Pattern of mtDNA Variation in Three Populations from São Tomé e Príncipe

We have analysed the matrilineal genetic composition of three self-reported ethnic groups from São Tomé e Príncipe (Gulf of Guinea), an African archipelago whose settlement begun in the late fifteenth century. Sequence data from the hypervariable segments I (HVS-I) and II (HVS-II) were obtained for 30 Angolares, 35 Forros and 38 Tongas. The repertory of mtDNA lineages in São Tomé e Príncipe denoted a fully African maternal pool, primarily arisen from a Central/Southwestern substratum. The absence of any lineages of putative European descent means that the European impact at the mitochondrial pool was virtually nil. Angolares showed a clear reduction of mtDNA diversity and a slight genetic differentiation relative to Tongas or Forros, whereas the latter two groups did not present any signs of genetic boundaries between each other. The data obtained here reinforce the depiction of genetic substructuring in São Tomé e Príncipe previously derived from Y-chromosome STRs. In addition, the crossing of mtDNA and Y-STR information led to the inference that the female mediated gene flow within the archipelago was less restricted than the male, a pattern that could be framed in the cultural traditions and socio-historical interactions among the groups

Supporting the design of an ambient assisted living system using virtual reality prototypes

APEX, a framework for prototyping ubiquitous environments, is used to design an Ambient Assisted Living (AAL) system to enhance a care home for older people. The environment allows participants in the design process to experience the proposed design and enables developers to explore the design by rapidly developing alternatives. APEX provided the means to explore alternative designs through a virtual environment. It provides a mediating representation (a boundary object) allowing users to be involved in the design process. A group of residents in a city-based care home were involved in the design. The paper describes the design process and lessons learnt for the design of AAL systems.info:eu-repo/semantics/acceptedVersio

Rotational and translational self-diffusion in concentrated suspensions of permeable particles

In our recent work on concentrated suspensions of uniformly porous colloidal spheres with excluded volume interactions, a variety of short-time dynamic properties were calculated, except for the rotational self-diffusion coefficient. This missing quantity is included in the present paper. Using a precise hydrodynamic force multipole simulation method, the rotational self-diffusion coefficient is evaluated for concentrated suspensions of permeable particles. Results are presented for particle volume fractions up to 45%, and for a wide range of permeability values. From the simulation results and earlier results for the first-order virial coefficient, we find that the rotational self-diffusion coefficient of permeable spheres can be scaled to the corresponding coefficient of impermeable particles of the same size. We also show that a similar scaling applies to the translational self-diffusion coefficient considered earlier. From the scaling relations, accurate analytic approximations for the rotational and translational self-diffusion coefficients in concentrated systems are obtained, useful to the experimental analysis of permeable-particle diffusion. The simulation results for rotational diffusion of permeable particles are used to show that a generalized Stokes-Einstein-Debye relation between rotational self-diffusion coefficient and high-frequency viscosity is not satisfied.Comment: 4 figure

Supporting the design of an ambient assisted living system using virtual reality prototypes

APEX, a framework for prototyping ubiquitous environments, is used to design an Ambient Assisted Living (AAL) system to enhance a care home for older people. The environment allows participants in the design process to experience the proposed design and enables developers to explore the design by rapidly developing alternatives. APEX provided the means to explore alternative designs through a virtual environment. It provides a mediating representation (a boundary object) allowing users to be involved in the design process. A group of residents in a city-based care home were involved in the design. The paper describes the design process and lessons learnt for the design of AAL systems.EPSRC - Engineering and Physical Sciences Research Council(EP/G059063/1)Jose C. Campos acknowledges support by the FCT – Fundação para a Ciência e a Tecnologia (Portuguese Foundation for Science and Technology) within project UID/EEA/50014/2013. José Luís Silva acknowledges support from project PEST-OE/EEI/LA0009/2015. Michael Harrison was also funded by EPSRC research grant EP/G059063/1: CHI+MED (Computer–Human Interaction for Medical Devices)

