GIS-FA: an approach to integrating thematic maps, factor-analytic, and envirotyping for cultivar targeting.

KEY MESSAGE: We propose an "enviromics" prediction model for recommending cultivars based on thematic maps aimed at decision-makers. Parsimonious methods that capture genotype-by-environment interaction (GEI) in multi-environment trials (MET) are important in breeding programs. Understanding the causes and factors of GEI allows the utilization of genotype adaptations in the target population of environments through environmental features and factor-analytic (FA) models. Here, we present a novel predictive breeding approach called GIS-FA, which integrates geographic information systems (GIS) techniques, FA models, partial least squares (PLS) regression, and enviromics to predict phenotypic performance in untested environments. The GIS-FA approach enables: (i) the prediction of the phenotypic performance of tested genotypes in untested environments, (ii) the selection of the best-ranking genotypes based on their overall performance and stability using the FA selection tools, and (iii) the creation of thematic maps showing overall or pairwise performance and stability for decision-making. We exemplify the usage of the GIS-FA approach using two datasets of rice [Oryza sativa (L.)] and soybean [Glycine max (L.) Merr.] in MET spread over tropical areas. In summary, our novel predictive method allows the identification of new breeding scenarios by pinpointing groups of environments where genotypes demonstrate superior predicted performance. It also facilitates and optimizes cultivar recommendations by utilizing thematic maps.

Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies.

Understanding SARS-CoV-2 evolution and host immunity is critical to control COVID-19 pandemics. At the core is an arms-race between SARS-CoV-2 antibody and angiotensin-converting enzyme 2 (ACE2) recognition, a function of the viral protein spike. Mutations in spike impacting antibody and/or ACE2 binding are appearing worldwide, imposing the need to monitor SARS-CoV2 evolution and dynamics in the population. Determining signatures in SARS-CoV-2 that render the virus resistant to neutralizing antibodies is critical. We engineered 25 spike-pseudotyped lentiviruses containing individual and combined mutations in the spike protein, including all defining mutations in the variants of concern, to identify the effect of single and synergic amino acid substitutions in promoting immune escape. We confirmed that E484K evades antibody neutralization elicited by infection or vaccination, a capacity augmented when complemented by K417N and N501Y mutations. In silico analysis provided an explanation for E484K immune evasion. E484 frequently engages in interactions with antibodies but not with ACE2. Importantly, we identified a novel amino acid of concern, S494, which shares a similar pattern. Using the already circulating mutation S494P, we found that it reduces antibody neutralization of convalescent and post-immunization sera, particularly when combined with E484K and with mutations able to increase binding to ACE2, such as N501Y. Our analysis of synergic mutations provides a signature for hotspots for immune evasion and for targets of therapies, vaccines and diagnostics.

Design of an interferometric fiber optic parametric amplifier for the rejection of unwanted four-wave mixing products.

We introduce a novel (to our knolwedge) interferometric fiber optic parametric amplifier (FOPA), allowing for the suppression of unwanted four-wave mixing products. We perform simulations of two configurations where one rejects idlers and, the other rejects nonlinear crosstalk from the signal output port. The numerical simulations presented here demonstrate the practical feasibility of suppressing idlers by >28 dB across at least 10 THz enabling the reuse of the idler frequencies for signal amplification and thus doubling the employable FOPA gain bandwidth. We demonstrate it can be achieved even when the interferometer employs real-world couplers by introducing a small attenuation in one of the interferometer arms.

Design and transmission analysis of trench-assisted multi-core fibre in standard cladding diameter.

6-core and 8-core trench-assisted heterogeneous fibres in standard cladding diameter are designed using artificial intelligence-based techniques including a cut-off wavelength regressor. The designs proposed here, for the first time, suppress crosstalk at 1550 nm of 8-core fibre to as low as -55 dB/km covering the whole S+C+L band while keeping coating loss below 0.001 dB/km. We compare them to reveal the influence of the additional cores in the 125 µm cladding diameter scenario. We report on the transmission characteristics and performance of the MCFs in terms of capacity and spatial spectral efficiency, including the influence of bandwidth, effective mode area, distance and crosstalk, for a range of transmission distances. The artificial intelligence-based method and insights given can be used to significantly speed up and tailor designs for a variety of telecom and datacom applications.

