Miracle-dz/UniFAR-FTUs huggingface dataset:
The relationship between population size and rates of language evolution

Languages change over time, and the evolution of languages is similar in many ways to biological evolution. But are all patterns predicted by evolutionary theory also seen in language evolution? One well-known biological pattern is that smaller populations tend to lose genetic diversity, and large populations tend to become more genetically diverse, but the effect of population size on language evolution is highly debated. Do small populations have faster rates of change through greater diffusion of new words, or slower rates of change due to strict language transmission? Do large populations gain words faster through more innovators, or lose faster due to simplification across varied speaker communities? This extract, taken from Welsh’s (2015) Honours thesis, provides the background on the relationship between population size and rate of language change, discusses some of the contrasting hypotheses and methodological techniques and explains the research currently being conducted that attempts to clarify the relationship.
PEA3 Subfamily Transcriptional Activation of Osteopontin, A Transformation-Associated Protein

PEA3, ERM, and ER81 comprise a subfamily ofETS transcription factors that upregulate genes correlated with an increased metastastic potential of tumors. In mouse embryo fibroblast (MEF) cells, PEA3 is required for transformation by activated Ras or Neu, but the means by which PEA3 mediates Ras-transformation is not clear. Osteopontin (OPN) expression is induced upon B-ras-transformation and purified PEA3 can bind the OPN promoter by gel-shift analysis. In this study, OPN expressed higher transcript levels in the wildtype MEF 4 cell line than the PEA3 null MEF 1 cell line and was further characterized as a potential PEA3 target gene by Northern blot analyses and transient transfection studies. Northern blot analyses of4 wildtype MEF (4, 100, 101, 104), 5 FEA3 null MEF (1, 115, B5, B10, B12), and 5 MEF 1 retransformant cell lines that stab'y reexpress PEA3 showed a good correlation between OPN and ERM transcript levels in 9/11 cell lines although at least 2 PEA3 subfamily members were coexpressed in 8/11 cell lines that expressed high OPN transcript levels. This suggested that the PEA3 subfamily additively regulated OPN and that ERM protein was more abundant than PEA3 and ER81 protein levels in the MEF cell lines. The relative PEA3 subfamily protein levels remain to be clarified. Transient transfection assays in the HEK 293-1 C cell line indicated that the OPN promoter was responsive to PEA3 and that the promoter region between -258 to -88 was required for maximal OPNpromoter activity. There are 16 candidate core ETS binding sites in the -777 /+79 OPN promoter which could be responsible for PEA3 subfamily transactivation. The OPN promoter was more active in the MEF 4 cell line than the MEF 1 cell line, corresponding to their relative number of
Elaboração de queijo de coalho probiótico com leite de cabras em dieta para aumento do teor de ácido linoléico conjugado.

A suplementacao da dieta de cabras leiteiras com oleos vegetais, particularmente o oleo de soja, eleva o teor de acido linoleico conjugado (CLA) na gordura do leite, bem como o proprio teor de gordura e o total de acidos graxos (AG) insaturados. Este trabalho teve como objetivo avaliar a sobrevivencia de Bifidobacterium animalis BB12 ao processamento de queijo de coalho a partir do leite de cabras em dieta suplementada com oleo de soja e sem essa suplementacao. com o uso de leite normal e com estrategia para o aumento de acido linoleico conjugado (CLA), verificar se haveria interferencia dos probioticos em relacao a sobrevivencia das bacterias do fermento e avaliacao do potencial de probioticos no soro. As culturas probioticas sao suplementos microbianos que aumentam de maneira significativa o valor nutritivo e terapeutico dos alimentos. Produtos lacteos fermentados sao geralmente considerados como sendo um dos veiculos mais adequados para a administracao de um numero suficiente de bacterias probioticas para o consumidor. O que pode influenciar na viabilidade de bacterias probioticas em queijos, veiculo promissor para estes microrganismos.
Genomes & Developmental Control Computational analysis of EGFR inhibition by Argos