Applying artificial intelligence to determination of legal age of majority from radiographic

Forensic odontologists use biological patterns to estimate chronological age for the judicial system. The age of majority is a legally significant period with a limited set of reliable oral landmarks. Currently, experts rely on the questionable development of third molars to assess whether litigants can be prosecuted as legal adults. Identification of new and novel patterns may illuminate features more dependably indicative of chronological age, which have, until now, remained unseen. Unfortunately, biased perceptions and limited cognitive capacity compromise the ability of researchers to notice new patterns. The present study demonstrates how artificial intelligence can break through identification barriers and generate new estimation modalities. A convolutional neural network was trained with 4003 panoramic-radiographs to sort subjects into 'under-18' and 'over-18' age categories. The resultant architecture identified legal adults with a high predictive accuracy equally balanced between precision, specificity and recall. Moving forward, AI-based methods could improve courtroom efficiency, stand as automated assessment methods and contribute to our understanding of biological ageing.</p

Co‐infection by classic MYXV and ha‐MYXV in Iberian hare (Lepus granatensis) and European wild rabbit (Oryctolagus cuniculus algirus)

Research Areas: Infectious Diseases ; Veterinary SciencesMyxomatosis is an emergent disease in the Iberian hare (Lepus granatensis). In this species, the disease is caused by a natural recombinant virus (ha-myxoma virus [MYXV]) identified for the first time in 2018 and has since been responsible for a large number of outbreaks in Spain and Portugal. The ha-MYXV, which harbours a 2.8 Kb insert-disrupting gene M009L, can also infect and cause disease in wild and domestic rabbits, despite being less frequently identified in rabbits. During the laboratory investigations of wild leporids found dead in Portugal carried out within the scope of a Nacional Surveillance Plan (Dispatch 4757/17, MAFDR), co-infection events by classic (MYXV) and naturally recombinant (ha-MYXV) strains were detected in both one Iberian hare and one European wild rabbit (Oryctolagus cuniculus algirus). These two cases were initially detected by a multiplex qPCR detection of MYXV and ha-MYXV and subsequently confirmed by conventional PCR and sequencing of the M009L gene, which contains an ha-MYXV-specific insertion. To our knowledge, this is the first documented report of co-infection by classic MYXV and ha-MYXV strains either in Iberian hare or in European wild rabbit. It is also the first report of infection of an Iberian hare by a classic MYXV strain. These findings highlight the continuous evolution of the MYXV and the frequent host range changes that justify the nonstop monitoring of the sanitary condition of wild Leporidae populations in the Iberian Peninsula.info:eu-repo/semantics/acceptedVersio

A quadruplex qPCR for detection and differentiation of classic and natural recombinant Myxoma Virus Strains of leporids

Research Areas: Biochemistry & Molecular Biology ; ChemistryA natural recombinant myxoma virus (referred to as ha-MYXV or MYXV-Tol08/18) emerged in the Iberian hare (Lepus granatensis) and the European rabbit (Oryctolagus cuniculus) in late 2018 and mid-2020, respectively. This new virus is genetically distinct from classic myxoma virus (MYXV) strains that caused myxomatosis in rabbits until then, by acquiring an additional 2.8 Kbp insert within the m009L gene that disrupted it into ORFs m009L-a and m009L-b. To distinguish ha-MYXV from classic MYXV strains, we developed a robust qPCR multiplex technique that combines the amplification of the m000.5L/R duplicated gene, conserved in all myxoma virus strains including ha-MYXV, with the amplification of two other genes targeted by the real-time PCR systems designed during this study, specific either for classic MYXV or ha-MYXV strains. The first system targets the boundaries between ORFs m009L-a and m009L-b, only contiguous in classic strains, while the second amplifies a fragment within gene m060L, only present in recombinant MYXV strains. All amplification reactions were validated and normalized by a fourth PCR system directed to a housekeeping gene (18S rRNA) conserved in eukaryotic organisms, including hares and rabbits. The multiplex PCR (mPCR) technique described here was optimized for Taqman® and Evagreen® systems allowing the detection of as few as nine copies of viral DNA in the sample with an efficiency > 93%. This real-time multiplex is the first fast method available for the differential diagnosis between classic and recombinant MYXV strains, also allowing the detection of co-infections. The system proves to be an essential and effective tool for monitoring the geographical spread of ha-MYXV in the hare and wild rabbit populations, supporting the management of both species in the field.info:eu-repo/semantics/publishedVersio