Fibre optic parametric amplifier for high capacity burst-mode access networks.

We compare performance of a polarization insensitive fiber optic parametric amplifier (PI-FOPA), a commercial erbium doped fiber amplifier (EDFA) and a discrete Raman amplifier (DRA) in a 50 km long-reach optical access network transmitting bursts of 10 Gbps signal with traffic density ranged from 5% to 97%. We demonstrate that for the same power budget the PI-FOPA allows for transmission of bursty traffic with density up to 97% while DRA and EDFA are limited to 30% and 15%, respectively. Alternatively, we demonstrate PI-FOPA to allow for 3 dB and 5 dB higher power budget than the DRA and EDFA, respectively, for the worst case scenario of 75% traffic density.

Experimental Study on Wound Area Measurement with Mobile Devices.

Healthcare treatments might benefit from advances in artificial intelligence and technological equipment such as smartphones and smartwatches. The presence of cameras in these devices with increasingly robust and precise pattern recognition techniques can facilitate the estimation of the wound area and other telemedicine measurements. Currently, telemedicine is vital to the maintenance of the quality of the treatments remotely. This study proposes a method for measuring the wound area with mobile devices. The proposed approach relies on a multi-step process consisting of image capture, conversion to grayscale, blurring, application of a threshold with segmentation, identification of the wound part, dilation and erosion of the detected wound section, identification of accurate data related to the image, and measurement of the wound area. The proposed method was implemented with the OpenCV framework. Thus, it is a solution for healthcare systems by which to investigate and treat people with skin-related diseases. The proof-of-concept was performed with a static dataset of camera images on a desktop computer. After we validated the approach's feasibility, we implemented the method in a mobile application that allows for communication between patients, caregivers, and healthcare professionals.

Experimental comparison of fiber optic parametric, Raman and erbium amplifiers for burst traffic for extended reach PONs.

We experimentally compare the performance of a polarization-independent fiber optic parametric amplifier (FOPA), a discrete Raman amplifier and a commercial erbium doped fiber amplifier (EDFA) for burst traffic amplification in extended reach passive optical networks (PON). We demonstrate that EDFA and Raman amplifiers suffer from severe transient effects, causing penalty on receiver sensitivity >5 dB for traffic bursts of 10 Gbps on-off keying signal shorter than 10 µs. On the other hand, we demonstrate that FOPA does not introduce a penalty on receiver sensitivity when amplifying signal bursts as short as 5 µs as compared to a non-burst signal. Therefore, FOPA used as a drop-in replacement for an EDFA or Raman amplifier allows us to improve receiver sensitivity by >3 dB for short signal bursts. We conclude that FOPA allows substantially increased power budget for an extended reach PON transmitting variable duration bursts. In addition, we identify the maximum burst duration tolerated by each examined amplifier.

KIF13A mediates trafficking of influenza A virus ribonucleoproteins.

Influenza A is a rapidly evolving virus that is successful in provoking periodic epidemics and occasional pandemics in humans. Viral assembly is complex as the virus incorporates an eight-partite genome of RNA (in the form of viral ribonucleoproteins, vRNPs), and viral genome assembly - with its implications to public health - is not completely understood. It has previously been reported that vRNPs are transported to the cell surface on Rab11-containing vesicles by using microtubules but, so far, no molecular motor has been assigned to the process. Here, we have identified KIF13A, a member of the kinesin-3 family, as the first molecular motor to efficiently transport vRNP-Rab11 vesicles during infection with influenza A. Depletion of KIF13A resulted in reduced viral titers and less accumulation of vRNPs at the cell surface, without interfering with the levels of other viral proteins at sites of viral assembly. In addition, when overexpressed and following two separate approaches to displace vRNP-Rab11 vesicles, KIF13A increased levels of vRNP at the plasma membrane. Together, our results show that KIF13A plays an important role in the transport of influenza A vRNPs, a crucial step for viral assembly.This article has an associated First Person interview with the first author of the paper.

Near-ML detection for MDL-impaired few-mode fiber transmission.

