Miracle-dz/UniFAR-FTUs huggingface dataset:
Antiviral Therapeutic Approaches for SARS-CoV-2 Infection: A Systematic Review

Due to the lack of an etiologic treatment for SARS-CoV-2 and the difficulties involved in developing new drugs, some drugs already approved for other diseases or with efficacy against SARS and MERS, have been used in patients with COVID-19. This systematic review aims to summarize evidence on the efficacy and safety of five antivirals applied to patients with COVID-19, that have proven to be effective either in vitro studies or in studies on SARS-CoV and MERS. ; An intensive search of different databases (Pub Med, WoS, MEDLINE and Cochrane COVID-19 Study Register) has been carried out until the end of April 2021. This systematic review has been conducted according to the PRISMA statement. From each of the included studies, the characteristics of the intervention and comparison groups, demographic data and results were extracted independently; Remdesivir is well tolerated and helps to accelerate clinical improvement but is ineffective in reducing mortality. Favipiravir is safe and shows promising results regarding symptom resolution but does not improve viral clearance. The use of lopinavir/ritonavir has been associated with an increased risk of gastrointestinal adverse events and it has not proven to be effective. No significant differences were observed between patients treated with ribavirin or umifenovir and their respective control groups; Remdesivir and favipiravir are well tolerated and effective in accelerating clinical improvement. This systematic review does not support the use of lopinavir/ritonavir, ribavirin and umifenovir in hospitalized patients with COVID-19.
BRIE2: computational identification of splicing phenotypes from single-cell transcriptomic experiments

RNA splicing is an important driver of heterogeneity in single cells through the expression of alternative transcripts and as a determinant of transcriptional kinetics. However, the intrinsic coverage limitations of scRNA-seq technologies make it challenging to associate specific splicing events to cell-level phenotypes. BRIE2 is a scalable computational method that resolves these issues by regressing single-cell transcriptomic data against cell-level features. We show that BRIE2 effectively identifies differential disease-associated alternative splicing events and allows a principled selection of genes that capture heterogeneity in transcriptional kinetics and improve RNA velocity analyses, enabling the identification of splicing phenotypes associated with biological changes.
Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2

An Emergency Use Authorization was issued in the United States and in Europe for a monoclonal antibody monotherapy to prevent severe COVID-19 in high-risk patients. This study aimed to assess the risk of emergence of mutations following treatment with a single monoclonal antibody. Bamlanivimab was administered at a single dose of 700 mg in a one-hour IV injection in a referral center for the management of COVID-19 in France. Patients were closely monitored clinically and virologically with nasopharyngeal RT-PCR and viral whole genome sequencing. Six patients were treated for a nosocomial SARS-CoV-2 infection, all males, with a median age of 65 years and multiple comorbidities. All patients were infected with a B.1. 1.7 variant, which was the most frequent variant in France at the time, and no patients had E484 mutations at baseline. Bamlanivimab was infused in the six patients within 4 days of the COVID-19 diagnosis. Four patients had a favorable outcome, one died of complications unrelated to COVID-19 or bamlanivimab, and one kidney transplant patient treated with belatacept died from severe COVID-19 more than 40 days after bamlanivimab administration. Virologically, four patients cleared nasopharyngeal viral shedding within one month after infusion, while two presented prolonged viral excretion for more than 40 days. The emergence of E484K mutants was observed in five out of six patients, and the last patient presented a Q496R mutation potentially associated with resistance. CONCLUSIONS: These results show a high risk of emergence of resistance mutants in COVID-19 patients treated with monoclonal antibody monotherapy.
Serological Screening for Antibodies against SARS-CoV-2 in Dutch Shelter Cats

