Miracle-dz/UniFAR-FTUs huggingface dataset:
Cálculo da distância de reversão e construção de árvores filogenéticas usando a ordem dos genes

Calculating evolutionary distances, such as the reversal distance or the double cut and join distance, between the gene orders of two organisms is a complex combinatory problem. This scenario can be even more complicated if we want to build phylogenetic trees, since most of the approaches in the literature first solves the median problem for three genomes, which was shown to be NP-Hard for various evolutionary models. In this work, we are proposing several evolutionary algorithms for the problem of sorting (unsigned) permutations by reversals, whose output is the reversal distance. These algorithms are based on a simple genetic algorithm, on which were embedded different heuristics such as local search, opposition-based learning, and elimination of breakpoints. Experiments were performed using different types of data (permutations) based on gene orders which were generated artificially (in a random way) and also from biological data. From these algorithms, the ones with the best results for practical cases, that is, permutations of length up to 120, are called as AMBO and AMBO-Híbrido. These results were validated by applying the Friedman and Holm statistical tests. Moreover, a software called HELPHY for building phylogenetic trees was implemented, which takes as input data based on gene order (signed permutations). First, an greedy algorithm was proposed for the small phylogeny problem, whose aim is to calculate the cost (score) of a given tree structure. Then, an approach based on variable neighborhood search was proposed for the large phylogeny problem, whose aim is to explore the search space of tree structures. Results of the experiments showed that HELPHY improved the execution time for finding good scores (reversal distance) for the dataset Campanulaceae; besides, a new tree structure with the best score (double cut and join distance) in the literature was found for the dataset Hemiascomycetes.
Temperature regulating floral bud differentiation in loquat (Eriobotrya japonica Lindl.). Hormonal and genetic aspects.

In loquat, apex of a current shoot changes from vegetative to reproductive stage during summer, i.e. under high temperature conditions. Indeed, just before floral bud differentiation, a decline in the growth rate due to high temperature takes place. The aim of this work is to study the role of this 'summer rest period' on the apex transition from vegetative to reproductive stage. For this purpose 1) sprouting of secondary shoots was promoted at different times, removing the main shoot, before, during and after floral bud differentiation occurred and 2) groups of trees were shifted to a greenhouse under average maximum temperature not exceeding 25 ° C during different periods from June to October. Floral bud differentiation was evaluated. LEAFY (LFY), APETALA (AP1), TERMINAL FLOWERING 1 (TFL1) and FLOWERING LOCUS T (FT1) expression and hormonal content in abscisic acid (ABA), gibberellins (GAs), indoleacetic acid (IAA) and cytokinins (CKs) were analyzed in bud collected during the summer. Results suggest that the date of shoot apex removal determining floral bud differentiation of new shoots, so that the percentage of the new reproductive shoots reduced with the delaying of apex removal. On the other hand, maximum average temperature not exceeding 25 ° C prevented floral bud differentiation. Buds of the trees under indoors conditons displayed lower expression of identity floral genes EjLFY and EjAP1 than buds of trees grown in field. On the contrary, the floral repressor EjTFL1 and EjFT1 gene expressed higher in buds of the trees grown indoors. Time-course of ABA decreased in buds of trees grown in field during studied period while in buds of trees under greenhouse conditions displayed a growing trend. Time-course of GAs, IAA and CKs concentrations did not show remarkable differences between buds of trees growing under field and indoors conditions. Accordingly, 1) secondary shoots emerged from mid- August are unfitness to flower and 2) maximum average tempertature 25±1 °C during the summer prevents floral bud differentiation, enhances ABA biosynthesis, reduces EjLFY and EjAP1 expression and enhance EjTFL1 expression in the apex.
Impact of food environmental factors related to fermented sausages on Salmonella stress and virulence response

