Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity.

SARS-CoV-2 can mutate and evade immunity, with consequences for efficacy of emerging vaccines and antibody therapeutics. Here, we demonstrate that the immunodominant SARS-CoV-2 spike (S) receptor binding motif (RBM) is a highly variable region of S and provide epidemiological, clinical, and molecular characterization of a prevalent, sentinel RBM mutation, N439K. We demonstrate N439K S protein has enhanced binding affinity to the hACE2 receptor, and N439K viruses have similar in vitro replication fitness and cause infections with similar clinical outcomes as compared to wild type. We show the N439K mutation confers resistance against several neutralizing monoclonal antibodies, including one authorized for emergency use by the US Food and Drug Administration (FDA), and reduces the activity of some polyclonal sera from persons recovered from infection. Immune evasion mutations that maintain virulence and fitness such as N439K can emerge within SARS-CoV-2 S, highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics.

Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology.

Analysis of the specificity and kinetics of neutralizing antibodies (nAbs) elicited by SARS-CoV-2 infection is crucial for understanding immune protection and identifying targets for vaccine design. In a cohort of 647 SARS-CoV-2-infected subjects, we found that both the magnitude of Ab responses to SARS-CoV-2 spike (S) and nucleoprotein and nAb titers correlate with clinical scores. The receptor-binding domain (RBD) is immunodominant and the target of 90% of the neutralizing activity present in SARS-CoV-2 immune sera. Whereas overall RBD-specific serum IgG titers waned with a half-life of 49 days, nAb titers and avidity increased over time for some individuals, consistent with affinity maturation. We structurally defined an RBD antigenic map and serologically quantified serum Abs specific for distinct RBD epitopes leading to the identification of two major receptor-binding motif antigenic sites. Our results explain the immunodominance of the receptor-binding motif and will guide the design of COVID-19 vaccines and therapeutics.

Neutralization, effector function and immune imprinting of Omicron variants.

Currently circulating SARS-CoV-2 variants have acquired convergent mutations at hot spots in the receptor-binding domain1 (RBD) of the spike protein. The effects of these mutations on viral infection and transmission and the efficacy of vaccines and therapies remains poorly understood. Here we demonstrate that recently emerged BQ.1.1 and XBB.1.5 variants bind host ACE2 with high affinity and promote membrane fusion more efficiently than earlier Omicron variants. Structures of the BQ.1.1, XBB.1 and BN.1 RBDs bound to the fragment antigen-binding region of the S309 antibody (the parent antibody for sotrovimab) and human ACE2 explain the preservation of antibody binding through conformational selection, altered ACE2 recognition and immune evasion. We show that sotrovimab binds avidly to all Omicron variants, promotes Fc-dependent effector functions and protects mice challenged with BQ.1.1 and hamsters challenged with XBB.1.5. Vaccine-elicited human plasma antibodies cross-react with and trigger effector functions against current Omicron variants, despite a reduced neutralizing activity, suggesting a mechanism of protection against disease, exemplified by S309. Cross-reactive RBD-directed human memory B cells remained dominant even after two exposures to Omicron spikes, underscoring the role of persistent immune imprinting.

Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift.

The recently emerged SARS-CoV-2 Omicron variant encodes 37 amino acid substitutions in the spike protein, 15 of which are in the receptor-binding domain (RBD), thereby raising concerns about the effectiveness of available vaccines and antibody-based therapeutics. Here we show that the Omicron RBD binds to human ACE2 with enhanced affinity, relative to the Wuhan-Hu-1 RBD, and binds to mouse ACE2. Marked reductions in neutralizing activity were observed against Omicron compared to the ancestral pseudovirus in plasma from convalescent individuals and from individuals who had been vaccinated against SARS-CoV-2, but this loss was less pronounced after a third dose of vaccine. Most monoclonal antibodies that are directed against the receptor-binding motif lost in vitro neutralizing activity against Omicron, with only 3 out of 29 monoclonal antibodies retaining unaltered potency, including the ACE2-mimicking S2K146 antibody1. Furthermore, a fraction of broadly neutralizing sarbecovirus monoclonal antibodies neutralized Omicron through recognition of antigenic sites outside the receptor-binding motif, including sotrovimab2, S2X2593 and S2H974. The magnitude of Omicron-mediated immune evasion marks a major antigenic shift in SARS-CoV-2. Broadly neutralizing monoclonal antibodies that recognize RBD epitopes that are conserved among SARS-CoV-2 variants and other sarbecoviruses may prove key to controlling the ongoing pandemic and future zoonotic spillovers.

