Miracle-dz/UniFAR-FTUs huggingface dataset:
Nested oscillatory dynamics in cortical organoids model early human brain network development

Structural and transcriptional changes during early brain maturation follow fixed developmental programs defined by genetics. However, whether this is true for functional network activity remains unknown, primarily due to experimental inaccessibility of the initial stages of the living human brain. Here, we developed cortical organoids that spontaneously display periodic and regular oscillatory network events that are dependent on glutamatergic and GABAergic signaling. These nested oscillations exhibit cross-frequency coupling, proposed to coordinate neuronal computation and communication. As evidence of potential network maturation, oscillatory activity subsequently transitioned to more spatiotemporally irregular patterns, capturing features observed in preterm human electroencephalography (EEG). These results show that the development of structured network activity in the human neocortex may follow stable genetic programming, even in the absence of external or subcortical inputs. Our approach provides novel opportunities for investigating and manipulating the role of network activity in the developing human cortex. HIGHLIGHTS Early development of human functional neural networks and oscillatory activity can be modeled in vitro. Cortical organoids exhibit phase-amplitude coupling between delta oscillation (2 Hz) and high-frequency activity (100-400 Hz) during network-synchronous events. Differential role of glutamate and GABA in initiating and maintaining oscillatory network activity. Developmental impairment of MECP2-KO cortical organoids impacts the emergence of oscillatory activity. Cortical organoid network electrophysiological signatures correlate with human preterm neonatal EEG features. eTOC Brain oscillations are a candidate mechanism for how neural populations are temporally organized to instantiate cognition and behavior. Cortical organoids initially exhibit periodic and highly regular nested oscillatory network events that eventually transition to more spatiotemporally complex activity, capturing features of late-stage preterm infant electroencephalography. Functional neural circuitry in cortical organoids exhibits emergence and development of oscillatory network dynamics similar to those found in the developing human brain.
Effects of rare earth elements on growth rate, lipids, fatty acids and pigments in microalgae

The extensive exploitation of rare earth elements (REEs), particularly in electronic technologies and agriculture has concomitantly raised the environmental load. Their resulting effects on primary producers such as microalgae are, however, poorly understood. We have studied these effects on two microalgae of biotechnological interest. The yellow‐green alga Trachydiscus minutus (Eustigmatophyceae, Ochrophyta), and the green alga Parachlorella kessleri (Trebouxiophyceae, Chlorophyta) were cultivated in mineral medium supplemented with 10 μmol L−1 chlorides of REEs: cerium, gadolinium, lanthanum, lutetium, praseodymium, scandium, and with monazite, which is a mineral rich in those elements. We observed growth rates at different mean light intensities (20, 50, 150 and 300 μmol m−2 s−1). The high growth rate of P. kessleri was not affected by the presence of any lanthanide, and decreased proportionally with light intensity (from 0.2 to 0.04 doublings per hour). In contrast, the growth rate of T. minutus was about three times lower compared with P. kessleri, with an optimum at 50 μmol m−2 s−1 and decreased at higher or lower light intensities. In the presence of Ce3+, La3+ and Sc3+, the growth rate markedly increased to a value that corresponded to the growth rate in P. kessleri at the same light intensity. The composition and content of pigments and lipids were followed at the optimum light intensity for both species. The lipid content (percentage of dry weight) varied only slightly in the presence of individual rare earths. There was, however, an increase in saturated fatty acids at the expense of polyunsaturated fatty acids. The effect of REEs on pigments was variable: the presence of Ce3+, Gd3+, La3+ and Sc3+ caused an increase in the concentrations of major pigments such as lutein, violaxanthin, β‐carotene or chlorophylls, while Pr3+ and Lu3+ reduced them.
Distribution of estuarine fish fauna along coast of Brazil