Few-mode fiber transmission systems are typically impaired by mode-dependent loss (MDL). In an MDL-impaired link, maximum-likelihood (ML) detection yields a significant advantage in system performance compared to linear equalizers, such as zero-forcing and minimum-mean square error equalizers. However, the computational effort of the ML detection increases exponentially with the number of modes and the cardinality of the constellation. We present two methods that allow for near-ML performance without being afflicted with the enormous computational complexity of ML detection: improved reduced-search ML detection and sphere decoding. Both algorithms are tested regarding their performance and computational complexity in simulations of three and six spatial modes with QPSK and 16QAM constellations.

Recommendation of Tahiti acid lime cultivars through Bayesian probability models.

Probabilistic models enhance breeding, especially for the Tahiti acid lime, a fruit essential to fresh markets and industry. These models identify superior and persistent individuals using probability theory, providing a measure of uncertainty that can aid the recommendation. The objective of our study was to evaluate the use of a Bayesian probabilistic model for the recommendation of superior and persistent genotypes of Tahiti acid lime evaluated in 12 harvests. Leveraging the Monte Carlo Hamiltonian sampling algorithm, we calculated the probability of superior performance (superior genotypic value), and the probability of superior stability (reduced variance of the genotype-by-harvests interaction) of each genotype. The probability of superior stability was compared to a measure of persistence estimated from genotypic values predicted using a frequentist model. Our results demonstrated the applicability and advantages of the Bayesian probabilistic model, yielding similar parameters to those of the frequentist model, while providing further information about the probabilities associated with genotype performance and stability. Genotypes G15, G4, G18, and G11 emerged as the most superior in performance, whereas G24, G7, G13, and G3 were identified as the most stable. This study highlights the usefulness of Bayesian probabilistic models in the fruit trees cultivars recommendation.

Biodegradation of e-waste microplastics by Penicillium brevicompactum.

Electronic and electric waste (e-waste) management strategies often fall short in dealing with the plastic constituents of printed circuit boards (PCB). Some plastic materials from PCB, such as epoxy resins, may release contaminants, but neither potential environmental impact has been assessed nor mitigation strategies have been put forward. This study assessed the biodegradation of microplastics (1-2 mm in size) from PCB by the fungus Penicillium brevicompactum over 28 days, thus contributing to the discussion of mitigation strategies for decreasing the environmental impact of such plastics in the environment. The capacity of P. brevicompactum to induce microplastic fragmentation and degradation has been determined by the increased the number of smaller-sized particles and microplastic mass reduction (up to 75 % within 14 days), respectively. The occurrence of chain scission and oxidation of microplastics exposed to P. brevicompactum when compared with the control conditions (which occurred only after 28 days of exposure) can be observed. Furthermore, Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopy performed in dried biomass put in evidence an increase in the absorption intensities in regions that could be attributed to functional groups associated with carbohydrates. The results underline the potential role of the genus Penicillium, particularly P. brevicompactum, in the biodegradation of microplastics from PCB, thus providing the basis for further exploration of its potential for e-waste bioremediation and research on the underlying mechanisms for sustainable approaches to mitigate e-waste pollution.

Microplastics from agricultural mulch films: Biodegradation and ecotoxicity in freshwater systems.

The application of bio-based biodegradable mulch films in agriculture has raised environmental concerns regarding their potential impacts on adjacent freshwater ecosystems. This study investigated the biodegradation of microplastics derived from a bio-based biodegradable mulch (bio-MPs) and its acute and chronic ecotoxicity considering relevant scenarios (up to 200 and 250 mg/kg of sediment, using pristine and/or UV-aged particles), using the fungus Penicillium brevicompactum and the dipteran Chironomus riparius as model organisms, respectively, due to their ecological relevance in freshwater environments. Fourier-transform infrared spectroscopy analysis suggested changes in the fungus's carbohydrate reserves and bio-MP degradation through the appearance of low molecular weight esters throughout a 28 day biodegradation test. In a short-term exposure (48 h), C. riparius larvae exposed to pristine or UV-aged bio-MPs had up to 2 particles in their gut. Exposure to pristine bio-MPs decreased larval aerobic metabolism (<20 %) and increased neurotransmission (>15 %), whereas exposure to UV-aged bio-MPs activated larval aerobic metabolism (>20 %) and increased antioxidant defences (catalase activity by >30 % and glutathione-s-transferase by >20 %) and neurotransmission (>30 %). Longer-term (28-d) exposure to UV-aged bio-MPs did not affect larval survival and growth nor the dipteran's emergence but increased male numbers (>30 %) at higher concentrations. This study suggests that the selected agricultural bio-based mulch film is prone to biodegradation by a naturally occurring fungus. However, there is a potential for endocrine disruption in the case of prolonged exposures to UV-aged microplastics. This study emphasises the importance of further research to elucidate the potential ecological effects of these plastic products, to ensure effective management practices, and to establish new regulations governing their use.