Personalising circadian hygiene educational initiatives aimed at university students-"He who has ears to hear, let him hear".

The aim of the present study was to characterise "early drop-outs" (n = 3185) out of a group of university students (n = 7766) engaged in an ongoing circadian education initiative, to evaluate its efficacy and direct its developments. The initiative is aimed at improving sleep timing/quality through one of two sets of circadian hygiene advice covering the timing of sleep, meals, exercise and light exposure, and it has already been shown to have a positive effect on sleep timing. This second, interim analysis confirmed the high prevalence of disturbed night sleep and social jetlag amongst students at Padova University. Three-thousand, one-hundred and eighty-five (41.0%) students were early drop-outs. These were more commonly males (46.4 versus 37.6%; χ2 = 58, p < 0.0001), had later sleep-wake habits, more daytime sleepiness and worse night sleep quality. Chronotype distribution was also different, with a slight but significantly higher proportion of extremely evening/evening types amongst early drop-outs (χ2 = 10, p < 0.05). These results suggest that the more evening the student, the lower their likelihood of choosing/being able to follow circadian advice.

A data-driven approach to identify risk profiles and protective drugs in COVID-19.

As the COVID-19 pandemic is spreading around the world, increasing evidence highlights the role of cardiometabolic risk factors in determining the susceptibility to the disease. The fragmented data collected during the initial emergency limited the possibility of investigating the effect of highly correlated covariates and of modeling the interplay between risk factors and medication. The present study is based on comprehensive monitoring of 576 COVID-19 patients. Different statistical approaches were applied to gain a comprehensive insight in terms of both the identification of risk factors and the analysis of dependency structure among clinical and demographic characteristics. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus enters host cells by binding to the angiotensin-converting enzyme 2 (ACE2), but whether or not renin-angiotensin-aldosterone system inhibitors (RAASi) would be beneficial to COVID-19 cases remains controversial. The survival tree approach was applied to define a multilayer risk stratification and better profile patient survival with respect to drug regimens, showing a significant protective effect of RAASi with a reduced risk of in-hospital death. Bayesian networks were estimated, to uncover complex interrelationships and confounding effects. The results confirmed the role of RAASi in reducing the risk of death in COVID-19 patients. De novo treatment with RAASi in patients hospitalized with COVID-19 should be prospectively investigated in a randomized controlled trial to ascertain the extent of risk reduction for in-hospital death in COVID-19.

End-to-End Emulation of LoRaWAN Architecture and Infrastructure in Complex Smart City Scenarios Exploiting Containers.

In a LoRaWAN network, the backend is generally distributed as Software as a Service (SaaS) based on container technology, and recently, a containerized version of the LoRaWAN node stack is also available. Exploiting the disaggregation of LoRaWAN components, this paper focuses on the emulation of complex end-to-end architecture and infrastructures for smart city scenarios, leveraging on lightweight virtualization technology. The fundamental metrics to gain insights and evaluate the scaling complexity of the emulated scenario are defined. Then, the methodology is applied to use cases taken from a real LoRaWAN application in a smart city with hundreds of nodes. As a result, the proposed approach based on containers allows for the following: (i) deployments of functionalities on diverse distributed hosts; (ii) the use of the very same SW running on real nodes; (iii) the simple configuration and management of the emulation process; (iv) affordable costs. Both premise and cloud servers are considered as emulation platforms to evaluate the resource request and emulation cost of the proposed approach. For instance, emulating one hour of an entire LoRaWAN network with hundreds of nodes requires very affordable hardware that, if realized with a cloud-based computing platform, may cost less than USD 1.

Patient-reported persistent symptoms after radiotherapy and association with quality of life for prostate cancer survivors.

