Pre-Omicron Vaccine Breakthrough Infection Induces Superior Cross-Neutralization against SARS-CoV-2 Omicron BA.1 Compared to Infection Alone

SARS-CoV-2 variants raise concern because of their high transmissibility and their ability to evade neutralizing antibodies elicited by prior infection or by vaccination. Here, we compared the neutralizing abilities of sera from 70 unvaccinated COVID-19 patients infected before the emergence of variants of concern (VOCs) and of 16 vaccine breakthrough infection (BTI) cases infected with Gamma or Delta against the ancestral B.1 strain, the Gamma, Delta and Omicron BA.1 VOCs using live virus. We further determined antibody levels against the Nucleocapsid (N) and full Spike proteins, the receptor-binding domain (RBD) and the N-terminal domain (NTD) of the Spike protein. Convalescent sera featured considerable variability in the neutralization of B.1 and in the cross-neutralization of different strains. Their neutralizing capacity moderately correlated with antibody levels against the Spike protein and the RBD. All but one convalescent serum failed to neutralize Omicron BA.1. Overall, convalescent sera from patients with moderate disease had higher antibody levels and displayed a higher neutralizing ability against all strains than patients with mild or severe forms of the disease. The sera from BTI cases fell into one of two categories: half the sera had a high neutralizing activity against the ancestral B.1 strain as well as against the infecting strain, while the other half had no or a very low neutralizing activity against all strains. Although antibody levels against the spike protein and the RBD were lower in BTI sera than in unvaccinated convalescent sera, most neutralizing sera also retained partial neutralizing activity against Omicron BA.1, suggestive of a better cross-neutralization and higher affinity of vaccine-elicited antibodies over virus-induced antibodies. Accordingly, the IC50: antibody level ratios were comparable for BTI and convalescent sera, but remained lower in the neutralizing convalescent sera from patients with moderate disease than in BTI sera. The neutralizing activity of BTI sera was strongly correlated with antibodies against the Spike protein and the RBD. Together, these findings highlight qualitative differences in antibody responses elicited by infection in vaccinated and unvaccinated individuals. They further indicate that breakthrough infection with a pre-Omicron variant boosts immunity and induces cross-neutralizing antibodies against different strains, including Omicron BA.1.     

Trypsin-like Inhibitor Domain (TIL)-Harboring Protein Is Essential for Aedes aegypti Reproduction

Cysteine-rich trypsin inhibitor-like domain (TIL)-harboring proteins are broadly distributed in nature but remain understudied in vector mosquitoes. Here we have explored the biology of a TIL domain-containing protein of the arbovirus vector Aedes aegypti, cysteine-rich venom protein 379 (CRVP379). CRVP379 was previously shown to be essential for dengue virus infection in Ae. aegypti mosquitoes. Gene expression analysis showed CRVP379 to be highly expressed in pupal stages, male testes, and female ovaries. CRVP379 expression is also increased in the ovaries at 48 h post-blood feeding. We used CRISPR-Cas9 genome editing to generate two mutant lines of CRVP379 with mutations inside or outside the TIL domain. Female mosquitoes from both mutant lines showed severe defects in their reproductive capability; mutant females also showed differences in their follicular cell morphology. However, the CRVP379 line with a mutation outside the TIL domain did not affect male reproductive performance, suggesting that some CRVP379 residues may have sexually dimorphic functions. In contrast to previous reports, we did not observe a noticeable difference in dengue virus infection between the wild-type and any of the mutant lines. The importance of CRVP379 in Ae. aegypti reproductive biology makes it an interesting candidate for the development of Ae. aegypti population control methods.     

MicroRNAs as Potential Biomarkers in the Differential Diagnosis of Lipomatous Tumors and Their Mimics

Adipocytic tumors are the most common subtype of soft tissue tumors. In current clinical practice, distinguishing benign lipomas from well-differentiated liposarcomas (WDLPS), as well as dedifferentiated liposarcomas (DDLPS) from their morphologic mimics, remains a significant diagnostic challenge. This is especially so when examining small biopsy samples and without the aid of additional ancillary tests. Recognizing the important role that microRNAs (miRNAs) play in tumorigenesis and their potential utility in tumor classification, we analyzed routine clinical tissue samples of benign and malignant lipomatous tumors, as well as other sarcoma mimics, to identify distinguishing miRNA-based signatures that can aid in the differential diagnosis of these entities. We discovered a 6-miRNA signature that separated lipomas from WDLPS with high confidence (AUC of 0.963), as well as a separate 6-miRNA signature that distinguished DDLPS from their more aggressive histologic mimics (AUC of 0.740). Functional enrichment analysis unveiled possible mechanistic involvement of these predictive miRNAs in adipocytic cancer-related biological processes and pathways such as PI3K/AKT/mTOR and MAPK signaling, further supporting the relevance of these miRNAs as biomarkers for adipocytic tumors. Our results demonstrate that miRNA expression profiling may potentially be used as an adjunctive tool for the diagnosis of benign and malignant adipocytic tumors. Further validation studies are warranted.     

