TypeTaxonScript: sugarifying and enhancing data structures in biological systematics and biodiversity research.

Object-oriented programming (OOP) embodies a software development paradigm grounded in representing real-world entities as objects, facilitating a more efficient and structured modelling approach. In this article, we explore the synergy between OOP principles and the TypeScript (TS) programming language to create a JSON-formatted database designed for storing arrays of biological features. This fusion of technologies fosters a controlled and modular code script, streamlining the integration, manipulation, expansion, and analysis of biological data, all while enhancing syntax for improved human readability, such as through the use of dot notation. We advocate for biologists to embrace Git technology, akin to the practices of programmers and coders, for initiating versioned and collaborative projects. Leveraging the widely accessible and acclaimed IDE, Visual Studio Code, provides an additional advantage. Not only does it support running a Node.js environment, which is essential for running TS, but it also efficiently manages GitHub versioning. We provide a use case involving taxonomic data structure, focusing on angiosperm legume plants. This method is characterized by its simplicity, as the tools employed are both fully accessible and free of charge, and it is widely adopted by communities of professional programmers. Moreover, we are dedicated to facilitating practical implementation and comprehension through a comprehensive tutorial, a readily available pre-built database at GitHub, and a new package at npm.

Precipitation is the main axis of tropical plant phylogenetic turnover across space and time.

Early natural historians-Comte de Buffon, von Humboldt, and De Candolle-established environment and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, a pantropical plant clade of c. 3500 species, we show that the water availability gradient from deserts to rain forests dictates turnover of lineages within continents across the tropics. We demonstrate that 95% of speciation occurs within a precipitation niche, showing profound phylogenetic niche conservatism, and that lineage turnover boundaries coincide with isohyets of precipitation. We reveal similar patterns on different continents, implying that evolution and dispersal follow universal processes.

Quantifying and mapping species threat abatement opportunities to support national target setting.

The successful implementation of the Convention on Biological Diversity's post-2020 Global Biodiversity Framework will rely on effective translation of targets from global to national level and increased engagement across diverse sectors of society. Species conservation targets require policy support measures that can be applied to a diversity of taxonomic groups, that link action targets to outcome goals, and that can be applied to both global and national data sets to account for national context, which the species threat abatement and restoration (STAR) metric does. To test the flexibility of STAR, we applied the metric to vascular plants listed on national red lists of Brazil, Norway, and South Africa. The STAR metric uses data on species' extinction risk, distributions, and threats, which we obtained from national red lists to quantify the contribution that threat abatement and habitat restoration activities could make to reducing species' extinction risk. Across all 3 countries, the greatest opportunity for reducing plant species' extinction risk was from abating threats from agricultural activities, which could reduce species' extinction risk by 54% in Norway, 36% in South Africa, and 29% in Brazil. Species extinction risk could be reduced by a further 21% in South Africa by abating threats from invasive species and by 21% in Brazil by abating threats from urban expansion. Even with different approaches to red-listing among countries, the STAR metric yielded informative results that identified where the greatest conservation gains could be made for species through threat-abatement and restoration activities. Quantifiably linking local taxonomic coverage and data collection to global processes with STAR would allow national target setting to align with global targets and enable state and nonstate actors to measure and report on their potential contributions to species conservation.

On-chip scalable highly pure and indistinguishable single-photon sources in ordered arrays: Path to quantum optical circuits.

Realization of quantum optical circuits is at the heart of quantum photonic information processing. A long-standing obstacle, however, has been the absence of a suitable platform of single photon sources (SPSs). Such SPSs need to be in spatially ordered arrays and produce, on-demand, highly pure, and indistinguishable single photons with sufficiently uniform emission characteristics to enable controlled interference between photons from distinct sources underpinning functional quantum optical networks. We report on such a platform of SPSs based on a unique class of epitaxial quantum dots dubbed mesa-top single quantum dot. Under resonant excitation, the spatially ordered SPSs (without Purcell enhancement) show single photon purity of >99% [g(2)(0) ~ 0.015], high two-photon Hong-Ou-Mandel interference visibilities of 0.82 ± 0.03 (at 11.5 kelvin, without cavity), and spectral nonuniformity of <3 nanometers, within established locally tunable technology. Our platform of SPSs paves the path to creating on-chip scalable quantum photonic networks for communication, computation, simulation, sensing and imaging.

Effects of enriched environment on maximal lactate steady state of wistar rats / Efeitos do ambiente enriquecido na máxima fase estável do lactato de ratos wistar

The enriched environment (EE) is a combination of stimulations inserted in the cage, such as tunnels, exercise wheel and color objects, increased cage size and the number of rats. Although the EE can be promoter of physical activity (PA), the literature lacks studies showing the effects of this accumulation of PA in the rats. In this way, the present study aims to investigate the effects of EE on maximal lactate steady state in rats. To this, adult Wistar rats were randomly distributed into control group (CG), kept in conventional cages, and EE group (EEG), kept in enriched cages. Before and after the experimental period (six weeks) the animals were submitted for the maximal lactate steady state (MLSS) test. In the last week, length and body mass was measured. At the end of the experimental period, after euthanasia, blood sample was collected for the analyses of glucose and heart was weighted. To statistical analyses, after the test of normality, the parametric results were analyzed by Student's t test and nonparametric through Mann-Whintey test. There were no differences in serum glucose, body length, body and heart mass. The groups presented similar MLSS at beginning of experiment, however, MLSS load was higher in EE than CG at end of experiment. In conclusion, PA performed in the enriched cage increased the aerobic capacity in comparing to the conventional cage, even in the absence of significant changes in length and body weight and blood glucose.