The COVID-19 pandemic raised concerns that companion animals might be infected with, and could become a reservoir of, SARS-CoV-2. As cats are popular pets and susceptible to Coronavirus, we investigated the seroprevalence of SARS-CoV-2 antibodies in shelter cats housed in Dutch animal shelters during the COVID-19 pandemic. In this large-scale cross-sectional study, serum samples of shelter cats were collected during the second wave of human COVID-19 infections in The Netherlands. Seroprevalence was determined by using an indirect protein-based ELISA validated for cats, and a Virus Neutralization Test (VNT) as confirmation. To screen for feline SARS-CoV-2 shedding, oropharyngeal and rectal swabs of cats positive for ELISA and/or VNT were analyzed using PCR tests. In 28 Dutch animal shelters, 240 shelter cats were convenience sampled. Two of these cats (0.8%; CI 95%: 0.1–3.0%) were seropositive, as evidenced by the presence of SARS-CoV-2 neutralizing antibodies. The seropositive animals tested PCR negative for SARS-CoV-2. Based on the results of this study, it is unlikely that shelter cats could be a reservoir of SARS-CoV-2 or pose a (significant) risk to public health.
Mandate or Not Mandate: Knowledge, Attitudes, and Practices of Italian Occupational Physicians towards SARS-CoV-2 Immunization at the Beginning of Vaccination Campaign

Vaccinations used to prevent coronavirus disease (COVID-19)—the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)—are critical in order to contain the ongoing pandemic. However, SARS-CoV-2/COVID-19 vaccination rates have only slowly increased since the beginning of the vaccination campaign, even with at-risk workers (e.g., HCWs), presumptively because of vaccine hesitancy. Vaccination mandates are considered instrumental in order to rapidly improve immunization rates (but they minimize the impact of vaccination campaigns). In this study, we investigated the acceptance (i.e., knowledge, attitudes, and practices) from occupational physicians (OPs)) in regard to SARS-CoV-2/COVID-19 vaccination mandates. A total of 166 OPs participated in an internet-based survey by completing structured questionnaires. Adequate, general knowledge of SARS-CoV-2/COVID-19 was found in the majority of OPs. High perception of SARS-CoV-2 risk was found in around 80% of participants (79.5% regarding its occurrence, 81.9% regarding its potential severity). SARS-CoV-2/COVID-19 vaccination was endorsed by 90.4% of respondents, acceptance for SARS-CoV-2 vaccine was quite larger for mRNA formulates (89.8%) over adenoviral ones (59.8%). Endorsement of vaccination mandates was reported by 60.2% of respondents, and was more likely endorsed by OPs who exhibited higher concern for SARS-CoV-2 infection occurrence (odds ratio 3.462, 95% confidence intervals 1.060–11.310), who were likely to accept some sort of payment/copayment for SARS-CoV-2/COVID-19 vaccination (3.896; 1.607; 9.449), or who were more likely to believe HCWs not vaccinates against SARS-CoV-2 as unfit for work (4.562; 1.935; 10.753). In conclusion, OPs exhibited wide acceptance of SARS-CoV-2/COVID-19 vaccinations, and the majority endorsed vaccination mandates for HCWs, which may help improve vaccination rates in occupational settings.
Cross-Sectional Study to Establish the Utility of Serum Tumor Markers in the Diagnosis of Lung Cancer

Background: Reliable blood markers for aiding lung cancer (LC) diagnosis and differentiating LC from tuberculosis are lacking in India. Methodology: In this single-centre, cross-sectional, real-world study, serum levels of 5 TMs (CEA, CYFRA 21-1, SCC, ProGRP, NSE) were measured from consented patients with suspicious lung nodules who were candidates for biopsy, and also from healthy controls. TM level measurement was done through electrochemiluminescent immunoassay, followed by histological diagnosis on the biopsied specimen. Using package insert cut-offs, sensitivity and specificity of the 5 TMs were evaluated individually and in combination. Using receiver operating characteristic (ROC) curves of individual TMs, the ability of CEA, CYFRA 21-1, and ProGRP taken together was evaluated for its ability to differentiate LC from no-LC. Results: Out of 178 subjects, 160 had LC (147 NSCLC; 13 SCLC). NSCLC patients had higher median values of CYFRA 21-1 and SCC; SCLC patients had higher median values of CEA, NSE, and ProGRP. Adenocarcinoma-NSCLC patients had higher median values of CEA, CYFRA 21-1, NSE, and ProGRP; squamous-NSCLC patients had higher median value of SCC. For differentiating LC from no-LC, the combination of all 5 TMs (sensitivity:97.5%, specificity:33.3%) and combination of CEA, CYFRA 21-1 and ProGRP (sensitivity:91.3%, specificity:88.9%) were found suitable. Conclusion: Combination of all 5 TMs, and combination of CEA, CYFRA 21-1, and ProGRP represents an easy and non-invasive method for aid in LC diagnosis that does not require technical expertise. TM evaluation can also supplement histological diagnosis of LC.
Frequency of persistent obesity 5 years after first time diagnosis of status asthmaticus