Nanocellulose-based porous materials: Regulation and pathway to commercialization in regenerative medicine.

We review the recent progress that have led to the development of porous materials based on cellulose nanostructures found in plants and other resources. In light of the properties that emerge from the chemistry, shape and structural control, we discuss some of the most promising uses of a plant-based material, nanocellulose, in regenerative medicine. Following a brief discussion about the fundamental aspects of self-assembly of nanocellulose precursors, we review the key strategies needed for material synthesis and to adjust the architecture of the materials (using three-dimensional printing, freeze-casted porous materials, and electrospinning) according to their uses in tissue engineering, artificial organs, controlled drug delivery and wound healing systems, among others. For this purpose, we map the structure-property-function relationships of nanocellulose-based porous materials and examine the course of actions that are required to translate innovation from the laboratory to industry. Such efforts require attention to regulatory aspects and market pull. Finally, the key challenges and opportunities in this nascent field are critically reviewed.

Balance between maternal antiviral response and placental transfer of protection in gestational SARS-CoV-2 infection.

The intricate interplay between maternal immune response to SARS-CoV-2 and the transfer of protective factors to the fetus remains unclear. By analyzing mother-neonate dyads from second and third trimester SARS-CoV-2 infections, our study shows that neutralizing antibodies (NAbs) are infrequently detected in cord blood. We uncovered that this is due to impaired IgG-NAb placental transfer in symptomatic infection and to the predominance of maternal SARS-CoV-2 NAbs of the IgA and IgM isotypes, which are prevented from crossing the placenta. Crucially, the balance between maternal antiviral response and transplacental transfer of IgG-NAbs appears to hinge on IL-6 and IL-10 produced in response to SARS-CoV-2 infection. In addition, asymptomatic maternal infection was associated with expansion of anti-SARS-CoV-2 IgM and NK cell frequency. Our findings identify a protective role for IgA/IgM-NAbs in gestational SARS-CoV-2 infection and open the possibility that the maternal immune response to SARS-CoV-2 infection might benefit the neonate in 2 ways, first by skewing maternal immune response toward immediate viral clearance, and second by endowing the neonate with protective mechanisms to curtail horizontal viral transmission in the critical postnatal period, via the priming of IgA/IgM-NAbs to be transferred by the breast milk and via NK cell expansion in the neonate.

Defining basic rules for hardening influenza A virus liquid condensates.

In biological systems, liquid and solid-like biomolecular condensates may contain the same molecules but their behaviour, including movement, elasticity, and viscosity, is different on account of distinct physicochemical properties. As such, it is known that phase transitions affect the function of biological condensates and that material properties can be tuned by several factors including temperature, concentration, and valency. It is, however, unclear if some factors are more efficient than others at regulating their behaviour. Viral infections are good systems to address this question as they form condensates de novo as part of their replication programmes. Here, we used influenza A virus (IAV) liquid cytosolic condensates, AKA viral inclusions, to provide a proof of concept that liquid condensate hardening via changes in the valency of its components is more efficient than altering their concentration or the temperature of the cell. Liquid IAV inclusions may be hardened by targeting vRNP (viral ribonucleoprotein) interactions via the known NP (nucleoprotein) oligomerising molecule, nucleozin, both in vitro and in vivo without affecting host proteome abundance nor solubility. This study is a starting point for understanding how to pharmacologically modulate the material properties of IAV inclusions and may offer opportunities for alternative antiviral strategies.

