Tensor-Based Methods for Blind Spatial Signature Estimation in Multidimensional Sensor Arrays

The estimation of spatial signatures and spatial frequencies is crucial for several practical applications such as radar, sonar, and wireless communications. In this paper, we propose two generalized iterative estimation algorithms to the case in which a multidimensional (R-D) sensor array is used at the receiver. The first tensor-based algorithm is an R-D blind spatial signature estimator that operates in scenarios where the source’s covariance matrix is nondiagonal and unknown. The second tensor-based algorithm is formulated for the case in which the sources are uncorrelated and exploits the dual-symmetry of the covariance tensor. Additionally, a new tensor-based formulation is proposed for an L-shaped array configuration. Simulation results show that our proposed schemes outperform the state-of-the-art matrix-based and tensor-based techniques

Epigenetic reprogramming by TET enzymes impacts co-transcriptional R-loops

PTDC/BIA-MOL/30438/2017 PTDC/MED-OUT/4301/2020 RiboMed 857119 PD/BD/128292/2017 LCF/PR/HP21/52310016 PTDC/BIA-MOL/6624/2020 PTDC/MED-ONC/7864/2020DNA oxidation by ten-eleven translocation (TET) family enzymes is essential for epigenetic reprogramming. The conversion of 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) initiates developmental and cell-type-specific transcriptional programs through mechanisms that include changes in the chromatin structure. Here, we show that the presence of 5hmC in the transcribed gene promotes the annealing of the nascent RNA to the template DNA strand, leading to the formation of an R-loop. Depletion of TET enzymes reduced global R-loops in the absence of gene expression changes, whereas CRISPR-mediated tethering of TET to an active gene promoted the formation of R-loops. The genome-wide distribution of 5hmC and R-loops shows a positive correlation in mouse and human stem cells and overlap in half of all active genes. Moreover, R-loop resolution leads to differential expression of a subset of genes that are involved in crucial events during stem cell proliferation. Altogether, our data reveal that epigenetic reprogramming via TET activity promotes co-transcriptional R-loop formation, disclosing new mechanisms of gene expression regulation.publishersversionpublishe

Spectral analysis methods for improved resolution and sensitivity: enhancing SPR and LSPR optical fiber sensing

Biochemical–chemical sensing with plasmonic sensors is widely performed by tracking the responses of surface plasmonic resonance peaks to changes in the medium. Interestingly, consistent sensitivity and resolution improvements have been demonstrated for gold nanoparticles by analyzing other spectral features, such as spectral inflection points or peak curvatures. Nevertheless, such studies were only conducted on planar platforms and were restricted to gold nanoparticles. In this work, such methodologies are explored and expanded to plasmonic optical fibers. Thus, we study—experimentally and theoretically—the optical responses of optical fiber-doped gold or silver nanospheres and optical fibers coated with continuous gold or silver thin films. Both experimental and numerical results are analyzed with differentiation methods, using total variation regularization to effectively minimize noise amplification propagation. Consistent resolution improvements of up to 2.2× for both types of plasmonic fibers are found, demonstrating that deploying such analysis with any plasmonic optical fiber sensors can lead to sensing resolution improvements.Fundação para a Ciência e Tecnologia | Ref. UIDB/50014/2020Fundação para a Ciência e Tecnologia | Ref. SFRH/BD/130674/2017Fundação para a Ciência e Tecnologia | Ref. CEECIND/00471/2017Xunta de Galicia | Ref. GRC ED431C 2020/09Fundação para a Ciência e Tecnologia | Ref. SFRH/BD/146784/201

Calcification in free‑living coralline algae is strongly influenced by morphology: Implications for susceptibility to ocean acidification

Rhodolith beds built by free-living coralline algae are important ecosystems for marine biodiversity and carbonate production. Yet, our mechanistic understanding regarding rhodolith physiology and its drivers is still limited. Using three rhodolith species with different branching morphologies, we investigated the role of morphology in species’ physiology and the implications for their susceptibility to ocean acidification (OA). For this, we determined the effects of thallus topography on diffusive boundary layer (DBL) thickness, the associated microscale oxygen and pH dynamics and their relationship with species’ metabolic and light and dark calcification rates, as well as species’ responses to short-term OA exposure. Our results show that rhodolith branching creates low-flow microenvironments that exhibit increasing DBL thickness with increasing branch length. This, together with species’ metabolic rates, determined the light-dependent pH dynamics at the algal surface, which in turn dictated species’ calcification rates. While these differences did not translate in species-specific responses to short-term OA exposure, the differences in the magnitude of diurnal pH fluctuations (~ 0.1–1.2 pH units) between species suggest potential differences in phenotypic plasticity to OA that may result in different susceptibilities to long-term OA exposure, supporting the general view that species’ ecomechanical characteristics must be considered for predicting OA responses

Forage Intake and Nitrogen Retention in Wethers Fed Ryegrass Haylage Supplemented with Maize Silage

Many decision support tools have been developed to predict herbage intake with herbivore ruminants indoors (Faverdin 1992) or at grazing, both using short-term (Baumont et al. 2004) or daily scale input variables (Heard et al. 2004; Delagarde et al. 2011). However, the ingestive and digestive interactions when diets with more than one type of forage are used have not been sufficiently studied. The aim of this study was to assess the effects of maize silage supplementation to wethers receiving ryegrass haylage on OM intake, OM digestibility, microbial protein synthesis and N retention

Identification and analysis of seven effector protein families with different adaptive and evolutionary histories in plant-associated members of the Xanthomonadaceae.

