Multivariate phase space reconstruction by nearest neighbor embedding with different time delays

A recently proposed nearest neighbor based selection of time delays for phase space reconstruction is extended to multivariate time series, with an iterative selection of variables and time delays. A case study of numerically generated solutions of the x- and z coordinates of the Lorenz system, and an application to heart rate and respiration data, are used for illustration.Comment: 4 pages, 3 figure

Ciência na Ponta dos Dedos: Scientific Activities for Children under 10

In the context of the “Projeto” of the 3rd year of “Licenciatura em Biologia Aplicada” it was proposed to develop experimental activities connected with science for 1st to 4th grade students. This initiative was named Ciência na Ponta dos Dedos and was presented in the scope of “Festa da Ciência 2014”, an event of the Escola de Ciências of Universidade do Minho, which happens every year during May (and lasted this year from 12th to 14th of May). The first edition of Ciência na Ponta dos Dedos was offered to 1st grade students (6-7 years old). A mini laboratory where children could see, try and participate in scientific hands-on activities was created for the initiative. The experimental activities were designed and settled in accordance with curricular guidelines, age [1,2,3] and in the scope of the theme “water source of life” through the development of six different activities where the children, organized in groups, had the opportunity to explore aspects connected with the (i) reaction of an acid with sodium bicarbonate in water, (ii) dissolution of different substances in water,(iii) permeability of different soils, (iv) water cycle through the observation of a mini ecosystem, (v) observation on the microscope of the stoma of the plants and (vi) the colouring of carnations by capillarity using several dyes. These activities were carried out in such an environment that kids’ eyes had light up as brightly when doing the science lab activities Children could feel free to express their ideas and participate in the activities to build applicable knowledge in the context of experimental science. This kind of learning comes easier to children if they can touch and make the experiments by themselves, though with a proper supervision, allowing the children to think and to learn that “if I do this, that will happen“, so “in order that to happen, I will have to make this” [2]. In the sequence of these experimental activities, children were asked to fill in an inquiry, previously prepared in order to know their opinion about the activities they performed, including their favourite ones. This survey will also provide some new ideas to improve future similar events.The present communication intends to present the project and its success near the children and their teachers, as well as to highlight the importance of scientific knowledge. Quoting some children: “the activities were very funny and I learned new things”, “I learned why oil does not mix with water” and “I learned that the noses of the plants are in their leaves”. In a developing society it is more and more important that the education system makes science stand out from the early years of school in order to form citizens able to deal efficiently with the challenges and the necessities of the current society [2].info:eu-repo/semantics/publishedVersio

Establishment of a new PNA-FISH method for Aspergillus fumigatus identification: first insights for future use in pulmonary samples

Aspergillus fumigatus is the main causative agent of Invasive Aspergillosis. This mold produces conidia that when inhaled by immunocompromized hosts can be deposited in the lungs and germinate, triggering disease. In this paper, the development of a method using peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH) is described. The PNA-FISH probe was tested in several strains and a specificity and sensitivity of 100% was obtained. Detection of A. fumigatussensu stricto was then achieved in artificial sputum medium (ASM) pre-inoculated with 1 × 102 conidia·mL−1–1 × 103 conidia·mL−1, after a germination step of 24 h. The PNA-FISH method was evaluated in 24 clinical samples (10 sputum, 8 bronchoalveolar lavage (BAL), and 6 bronchial lavage (BL)) that were inoculated with 1 × 104 conidia·mL−1 in sputum; 1 × 103 conidia·mL−1 in BL and BAL, for 24 h. Despite a specificity of 100%, the sensitivity was 79%. This relatively low sensitivity can be explained by the fact that hyphae can yield “fungal ball“ clusters, hindering pipetting procedures and subsequent detection, leading to false negative results. Nonetheless, this study showed the potential of the PNA-FISH method for A. fumigatussensu stricto detection since it takes only 1 h 30 m to perform the procedure with a pre-enrichment step of 6 h (pure cultures) and 24 h (clinical samples), and might provide a suitable alternative to the existing methods for studies in pure cultures and in clinical settings.This research was funded by: Base Funding — UIDB/00511/2020 of the Laboratory for Process Engineering, Environment, Biotechnology and Energy—LEPABE—funded by national funds through the FCT/MCTES (PIDDAC)—Projects POCI-01-0145-FEDER-029961 and POCI-01-0145-FEDER-031011, funded by FEDER funds through COMPETE2020—Programa Operacional Competitividade e Internacionalização (POCI) and by national funds (PIDDAC) through FCT/MCTES. Laura Cerqueira is also financed by Project POCI-01-0145-FEDER-029961.info:eu-repo/semantics/publishedVersio