Cells are organized into compartments that carry out specific functions. Envelope-like membranes enclose some of those compartments, while others remain unenclosed. The latter are called biomolecular condensates, and they can shift their physical states from a more liquid to a more solid form, which may affect how well they function. Temperature, molecular concentration and molecular interactions affect the physical state of condensates. Understanding what causes physical shifts in biomolecular condensates could have important implications for human health. For example, many viruses, including influenza, HIV, rabies, measles and the virus that causes COVID-19, SARS-CoV-2, use biomolecular condensates to multiply in cells. Changing the physical state of biomolecular condensates to one that hampers viruses' ability to multiply could be an innovative approach to treating viruses. Etibor et al. show that it is possible to harden condensates produced by influenza A virus. In the experiments, the researchers manipulated the temperature, molecular concentration and strength of connections between molecules in condensates created by influenza A-infected cells. Then, they measured their effects on the condensate's physical state. The experiments showed that using drugs that strengthen the bonds between molecules in condensates was the most effective strategy for hardening. Studies in both human cells and mice showed that using drugs to harden condensate in infected cells did not harm the cells or the animal and disabled the virus. The experiments provide preliminary evidence that using drugs to harden biomolecular condensates may be a potential treatment strategy for influenza A. More studies are necessary to test this approach to treating influenza A or other viruses that use condensates. If they are successful, the drug could add a new tool to the antiviral treatment toolbox.

Facemasks: An insight into their abundance in wetlands, degradation, and potential ecotoxicity.

Disposable facemasks represent a new form of environmental contamination worldwide. This study aimed at addressing the abundance of facemasks in an overlooked natural environment with high ecological and economic value - the wetlands (Ria de Aveiro, Portugal, as study case), evaluating their potential biodegradation using naturally occurring fungi and assessing the potential ecotoxicity of released microfibres on local bivalves. All masks collected within 6500 m2 area of Aveiro wetland were 100 % disposable ones (PP-based, confirmed by Fourier transform infrared spectroscopy - FTIR) with an initial abundance of 0.0023 items/m2 in Sept. 2021, which was reduced by ∼40 % in Apr. 2022 and ∼87 % in Sept. 2022, as a reflection of the government policies. Analysis of the carbonyl index (0.03 to 1.79) underlined their state of degradation, primarily due to sun exposure during low tides. In laboratory conditions, 1 mm2 microplastics obtained from new disposable facemasks were prone to biodegradation by Penicillium brevicompactum and Zalerion maritimum inferred from microplastics mass loss (∼22 to -26 % and ∼40 to 50 %, respectively) and FTIR spectra (particularly in the hydroxyl and carbonyl groups). In addition, microfibres released from facemasks induced sublethal effects on the clam, Venerupis corrugata, mostly in their UV-aged form when compared to pristine ones, characterised by a decrease in cellular energy allocation (CEA) and an increase in aerobic energy metabolism (ETS). Concomitantly, clams exposed to 1250 items/L of UV-aged microplastics (similar to field-reported concentrations) expressed greater clearance capacity, indicating a need to compensate for the potential energy unbalance. This study provides the first baseline monitoring of facemasks in wetlands while bringing new evidence on their biodegradation and ecotoxicity, considering environmentally relevant conditions and keystone organisms in such environments. Such studies require scientific attention for rapid regulatory action against this emerging and persistent pollutant, also targeting remediation and mitigation strategies considering these items under pandemic scenarios.

Impact of mode coupling on the mode-dependent loss tolerance in few-mode fiber transmission.

Spatial-division multiplexing in the form of few-mode fibers has captured the attention of researchers since it is an attractive approach to significantly increase the channel capacity. However, the optical components employed in such systems introduce mode-dependent loss or gain (MDL) due to manufacturing imperfections, leading to significant system impairments. In this work the impact of MDL from optical amplifiers in few-mode fibers with either weak or strong mode coupling is analyzed for a 3x136-Gbit/s DP-QPSK mode-division multiplexed transmission system. It is shown that strong mode coupling reduces the impact of MDL in a similar manner as that polarization-dependent loss is reduced in single mode fibers by polarization-mode dispersion.

DSP complexity of mode-division multiplexed receivers.