PURPOSE: To evaluate the persistence of symptoms after radiotherapy (RT) for localised prostate cancer (PCa) and the association with quality of life (QOL). MATERIALS AND METHODS: Prospective patient-reported outcome (PRO) from a multi-institutional study on PCa treated with radical RT (2010-2014) was analysed. Data was collected at baseline (BL) and follow-ups (FUPs) up to 5 years. Patients with BL and ≥3 late FUPs (≥6 months) were analysed. PRO was scored by means of the IPSS and ICIQ-SF (urinary), LENT-SOMA (gastrointestinal [GI]), and EORTC-C30 (pain, insomnia, fatigue, and QOL) questionnaires. Symptoms were defined 'persistent' if the median score over FUPs was ≥3 (urinary) or ≥2 (GI, pain, insomnia, and fatigue), and worse than BL. Different thresholds were chosen to have enough events for each symptom. QOL was linearly transformed on a continuous scale (0-100). Linear-mixed models were used to identify significant differences between groups with and without persistent symptoms including age, smoking status, previous abdominal surgery, and diabetes as confounders. Mean QOL differences between groups were evaluated longitudinally over FUPs. RESULTS: The analysis included 293 patients. Persistent urinary symptoms ranged from 2% (straining) to 12% (weak stream, and nocturia). Gastrointestinal symptoms ranged from 7% (rectal pain, and incontinence) to 30% (urgency). Proportions of pain, insomnia, and fatigue were 6, 13, and 18%. Significant QOL differences of small-to-medium clinical relevance were found for urinary incontinence, frequency, urgency, and nocturia. Among GI symptoms, rectal pain and incontinence showed small-to-medium differences. Fatigue was associated with the largest differences. CONCLUSIONS: The analysis showed that symptoms after RT for PCa occur with different persistence and their association with QOL varies in magnitude. A number of persistent urinary and GI symptoms showed differences in a comparable range. Urinary incontinence and frequency, rectal pain, and faecal incontinence more often had significant associations. Fatigue was also prevalent and associated with largely deteriorated QOL.

Residues of veterinary antibiotics in manures from pig and chicken farms in a context of antimicrobial use reduction by implementation of health and welfare plans.

The use of antibiotics in food-producing animals can induce the presence of residual substances in manure, which are then released into the environment and may contribute to soil and groundwater contamination. During the on-farm implementation of strategies to improve animal health and welfare in chicken and pig farms, the consequences of antibiotic use were evaluated in terms of the occurrence and levels of antibiotic residues in manure. A set of 35 broiler farms from Cyprus, Greece, the Netherlands and 40 pig farms from France and Italy provided a total of 350 manure samples. The primary objective was to develop a specific LC/MS/MS method capable of quantifying antibiotic residues in both types of manure. The method was able to detect fifteen antibiotics belonging to nine classes, with validated limits of quantification of 10-20 µg/kg, and accuracies ranging from 81% to 138%. With the exception of amoxicillin, which was never detected in any manure, all antibiotics used were detected in manure from treated animals with typical concentrations ranging from 10 to 99198 µg/kg for both chickens and pigs. The occurrence of residual antibiotics was higher in chicken than in pig manure, especially for fluoroquinolones and doxycycline which were detected in 89% and 100% of the chicken manure, respectively, and in 28% of the pig manure. The impact of the health plans on the antibiotic load manure was assessed by measuring for each farm the ratio of the sum of all antibiotic concentrations measured after and before the implementation of the plan. The results showed that, in addition to the frequency of treatments, the class of antibiotic used is an important factor to consider as it strongly influences the stability/instability of the compounds, i.e. their ability to persist in the manure of food-producing animals.

HCM-associated ALMS1 variant: Allele drop-out and frequency in Italian Sphynx cats.