The raw meat used for fermented sausages will often contain leftovers from cutting up meat. During handling practices the microbiological food safety may be compromised if too high temperatures allow growth of pathogens such as Salmonella. High counts of Salmonella in exponential growth phase have been shown to be particular infectious compared to Salmonella in stationary phase. Also, adaptation can increase bacterial tolerance to environmental stress and inherent variability exists between exponential and stationary phase cells, with stationary phase cells generally being more resilient. To allow proper blending of ingredients during mincing, the meat has to be frozen and the stress encountered during freezing and thawing and exposure to ingredients as salt and nitrite could impose different bacterial survival depending on the growth phase. The aim of this study was to investigate the survival of exponential and stationary phase Salmonella during freezing and subsequent sausage fermentation. Minced meat was inoculated with exponential or stationary phase Salmonella Typhimurium and frozen at -18oC for up to 35 days. The sausages were fermented at 25oC, and survival of Salmonella was followed during fermentation for 3 days. During both shortand long-term freezing, no reduction of stationary phase cells was observed whereas exponential phase cells were reduced by more than 1.5 log10 units (30 fold). Without starter culture, growth of Salmonella in both growth phases was observed during the course of fermentation reaching comparable maximum population densities. This indicate that a disrupted or delayed fermentation may support growth of Salmonella, regardless of the growth phase of the organism, but also that in spite of a higher growth capacity of exponential cells their level of contamination in the raw material should be more than 30 fold higher than stationary cells to impose a higher risk. In contrast, when applying a commercial starter culture, a
Lineage-Specific Expression and Functional Relevance of MicroRNA Genes in Normal Hematopoiesis.

MicroRNAs (miRs) are a class of a small (~ 22nt) RNAs, which play an important role in the negative regulation of gene expression by base-pairing to complementary sites on the target mRNAs. While it is established that miRs are involved in a variety of basic processes, e.g., cell proliferation and apoptosis, neural development, fat metabolism and stress response, little is known on their expression and function in hematopoiesis. In order to investigate miR expression in erythropoietic (E), megakaryocytic (Mk), granulopoietic (G) and monocytopoietic (Mo) lineages, we have assayed their level at discrete sequential stages of the E, Mk, G or Mo series in unilineage differentiation/maturation cultures of cord blood (CB) CD34+ cells. The analysis was performed using a microarray chip containing as probes gene-specific 40mer oligonucleotides, generated from 161 human and 84 mouse precursors miRs (Liu GC et al., PNAS, 2004). Northern blot analysis confirmed the microarray data. The results indicate that the majority of the analyzed miRs is not expressed in CB hematopoietic cells. However, 49 miRs are expressed at significant levels in CD34+ cells: in most cases the expression level declines during hematopoietic differentiation according to diverse patterns, i.e., the decline may be more or less pronounced, more or less rapid and differ in the diverse hematopoietic lineages. As expression pattern examples, we observed that: (a) miR 223 is strongly downmodulated in the E lineage, whereas its level is not affected or increased in the other series; (b) miR 221 and 222 level sharply declines in the E lineage, while the drop is less pronounced in the Mk, G and Mo series; conversely, (c) miR 17, 20, 106 are downmodulated prevalentely in the G/Mo series, as compared to the E/Mk lineages. Interestingly, cluster analysis indicates that miR expression in hematopoietic cells is sharply different from that observed in CB T lymphocytes. The lineage- and stage-specific pattern of miR expression is of functional relevance. As an example, transfection of miR 222 oligonucleotide into CD34+ cells grown in multilineage clonogenic culture causes a pronounced shift from E to GM colony formation, indicating modulation of the lineage commitment of hematopoietic progenitors. The target genes of miRs expressed in hematopoietic cells are often of pivotal functional significance, e.g., miR 222 targets the kit receptor (N. Felli et al., this Meeting). A single miR may target diverse mRNAs, e.g., miR 222 targets kit, Ets1 and Fli1. Conversely, a single mRNA may be targeted by different miRs, e.g.,, kit is targeted by miR 146, 221 and 222. Noterworthily, the miR expression pattern in primitive hematopoietic cells and their progeny is fully distinct from that observed in primitive mesenchymal and neural cells (i.e., “neurospheres”) and their progeny: this suggests that miR downmodulation during differentiation of primitive cells contributes to tissue-specific gene expression by unblocking translational repression of the target mRNAs.
Ventilatory Currents in the Mantle of Cephalopods