Argos, a secreted inhibitor of the Drosophila epidermal growth factor receptor, and the only known secreted receptor tyrosine kinase inhibitor, acts by sequestering the EGFR ligand Spitz. We use computational modeling to show that this biochemically-determined mechanism of Argos action can explain available genetic data for EGFR/Spitz/Argos interactions in vivo. We find that efficient Spitz sequestration by Argos is key for explaining the existing data and for providing a robust feedback loop that modulates the Spitz gradient in embryonic ventral ectoderm patterning. Computational analysis of the EGFR/Spitz/Argos module in the ventral ectoderm shows that Argos need not be long-ranged to account for genetic data, and can actually have very short range. In our models, Argos with long or short length scale functions to limit the range and action of secreted Spitz. Thus, the spatial range of Argos does not have to be tightly regulated or may act at different ranges in distinct developmental contexts.
Analysis of the role of potential phytohormone and light-signalling components in photosynthetic organisms

This thesis investigates two signalling components of the cyanobacterium Synechocystis sp. PCC 6803, the phytochrome photoreceptor CPH2 and the histidine kinase 12 (HIK12). Knockout and overexpression mutants of both proteins were analysed under distinct growth conditions, focusing on the central carbon metabolism and the transition from fast exponential to slowed-down growth in biomats. The results show a clear regulatory function of both proteins on the central carbon metabolism, which is substantiated in a strongly retarded growth phenotype in the knockout mutants, correlating with a reduced glucose-6-phosphate dehydrogenase activity and changes in the transcript level of cytochrome c oxidase encoding CtaDI. These phenotypes manifest under biomatforming conditions, together with heterotrophic conditions for CPH2 and photomixotrophic conditions for HIK12. Both can be complemented by overexpression of the respective protein in the knockout background. Furthermore, the phytohormone cytokinin and its histidine kinase receptor AHK3 were shown to be involved in plant pathogen defense.
Hipótesis: la agrupación Microcystis aeruginosa Kütz.-Nitzschia palea (Kütz.) W. Sm.-bacterias en la laguna Alalay, Cochabamba, Bolivia es de tipo simbiótico

A bloom of Microcystis aeruginosa Kütz. is reported from the plankton of Alalay Pond, a brackish, urban and highly eutrophic ecosystem. The cyanobacterial colonies were in turn colonized by the diatom Nitzschia palea (Kütz.) W. Sm. This co-occurrence has been previously reported only twice in the literature. As part of the grouping, pleomorphic bacteria were also observed, but their identity could not be established. Field and laboratory observations, as well as a literature revision, suggest that the association of the three types of organisms is symbiotic, assuring a continuous supply of nutrients of exogenous and endogenous origin. Besides obtaining nutrients, Nitzschia palea also benefits from suspension in the upper part of the photic zone, where availability of light and nutrients is higher. In this manuscript, diverse arguments to support the symbiosis hypothesis are explored as a first step towards the physiological and molecular investigation of the association.
Epstein‐Barr virus infection and human malignancies

The Epstein‐Barr virus (EBV) is a herpes virus which establishes a life‐long persistent infection in over 90% of the human adult population world‐wide. Based on its association with a variety of lymphoid and epithelial malignancies, EBV has been classified as a group 1 carcinogen by the International Agency for Research on Cancer. In this article we discuss the evidence supporting an aetiological role for EBV in the pathogenesis of human tumours. The biology of EBV infection will be described with special emphasis on viral transforming gene products. A brief survey of EBV‐associated tumours is followed by a discussion of specific problems. Evidence is presented which suggests that failures of the EBV‐specific immunity may play a role in the pathogenesis of EBV‐associated tumours also in patients without clinically manifest immunodeficiencies. Finally, the timing of EBV infection in the pathogenesis of virus‐associated malignancies is discussed. There is good evidence that EBV infection precedes expansion of the malignant cell populations in some virus‐associated tumours. However, this is clearly not always the case and for some of these tumours there are indications that clonal genetic alterations may occur prior to EBV infection. Thus, whilst there is good evidence to suggest that EBV is a human carcinogen, its precise role(s) in the development of virus‐associated human tumours requires clarification. <
Effect of concomitant application of Pseudomonas fluorescens and Purpureocillium lilacinum in carrot fields infested with Meloidogyne hapla