The complexities of common equalizer schemes are analytically analyzed in this paper in terms of complex multiplications per bit. Based on this approach we compare the complexity of mode-division multiplexed digital signal processing algorithms with different numbers of multiplexed modes in terms of modal dispersion and distance. It is found that training symbol based equalizers have significantly lower complexity compared to blind approaches for long-haul transmission. Among the training symbol based schemes, OFDM requires the lowest complexity for crosstalk compensation in a mode-division multiplexed receiver. The main challenge for training symbol based schemes is the additional overhead required to compensate modal crosstalk, which increases the data rate. In order to achieve 2000 km transmission, the effective modal dispersion must therefore be below 6 ps/km when the OFDM specific overhead is limited to 10%. It is concluded that for few mode transmission systems the reduction of modal delay is crucial to enable long-haul performance.

Cancer Inhibition and In Vivo Osteointegration and Compatibility of Gallium-Doped Bioactive Glasses for Osteosarcoma Applications.

Traditional osteosarcoma therapies tend to focus solely on eradicating residual cancer cells and often fail to promote local bone regeneration and even inhibit it due to lack of precise control over target cells, i.e., the treatment affects both normal and cancer cells. Typically, multistep procedures are required for optimal efficacy. Here, we found that a silica-based bioactive material containing 3 mol % gallium oxide selectively kills human osteosarcoma cells and presents excellent in vivo osteointegration, while showing no local or systemic toxicity. Cell culture media conditioned with the proposed material was able to kill 41% of osteosarcoma cells, and no significant deleterious effect on normal human osteoblasts was observed. In addition, rats treated with the gallium-doped material showed excellent material-bone integration with no sign of local toxicity or implant rejection. Systemic biocompatibility investigation did not indicate any sign of toxicity, with no presence of fibrosis or cellular infiltrate in the histological microstructure of the liver and kidneys after 56 days of observation. Taken together, these results show that synergistic bone regeneration and targeted cancer therapy can be combined, paving the way toward new bone cancer treatment approaches.

Saliva molecular testing bypassing RNA extraction is suitable for monitoring and diagnosing SARS-CoV-2 infection in children.

BACKGROUND: Adults are being vaccinated against SARS-CoV-2 worldwide, but the longitudinal protection of these vaccines is uncertain, given the ongoing appearance of SARS-CoV-2 variants. Children remain largely unvaccinated and are susceptible to infection, with studies reporting that they actively transmit the virus even when asymptomatic, thus affecting the community. METHODS: We investigated if saliva is an effective sample for detecting SARS-CoV-2 RNA and antibodies in children, and associated viral RNA levels to infectivity. For that, we used a saliva-based SARS-CoV-2 RT-qPCR test, preceded or not by RNA extraction, in 85 children aged 10 years and under, admitted to the hospital regardless of COVID-19 symptomatology. Amongst these, 29 (63.0%) presented at least one COVID-19 symptom, 46 (54.1%) were positive for SARS-CoV-2 infection, 28 (32.9%) were under the age of 1, and the mean (SD) age was 3.8 (3.4) years. Saliva samples were collected up to 48 h after a nasopharyngeal swab-RT-qPCR test. RESULTS: In children aged 10 years and under, the sensitivity, specificity, and accuracy of saliva-RT-qPCR tests compared to NP swab-RT-qPCR were, respectively, 84.8% (71.8%-92.4%), 100% (91.0%-100%), and 91.8% (84.0%-96.6%) with RNA extraction, and 81.8% (68.0%-90.5%), 100% (91.0%-100%), and 90.4% (82.1%-95.0%) without RNA extraction. Rescue of infectious particles from saliva was limited to CT values below 26. In addition, we found significant IgM positive responses to SARS-CoV-2 in children positive for SARS-CoV-2 by NP swab and negative by saliva compared to other groups, indicating late infection onset (>7-10 days). CONCLUSIONS: Saliva is a suitable sample type for diagnosing children aged 10 years and under, including infants aged <1 year, even bypassing RNA extraction methods. Importantly, the detected viral RNA levels were significantly above the infectivity threshold in several samples. Further investigation is required to correlate SARS-CoV-2 RNA levels to viral transmission.