Grid structure impact in sparse point representation of derivatives

In the Sparse Point Representation (SPR) method the principle is to retain the function data indicated by significant interpolatory wavelet coefficients, which are defined as interpolation errors by means of an interpolating subdivision scheme. Typically, a SPR grid is coarse in smooth regions, and refined close to irregularities. Furthermore, the computation of partial derivatives of a function from the information of its SPR content is performed in two steps. The first one is a refinement procedure to extend the SPR by the inclusion of new interpolated point values in a security zone. Then, for points in the refined grid, such derivatives are approximated by uniform finite differences, using a step size proportional to each point local scale. If required neighboring stencils are not present in the grid, the corresponding missing point values are approximated from coarser scales using the interpolating subdivision scheme. Using the cubic interpolation subdivision scheme, we demonstrate that such adaptive finite differences can be formulated in terms of a collocation scheme based on the wavelet expansion associated to the SPR. For this purpose, we prove some results concerning the local behavior of such wavelet reconstruction operators, which stand for SPR grids having appropriate structures. This statement implies that the adaptive finite difference scheme and the one using the step size of the finest level produce the same result at SPR grid points. Consequently, in addition to the refinement strategy, our analysis indicates that some care must be taken concerning the grid structure, in order to keep the truncation error under a certain accuracy limit. Illustrating results are presented for 2D Maxwell's equation numerical solutions

Laser-induced graphene from paper for non-enzymatic uric acid electrochemical sensing in urine

This work was developed within the scope of project i3N (LA/P/0037/2020. I.P. N. F. Santos thanks i3N for the BPD Grant BPD/UI96/5177/2020. S. O. Pereira thanks i3N for the BPD Grant BPD/UI96/5808/2017. The authors also thank Jonas Deuermeier for the XPS measurements. Publisher Copyright: © 2022 Elsevier LtdLaser-induced graphene from paper (paper-LIG) was applied in non-enzymatic electrochemical sensing of uric acid (UA) in human urine. Paper-LIG was formed by CO2 laser modification of paper into a 3D graphene arrangement. Kinetic analysis of paper-LIG electrodes returned effective heterogeneous electron transfer standard rate constants of 1.4 × 10−3 cm s−1 and 7.8 × 10−4 cm s−1 for [Ru(NH3)6]2+/3+ and [Fe(CN)6]4−/3− redox probes, respectively. These electrodes were able to detect and quantify uric acid in PBS within the 10–300 μM range at pH between 5.6 and 7.4. At pH 7.4, a linear response (R2 = 0.999) from 10 to 250 μM was achieved, with a limit of detection of 3.97 μM and a sensitivity of 0.363 μA cm−2 μM−1. Paper-LIG electrodes denoted adequate selectivity in synthetic urine as well as in ascorbic acid (AA) and dopamine (DA)-containing electrolytes. Determination of urinary UA content in human samples returned a concentration of c.a. 1.8–1.9 mM, within the range for healthy individuals. Recoveries of samples spiked with 50 and 100 μM UA were 100.6% and 95.4%, respectively, with satisfactory reproducibility and stability. These cheap, lightweight, flexible, and eco-friendly paper-LIG biosensors for non-enzymatic quantification of UA in human urine pave the way to widespread application in the detection of other important biomarkers.publishersversionpublishe

Optical Studies in Red/NIR Persistent Luminescent Cr‐Doped Zinc Gallogermanate (ZGGO:Cr)

Zn1+xGa2‐2xGexO4 (ZGGO:Cr)‐persistent phosphor, with a molar fraction, x, of x = 0.1, doped with a 0.5% molar of chromium, was synthesised via solid‐state reaction at 1350 °C for 36 h. X‐ray diffraction measurements and Raman spectroscopy evidence a single crystalline phase corresponding to the cubic spinel structure. Room temperature (RT) photoluminescence (PL) and afterglow decay profiles were investigated using above and below bandgap excitation. In both cases, persistent PL was observed for almost 8 h, mainly originating from a Cr3+ defect, the so‐called N2 optical centre. RT PL excitation and diffuse reflectance allow identification of the best pathways of Cr3+ red/NIR emission, as well as estimation of the ZGGO bandgap energy at 4.82 eV. An in‐depth investigation of the observed luminescence at 15 K and temperature‐dependent PL under site‐selective excitation reveals the spectral complexity of the presence of several optically active Cr3+ centres in the ZGGO host that emit in almost the same spectral region. Furthermore, the temperature dependence of the R‐lines’ intensity indicates the existence of thermal populating processes between the different optical centres. Such observations well account for a wide distribution of defect trap levels available for carrier capture/release, as measured by the persistent luminescence decay, from which the carriers are released preferentially to the N2 Cr3+‐related optical centre.publishersversionpublishe

Chemical characterisation, antioxidant and antibacterial activities of Pinus pinaster Ait. and Pinus pinea L. bark polar extracts: prospecting Forestry by-products as renewable sources of bioactive compounds