When a severe asthma exacerbation occurs in an obese pediatric patient, it is unknown if this body type persists in future encounters. Persistent obesity can lead to future asthma exacerbations. The main study objective is to evaluate the persistence of a BMI percentile ≥85th in children 5 years after the first reported diagnosis of status asthmaticus. We hypothesized that a hospital admission for status asthmaticus was associated with persistence of a BMI percentile ≥85th.
Sensor-Based Gait Retraining Lowers Knee Adduction Moment and Improves Symptoms in Patients with Knee Osteoarthritis: A Randomized Controlled Trial

The present study compared the effect between walking exercise and a newly developed sensor-based gait retraining on the peaks of knee adduction moment (KAM), knee adduction angular impulse (KAAI), knee flexion moment (KFM) and symptoms and functions in patients with early medial knee osteoarthritis (OA). Eligible participants (n = 71) with early medial knee OA (Kellgren-Lawrence grade I or II) were randomized to either walking exercise or gait retraining group. Knee loading-related parameters including KAM, KAAI and KFM were measured before and after 6-week gait retraining. We also examined clinical outcomes including visual analog pain scale (VASP) and Knee Injury and Osteoarthritis Outcome Score (KOOS) at each time point. After gait retraining, KAM1 and VASP were significantly reduced (both Ps < 0.001) and KOOS significantly improved (p = 0.004) in the gait retraining group, while these parameters remained similar in the walking exercise group (Ps ≥ 0.448). However, KAM2, KAAI and KFM did not change in both groups across time (Ps ≥ 0.120). A six-week sensor-based gait retraining, compared with walking exercise, was an effective intervention to lower medial knee loading, relieve knee pain and improve symptoms for patients with early medial knee OA.
In Silico Approaches: A Way to Unveil Novel Therapeutic Drugs for Cervical Cancer Management

Cervical cancer (CC) is the fourth most common pathology in women worldwide and presents a high impact in developing countries due to limited financial resources as well as difficulties in monitoring and access to health services. Human papillomavirus (HPV) is the leading cause of CC, and despite the approval of prophylactic vaccines, there is no effective treatment for patients with pre-existing infections or HPV-induced carcinomas. High-risk (HR) HPV E6 and E7 oncoproteins are considered biomarkers in CC progression. Since the E6 structure was resolved, it has been one of the most studied targets to develop novel and specific therapeutics to treat/manage CC. Therefore, several small molecules (plant-derived or synthetic compounds) have been reported as blockers/inhibitors of E6 oncoprotein action, and computational-aided methods have been of high relevance in their discovery and development. In silico approaches have become a powerful tool for reducing the time and cost of the drug development process. Thus, this review will depict small molecules that are already being explored as HR HPV E6 protein blockers and in silico approaches to the design of novel therapeutics for managing CC. Besides, future perspectives in CC therapy will be briefly discussed.
A Lightweight Fusion Distillation Network for Image Deblurring and Deraining

Recently, deep learning-based image deblurring and deraining have been well developed. However, most of these methods fail to distill the useful features. What is more, exploiting the detailed image features in a deep learning framework always requires a mass of parameters, which inevitably makes the network suffer from a high computational burden. We propose a lightweight fusion distillation network (LFDN) for image deblurring and deraining to solve the above problems. The proposed LFDN is designed as an encoder–decoder architecture. In the encoding stage, the image feature is reduced to various small-scale spaces for multi-scale information extraction and fusion without much information loss. Then, a feature distillation normalization block is designed at the beginning of the decoding stage, which enables the network to distill and screen valuable channel information of feature maps continuously. Besides, an information fusion strategy between distillation modules and feature channels is also carried out by the attention mechanism. By fusing different information in the proposed approach, our network can achieve state-of-the-art image deblurring and deraining results with a smaller number of parameters and outperform the existing methods in model complexity.
The Therapeutic Effect of Human Serum Albumin Dimer-Doxorubicin Complex against Human Pancreatic Tumors