O ambiente enriquecido (EE) é uma combinação de estímulos inseridos na gaiola, tais como túneis, roda de exercício e objetos coloridos, além de aumento do tamanho da gaiola e do número de ratos. Embora o EE possa ser promotor de atividade física (PA), a literatura carece de estudos mostrando os efeitos dessa acumulação de PA em ratos mantidos no EE. Desta forma, o presente estudo tem como objetivo investigar os efeitos do EE sobre a máxima fase estável do lactato. Para isso, ratos Wistar adultos foram distribuídos aleatoriamente em grupo controle (CG), mantidos em gaiolas convencionais e grupo AE (EEG), mantidos em gaiolas enriquecidas. Antes e após o período experimental (seis semanas), os animais foram submetidos ao teste de máxima fase estável do lactato (MLSS). Na última semana, comprimento e massa corporal foram registradas. No final do período experimental, após a eutanásia, amostra de sangue foi coletada para análise de glicose e a massa do coração foi registrada. Para as análises estatísticas, após o teste de normalidade, os resultados paramétricos foram analisados pelo teste t de Student e não paramétrico através do teste de Mann-Whintey. Não houve diferença nos níveis de glicose no soro, comprimento corporal e massa cardíaca. Os grupos apresentaram MLSS semelhante no início do experimento, no entanto, no final do experimento, a carga da MLSS foi maior no EEG comparado ao GC. Em conclusão, PA realizada na gaiola enriquecido aumentou a capacidade aeróbia em comparação com o grupo mantido em gaiolas convencionais, mesmo na ausência de mudanças significativas na massa e comprimento corporal e da glicemia.

Efeitos da ingestão de óleo de linhaça e treinamento físico sobre a massa óssea de ratos Wistar / Effects of flaxseed oil intake and exercise training on bone mass of wistar rats

O treinamento físico é reconhecido como fator importante para prevenção e tratamento de doenças ósseas, como osteoporose. O Ômega 3, presente em alimentos como óleo de linhaça, também pode contribuir para manutenção da saúde óssea. Todavia, poucos estudos investigaram possíveis efeitos sinérgicos de ambos. Objetivo: objetiva-se investigar os efeitos da administração do óleo de linhaça e do treinamento físico sobre a massa óssea de ratos wistar saudáveis. Método: os ratos foram distribuídos em quatro grupos: controle (C), linhaça (L), treinado (T) e linhaça treinado (LT). O treinamento físico consistiu de 30 min/dia, 5 dias/semana, durante 8 semanas, suportando sobrecarga equivalente à 2,5 por cento massa corporal. O óleo de linhaça foi administrado via orogástrica por gavagem (0,5 ml/kg) durante 8 semanas. Os animais tiveram massa corporal registrada no início e final do período experimental e ingestões hídrica e alimentar foram coletadas na última semana de experimento. Após período experimental, os animais foram eutanasiados e a tíbia foi coletada para registros de comprimento e massa. Resultados e Discussão: nos parâmetros peso corporal, ingestões hídrica e alimentar e comprimento ósseo, a administração de linhaça e treinamento físico não causaram efeitos que promovessem diferença significativa nos valores. Todavia, o grupo que recebeu óleo de linhaça e foi submetido ao treinamento físico apresentou massa óssea da tíbia maior que os demais grupos. Conclusão: desta forma, pode ser concluído que, em animais saudáveis, este volume de treinamento físico e administração de óleo de linhaça concomitantemente promoveram aumento na massa tibial, sem provocar alterações nos demais parâmetros estudados...

Physical training is an important factor for the prevention and treatment of bone diseases like osteoporosis. Omega 3 found in foods such as flaxseed oil can also contribute to maintaining bone health. However, few studies have investigated possible synergistic effects of both. Objective: it aimed to verify the effects of administration of flaxseed oil and physical training in bone mass from healthy rats. Method: Wister rats were divided into four groups: control (C), linseed (L), trained (T) and flaxseed trained (LT). Exercise training consisted of 30 min / day, 5 days / week during 8 weeks supporting a load corresponding to 2.5 percent of the body weight. The flaxseed oil was administered via orogastric gavage (0.5 ml / kg) for 8 weeks. The animals had body mass recorded at the beginning and end of the experimental period, and water and food intakes collected in the last week of the experiment. After the experimental period, the animals were sacrificed and the tibia is removed to length and weight records. Results and Discussion: to body weight, water intake, food intake and bone length, the administration of flaxseed and/or physical training did not cause significant differences between the groups studied. However, the group that received flaxseed oil and was subjected to physical training had greater tibial bone mass than the other groups. Conclusion: it is concluded that this volume of physical training and administration of flaxseed oil concomitantly caused an increase in tibial mass without causing changes in other studied parameters in heathy rats...