Agroforestry by-products have gained rising attention in recent years as they represent inexpensive and abundant raw materials that are a source of added-value chemicals, e.g., for food and pharmaceutical applications, as well as for bioenergy generation. Pinus pinaster Ait. bark extracts are consumed worldwide for their cardiovascular benefits, whilst the health potential of Pinus pinea L. bark has not yet been deeply exploited. Therefore, this study highlights the chemical characterisation of Portuguese P. pinaster Ait. and P. pinea L. bark polar extracts, via ultra-high performance liquid chromatography-diode array detection-tandem mass spectrometry (UHPLC-DAD-MSn) analysis, and their antioxidant and antibacterial activities. Quinic acid, an A-type procyanidin dimer isomer, protocatechuic acid, and quercetin were identified for the first time as P. pinea L. bark components. Moreover, this bark demonstrated a higher total content of identified polar compounds than P. pinaster Ait. bark, with quinic acid being the most abundant compound identified. Regarding antioxidant activity, the pine bark polar extracts exhibited strong reducing power and 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2-azinobis-(3-ethyl-benzothiazoline-6-sulfonic acid (ABTS) radical scavenging effects compared to natural antioxidants. Moreover, the bactericidal actions of pine bark extracts were shown against Staphylococcus aureus and Escherichia coli at a 3.13–25 mg mL−1 range. Globally, these promising insights can boost the sustainable exploitation of P. pinea L. bark, as already occurs with P. pinaster Ait. bark, for the food and biomedical fields.publishe

Extraction and purification of violacein from Yarrowia lipolytica cells using aqueous solutions of surfactants

BACKGROUND: L-Asparaginase (ASNase) is an important biopharmaceutical for the treatment of acute lymphoblastic leukemia (ALL); however, with some restrictions due to its high manufacturing costs. Aqueous biphasic systems (ABS) have been suggested as more economical platforms for the separation/purification of proteins, but a full understanding of the mechanisms behind the ASNase partition is still a major challenge. Polymer/salt-based ABS with different driving-forces (salting-out and hydrophilicity/hydrophobicity effects) were herein applied to control the partition of commercial ASNase. RESULTS: The main results showed the ASNase partition to the salt- or polymer-rich phase depending on the ABS studied, with extraction efficiencies higher than 95%. For systems composed of inorganic salts, the ASNase partition was controlled by the polyethylene glycol (PEG) molecular weight used. Cholinium-salts-based ABS were able to promote a preferential ASNase partition to the polymer-rich phase using PEG-600 and to the salt-rich phase using a more hydrophobic polypropylene glycol (PPG)-400 polymer. It was possible to select the ABS composed of PEG-2000 + potassium phosphate buffer as the most efficient to separate the ASNase from the main contaminant proteins (purification factor = 2.4 ± 0.2), while it was able to maintain the enzyme activity for posterior application as part of a therapeutic. CONCLUSION: Polymer/salt ABS can be used to control the partition of ASNase and adjust its purification yields, demonstrating the ABS potential as more economic platform for the selective recovery of therapeutic enzymes from complex broths.publishe

Chemical characterization of Sambucus nigra L. flowers aqueous extract and its biological implications

The main goal of this study was to chemically characterize an aqueous S. nigra flower extract and validate it as a bioactive agent. The elderflower aqueous extraction was performed at different temperatures (50, 70 and 90 °C). The extract obtained at 90 °C exhibited the highest phenolic content and antiradical activity. Therefore, this extract was analyzed by GC-MS and HPLC-MS, which allowed the identification of 46 compounds, being quercetin and chlorogenic acid derivatives representative of 86% of the total of phenolic compounds identified in hydrophilic fraction of the aqueous extract. Naringenin (27.2%) was the major compound present in the lipophilic fraction. The antiproliferative effects of the S. nigra extract were evaluated using the colon cancer cell lines RKO, HCT-116, Caco-2 and the extracts antigenotoxic potential was evaluated by the Comet assay in RKO cells. The RKO cells were the most susceptible to S. nigra flower extract (IC50=1250 µg mL1). Moreover, the extract showed antimicrobial activity against Gram-positive bacteria, particularly Staphylococcus aureus and S. epidermidis. These results show that S. nigra-based extracts can be an important dietary source of bioactive phenolic compounds that contribute to health-span improving life quality, demonstrating their potential as nutraceutical, functional foods and/or cosmetic components for therapeutic purposes.This research was funded by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UIDB/04469/2020 unit and for Scientific Employment Stimulus 2017 (CEECIND/01507/2017) provided to Ana M. Sousa.info:eu-repo/semantics/publishedVersio

Conservation Biogeography of the Sahara‐Sahel: additional protected areas are needed to secure unique biodiversity