Methodology to identify a gene expression signature by merging microarray datasets

A vast number of microarray datasets have been produced as a way to identify differentially expressed genes and gene expression signatures. A better understanding of these biological processes can help in the diagnosis and prognosis of diseases, as well as in the therapeutic response to drugs. However, most of the available datasets are composed of a reduced number of samples, leading to low statistical, predictive and generalization power. One way to overcome this problem is by merging several microarray datasets into a single dataset, which is typically a challenging task. Statistical methods or supervised machine learning algorithms are usually used to determine gene expression signatures. Nevertheless, statistical methods require an arbitrary threshold to be defined, and supervised machine learning methods can be ineffective when applied to high-dimensional datasets like microarrays. We propose a methodology to identify gene expression signatures by merging microarray datasets. This methodology uses statistical methods to obtain several sets of differentially expressed genes and uses supervised machine learning algorithms to select the gene expression signature. This methodology was validated using two distinct research applications: one using heart failure and the other using autism spectrum disorder microarray datasets. For the first, we obtained a gene expression signature composed of 117 genes, with a classification accuracy of approximately 98%. For the second use case, we obtained a gene expression signature composed of 79 genes, with a classification accuracy of approximately 82%. This methodology was implemented in R language and is available, under the MIT licence, at https://github.com/bioinformatics-ua/MicroGES.info:eu-repo/semantics/publishedVersio

Preparação de sabão com propriedades fitoterápicas e emolientes a partir do óleo vegetal de cozinha.

Diariamente são descartados litros e litros de óleo doméstico usado, uma parte desse descarte se dá em latas de lixo, rede de esgoto, poucos são aqueles que reservam esse tipo de material para reciclagem, uma parte é por não saber como tratar os resíduos contidos em seu meio. Os projetos de preparação de sabão com propriedades fitoterápicas têm por objetivo dar um destino ao descarte desse óleo residual doméstico, promovendo a interação da comunidade local da região da Vila C a fazer desde a parte do tratamento de resíduo do óleo até a mistura de outros reagentes para a produção de um sabão para o banho de animais domésticos e que possa ser utilizável para limpeza de utensílios domésticos. Para a preparação deste material é considerado o fácil acesso aos reagentes envolvidos como a soda cáustica, a qual ainda é comercialmente vendida em mercearias locais e acesso às plantas medicinais que já tem suas propriedades conhecidas, como no caso a erva baleeira, calêndula, e citronela, também é realizado junto a comunidade, oficinas informando sobre os cuidados em manipular produtos químicos, como agir em caso de acidentes durante o manuseio, a quem é indicado a fazer esse tipo de tratamento e como preparar o produto. Existem análises laboratoriais que são acompanhadas e orientadas, as quais são necessárias para testes em pequena escala antes de cada oficina, essas análises são feitas para poder corrigir o pH do produto e mensurar a quantidade de aditivos na produção do sabão, após essas análises o modelo de produção é replicado em escala maior, já com a certeza dos resultados na qualidade do produto final. Desta forma se faz necessário uma investigação mais detalhada ao produto final, por meio de utilização de equipamentos cromatográficos e espectrofotômetros, como ferramenta na identificação dos compostos e/ou princípios ativos na composição, os quais dão a característica de fitoterápicos e comparar desta forma, com o que já temos em literatura conhecida

MAMMALS IN PORTUGAL: A data set of terrestrial, volant, and marine mammal occurrences in Portugal