O presente estudo teve como objetivos: listar a ictiofauna estuarina que ocorre no Brasil, a partir de dados compilados de artigos publicados em periodicos e em livros; rever a nomenclatura taxonomica valida das especies; alem de analisar ecologicamente as similaridades entre os segmentos ictiofaunisticos. Foram compilados os dados de 52 artigos cientificos e livros, que tratam sobre assembleias de peixes estuarinos ou listas com abundância por especie. Os trabalhos registraram 451 especies validas, sendo 225 associadas aos ambientes recifais, e 64 exclusivamente dulciaquicolas. Quatro especies: Lutjanus apodus, L. griseus, Scartella nuchifilis e Scomberomorus maculatus nao ocorrem na costa brasileira. Dentre as 104 familias registradas, Sciaenidae foi predominante em todos os segmentos, exceto no V e no VIII. A analise de agrupamento indicou uma maior similaridade entre os segmentos II e III, e entre os segmentos V e VII. Palavras chave: Estuarios, Peixes recifais, Similaridade.
Where Fossils Dare and Males Matter: combined morphological and molecular analysis untangles the evolutionary history of the spider ant genus Leptomyrmex Mayr (Hymenoptera : Dolichoderinae)

Abstract. The distinctive ant genus Leptomyrmex Mayr, 1862 had been thought to be endemic to Australasia for over 150 years, but enigmatic Neotropical fossils have challenged this view for decades. The present study responds to a recent and surprising discovery of extant Leptomyrmex species in Brazil with a thorough evaluation of the Dominican Republic fossil material, which dates to the Miocene. In the first case study of direct fossil inclusion within Formicidae Latreille, 1809, we incorporated both living and the extinct Leptomyrmex species. Through simultaneous analysis of molecular and morphological characters in both Bayesian and parsimony frameworks, we recovered the fossil taxon as sister-group to extant Leptomyrmex in Brazil while considering the influence of taxonomic and character sampling on inferred hypotheses relating to tree topology, biogeography and morphological evolution. We also identified potential loss of signal in the binning of morphological characters and tested the impact of parameterisation on divergence date estimation. Our results highlight the importance of securing sufficient taxon sampling for extant lineages when incorporating fossils and underscore the utility of diverse character sources in accurate placement of fossil terminals. Specifically, we find that fossil placement in this group is influenced by the inclusion of male-based characters and the newly discovered Neotropical ‘Lazarus taxon’.
Pattern separation of spiketrains in hippocampal neurons

Pattern separation is a process that minimizes overlap between patterns of neuronal activity representing similar experiences. Theoretical work suggests that the dentate gyrus (DG) performs this role for memory processing but a direct demonstration is lacking. One limitation is the difficulty to measure DG inputs and outputs simultaneously. To rigorously assess pattern separation by DG circuitry, we used mouse brain slices to stimulate DG afferents and simultaneously record DG granule cells (GCs) and interneurons. Output spiketrains of GCs are more dissimilar than their input spiketrains, demonstrating for the first time temporal pattern separation at the level of single neurons in the DG. Pattern separation is larger in GCs than in fast-spiking interneurons and hilar mossy cells, and is amplified in CA3 pyramidal cells. Analysis of the neural noise and computational modelling suggest that this form of pattern separation is not explained by simple randomness and arises from specific presynaptic dynamics.
Population genomics of rapidly invading lionfish in the Caribbean reveals signals of range expansion in the absence of spatial population structure

Range expansions driven by global change and species invasions are likely to have significant genomic, evolutionary, and ecological implications. During range expansions, strong genetic drift characterized by repeated founder events can result in decreased genetic diversity with increased distance from the center of the historic range, or the point of invasion. The invasion of the Indo-Pacific lionfish, Pterois volitans, into waters off the U.S. East Coast, Gulf of Mexico, and Caribbean Sea provides a natural system to study rapid range expansion in an invasive marine fish with high dispersal capabilities. We report results from 12,759 loci sequenced by restriction enzyme associated DNA sequencing for nine P. volitans populations in the invaded range, including Florida and other Caribbean sites, as well as mitochondrial control region D-loop data. Analyses revealed low to no spatially explicit metapopulation genetic structure in the study area, which is partly consistent with previous finding of little structure within ocean basins, but partly divergent from reports of between-basin structure. Genetic diversity, however, was not homogeneous across all sampled sites. Patterns of genetic diversity correlate with invasion pathway. Observed heterozygosity, averaged across all loci within a population, decreases with distance from Florida while expected heterozygosity is mostly constant throughout sampled populations, indicating population genetic disequilibrium correlated with distance from the point of invasion. Using an FST outlier analysis and a Bayesian environmental correlation analysis, we identified 256 and 616 loci, respectively, that could be experiencing selection or genetic drift. Of these, 24 loci were shared between the two methods.
A Cu/Zn superoxide dismutase gene from Saussurea involucrata Kar. & Kir., SiCSD, enhances drought, cold, and oxidative stress in transgenic tobacco