In Octopus and Sepia the inhalant water stream is sucked in to each side of the mantle cavity and passes into the centre of the corresponding gill. From here it runs counter-current to the blood vessels in the secondary gill lamellae and out into a common cavity created by expansion of the posterior part of the mantle. On exhalation the flow runs centrally, bypassing the gills and out through the funnel. This paper deals with the anatomy that ensures this pattern of flow, and with measurement of the P O O2 at various points in the mantle in normoxia and hypoxia. Utilization of oxygen from the respiratory stream is often better than 50% and the P O O2 of the exhalant water is regularly lower than the likely arterial P O O2 .
Genetic variability and evidence of founder effect in Hemiodus orthonops (Characiformes: Hemiodontidae) from the upper Paraná River basin, Brazil

Hemiodus orthonops is a small fish of the Hemiodontidae family, order Characiformes, with a maximum of 25 cm standard length. Until recently, H . orthonops was an endemic species from the Parana-Paraguay basin and it was absent from the upper Parana River basin. Since 2008, it has started to be collected in the upper Parana River, representing up to 10% of catches. Two population samples of H. orthonops from two localities of the upper Parana River basin (Porto Camargo and Porto Figueira) were analyzed using the allozymes electrophoresis technique. Twenty-one enzymatic loci were detected. The population sample from Porto Camargo displayed a genetic variability (He = 0.1061) higher than that from Porto Figueira (He = 0.0580) and homozygote excess in both of them. The F ST value (0.2081) indicated genetic structure. The excess of homozygotes in both samples was probably due to founder effect in the population.
Smad9 is a key player of follicular selection in goose via keeping the balance of LHR transcription

The egg production of poultry depends on follicular development and selection. However, the mechanism of selecting the priority of hierarchical follicles is completely unknown. Smad9 is one of the important transcription factors in BMP/Smads pathway and involved in goose follicular initiation. To explore its potential role in goose follicle hierarchy determination, we first blocked Smad9 expression using BMP typeⅠreceptor inhibitor LDN–193189 both in vivo and in vitro. Unexpectedly, LDN–193189 administration could dramatically suppress Smad9 level and elevate egg production (7.08 eggs / bird, P< 0.05) of animals, and the estradiol (E2) and luteinizing hormone receptor (LHR) level were significantly increased (P< 0.05), but the progesterone (P4) and follicle stimulating hormone receptor (FSHR) mRNA remain unchanged. Surprisingly, Smad9 knockdown notably attenuated (P< 0.05) in E2, P4, FSHR and LHR level in goose granulosa cells (gGCs). Further chromatin immunoprecipitation (ChIP) assay of gGCs revealed that Smad9, served as a sensor of balance, bound to the LHR promoter regulating its transcription. These findings demonstrated that Smad9 is differentially expressed in goose follicles, and acts as a key player in controlling goose follicular selection. SUMMARY STATEMENT To study the hierarchical development mechanism of avian follicle, new strategies can be found to improve the egg production of low-yielding poultry, such as geese.
An exploration of Echinoderes (Kinorhyncha: Cyclorhagida) in Korean and neighboring waters, with the description of four new species and a redescription of E. tchefouensis Lou, 1934

A large collection of kinorhynch specimens from coastal and subtidal localities around the Korean Peninsula and in the East China Sea was examined, and the material included several species of undescribed or poorly known species of Echinoderes Claparède, 1863. The present paper is part of a series dealing with echinoderid species from this material, and inludes descriptions of four new species of Echinoderes , E. aspinosus sp. nov. , E. cernunnos sp. nov. , E. microaperturus sp. nov. and E. obtuspinosus sp. nov. , and redescriprion of the poorly known Echinoderes tchefouensis Lou, 1934. Sensory spots present in the subdorsal positions only. Two middorsal glandular cell outlets type 1 fields) are present on the anterior part of the segment; anteriormost outlet may be covered by pectinate fringe of preceding segment (Fig. 9C). Cuticular hairs and extensions as on preceding segment. Pectinate fringe of posterior segment margin much shorter than on preceding segments.
How many insect species are in your country? The example of Trinidad and Tobago