Human serum albumin (HSA) is a versatile drug carrier with active tumor targeting capacity for an antitumor drug delivery system. Nanoparticle albumin-bound (nab)-technology, such as nab-paclitaxel (Abraxane®), has attracted significant interest in drug delivery research. Recently, we demonstrated that HSA dimer (HSA-d) possesses a higher tumor distribution than HSA monomer (HSA-m). Therefore, HSA-d is more suitable as a drug carrier for antitumor therapy and can improve nab technology. This study investigated the efficacy of HSA-d-doxorubicin (HSA-d-DOX) as next-generation nab technology for tumor treatment. DOX conjugated to HSA-d via a tunable pH-sensitive linker for the controlled release of DOX. Lyophilization did not affect the particle size of HSA-d-DOX or the release of DOX. HSA-d-DOX showed significantly higher cytotoxicity than HSA-m-DOX in vitro. In the SUIzo Tumor-2 (SUIT2) human pancreatic tumor subcutaneous inoculation model, HSA-d-DOX could significantly inhibit tumor growth without causing serious side effects, as compared to the HSA binding DOX prodrug, which utilized endogenous HSA as a nano-drug delivery system (DDS) carrier. These results indicate that HSA-d could function as a natural solubilizer of insoluble drugs and an active targeting carrier in intractable tumors with low vascular permeability, such as pancreatic tumors. In conclusion, HSA-d can be an effective drug carrier for the antitumor drug delivery system against human pancreatic tumors.
Visualization of Activated Area on Polymers for Evaluation of Atmospheric Pressure Plasma Jets

The treatment of a polymer surface using an atmospheric pressure plasma jet (APPJ) causes a local increase of the surface free energy (SFE). The plasma-treated zone can be visualized with the use of a test ink and quantitatively evaluated. However, the inked area is shrinking with time. The shrinkage characteristics are collected using activation image recording (AIR). The recording is conducted by a digital camera. The physical mechanisms of activation area shrinkage are discussed. The error sources are analyzed and methods of error reduction are proposed. The standard deviation of the activation area is less than 3%. Three polymers, acrylonitrile butadiene styrene (ABS), high-density polyethylene (HDPE), and polyoxymethylene (POM), are examined as a test substrate material. Due to a wide variation range of SFE and a small hydrophobic recovery, HDPE is chosen. Since the chemical mixtures tend to temporal changes of the stoichiometry, the pure formamide test ink with 58 mN/m is selected. The method is tested for the characterization of five different types of discharge: (i) pulsed arc APPJ with the power of about 700 W; (ii) piezoelectric direct discharge APPJ; (iii) piezoelectric driven needle corona in ambient air; (iv) piezoelectric driven plasma needle in argon; and (v) piezoelectric driven dielectric barrier discharge (DBD). For piezoelectrically driven discharges, the power was either 4.5 W or 8 W. It is shown how the AIR method can be used to solve different engineering problems.
Stimuli-Aware Visual Emotion Analysis

Visual emotion analysis (VEA) has attracted great attention recently, due to the increasing tendency of expressing and understanding emotions through images on social networks. Different from traditional vision tasks, VEA is inherently more challenging since it involves a much higher level of complexity and ambiguity in human cognitive process. Most of the existing methods adopt deep learning techniques to extract general features from the whole image, disregarding the specific features evoked by various emotional stimuli. Inspired by the Stimuli-Organism-Response (S-O-R) emotion model in psychological theory, we proposed a stimuli-aware VEA method consisting of three stages, namely stimuli selection (S), feature extraction (O) and emotion prediction (R). First, specific emotional stimuli (i. e., color, object, face) are selected from images by employing the off-the-shelf tools. To the best of our knowledge, it is the first time to introduce stimuli selection process into VEA in an end-to-end network. Then, we design three specific networks, i. e. , Global-Net, Semantic-Net and Expression-Net, to extract distinct emotional features from different stimuli simultaneously. Finally, benefiting from the inherent structure of Mikel’s wheel, we design a novel hierarchical cross-entropy loss to distinguish hard false examples from easy ones in an emotion-specific manner. Experiments demonstrate that the proposed method consistently outperforms the state-of-the-art approaches on four public visual emotion datasets. Ablation study and visualizations further prove the validity and interpretability of our method.
Obstacle Detection System for Agricultural Mobile Robot Application Using RGB-D Cameras