Hypertrophic cardiomyopathy (HCM) is the most common cardiomyopathy in domestic cats, and some inherited variants are available for genetic testing. A variant of the Alstrom syndrome protein 1 gene (ALMS1) was recently reported to be associated with HCM in the Sphynx cat breed (A3: g.92439157G>C). Genetic screening of the variant, promoted by the Osservatorio Veterinario Italiano Cardiopatie and Genefast Laboratory, was offered to Sphynx cat owners and breeders in Italy. Genotype data were initially obtained by Sanger sequencing. In one case where the samples of a trio were available, inconsistency in the vertical transmission of the variant suggested an allele dropout (ADO) of the wt allele. A new external primer pair was designed as an alternative to the original. The larger PCR product obtained was sanger sequenced, and five novel single nucleotide variants (SNVs) not yet annotated in open-access databases were detected. Three of these SNVs were within the original primer-binding regions and were assumed to have caused ADO. The haplotype, including the ADO SNVs, was detected in two cats belonging to different lineages. To accurately genotype ALMS1 g.92439157G>C in the samples, we set up a real-time TaqMan MGB assay while avoiding all surrounding SNVs. At g.92439157G>C, for 136 Sphynx cats, g.92439157 C variant was highly widespread (freq. >0.50). The present study reports five new variants surrounding ALMS1 g.92439157G>C that must be considered when designing the test. The study also indicates the need to verify the correspondence between the g.92439157 C variant frequency and the prevalence of HCM by increasing clinical visits and follow-ups and finally to promote genetic counselling for accurate management of mating plans in Italian Sphynx cats.

Assessing a Methodology for Evaluating the Latency of IPv6 with SCHC Compression in LoRaWAN Deployments.

The Internet of Things (IoT) approach relies on the use of the Internet Protocol (IP) as a pervasive network protocol. IP acts as a "glue" for interconnecting end devices (on the field side) and end users, leveraging on very diverse lower-level and upper-level protocols. The need for scalability would suggest the adoption of IPv6, but the large overhead and payloads do not match with the constraints dictated by common wireless solutions. For this reason, compression strategies have been proposed to avoid redundant information in the IPv6 header and to provide fragmentation and reassembly of long messages. For example, the Static Context Header Compression (SCHC) protocol has been recently referenced by the LoRa Alliance as a standard IPv6 compression scheme for LoRaWAN-based applications. In this way, IoT end points can seamlessly share an end-to-end IP link. However, implementation details are out of the specifications' scope. For this reason, formal test procedures for comparing solutions from different providers are important. In this paper, a test method for assessing architectural delays of real-world deployments of SCHC-over-LoRaWAN implementations is presented. The original proposal includes a mapping phase, for identifying information flows, and a subsequent evaluation phase, in which flows are timestamped and time-related metrics are computed. The proposed strategy has been tested in different use cases involving LoRaWAN backends deployed all around the world. The feasibility of the proposed approach has been tested by measuring the end-to-end latency of IPv6 data in sample use cases, obtaining a delay of less than 1 s. However, the main result is the demonstration that the suggested methodology permits a comparison of the behavior of IPv6 with SCHC-over-LoRaWAN, allowing the optimization of choices and parameters during deployment and commissioning of both infrastructure components and software.

The TNNT2:c.95-108G>A variant is common in Maine Coons and shows no association with hypertrophic cardiomyopathy.

Hypertrophic cardiomyopathy (HCM) is a common and potentially fatal heart disease in many cat breeds. An intronic variant in TNNT2, c.95-108G>A, was recently reported as the cause of HCM in the Maine Coon. The aim of this study was to determine this variant's allele frequency in different populations and its possible association with HCM. Based on 160 Maine Coon samples collected in Belgium, Italy, Sweden and the USA, the variant's allele frequency was estimated to be 0.32. Analysis of the 99 Lives feline whole genome sequencing database showed that the TNNT2 variant also occurs in other breeds, as well as mixed-breed cats. Comparison of 31 affected and 58 healthy cats did not reveal significantly increased odds for HCM in homozygotes. Based on the combined evidence and in agreement with the standards and guidelines for the interpretation of sequence variants, this variant is currently classified as a variant of unknown significance and should not be used for breeding decisions regarding HCM.

Italian survey on non-intubated thoracic surgery: results from INFINITY group.