Abstract Root-knot nematode, Meloidogyne hapla remains a major limiting factor to obtain the estimated yield and quality of carrots in many countries. Effective use of nematode antagonistic bio-agents is a potentially important component of the eco-friendly agro-farming. The effect of seed treatment (ST) with liquid Pseudomonas fluorescens at 100 ml/kg seeds and soil drenching (SD) with Purpureocillium lilacinum at 5 l/ha, singly and jointly, was studied to minimise the damage caused by M. hapla in carrot plants under field conditions. The concomitant application of P. fluorescens ST + P. lilacinum SD reduced 70% of second stage juvenile (J2) population in soil, 71% of female population in root and 74% of egg numbers in roots. The carrot plants from P. fluorescens ST + P. lilacinum SD plots were 36% taller with 39% more leafs and 30% longer leaves than untreated plants. The yield was also 29% higher in concomitant application. There was no significant difference in the root colonisation of P. fluorescens and P. lilacinum in solo and combined treatments. It concludes that the concomitant application of P. fluorescens ST and P. lilacinum SD is more effective to suppress M. hapla infection and enhance the yield of carrot.
Large male bias in collection of Micropterix facetella Zeller, 1851 (Lepidoptera, Micropterigidae)

1 Florida Museum of Natural History, University of Florida, Gainesville, FL, U.S.A. ; dplotkin@ufl.edu 2 Department of Entomology and Nematology, University of Florida, Gainesville, FL, U.S.A. ; nhomziak@ufl.edu, kawahara@flmnh.ufl.edu 3 Canadian National Collection of Insects, Arachnids and Nematodes; Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada; vazrick.nazari@agr.gc. ca
PHF6 modulates the chromatin landscape in B-cell leukemia

Developmental and lineage plasticity have been observed in numerous malignancies, and have been correlated with tumor progression and drug resistance. However, little is known about the molecular mechanisms that enable such plasticity to occur. Here, we describe the function of the Plant Homeodomain Finger Protein 6 (PHF6) in leukemia and define its role in regulating chromatin accessibility to lineage-specific transcription factors. We show that loss of Phf6 in B-cell leukemia results in systematic changes in gene expression via alteration of the chromatin landscape at the transcriptional start sites of Band T-cell specific factors. Additionally, Phf6KO cells show significant downregulation of genes involved in the development and function of normal B-cells, upregulation of genes involved in T-cell signaling, and give rise to mixed-lineage lymphoma in vivo. Engagement of divergent transcriptional programs results in phenotypic plasticity that leads to altered disease presentation in vivo, tolerance of aberrant oncogenic signaling, and differential sensitivity to frontline and targeted therapies. These findings suggest that active maintenance of a precise chromatin landscape is essential for sustaining proper leukemia cell identity, and that loss of a single factor (PHF6) can cause focal changes in chromatin accessibility and nucleosome positioning that render cells susceptible to lineage transition. Thesis Supervisor: Michael Hemann Title: Associate Professor of Biology
Turing-like patterns can arise from purely bioelectric mechanisms

Turing-like patterns can potentially occur in non-neural (non-excitable) tissues through strictly bioelectric processes, without involving transcriptional (gene) regulation, cell migration, or traditional reaction-diffusion mechanisms. Small molecules that gate transmembrane ion channels are often charged and capable of passing through intercellular gap junctions, and their transport under the influence of trans-junction electric fields furnishes a bioelectric feedback loop. We develop an analytically tractable, circuit-based model of this phenomenon and show that it can lead to spontaneous formation of spatial patterns in ligand density and membrane voltage under physiologically plausible conditions. The process is distinct from Turing’s reaction-diffusion paradigm but closely analogous to the spontaneous formation of patterns in colonies of chemotactic bacteria.
Current methods for the prediction of T‐cell epitopes