Alchemical Design of Pharmacological Chaperones with Higher Affinity for Phenylalanine Hydroxylase

Phenylketonuria (PKU) is a rare metabolic disease caused by variations in a human gene, PAH, encoding phenylalanine hydroxylase (PAH), and the enzyme converting the essential amino acid phenylalanine into tyrosine. Many PKU-causing variations compromise the conformational stability of the encoded enzyme, decreasing or abolishing its catalytic activity, and leading to an elevated concentration of phenylalanine in the blood, which is neurotoxic. Several therapeutic approaches have been developed to treat the more severe manifestations of the disorder, but they are either not entirely effective or difficult to adhere to throughout life. In a search for novel pharmacological chaperones to treat PKU, a lead compound was discovered (compound IV) that exhibited promising in vitro and in vivo chaperoning activity on PAH. The structure of the PAH-IV complex has been reported. Here, using alchemical free energy calculations (AFEC) on the structure of the PAH-IV complex, we design a new generation of compound IV-analogues with a higher affinity for the enzyme. Seventeen novel analogues were synthesized, and thermal shift and isothermal titration calorimetry (ITC) assays were performed to experimentally evaluate their stabilizing effect and their affinity for the enzyme. Most of the new derivatives bind to PAH tighter than lead compound IV and induce a greater thermostabilization of the enzyme upon binding. Importantly, the correspondence between the calculated alchemical binding free energies and the experimentally determined ΔΔG_b values is excellent, which supports the use of AFEC to design pharmacological chaperones to treat PKU using the X-ray structure of their complexes with the target PAH enzyme.     

Estimating above‐ground burned biomass and CO2 emissions for tropical Africa for the year 1990 with the NOAA–NASA Pathfinder AVHRR 8 km land dataset

Biomass burning combusts Earth's vegetation (in forests, savannas and agricultural lands) and occurs over huge areas of the Earth's surface. Global estimates of biomass burning are thus required in order to provide exact figures of the gas fluxes derived from this source. In this paper we use coarse resolution images for estimating above‐ground burned biomass and CO₂ emissions for tropical Africa for the year 1990. The burned land cover areas have been derived from burn scar and land cover maps using the global daily National Oceanic and Atmospheric Administration–National Aeronautics and Space Administration (NOAA–NASA) Pathfinder AVHRR 8?km land dataset. A burned area estimation of (742±222)?Mha has been considered. Monthly maximum Normalized Difference Vegetation Index (NDVI) composites and biomass density measurements have been used for modelling the temporal behaviour of above‐ground biomass for the main seasonal vegetation classes in Africa (humid savanna, derived humid savanna, dry savanna grassland and broadleaf savanna). The amount of above‐ground burned biomass and therefore CO₂ emissions can be estimated from burned land cover area, above‐ground biomass density, burn efficiency and emission factor of trace gas by land cover class. A total of 6494 (3675–9312) Tg for CO₂ emissions was computed for tropical Africa for the year 1990.     

5G Based on Cognitive Radio

Both the cognitive radio (CR) and the fifth generation of cellular wireless standards (5G) are considered to be the future technologies: on one hand, CR offers the possibility to significantly increase the spectrum efficiency, by smart secondary users (CR users) using the free licensed users spectrum holes; on the other hand, the 5G implies the whole wireless world interconnection (WISDOM—Wireless Innovative System for Dynamic Operating Megacommunications concept), together with very high data rates Quality of Service (QoS) service applications. In this paper, they are combined together into a “CR based 5G”. With this aim, two novel ideas are advanced: the 5G terminal is a CR terminal and the CR technology is chosen for WISDOM concept. Thus, the 5G takes CR flexibility and adaptability and makes the first step through a commercial and tangible form.     

Strategic justification of advanced manufacturing technology using an extended AHP model

Layered manufacturing has emerged as a highly versatile process to produce complex parts compared with conventional manufacturing processes, which are either too costly to implement or just downright not possible. However, this relatively new manufacturing process is characterized by a few outstanding issues that have kept the process from being widely applied. One such issue is the reduced part accuracy caused by the primitive method of generating the layer contours. Current practice generates the layer contours by simply intersecting a set of parallel planes through the computer model of the design part. The volumetric geometry of each layer is then constructed by extruding the layer contour by the layer thickness in the part building direction. This practice often leads to distorted part geometry due to the unidirectional bias of the extruded layers. This paper proposes a novel scheme to correct the systematic part distortion of layered manufactured parts resulting from the improperly generated layer contours. A new layer contour generation method utilizing the sectional projected data of a point cloud representation of the part surface is introduced. The systematic part distortion is reduced by extruding the outer boundary of the projected point data into the layer volumetric geometry. The boundary contour construction algorithm is able to adapt to changing density of the point set in order to keep the captured level of detail consistent. Specifically devised case studies were carried out to validate the proposed method.     

Optimized allylamine deposition for improved pluripotential cell culture

Deposition of allylamine (ALL) by plasma enhanced chemical vapor deposition has been optimized on silicon based models. Simultaneous energy recoil detection analysis and Rutherford backscattering spectra show that 100 W deposition is ideal in terms of polymerized film formation and H content while, lower or higher power induce reduced film retention or excessive cross linking, respectively. Surface composition of the ALL film was further probed by X-ray photoelectron spectroscopy revealing a monocomponent N 1s spectrum compatible with the presence of primary amines. Optimized ALL films were applied to polycaprolactone (PCL) surfaces after Ar plasma activation with implications in the chemistry and wettability of this biocompatible polymer. Human mesenchymal stem cells (hMSCs) were cultured on ALL coated PCL surface and controls. ALL functionalized PCL was found to be especially attractive for the formation of confluent monolayers of hMSCs after 72 h of culture.