Mammals are threatened worldwide, with ca. 26% of all species being included in the IUCN threatened categories. This overall pattern is primarily associated to habitat loss or degradation, and human persecution for terrestrial mammals, and pollution, open net fishing, climate change and prey depletion for marine mammals. Mammals play a key role in maintaining ecosystems functionality and resilience, and therefore information on their distribution is crucial to delineate and support conservation actions. MAMMALS IN PORTUGAL is a publicly available data set compiling unpublished geo-referenced occurrence records of 92 terrestrial, volant, and marine mammals in mainland Portugal and archipelagos of Azores and Madeira that includes 107,852 data entries between 1873 and 2021 (72% of the data occurring in 2000 and 2021). The methods used to collect the data were: live observations/captures (42%), sign surveys (38%), camera trapping (16%), bioacoustics surveys (4%) and radio-tracking and inquiries that represent less than 1% of the records. The data set includes 13 types of records: 1) burrows | soil mounds | tunnel, 2) capture, 3) colony, 4) dead animal | hair | skulls | jaws, 5) genetic confirmation, 6) inquiries, 7) observation of live animal, 8), observation in shelters, 9) photo trapping | video, 10), predators diet | pellets | pine cones/nuts, 11) scat | track | ditch, 12) telemetry and 13) vocalization | echolocation. The spatial uncertainty of most records ranges between 0 and 100 m (76%). Rodentia (n = 34,754) has the highest number of records followed by Chiroptera (n = 18,858), Carnivora (n = 18,594), Lagomorpha (n = 17,679), Cetartiodactyla (n = 11,568) and Eulipotyphla (n = 6400). The data set includes records of species classified by the IUCN as threatened (e.g., Oryctolagus cuniculus (n = 12,407), Monachus monachus (n = 1512), and Lynx pardinus (n = 197)]. We believe that this data set may stimulate the publication of other European countries data sets which would certainly contribute to ecology and conservation-related research, and therefore assisting on the development of more accurate and tailored conservation management strategies for each species. There are no copyright restrictions; please cite this data paper when the data are used in publications

Bacteriocin production by Escherichia coli during biofilm development

Escherichia coli is a highly versatile bacterium ranging from commensal to intestinal pathogen, and is an important foodborne pathogen. E. coli species are able to prosper in multispecies biofilms and secrete bacteriocins that are only toxic to species/strains closely related to the producer strain. In this study, 20 distinct E. coli strains were characterized for several properties that confer competitive advantages against closer microorganisms by assessing the biofilm-forming capacity, the production of antimicrobial molecules, and the production of siderophores. Furthermore, primer sets for E. coli bacteriocins–colicins were designed and genes were amplified, allowing us to observe that colicins were widely distributed among the pathogenic E. coli strains. Their production in the planktonic phase or single-species biofilms was uncommon. Only two E. coli strains out of nine biofilm-forming were able to inhibit the growth of other E. coli strains. There is evidence of larger amounts of colicin being produced in the late stages of E. coli biofilm growth. The decrease in bacterial biomass after 12 h of incubation indicates active type I colicin production, whose release normally requires E. coli cell lysis. Almost all E. coli strains were siderophore-producing, which may be related to the resistance to colicin as these two molecules may use the same transporter system. Moreover, E. coli CECT 504 was able to coexist with Salmonella enterica in dual-species biofilms, but Shigella dysenteriae was selectively excluded, correlating with high expression levels of colicin (E, B, and M) genes observed by real-time PCR.info:eu-repo/semantics/publishedVersio

Habitat Suitability of Threespine Stickleback (Gasterosteus aculeatus L.) in the Southern Limit of Its Global Distribution: Implications for Species Management and Conservation

The conservation of fish biodiversity requires reliable information on their distribution and habitat use, especially of endemic species that generally occur in restricted geographic areas and specific habitats. This is the case of threespine stickleback (G. aculeatus L.), that is a small freshwater fish listed as Endangered (EN) in Portugal, which represents the southern limit of the species global distribution. The monitoring and conservation of populations placed near to the species distribution limits is very important because in these places, small environmental changes can lead to the significant decline of local populations. However, due to the lack of knowledge about its regional distribution, ecology, and macrohabitat preferences, few measures have been proposed aiming the conservation of this species. This project aimed to identify which macro-scale environmental factors determine regional distribution of G. aculeatus, to predict their potential distribution and, therefore, define the most important areas for their protection and conservation. The occurrence data, from existing databases and specific sampling campaigns, together with 15 environmental macrohabitat predictors, were used to model the potential distribution of sticklebacks in Portugal, through an ensemble of species distributions models (SDM). Through the results of our ensemble model, we found that threespine stickleback may occur predominantly at lower stretches of river systems, where sandy substrate is dominant, and flow is higher. Sticklebacks are also more likely to occur in sites with high levels of rainfall in the driest month, thus avoiding locations with high potential for drying during summer, which tend to be common in the Iberian Peninsula. The species also tends to avoid steep slope areas, with high levels of annual precipitation. Based on our results, a probability map of occurrence was generated; from this, some river stretches were categorized into levels according to their importance for the conservation of the species. With the results obtained, it was also possible to identify some atypical populations, occurring in areas with low or null habitat suitability, which need to be further studied, because they must have developed physiological characteristics that allow them to subsist in places that are not conducive to their survival