Aim Identification of priority conservation areas and evaluation of coverage of the current protected areas are urgently needed to halt the biodiversity loss. Identifying regions combining similar environmental traits (climate regions) and species assemblages (biogroups) is needed for conserving the biodiversity patterns and processes. We identify climate regions and biogroups and map species diversity across the Sahara-Sahel, a large geographical area that exhibits wide environmental heterogeneity and multiple species groups with distinct biogeographical affinities, and evaluate the coverage level of current network of protected areas for biodiversity conservation. Location Sahara-Sahel, Africa. Methods We use spatially explicit climate data with the principal component analysis and model-based clustering techniques to identify climate regions. We use distributions of 1147 terrestrial vertebrates (and of 125 Sahara-Sahel endemics) and apply distance clustering methods to identify biogroups for both species groups. We apply reserve selection algorithms targeting 17% of species distribution, climate regions and biogroups to identify priority areas and gap analysis to assess their representation within the current protected areas. Results Seven climate regions were identified, mostly arranged as latitudinal belts. Concentrations of high species richness were found in the Sahel, but the central Sahara gathers most endemic and threatened species. Ten biogroups (five for endemics) were identified. A wide range of biogroups tend to overlap in specific climate regions. Identified priority areas are inadequately represented in protected areas, and six new top conservation areas are needed to achieve conservation targets. Main conclusions Biodiversity distribution in Sahara-Sahel is spatially structured and apparently related to environmental variation. Although the majority of priority conservation areas are located outside the areas of intense human activities, many cross multiple political borders and require internationally coordinated efforts for implementation and management. Optimized biodiversity conservation solutions at regional scale are needed. Our work contradicts the general idea that deserts are uniform areas and provide options for the conservation of endangered species.info:eu-repo/semantics/publishedVersio

A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing

Background: Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management. Results: We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of ~159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at http://www.corkoakdb.org. Conclusions: This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response.Peer Reviewe

Significance of glycolytic metabolism-related protein expression in colorectal cancer, lymph node and hepatic metastasis

Background: Colorectal cancer (CRC) is one of the most common malignancies and a leading cause of cancer death worldwide. Most cancer cells display high rates of glycolysis with production of lactic acid, which is then exported to the microenvironment by monocarboxylate transporters (MCTs). The main aim of this study was to evaluate the significance of MCT expression in a comprehensive series of primary CRC cases, lymph node and hepatic metastasis. Methods: Expressions of MCT1, MCT4, CD147 and GLUT1 were studied in human samples of CRC, lymph node and hepatic metastasis, by immunohistochemistry. Results: All proteins were overexpressed in primary CRC, lymph node and hepatic metastasis, when compared with non-neoplastic tissue, with exception of MCT1 in lymph node and hepatic metastasis. MCT1 and MCT4 expressions were associated with CD147 and GLUT1 in primary CRC. These markers were associated with clinical pathological features, reflecting the putative role of these metabolism-related proteins in the CRC setting. Conclusion: These findings provide additional evidence for the pivotal role of MCTs in CRC maintenance and progression, and support the use of MCTs as biomarkers and potential therapeutic targets in primary and metastatic CRC.This work was supported by the Fundação para a Ciência e a Tecnologia (FCT) grant ref. PTDC/SAU-FCF/104347/2008, under the scope of ‘Programa Operacional Temático Factores de Competitividade’ (COMPETE) of ‘Quadro Comunitário de Apoio III’ and co-financed by the Fundo Europeu De Desenvolvimento Regional (FEDER). Ricardo Amorim was recipient of the fellowship SFRH/BD/98002/2013, from Fundação para a Ciência e a Tecnologia (FCT Portugal).info:eu-repo/semantics/publishedVersio

Targeting Acanthamoeba proteins interaction with flavonoids of Propolis extract by in vitro and in silico studies for promising therapeutic effects

Background: Propolis is a natural resinous mixture produced by bees. It provides beneficial effects on human health in the treatment/management of many diseases. The present study was performed to demonstrate the anti-Acanthamoeba activity of ethanolic extracts of Propolis samples from Iran. The interactions of the compounds and essential proteins of Acanthamoeba were also visualized through docking simulation. Methods: The minimal inhibitory concentrations (MICs) of Propolis extract against Acanthamoeba trophozoites and cysts was determined in vitro. In addition, two-fold dilutions of each of agents were tested for encystment, excystment and adhesion inhibitions. Three major compounds of Propolis extract such as chrysin, tectochrysin and pinocembrin have been selected in molecular docking approach to predict the compounds that might be responsible for encystment, excystment and adhesion inhibitions of A. castellanii. Furthermore, to confirm the docking results, molecular dynamics (MD) simulations were also carried out for the most promising two ligand-pocket complexes from docking studies. Results: The minimal inhibitory concentrations (MICs) 62.5 and 125 µg/mL of the most active Propolis extract were assessed in trophozoites stage of Acanthamoeba castellanii ATCC30010 and ATCC50739, respectively. At concentrations lower than their MICs values (1/16 MIC), Propolis extract revealed inhibition of encystation. However, at 1/2 MIC, it showed a potential inhibition of excystation and anti-adhesion. The molecular docking and dynamic simulation revealed the potential capability of Pinocembrin to form hydrogen bonds with A. castellanii Sir2 family protein (AcSir2), an encystation protein of high relevance for this process in Acanthamoeba. Conclusions: The results provided a candidate for the development of therapeutic drugs against Acanthamoeba infection. In vivo experiments and clinical trials are necessary to support this claim