BACKGROUND: Non-Intubated Thoracic Surgery (NITS) is becoming increasingly adopted all over the world. Although it is mainly used for pleural operations,, non-intubated parenchymal lung surgery has been less frequently reported. Recently, NITS utilization seems to be increased also in Italy, albeit there are no multi-center studies confirming this finding. The objective of this survey is to assess quantitatively and qualitatively the performance of NITS in Italy. METHODS: In 2018 a web-based national survey on Non-Intubated management including both thoracic surgeons and anesthesiologists was carried out. Reference centers have been asked to answer 32 questions. Replies were collected from June 26 to November 31, 2019. RESULTS: We raised feedbacks from 95% (55/58) of Italian centers. Seventy-eight percent of the respondents perform NITS but only 38% of them used this strategy for parenchymal surgery. These procedures are more frequently carried out in patients with severe comorbidities and/or with poor lung function. Several issues as obesity, previous non-invasive ventilation and/or oxygen therapy are considered contraindications to NITS. The regional anesthesia technique most used to provide intra- and postoperative analgesia was the paravertebral block (37%). Conversion to general anesthesia is not anecdotal (31% of answerers). More than half of the centers believed that NITS may reduce postoperative intensive care unit admissions. Approximately a quarter of the centers are conducting trials on NITS and, three quarters of the respondent suppose that the number of these procedures will increase in the future. CONCLUSIONS: There is a growing interest in Italy for NITS and this survey provides a clear view of the national management framework of these procedures.

Present status and future directions: The restoration of root filled teeth.

This narrative review will focus on a number of contemporary considerations relating to the restoration of root filled teeth and future directions for research. Clinicians are now more than ever, aware of the interdependence of the endodontic and restorative aspects of managing root filled teeth, and how these aspects of treatment are fundamental to obtaining the best long-term survival. To obtain the optimal outcomes for patients, clinicians carrying out endodontic treatment should have a vested interest in the restorative phase of the treatment process, as well as an appreciation for the structural and biomechanical effects of endodontic-restorative procedures on restoration and tooth longevity. Furthermore, the currently available research, largely lacks appreciation of occlusal factors in the longevity of root filled teeth, despite surrogate outcomes demonstrating the considerable influence this variable has. Controversies regarding the clinical relevance of minimally invasive endodontic and restorative concepts are largely unanswered with respect to clinical data, and it is therefore, all too easy to dismiss these ideas due to the lack of scientific evidence. However, conceptually, minimally invasive endodontic-restorative philosophies appear to be valid, and therefore, in the pursuit of improved clinical outcomes, it is important that the efficacies of these treatment protocols are determined. Alongside an increased awareness of the preservation of tooth structure, developments in adhesive bonding, ceramic materials and the inevitable integration of digital dentistry, there is also a need to evaluate the efficacy of new treatment philosophies and techniques with well-designed prospective clinical studies.

Dissipation from Interlayer Friction in Graphene Nanoelectromechanical Resonators.

A unique feature of two-dimensional (2D) materials is the ultralow friction at their van der Waals interfaces. A key question in a new generation of 2D heterostructure-based nanoelectromechanical systems (NEMS) is how the low friction interfaces will affect the dynamic performance. Here, we apply the exquisite sensitivity of graphene nanoelectromechanical drumhead resonators to compare the dissipation from monolayer, Bernal-stacked bilayer, and twisted bilayer graphene membranes. We find a significant difference in the average quality factors of three resonator types: 53 for monolayer, 40 for twisted and 31 for Bernal-stacked membranes. We model this difference as a combination of change in stiffness and additional dissipation from interlayer friction during motion. We find even the lowest frictions measured on sliding 2D interfaces are sufficient to alter dissipation in 2D NEMS. This model provides a generalized approach to quantify dissipation in NEMS based on 2D heterostructures which incorporate interlayer slip and friction.

Buckling-Mediated Phase Transitions in Nano-Electromechanical Phononic Waveguides.

Waveguides for mechanical signal transmission in the megahertz to gigahertz regimes enable on-chip phononic circuitry, which brings new capabilities complementing photonics and electronics. Lattices of coupled nano-electromechanical drumhead resonators are suitable for these waveguides due to their high Q-factor and precisely engineered band structure. Here, we show that thermally induced elastic buckling of such resonators causes a phase transition in the waveguide leading to reversible control of signal transmission. Specifically, when cooled, the lowest-frequency transmission band associated with the primary acoustic mode vanishes. Experiments show the merging of the lower and upper band gaps, such that signals remain localized at the excitation boundary. Numerical simulations show that the temperature-induced destruction of the pass band is a result of inhomogeneous elastic buckling, which disturbs the waveguide's periodicity and suppresses the wave propagation. Mechanical phase transitions in waveguides open opportunities for drastic phononic band reconfiguration in on-chip circuitry and computing.