ABSTRACT Data from well-studied taxa are used together with explicit assumptions and estimates of the world fauna to estimate the number of insect species in Trinidad and Tobago. The median estimate of the world fauna is 4.8 million, while the median estimate of Trinidad and Tobago’s share in the world fauna is 4.8%. Accordingly, it is estimated within broad confidence limits that Trinidad and Tobago harbour 230,400 species. The approach used allows for a refinement of this estimate as new or better data become available.
Metabotropic glutamate receptors in oligodendrocytes and astrocytes in white and grey matter brain regions

I Table of contents II A – List of Tables VIII B – List of Figures X C – Declaration XVI D – Acknowledgements XVII E – Dissemination XVIII F – Glossary of Terms XIX Section 1 General introduction 1 1.1 CNS glial cells 2 1.1.1 General features of astrocytes 3 1.1.2 General features of oligodendrocytes 9 1.1.3 Adult OPCs 11 1.2 Myelination 11 1.3 Neurotransmitter receptors in glial cells 14 1.4 The glutamatergic system 17 1.4. 1 Metabotropic glutamate receptors 19 1.5 Hypoxia/ischaemia and glutamate excitotoxicity 27 1.6 The optic nerve as a model white matter 30 1.7 Hypothesis and aims 33 Section 2 Materials and methods 35 2.1 Animals 36 2.1.1 Declaration 36 2.1.2 Animal Strains 36 2.1.3 Animal Ages 37 2.1.4 Tissue Fixation Protocols 38 III 2.2 Molecular Biology 38 2.2.1 Total RNA Extraction 38 2.2.2 Quantitative real time PCR (qRT-PCR) 41
THE SURVIVAL OF VARIOUS PATHOGENIC ORGANISMS IN FATS AND OILS

OF THESIS THE SURVIVAL OF VARIOUS PATHOGENIC ORGANISMS IN FATS AND OILS The research within this thesis sought to determine the ability of various animal derived fats and plant derived oils to support the survival of several pathogenic cocktails over a multitude of storage times. The Salmonella study explored the survival rate of a four strain Salmonella cocktail in beef tallow, pig lard, duck fat, coconut oil, and extra virgin olive oil over seven days at 26 ̊C and 37 ̊C storage. The animal fats and the coconut oil supported the survival of the bacteria until the conclusion of the study. The Shiga-toxin producing Escherichia coli study explored the survival rate of a five strain STECs cocktail in extra virgin olive oil over seven days at 26 ̊C and 37 ̊C storage. The two Listeria studies explored the survival rate of a four strain Listeria monocytogenes cocktail in extra virgin olive oil over several time periods with different frequencies of sample mixing. In vitro, all genuses showed a 2.5-log cfu/mL to ≥ 7-log cfu/mL reduction in the extra virgin olive oil by the conclusion of the experiments. Extra virgin olive oil was then applied to cooked pork tenderloin, cheddar cheese snack squares, and turkey lunchmeat in hopes of inhibiting the L. monocytogenes cocktail. No reduction was observed.
-An Estimation of CGE Models

The Ramsey rule describes a system of optimal commodity taxation, in which the relative changes in compensated demands caused by extra commodity taxes are the same for all goods to minimize the deadweight loss. Although it contradicts the optimal commodity taxation theory, the uniform commodity taxation is widely implemented in practice. This paper applies Dynamic Computable General Equilibrium Model占to investigate the influences of uniform commodity taxation on labor and capital's prices and supplies, and consumer's utility level. We give a comparison to labor and capital taxation. It shows that increases in commodity taxation do much more harm to economic efficiency than labor and capital taxation.
RBCs as microlenses: wavefront analysis and applications

