration range of 1–1000 ppm and shows a detection limit of 0.32 ppm for CH4, 0.16 ppm for C2H2 and 0.23 ppm for NH3 at 1 s response time. The Allan–Werle deviation analysis verifies the long-term stability of the sensor, indicating a minimal detection limit of 20–34 ppb were achieved after 60–148 s integration time. Flow test of the portable multispecies sensor is also demonstrated in this work.
Validating a Traffic Conflict Prediction Technique for Motorways Using a Simulation Approach

With the ever-increasing advancements in the technology of driver assistant systems, there is a need for a comprehensive way to identify traffic conflicts to avoid collisions. Although significant research efforts have been devoted to traffic conflict techniques applied for junctions, there is dearth of research on these methods for motorways. This paper presents the validation of a traffic conflict prediction algorithm applied to a motorway scenario in a simulated environment. An automatic video analysis system was developed to identify lane change and rear-end conflicts as ground truth. Using these conflicts, the prediction ability of the traffic conflict technique was validated in an integrated simulation framework. This framework consisted of a sub-microscopic simulator, which provided an appropriate testbed to accurately simulate the components of an intelligent vehicle, and a microscopic traffic simulator able to generate the surrounding traffic. Results from this framework show that for a 10% false alarm rate, approximately 80% and 73% of rear-end and lane change conflicts were accurately predicted, respectively. Despite the fact that the algorithm was not trained using the virtual data, the sensitivity was high. This highlights the transferability of the algorithm to similar road networks, providing a benchmark for the identification of traffic conflict and a relevant step for developing safety management strategies for autonomous vehicles.
Low-Symmetry Phthalocyanines Bearing Carboxy-Groups: Synthesis, Spectroscopic and Quantum-Chemical Characterization

The synthesis and characterization of A3B-type phthalocyanines, ZnPc1–4, bearing bulky 2,6-diisopropylphenoxy-groups or chlorine atoms on isoindoline units “A” and either one or two carboxylic anchors on isoindoline unit “B” are reported. A comparison of molecular modelling with the conventional time dependent—density functional theory (TD-DFT) approach and its simplified sTD-DFT approximation provides further evidence that the latter method accurately reproduces the key trends in the spectral properties, providing colossal savings in computer time for quite large molecules. This demonstrates that it is a valuable tool for guiding the rational design of new phthalocyanines for practical applications.
Effect of soil mulching on agricultural greenhouse gas emissions in China: A meta-analysis

Human demand for food has been increasing as population grows around the world. Meanwhile, global temperature has been rising with the increase of greenhouse gas (GHG) emissions. Although soil mulching (SM) is an effective method to increase crop yield because it could conserve soil moisture and temperature, it is also an important factor affecting GHG productions and emissions. At present, research results in terms of the impact of SM on agricultural GHG emissions are still inconsistent. Therefore, a meta-analysis was used to quantitatively analyze the impact of SM on crop yield and GHG emissions in China. Overall, SM significantly enhanced not only crop yield, but also GHG emissions. Compared with no soil mulching (NSM), SM improved crop yield by 21.84%, while increased global warming potential (GWP) by 11.38%. To minimize the negative impact of SM on GHG, for maize and wheat in arid, semi-arid and semi-humid zones, it is recommended to use flat full mulching with grave or straw plus drip irrigation under neutral or weakly alkaline soil with bulk density <1.3g cm-3. For rice in humid regions, it is advisable to apply SM to minimize GHG emissions by significantly decreasing CH4 emissions.
Evidence-Based Mechanical Ventilatory Strategies in ARDS

Acute respiratory distress syndrome (ARDS) remains one of the leading causes of morbidity and mortality in critically ill patients despite advancements in the field. Mechanical ventilatory strategies are a vital component of ARDS management to prevent secondary lung injury and improve patient outcomes. Multiple strategies including utilization of low tidal volumes, targeting low plateau pressures to minimize barotrauma, using low FiO2 (fraction of inspired oxygen) to prevent injury related to oxygen free radicals, optimization of positive end expiratory pressure (PEEP) to maintain or improve lung recruitment, and utilization of prone ventilation have been shown to decrease morbidity and mortality. The role of other mechanical ventilatory strategies like non-invasive ventilation, recruitment maneuvers, esophageal pressure monitoring, determination of optimal PEEP, and appropriate patient selection for extracorporeal support is not clear. In this article, we review evidence-based mechanical ventilatory strategies and ventilatory adjuncts for ARDS.