Refractory Chylothorax Secondary to Sizeable Azygos Vein Hemangioma: Tailored Multimodal Treatment of a Challenging Case Report.

BACKGROUND: Mediastinal hemangiomas are rare, and their etiology remains unclear. Most patients affected have no pathognomonic clinical symptoms, and the diagnosis is often incidental. Due to the paucity of the available literature regarding the management of this disease, the choice and timing of treatment remains controversial. CASE PRESENTATION: Herein, we report the case of a hemangioma of the azygos vein arch in a 66-year-old woman who presented with dyspnea, chest discomfort, dysphagia, and weight loss. A simultaneous right chylothorax refractory to conservative management was found. A CT-guided biopsy of the mass was performed, and it confirmed the vascular nature of the lesion. Therefore, the patient underwent an angiography followed by endo-vascular embolization. Three days later, thoracoscopic surgical resection of the mass and the repair of the chyle leakage were performed safely. The patient was discharged uneventfully on postoperative day seven, with complete resolution of all the presenting symptoms. CONCLUSIONS: Treatment of symptomatic mediastinal hemangiomas could be mandatory, but a thorough multidisciplinary approach to these rare malformations is essential. Despite the risk of intraoperative bleeding, selective endovascular embolization followed by thoracoscopic surgery allowed for a complete and safe resection with a good outcome.

An Evolving TinyML Compression Algorithm for IoT Environments Based on Data Eccentricity.

Currently, the applications of the Internet of Things (IoT) generate a large amount of sensor data at a very high pace, making it a challenge to collect and store the data. This scenario brings about the need for effective data compression algorithms to make the data manageable among tiny and battery-powered devices and, more importantly, shareable across the network. Additionally, considering that, very often, wireless communications (e.g., low-power wide-area networks) are adopted to connect field devices, user payload compression can also provide benefits derived from better spectrum usage, which in turn can result in advantages for high-density application scenarios. As a result of this increase in the number of connected devices, a new concept has emerged, called TinyML. It enables the use of machine learning on tiny, computationally restrained devices. This allows intelligent devices to analyze and interpret data locally and in real time. Therefore, this work presents a new data compression solution (algorithm) for the IoT that leverages the TinyML perspective. The new approach is called the Tiny Anomaly Compressor (TAC) and is based on data eccentricity. TAC does not require previously established mathematical models or any assumptions about the underlying data distribution. In order to test the effectiveness of the proposed solution and validate it, a comparative analysis was performed on two real-world datasets with two other algorithms from the literature (namely Swing Door Trending (SDT) and the Discrete Cosine Transform (DCT)). It was found that the TAC algorithm showed promising results, achieving a maximum compression rate of 98.33%. Additionally, it also surpassed the two other models regarding the compression error and peak signal-to-noise ratio in all cases.

Crossing borders to facilitate live donor kidney transplantation: the Czech-Austrian kidney paired donation program - a retrospective study.

Kidney paired donation (KPD) is a valuable tool to overcome immunological barriers in living donor transplantation. While small national registries encounter difficulties in finding compatible matches, multi-national KPD may be a useful strategy to facilitate transplantation. The Czech (Prague) and Austrian (Vienna) KPD programs, both initiated in 2011, were merged in 2015. A bi-national algorithm allowed for ABO- and low-level HLA antibody-incompatible exchanges, including the option of altruistic donor-initiated domino chains. Between 2011 and 2019, 222 recipients and their incompatible donors were registered. Of those, 95.7% (Prague) and 67.9% (Vienna) entered into KPD registries, and 81 patients received a transplant (95% 3-year graft survival). Inclusion of ABO-incompatible pairs in the Czech program contributed to higher KPD transplant rates (42.6% vs. 23.6% in Austria). After 2015 (11 bi-national match runs), the median pool size increased to 18 pairs, yielding 33 transplants (8 via cross-border exchanges). While matching rates doubled in Austria (from 9.1% to 18.8%), rates decreased in the Czech program, partly due to implementation of more stringent HLA antibody thresholds. Our results demonstrate the feasibility of merging small national KPD programs to increase pool sizes and may encourage the implementation of multi-national registries to expand the full potential of KPD.