T‐cell epitopes are specific peptide sequences derived from foreign or own proteins that can initiate an immune response and which are recognized by specific T‐cells when displayed on the surface of other cells. The prediction of T‐cell epitopes is of particular interest in vaccine design, disease prevention and the development of immunotherapeutics. There are two principal categories of predictive methods: peptide‐sequence based and peptide‐structure‐based. Sequence‐based methods make use of various approaches to identify likely immunogenic amino acid sequences, such as sequence motifs, decision trees, partial least squares (PLS), quantitative matrices (QM), artificial neural networks (ANN), hidden Markov models (HMM), and support vector machines (SVM). Structure‐based methods are more diverse in nature and involve approaches such as quantitative structure‐activity relationships (QSAR), molecular modelling, molecular docking and molecular dynamics simulations (MD). This review highlights the key features of all of these approaches, provides some key examples of their application, and compares and contrasts the most important methods currently in use.
Returning to the Wild: Restoring Natural Levels of Immune Function to Laboratory Animals

Aims: The loss of biodiversity from the human body, caused by cultural factors in Western society such as widespread use of sewer systems and water treatment facilities, has resulted in a propensity for aberrant immune function, leading to pandemics of allergy, autoimmunity, (n=8), biota-enriched laboratory rats (n=15) and biota-depleted laboratory rats (n=20). Laboratory rats had approximately 33% of natural IgG and IgM levels compared to wild rodents. Biota enrichment in laboratory animals enhanced levels of natural IgG and IgM to similar extents. Immunization boosted the level to 47%, and co-housing with wild rodents coupled with exposure to helminths boosted the level further to within 72% of levels found in wild rodents. Conclusion: This study indicates that artificial biota enrichment in laboratory animals can significantly enhance immune function that is known to be important for cancer surveillance, wound healing, and a variety of other immune functions.
Partial migration in inexperienced pied avocetsRecurvirostra avosetta: distribution pattern and correlates

Birds exhibit a range of wintering behaviour from strictly migrant to strictly resident species. In partially migrating ones, some birds overwinter within their breeding region (resident birds) while others, although breeding in the same area, winter far away (migrant birds). Accordingly, choosing a wintering region is a key stage in the annual life cycle of birds, notably for inexperienced first-year individuals. The present study aimed to investigate this issue, and more specifically to study the distribution pattern during winter and factors influencing the wintering behaviour of first-year pied avocets Recurvirostra avosetta. Based on a 10-yr ringing study carried out on five of the major French breeding colonies distributed along the Atlantic coast, we showed the coexistence of different wintering tactics. The resident tactic was predominant (approximately 86% of the 575 birds re-sighted), while the other birds adopted migration. Among resident individuals, two different tactics occurred: 43% of birds overwintered within their natal colony, whereas the others wintered in another site located at relatively close proximity along the French Atlantic coast. Hatching date was a consistent predictor of all wintering tactics. More specifically, the probability of migrating was the highest for early-hatched birds, and for resident ones, the probability of wintering within their natal colony rather than in another French site was the highest for both median- and late-hatched individuals. In addition, a colony effect was demonstrated for resident birds. Several biological interpretations, including social system, variations in both individual body condition and habitat quality, were put forward to explain these correlates.
Heat Stress Biomarker Amino Acids and Neuropeptide Afford Thermotolerance in Chicks

With global warming, heat stress is becoming a pressing concern worldwide. In chickens, heat stress reduces food intake and growth, and increases body temperature and stress responses. Although it is believed that young chicks do not experience heat stress as they need a higher ambient temperature to survive, our series of studies in young chicks showed that they are sensitive to heat stress. This review summarizes current knowledge on amino acid metabolisms during heat stress, with special emphasis on the hypothermic functions of l-citrulline (l-Cit) and l-leucine (l-Leu), and the functions of neuropeptide Y (NPY) in terms of body temperature and heat stress regulation in chicks. Amino acid metabolism is severely affected by heat stress. For example, prolonged heat stress reduces plasma l-Cit in chicks and l-Leu in the brain and liver of embryos. l-Cit and l-Leu supplementation affords thermotolerance in young chicks. NPY expression is increased in the brains of heat-exposed chicks. NPY has a hypothermic action under control thermoneutral temperature and heat stress in chicks. The NPY-sub-receptor Y5 is a partial mediator of the hypothermic action of NPY. Further, NPY stimulates brain dopamine concentrations and acts as an anti-stress agent in heat-exposed fasted, but not fed chicks. In conclusion, young chicks can serve as a model animal for the study of heat stress in chickens. l-Cit, l-Leu, and NPY were identified as biomarkers of heat stress, with the potential to afford thermotolerance in chicks.
A phosphorylation site in the Ftz homeodomain is required for segmentation in Drosophila