Mobile robots designed for agricultural tasks need to deal with challenging outdoor unstructured environments that usually have dynamic and static obstacles. This assumption significantly limits the number of mapping, path planning, and navigation algorithms to be used in this application. As a representative case, the autonomous lawn mowing robot considered in this work is required to determine the working area and to detect obstacles simultaneously, which is a key feature for its working efficiency and safety. In this context, RGB-D cameras are the optimal solution, providing a scene image including depth data with a compromise between precision and sensor cost. For this reason, the obstacle detection effectiveness and precision depend significantly on the sensors used, and the information processing approach has an impact on the avoidance performance. The study presented in this work aims to determine the obstacle mapping accuracy considering both hardware- and information processing-related uncertainties. The proposed evaluation is based on artificial and real data to compute the accuracy-related performance metrics. The results show that the proposed image and depth data processing pipeline introduces an additional distortion of 38 cm.
Fully Recyclable Bio-Based Epoxy Formulations Using Epoxidized Precursors from Waste Flour: Thermal and Mechanical Characterization

Organic wastes represent an increasing pollution problem due to the exponential growth of their presence in the waste stream. Among these, waste flour cannot be easily reused by transforming it into high-value-added products. Another major problem is represented by epoxy-based thermosets, which have wide use but also poor recyclability. The object of the present paper is, therefore, to analyze both of these problems and come up with innovative solutions. Indeed, we propose a completely new approach, aimed at reusing the organic waste flour, by converting it into high-value epoxy-based thermosets that could be fully recycled into a reusable plastic matrix when added to the waste epoxy-based thermosets. Throughout the research activity, the organic waste was transformed into an epoxidized prepolymer, which was then mixed with a bio-based monomer cured with a cleavable ammine. The latter reactant was based on Recyclamine™ by Connora Technologies, and in this paper, we demonstrate that this original approach could work with the synthetized epoxy prepolymers derived from the waste flour. The cured epoxies were fully characterized in terms of their thermal, rheological, and flexural properties. The results obtained showed optimal recyclability of the new resin developed.
Influence of Herbicide Exposure and Ranavirus Infection on Growth and Survival of Juvenile Red-Eared Slider Turtles (Trachemys scripta elegans)

Ranaviruses are an important wildlife pathogen of fish, amphibians, and reptiles. Previous studies have shown that susceptibility and severity of infection can vary with age, host species, virus strain, temperature, population density, and presence of environmental stressors. Experiments are limited with respect to interactions between this pathogen and environmental stressors in reptiles. In this study, we exposed hatchling red-eared slider turtles (Trachemys scripta elegans) to herbicide and ranavirus treatments to examine direct effects and interactions on growth, morbidity, and mortality. Turtles were assigned to one of three herbicide treatments or a control group. Turtles were exposed to atrazine, Roundup ProMax®, or Rodeo® via water bath during the first 3 weeks of the experiment. After 1 week, turtles were exposed to either a control (cell culture medium) or ranavirus-infected cell lysate via injection into the pectoral muscles. Necropsies were performed upon death or upon euthanasia after 5 weeks. Tissues were collected for histopathology and detection of ranavirus DNA via quantitative PCR. Only 57.5% of turtles exposed to ranavirus tested positive for ranaviral DNA at the time of death. Turtles exposed to ranavirus died sooner and lost more mass and carapace length, but not plastron length, than did controls. Exposure to environmentally relevant concentrations of herbicides did not impact infection rate, morbidity, or mortality of hatchling turtles due to ranavirus exposure. We also found no direct effects of herbicide or interactions with ranavirus exposure on growth or survival time. Results of this study should be interpreted in the context of the modest ranavirus infection rate achieved, the general lack of growth, and the unplanned presence of an additional pathogen in our study.