Abstract: Superoxide dismutase (SOD) plays an important role in the stress tolerance of higher plants. In the present study, a novel Cu/Zn-SOD gene, SiCSD (accession no. KC912564), was cloned from Saussurea involucrata Kar. & Kir. The deduced amino acid sequence shared 85% identity with Cu/Zn-SOD of Solanum tuberosum L. and Solanum lycopersicum L. Quantitative real-time polymerase chain reaction showed that SiCSD was upregulated by treatments with cold, drought, and oxidative stresses. SiCSD transgenic tobacco plants improved tolerance to drought, freezing, and oxidative stresses and exhibited a higher survival rate, relative water content, photosynthesis efficiency, and higher activities of SODs, catalases, and ascorbate peroxidase, but lower ion leakage and malondialdehyde contents compared with the wild type. These data demonstrate that SiCSD may act as a positive regulator in drought and cold stress by reducing oxidant injury.
Greening Industry Without Enforcement? An Assessment of the World Bank's Pollution Regulation Model for Developing Countries

The best comparative and overview source now available for knowledge about pollution regulation in developing countries is the 2000 World Bank policy research report called Greening Industry. The World Bank finds that there is a new model for pollution regulation in lower- and middle-level income countries that is an alternative to “traditional” command and control regulation. The new model stresses flexible norms and nonstate pressures on regulated enterprises coming from communities and markets. This article presents an investigation into this new model. It finds that the prevalence of weak law enforcement may undermine the new model's potential to control pollution in developing countries. It also contends that social and market pressures only occur under certain circumstances often not found in lower- and middle-level income countries. Therefore, the article concludes that developing countries require smart mixes of various regulatory instruments appropriate in the given state and nonstate regulatory capacities, instead of contrasting state and nonstate regulation.
Mosaic chromosomal aneuploidy detection by sequencing (MAD-seq)

Current approaches to detect and characterize mosaic chromosomal aneuploidy are limited by sensitivity, efficiency, cost or the need to culture cells. We describe a combination of a new sequencing-based assay and a novel analytical approach that allows low levels of mosaicism for chromosomal aneuploidy to be detected, assigned to a meiotic or mitotic origin, and quantified as a proportion of the cells in the sample. We show results from a multi-ethnic assay design that is suitable for populations of diverse racial and ethnic origins, and how the MADSEQ analytical approach applied to exome sequencing data reveals unrecognized aneuploidy in 1000 Genomes samples and cell lines from public repositories. We have made the assay design and analytical software open for unrestricted use, with the goal that it can be applied in clinical samples to allow new insights into the unrecognized prevalence of mosaic chromosomal aneuploidy and its phenotypic associations.
Assessing haplotype-based models for genomic evaluation in Holstein cattle