The Xanthomonadaceae family consists of species of non-pathogenic and pathogenic γ-proteobacteria that infect different hosts, including humans and plants. In this study, we performed a comparative analysis using 69 fully sequenced genomes belonging to this family, with a focus on identifying proteins enriched in phytopathogens that could explain the lifestyle and the ability to infect plants. Using a computational approach, we identified seven phytopathogen-enriched protein families putatively secreted by type II secretory system: PheA (CM-sec), LipA/LesA, VirK, and four families involved in N-glycan degradation, NixE, NixF, NixL, and FucA1. In silico and phylogenetic analyses of these protein families revealed they all have orthologs in other phytopathogenic or symbiotic bacteria, and are involved in the modulation and evasion of the immune system. As a proof of concept, we performed a biochemical characterization of LipA from Xac306 and verified that the mutant strain lost most of its lipase and esterase activities and displayed reduced virulence in citrus. Since this study includes closely related organisms with distinct lifestyles and highlights proteins directly related to adaptation inside plant tissues, novel approaches might use these proteins as biotechnological targets for disease control, and contribute to our understanding of the coevolution of plant-associated bacteria

Isolation, absolute configuration and cytotoxic activities of alkaloids from Hippeastrum goianum (Ravenna) Meerow (Amaryllidaceae)

The phytochemical study of Hippeastrum goianum led to the identification of 13 compounds by means of gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR). Compounds 7-demethoxy-9-O-methylhostasine (1) and 7-deoxi-trans-dihydronarciclasine (2) had their absolute configurations determined by vibrational circular dichroism (VCD). This is the first time that compound 1 is described in the Amaryllidaceae family. The cytotoxicity of all isolated compounds was tested against colorectal carcinoma (HCT 116), breast carcinoma (MCF-7), and non-tumor human retinal pigment epithelium (RPE) cell lines. The half-maximum inhibitory concentration (IC50) of compound 2 against each cell line was equivalent to the positive control (doxorubicin), indicating a considerable cytotoxic activity. Keywords: narciclasine; galasine; cytotoxic activity; absolute configuration; vibrational circular dichrois

Identification of Eschweilenol C in derivative of Terminalia fagifolia Mart. and green synthesis of bioactive and biocompatible silver nanoparticles

A green synthetic route was developed to prepare silver nanoparticles (AgNPs) in aqueous solution for biological applications. Eschweilenol C, a compound derivative ellagic acid was identified as the main constituent of the aqueous fraction of the ethanolic extract of Terminalia fagifolia Mart. by NMR analysis. In the green synthesis, the ethanolic extract of T. fagifolia and its aqueous fraction were used to promote silver reduction and nanoparticle stabilization. The synthesized AgNPs presented a spherical or polygonal morphology shape by TEM analysis and AgNPs showed high levels of antioxidant and considerable antibacterial and antifungal activities. Synthesized nanoparticles presented significant antioxidant activity by sequestration of DPPH and ABTS radicals, in addition to iron reduction (FRAP assay) and measurement of antioxidant capacity in ORAC units, in addition, AgNP synthesized with the aqueous fraction also demonstrated antioxidant potential in microglial cells. Gram-positive and Gram-negative bacteria were susceptible to growth inhibition by the nanoparticles, among which the AgNPs formed by the ethanolic extract was the most effective. The data obtained by AFM images suggested that AgNPs could lead to the lysis of bacteria and subsequent death. The antifungal assays showed high efficiency against yeasts and dermatophytes. This work represents the first description of antifungal activity by AgNPs against Fonsecaea pedrosoi, the etiologic agent of chromoblastomycosis. In relation to biocompatibility, the AgNPs induced lower haemolysis than AgNO3.We thank Herbert Kogler and Reinhard Wimmer for the identification of Eschweilenol C. The NMR laboratory at Aalborg University is supported by the Obel Family, SparNord and Carlsberg foundations.The authors are grateful to Carla Eiras (LIMAV/CT/UFPI) and to FCT and EU for financial support through project UID/QUI/50006/2013– POCI-01-0145-FEDER-007265 from COMPETE and projectNORTE-01-0145-FEDER-000011 from COMPETE. Thanks to Andreia Pinto for help with the TEM measurements at Instituto de Medicina Molecular (IMM). This work was supported by the Histology and Comparative Pathology Laboratory of the IMMinfo:eu-repo/semantics/publishedVersio

Human Papillomavirus Genotype Distribution among Cervical Cancer Patients prior to Brazilian National HPV Immunization Program

To evaluate the impact of HPV immunization and possible changes in virus type-specific prevalence associated with cervical cancer, it is important to obtain baseline information based on socioeconomic, educational, and environmental characteristics in human populations. We describe these characteristics and the type-specific HPV distribution in 1,183 women diagnosed with cervical cancer in two Brazilian healthcare institutions located at the Southeastern (Rio de Janeiro/RJ) and the Amazonian (Belém/PA) regions. Large differences were observed between women in these regions regarding economic, educational, and reproductive characteristics. The eight most frequent HPV types found in tumor samples were the following: 16, 18, 31, 33, 35, 45, 52, and 58. Some HPV types classified as unknown or low risk were found in tumor samples with single infections, HPV 83 in RJ and HPV 11, 61, and 69 in PA. The proportion of squamous cervical cancer was lower in RJ than in PA (76.3% versus 87.3%, 푝 < 0.001). Adenocarcinoma was more frequent in RJ than in PA (13.5% versus 6.9%, 푝 < 0.001). The frequency of HPV 16 in PA was higher in younger women (푝 < 0.05). The success of a cervical cancer control program should consider HPV types, local health system organization, and sociodemographic diversity of Brazilian regions