The Drosophila homeodomain-containing protein Fushi tarazu (Ftz) is expressed sequentially in the embryo, first in alternate segments, then in specific neuroblasts and neurons in the central nervous system and finally in parts of the gut. During these different developmental stages, the protein is heavily phosphorylated on different subsets of Ser and Thr residues. This stage-specific phosphorylation suggests possible roles for signal transduction pathways in directing tissue-specific Ftz activities. The objective has been the testing of the importance of a single phosphorylation site for Ftz activity in the embryo. This was done by mapping Ftz phosphorylation sites, mutating the relevant Ser or Thr residues to Ala and Asp, and then testing the ability of the mutated proteins to rescuepz mutant embryos. My analysis has focused on T263, which is in the N-terminus of the Ftz homeodomain. This site is phosphorylated in vitro by Drosophila embryo extracts and by purified protein kinase A. In the embryo, mutagenesis of this site to the non-phosphorylatable residue Ala results in segmental defects. Conversely, replacement of T263 by Asp, which is also non-phosphorylatable, but which successfully mimics phosphorylated residues in a number of proteins, rescues the segmental phenotype. This suggests phosphorylation of Ftz on residue T263 is required for function in the ectoderm. In the CNS however, both T263A and T263D mutant proteins function normally, indicating that the requirement for T263 phosphorylation is stage-specific. In terms of molecular properties, mutation of T263 to Ala and Asp does not affect Ftz DNA binding activity in vim, nor do the mutations affect transcriptional activity in transfected S2 cells. I conclude that T263 phosphorylation is most likely required for a homeodomain-mediated interaction with an embryonically expressed protein.
Objective Classification of Neocortical Pyramidal Cells

A consensus on the number of morphologically different types of pyramidal cells (PCs) in the neocortex has not yet been reached, despite over a century of anatomical studies. This is because of a lack of agreement on the subjective classifications of neuron types, which is based on expert analyses of neuronal morphologies: the shapes of somata, dendrites, and axons. Even for neurons that are visually different to non-experts, there is no common ground to consistently distinguish morphological types. We found that objective classification is possible with methods from algebraic topology, and that the dendritic arbor is sufficient for reliable identification of distinct types of PCs. We also provide a solution for the more challenging problem of whether two similar neurons belong to different types or to a continuum of the same type. Using this scheme, we objectively identify seventeen types of PCs in the rat somatosensory cortex. Our topological classification does not require expert input, is stable, and helps settle the long-standing debate on whether cell-types are discrete or continuous morphological variations of each other.
Wild Medicinal Species Traded in the Balsas Basin, Mexico: Risk Analysis and Recommendations for Their Conservation

The Balsas River Basin (BRB) area is the major source of wild medicinal plants commercially sold in Mexico; thus, the region is important in the conservation of these high-demand resources. We studied wild medicinal plant species extracted from the BRB to document the species richness of traded plants and analyze the commercialization dynamics and socioecological vulnerability. We constructed a database of the medicinal plant species traded in the BRB and we developed a risk index from 14 different ethnobotanical, socioeconomic, and ecological variables to assess the vulnerability of each species. The medicinal flora that are traded in the BRB include 257 species, 176 genera, and 83 families. The use of 91% of these species is unregulated by the government. Tropical deciduous forests contribute the greatest number of taxa (38.5%) and herbs are the most harvested plants (45.9%). Less than 5% of these species are protected by national and international regulations. The highest-risk category primarily consists of tree species with the greatest number of uses and plant structures harvested and sold in the largest number of local and regional markets. Due to high commercial demand in the BRB, intensive harvesting is not compatible with conservation. Therefore, public policies that regulate trade and local practices to protect and preserve medicinal plant species must be developed. These policies should maintain people's livelihoods, especially in regions with high marginalization but great biological and cultural richness, such as the BRB.