Abstract: A single-nucleotide polymorphisms-based genomic relationship matrix (G SNP) discriminate less identity by state from identity by descent (IBD) alleles compared with a multi-locus haplotype-based relationship matrix (G HAP), which can better capture IBD alleles and recent relationships. We aimed to compare the prediction reliability and prediction bias of genomic best linear unbiased prediction (GBLUP) using either G SNP or G HAP in Holstein cattle. Therefore, a total of 57 traits with a wide range of heritability values were analyzed. Classical validation tests were done using a validation dataset comprised of 50k genotype records of 561–669 proven bulls born in 2010–2011 with an official estimated breeding value (EBV) in 2016 and a training set of 5314–19 678 bulls born before 2010, depending on the trait. The method for building the genomic relationship matrix (G) had significant, but small effect on observed reliability (r 2 GEBV) (p < 0.0001) and bias (p < 0.0001). A significant interaction between G and the level of trait heritability on r 2 GEBV and bias was also observed (p < 0.0001). The small gains in r 2 GEBV and small reductions in the bias by using GHAPBLUP were increased when predicting moderate to high-heritability traits compared with low-heritability traits.
Establishment and maintenance of an R6/1 transgenic mouse colony and validation of its progressive neurological phenotype to study Huntington’s disease

Veterinaria Mexico OA ISSN: 2448-6760 Cite this as: Garcia-Lara L, Morales-Martinez A, Angeles-Lopez QD, Pedraza-Espitia H, Perez-Neri I, Rodriguez-Balderas CA, Perez-Severiano F. Establishment and maintenance of an R6/1 transgenic mouse colony and validation of its progressive neurological phenotype to study Huntington’s disease. Veterinaria Mexico OA. 2018;5(1). doi: 10.21753/vmoa.5. 1.487 . Huntington’s disease (HD) is a hereditary neurodegenerative disorder of the central nervous system that mainly affects the basal ganglia and has no cure. The mutation is located at an abnormal expansion of the CAG triplet in the Huntingtin gene. Humans show psychiatric, behavioural and motor disorders. Transgenic animal models are essential to the study of HD since the disease only affects humans. Therefore, the aim of this article was to describe the formation and maintenance of and to validate the progressive neurological phenotype of an R6/1 transgenic mouse colony. To achieve our objective, the colony founder was imported from Jackson Laboratories, and the mice were kept under controlled environmental conditions. The animals were bred at the vivarium of the Instituto Nacional de Neurologia y Neurocirugia Man­uel Velasco Suarez. The R6/1 transgenic mice were successfully bred and showed genetic and phenotypic characteristics similar to the ones previously reported. Our colony is currently established and validated with the condi­tions of our vivarium and has produced more than four generations of R6/1 mice. The establishment of the R6/1 colony and its maintenance through generation is an advantage since it allows us to follow the authenticity of the transgenic mice regarding their phenotypic and motor behaviours. Fur­thermore, these animals can be compared with other transgenic mice that reproduce some of the main characteristics of the disease manifested in hu­mans, making these transgenic R6/1 mice a useful tool for the study of HD. Figure 2. D) Wt mouse with normal fur and weight.
Jatropha (Jatropha curcas) meal is an alternative protein source in poultry nutrition

The application of novel feedstuffs in poultry diets, especially in developing countries, has received attention in recent years. Jatropha (Jatropha curcas) is a non-edible oil seed, and its meal is a rich in protein. Jatropha meal (JM) has been characterised as a potentially useful animal feedstuff due to its high content of crude protein level (35-50%), essential amino acid and mineral content. However, jatropha kernel contains high amounts of phytate, ranging from 7 to 10%, which would require phytase supplementation for it to be used in feeds. Jatropha contains toxic compounds and anti-nutritional factors, including lectin, tannin, saponin, phorbol esters and trypsin inhibitors, which require different treatments (physical, chemical or biological) to make it suitable for poultry diets. As a result of the presence of detrimental compounds, only low levels of jatropha in feed are recommended from animal trials. It may be used to partially substitute soybean meal, but not maize. It has been suggested in the literature that, after physical or chemical treatment of jatropha seed meal, it may have other benefits, including as an immunomodulant and antioxidant, as well as hypocholestermic, antihypertensive, hepatoprotectant, antiretroviral, anti-inflammatory, analgesic and antibacterial properties. It appears that heat and enzyme treated jatropha could be used in poultry diets without detrimental effects on productive and reproductive performance and may promote health status in poultry.
A novel cell segmentation method for developing embryos using machine learning