Developing the recently discovered concept of RBCs as microlenses, we demonstrate further applications in wavefront analysis and diagnostics. Correlation between RBC’s morphology and its behavior as a refractive optical element has been established. In fact, any deviation from the healthy RBC morphology can be seen as additional aberration in the optical wavefront passing through the cell. By this concept, accurate localization of focal spots of RBCs can become very useful in blood disorders identification. Moreover, By modelling RBC as bio-lenses through Zernike polynomials it is possible to identify a series of orthogonal parameters able to recognise RBC shapes. The main improvement concerns the possibility to combine such parameters because of their independence conversely to standard image-based analysis where morphological factors are dependent each-others. We investigate the three-dimensional positioning of such focal spots over time for samples with two different osmolarity conditions, i.e. discocytes and spherocytes. Finally, Zernike polynomials wavefront analysis allows us to study the optical behavior of RBCs under an optically-induced mechanical stress. Detailed wavefront analysis provides comprehensive information about the aberrations induced by the deformation obtained using optical tweezers. This could open new routes for analyzing cell elasticity by examining optical parameters instead of direct but with low resolution strain analysis, thanks to the high sensitivity of the interferometric tool.
Complete genome sequence of an isolate of leek yellow stripe virus from garlic in India.

The complete genome sequence of leek yellow stripe virus (LYSV) isolate AC-50 from garlic in India was determined and the predicted amino acid (aa) sequence was analyzed. The LYSV RNA genome is 10,131 nucleotides (nt) long excluding the poly(A) tail (KP168261) and has a large open reading frame (ORF) encoding a putative polyprotein of 3152 aa with conserved motifs typical of members of the genus Potyvirus in the family Potyviridae. The pretty interesting Potyviridae ORF (PIPO) coding region was identified in the P3 coding region. LYSV isolate AC-50 shares maximum nt and aa sequence identity of 79.9% and 87.2% with a LYSV isolate from Australia (HQ258895) at the full genome and polyprotein level, respectively, and clusters with clade II isolates from China, Mexico, Australia, Brazil and Spain. The P1 coding region of isolate AC-50 was highly variable with an identity range of 48.9-70.9% with other LYSV isolates and a deletion of 204 nt compared to Japanese and Australian isolates. The ratio of nonsynonymous (dN) and synonymous (dS) polymorphic sites suggested that purifying selection dominates in the evolution of LYSV and the mean dN/dS ratio was highest for P1, confirming that this coding region is under less evolutionary constraints.
Age, sex and seasonal variation in the shape and size of erythrocytes of the alpine accentor, Prunella collaris (Passeriformes: Prunellidae)

Abstract The aim of our study was to analyse red blood cells from the high-altitude avian species alpine accentor (Prunella collaris). We caught 79 alpine accentors in the High Tatra Mountains (the West Carpathians, Slovakia) from 2001 to 2008. Blood samples were collected from the vena ulnaris cutanea. The cells and nuclei of juveniles tend to be wider and larger while adults, especially males, tend to have elongated (narrow) cells. The largest erythrocytes were found in winter and the smallest in summer, in June. Red blood cells with larger, elongated nuclei but overall smaller in size occurred at the beginning and the end of the breeding season, while larger, rounded cells with smaller nuclei were found in the middle of the breeding season. This kind of reshaping of erythrocytes of alpine accentors in summer is probably a response to hypoxia and elevated summer temperature in high mountains. As regards the length/width ratio, in August and September, erythrocytes were more elongated (both cell and nucleus) than in the other months. This study is probably the first assessment of seasonal effects on size and shape of red blood cells of bird species permanently living and breeding at high altitudes of the Palearctic mountains.
Application of the marine ecosystem services approach in the development of the maritime spatial plan of Latvia

ABSTRACT The Maritime Spatial Plan for Internal Waters, Territorial Waters and Economic Exclusive Zone of the Republic of Latvia is a long-term spatial planning document, which defines the permitted uses of the sea and conditions for development. Work on maritime spatial planning (MSP) in Latvia was a novel process from different aspects including incorporation of the concept of ecosystem services (ES) into MSP. In the course of the MSP process, marine ES were mapped and assessed, and impacts of proposed spatial solutions for the use of the sea were assessed. The scope of mapping and assessment of ES was limited by data availability and expert knowledge on marine ecosystems. MSP in Latvia was an open and transparent process with an active involvement of different stakeholder groups. Marine ES assessment results were visualized and used during the public consultations to highlight the marine areas providing the most significant social benefits as well as to facilitate debate about potential impacts arising from proposed uses of the sea. The marine ES approach, in a spatially explicit manner, provided stakeholders and policymakers with a strategic framework to address a complex social–ecological system. EDITED BY Joao Rodrigues