Efficacy, Stability, and Safety Evaluation of New Polyphenolic Xanthones Towards Identification of Bioactive Compounds to Fight Skin Photoaging

Antioxidants have long been used in the cosmetic industry to prevent skin photoaging, which is mediated by oxidative stress, making the search for new antioxidant compounds highly desirable in this field. Naturally occurring xanthones are polyphenolic compounds that can be found in microorganisms, fungi, lichens, and some higher plants. This class of polyphenols has a privileged scaffold that grants them several biological activities. We have previously identified simple oxygenated xanthones as promising antioxidants and disclosed as hit, 1,2-dihydroxyxanthone (1). Herein, we synthesized and studied the potential of xanthones with different polyoxygenated patterns as skin antiphotoaging ingredients. In the DPPH antioxidant assay, two newly synthesized derivatives showed IC₅₀ values in the same range as ascorbic acid. The synthesized xanthones were discovered to be excellent tyrosinase inhibitors and weak to moderate collagenase and elastase inhibitors but no activity was revealed against hyaluronidase. Their metal-chelating effect (FeCl₃ and CuCl₂) as well as their stability at different pH values were characterized to understand their potential to be used as future cosmetic active agents. Among the synthesized polyoxygenated xanthones, 1,2-dihydroxyxanthone (1) was reinforced as the most promising, exhibiting a dual ability to protect the skin against UV damage by combining antioxidant/metal-chelating properties with UV-filter capacity and revealed to be more stable in the pH range that is close to the pH of the skin. Lastly, the phototoxicity of 1,2-dihydroxyxanthone (1) was evaluated in a human keratinocyte cell line and no phototoxicity was observed in the concentration range tested.This research was supported by national funds through FCT, Foundation for Science and Technology, within the scope of UIDB/04423/2020 and UIDP/04423/2020 under the project PTDC/SAU-PUB/28736/2017 (reference POCI-01-0145-FEDER-028736), cofinanced by COMPETE 2020, Portugal 2020 and the European Union through the ERDF and by FCT through national funds, as well as CHIRALBIOACTIVE-PI-3RL-IINFACTS-2019, and supported by the Applied Molecular Biosciences Unit-UCIBIO which is financed by national funds from FCT/MCTES (UID/Multi/04378/2019). Thanks are also due to FCT, the European Union, QREN, FEDER, COMPETE, by funding cE3c center (Ref. UID/BIA/00329/2019) and Direcao Regional da Ciencia e Tecnologia (Azores Government) by funding Azorean Biodiversity Group.info:eu-repo/semantics/publishedVersio

ULK overexpression mitigates motor deficits and neuropathology in mouse models of Machado-Joseph disease

Machado-Joseph disease (MJD) is a fatal neurodegenerative disorder clinically characterized by prominent ataxia. It is caused by an expansion of a CAG trinucleotide in ATXN3, translating into an expanded polyglutamine (polyQ) tract in the ATXN3 protein, that becomes prone to misfolding and aggregation. The pathogenesis of the disease has been associated with the dysfunction of several cellular mechanisms, including autophagy and transcription regulation. In this study, we investigated the transcriptional modifications of the autophagy pathway in models of MJD and assessed whether modulating the levels of the affected autophagy-associated transcripts (AATs) would alleviate MJD-associated pathology. Our results show that autophagy is impaired at the transcriptional level in MJD, affecting multiple AATs, including Unc-51 like autophagy activating kinase 1 and 2 (ULK1 and ULK2), two homologs involved in autophagy induction. Reinstating ULK1/2 levels by adeno-associated virus (AAV)-mediated gene transfer significantly improved motor performance while preventing neuropathology in two in vivo models of MJD. Moreover, in vitro studies showed that the observed positive effects may be mainly attributed to ULK1 activity. This study provides strong evidence of the beneficial effect of overexpression of ULK homologs, suggesting these as promising instruments for the treatment of MJD and other neurodegenerative disorders