Cell segmentation is crucial in the study of morphogenesis in developing embryos, but it is limited in its accuracy. In this study we provide a novel method for cell segmentation using machine-learning, termed Cell Segmenter using Machine Learning (CSML). CSML performed better than state-of-the-art methods, such as RACE and watershed, in the segmentation of ectodermal cells in the Xenopus embryo. CSML required only one whole embryo image for training a Fully Convolutional Network classifier, and it took 20 seconds per each image to return a segmented image. To validate its accuracy, we compared it to other methods in assessing several indicators of cell shape. We also examined the generality by measuring its performance in segmenting independent images. Our data demonstrates the superiority of CSML, and we expect this application to significantly improve efficiency in cell shape studies.
In-silico based identification and functional analyses of miRNAs and their targets in Cowpea (Vigna unguiculata L.)

Abstract Cowpea (Vigna unguiculata L.) is an important leguminous plant and a good diet due to presence of carbohydrate and high protein contents. Currently, only few cowpea microRNAs (miRNAs) are reported. This study is intended to identify and functionally analyze new miRNAs and their targets in cowpea. An in-silico based homology search approach was applied and a total of 46 new miRNAs belonging to 45 families were identified and functionally annotated from the cowpea expressed sequence tags (ESTs). All these potential miRNAs are reported here for the first time in cowpea. The 46 new miRNAs were also observed with stable hairpin structures with minimum free energy, ranging from −10 to −132 kcal mol−1 with an average of −40 kcal mol−1. The length of new cowpea miRNAs are ranged from 18 to 26 nt with an average of 21 nt. The cowpea miRNA-vun-mir4414, is found as pre-miRNA cluster for the first time in cowpea. Furthermore, a set of 138 protein targets were also identified for these newly identified 46 cowpea miRNAs. These targets have significant role in various biological processes, like metabolism, transcription regulation as transcription factor, cell transport, signal transduction, growth & development and structural proteins. These findings are the significant basis to utilize and manage this important leguminous plant-cowpea for better nutritional properties and tolerance for biotic and abiotic stresses.
Determinación de los patrones de ácidos biliares en heces de distintas especies del superorden xenarthra (Mammalia)

The analysis of feces is a fundamental tool for field work, especially to identify the presence of certain species in an area. Fecal bile acids and their relative concentration follow patterns that are species-specific, and can be characterized by Thin Layer Chromatography (TLC) and High Performance Liquid Chromatography (HPLC). These techniques have been used for differentiating feces of several mammal species; however, it has never been used for Xenarthra species. In this thesis we identified, by those techniques, the fecal bile acid profile of 11 Xenarthra species, by the analysis of 107 feces from different individuals: Zaedyus pichiy (n=10), Chaetophractus vellerosus (n=5), Chaetophractus villosus (n=57), Dasypus hybridus (n=4), Priodontes maximus (n=2), Tamandua tetradactyla (n=14), Myrmecophaga tridactyla (n=4), Tolypeutes matacus (n=8), Euphractus sexcinctus (n=1), Choloepus didactylus (n=1) and C. hoffmanni (n=1). There were differences between the bile acid patterns of all the species, but not between males and females, nor between wild and captive animals of the same species. TLC was a useful, low cost and rapid technique to analyze fecal bile acid profiles. However, it showed some limitations in the resolution of tauroconjugated bile acids. HPLC was more resolute and sensitive than TLC, allowing separation and identification of tauroconjugated bile acids and of other compounds which were not visualized by TLC. 90% or more of the bile acids were of the type VI, with a structure C24. All species presented DHCA, UDCA, CA, GCA, TCA, TDCA and LCA. Similitude values among fecal bile acid profiles of all species reflected, in a great majority, phylogenetic relationships established for the Superorden Xenarthra. We established, for Xenarthra, that chromatographic determination of fecal bile acids is a precise method for specific identification of feces, being a useful ecological tool. These results are the first for Xenarthra and would be important for future studies about the physiology, ecology and conservation of the group.