Harmless or Threatening? Interpreting the Results of Molecular Diagnosis in the Context of Virus-Host Relationships

Molecular methods, established in the 1980s, expanded and delivered tools for the detection of vestigial quantities of nucleic acids in biological samples. Nucleotide sequencing of these molecules reveals the identity of the organism it belongs to. However, the implications of such detection are often misinterpreted as pathogenic, even in the absence of corroborating clinical evidence. This is particularly significant in the field of virology where the concepts of commensalism, and other benign or neutral relationships, are still very new. In this manuscript, we review some fundamental microbiological concepts including commensalism, mutualism, pathogenicity, and infection, giving special emphasis to their application in virology, in order to clarify the difference between detection and infection. We also propose a system for the correct attribution of terminology in this context.info:eu-repo/semantics/publishedVersio

Espectrometria de infravermelho próximo na predição da textura de solos desenvolvidos de basalto.

A textura dos solos tem sido determinada através de métodos analíticos que muitas vezes são caros e lentos. Ademais, em solos muito argilosos, a dispersão química e mecânica nem sempre é eficiente em separar a fração silte da fração argila, superestimando o conteúdo de silte dos solos. O objetivo do trabalho foi testar a espectroscopia de reflectância de infravermelho próximo (NIRS) na avaliação da textura de solos de basalto. Foram coletadas 214 amostras de terra na região Norte do Estado do Paraná, Brasil, nos municípios de Bela Vista do Paraíso e Londrina, em áreas com predominância de Latossolos, Nitossolos e Neossolos, classificados. As amostras foram coletadas nas profundidades de 0-20 cm e 60-80 cm. Foi realizada análise textural pela dispersão química e mecânica e em seguida as amostras foram escaneadas em um espectrômetro modelo FOSS NIRS SYSTENS XDS, na banda de reflectância entre 400 e 2500 nm. Os dados espectrais foram analisados e comparados aos resultados obtidos com o método da pipeta, através do software WinISI III v. 1.61e. Foi possível verificar que na camada 60-80 cm os teores de argila foram superiores aos da camada 0-20 cm, em função de pequenas translocações de argila verificadas nesses solos. Em relação à predição da textura pelo NIRS, não foi possível obter boa acurácia para nenhuma das frações granulométricas analisadas, uma vez que os coeficientes de correlação da calibração foram apenas 0,55; 0,55 e 0,53 para argila, silte e areia, respectivamente. Nesta situação o indicado seria testar novos métodos de análise de referência e novos tratamentos estatísticos para se ter um melhor indicativo do potencial de uso da técnica

Simple method for establishing primary Leporidae skin fibroblast cultures

Research Areas: Cell BiologyCommercial hare and rabbit immortalized cell lines are extremely limited regarding the many species within the lagomorpha order. To overcome this limitation, researchers and technicians must establish primary cell cultures derived from biopsies or embryos. Among all cell types, fibroblasts are plastic and resilient cells, highly convenient for clinical and fundamental research but also for diagnosis, particularly for viral isolation. Here, we describe a fast and cheap method to produce primary fibroblast cell cultures from leporid species, using dispase II, a protease that allows dermal–epidermal separation, followed by a simple enzymatic digestion with trypsin. This method allows for the establishment of an in vitro cell culture system with an excellent viability yield and purity level higher than 85% and enables the maintenance and even immortalization of leporid fibroblastic cells derived from tissues already differentiated.info:eu-repo/semantics/publishedVersio