Miracle-dz/UniFAR-FTUs huggingface dataset:
A permutation approach for inferring species networks from gene trees in polyploid complexes by minimising deep coalescences

Context and purpose. Due to ubiquity of polyploid species formation in angiosperms, reconstructing the evolutionary history of polyploid complexes is at the forefront of methodological field of activity in molecular phylogenetics and systematic botany. The advent of multilocus species tree reconstruction approaches motivated by next‐generation sequencing methods pave the way to species network inference methods, with which phylogenetics could accommodate to the necessity for reconstructing reticulate relationships among diploids and (allo‐)polyploids in an objective manner, simultaneously taking into account gene tree incongruences caused by incomplete lineage sorting and hybridisation. Methods used. The present contribution describes a relatively simple and fast workflow pipeline for the reconstruction of species networks in polyploid complexes based on multilocus gene trees. It uses a permutation strategy and a parsimony‐based principle in species tree reconstruction (Minimising Deep Coalescences, MDC) for the assignment of homoeologs to parental genomes in allopolyploids, which is a crucial step in species network inference for polyploid complexes. Simulations with varying effective population sizes, different temporal scenarios for diploid or polyploid formations and different types of allopolyploid speciation (sister‐species diploids, non‐sister diploids or polyploidisation under participation of ancestral diploids) are used to assess the reliability of the reconstruction. Main results. Simulations show that the proposed method leads to trustworthy reconstructions if effective populations sizes are not too large and divergences among ancestral taxa are not too shallow. The applicability of our method to a real data set is demonstrated by inferring the reticulate relationships among diploid, tetraploid and hexaploid representatives of the genus Leucanthemopsis (Compositae, Anthemideae) based on gene tree topologies from four nuclear single‐copy genes and two plastidic intergenic spacer regions. Conclusion. The proposed MDC‐based method for species network reconstruction in polyploids is fast and manages to trustworthily reconstruct parentage in polyploidisation events. Concerns with and possible improvements of the described method are discussed.
Phylogeny of amphisphaeriaceae (Sensu stricto) and related taxa revisited based on NRDNA sequences

To further test the phylogeny of Amphisphaeriaceae (sensu stricto) we determined the sequence of 1742 nucleotides from the 18S nrDNA of the type species Amphisphaeria umbrina. The phylogenetic analyses of 18S and ITS nrDNA sequences of the present and previous studies alongside other related ascomycete GenBank retrievals revealed that the Amphisphaeriaceae (sensu stricto) and Xylariaceae are related and should be placed in the Xylariales. Previous conclusions that the Amphisphaeriaceae and Xylariaceae were unrelated were incorrect as DNA sequences obtained from the ITS nrDNA of Apioclypea livistonae, Hypoxylon fragiforme, Myelosperma tumidum and Xylaria hypoxylon contained ambiguities or were contaminated. These sequences are therefore withdrawn from GenBank. With this new data in mind the phylogeny of Amphisphaeriaceae (sensu stricto) is re-visited.
IN VITRO ANTIBACTERIAL ACTIVITIES OF OPUNTIA FICUS INDICA STEM AND FRUIT EXTRACTS USING DISC DIFFUSION METHOD

Objective: Opuntia ficus indica is a medicinal plant belonging to family Cactaceae . It is a species of cactus that has long been a domesticated crop plant important in agricultural economies throughout arid and semiarid parts of the world. The fruit and stem are used to prepare worth added products, fruits jam, squash, drinks, preserve product of pickle, body lotion, shampoo and creams, etc. Methods: For the preliminary study, various extracts of stem and fruit has been used to check the efficacy of antibacterial activity against Bacillus subtilis, Pseudomonas aeruginosa and Escherichia coli bacteria of gram-positive and gram-negative strain respectively using disc diffusion method. Results: The stem and fruit extracts showed various levels of activity on different test organisms. The methanol fruit extracts showed high antibacterial activity against Escherichia Coli, Pseudomonas aeruginosa and Bacillus subtilis compared with other extracts. Aqueous extract of stem and fruit showed less antibacterial activity against the tested bacterial strains. Conclusion: The present study suggests that the methanol extracts of the fruit of Opuntia ficus indica contain compounds that can form the basis for the development of a novel broad-spectrum antibacterial formulation. Keywords: Opuntia ficus indica, Antibacterial activity, Methanol extract, Ethanol extract, Aqueous extract
Demographic analysis of Agave angustifolia (Agavaceae) with an emphasis on ecological restoration

We studied the demography of two populations of Agave angustifolia , one in a preserved tropical dry forest (Xochicalco), and the other one in a pastureland area used for cattle grazing (Tembembe), to test whether populations are likely to thrive on the deteriorated habitats left after cattle ranching. Seed germination and seedling survival experiments were carried out in different natural microsites (i.e. under tree canopies and in open microsites). We built Lefkovitch matrices and carried out prospective (elasticity) and retrospective (Life Table Response Experiments) analyses for both populations. Numerical simulations were performed to project the effect of inflorescences harvest and seedling introduction. Seedling survival and seed germination were highest in Tembembe. Population growth rate was slightly higher in Tembembe (lambda =1.268) than in Xochicalco (lambda =1.208). Prospective and retrospective analyses showed that stasis and growth contributed most to population growth rate and that the differences between the two populations were accounted for a lower fecundity and stasis in Xochicalco compared to Tembembe. Simulations of inflorescence harvest showed that lambda dropped below unity only when all inflorescences were eliminated. The simulated introduction of seedlings produced a substantial rise in lambda. As the lambda values reflect thriving populations at both sites, we suggest that this species could be successfully used in restoration programs.
Desempenho e divergência genética de genótipos de tomate para processamento industrial

O crescimento do mercado de tomate para processamento industrial desperta o interesse de instituicoes nacionais e empresas multinacionais produtoras de sementes de hortalicas no desenvolvimento de novos hibridos. Neste sentido, objetivou-se avaliar o desempenho e a divergencia genetica de genotipos de tomate, quanto as caracteristicas firmeza de fruto, concentracao de maturacao dos frutos, indice de retencao do pedunculo, vigor da planta, cobertura foliar do fruto, sanidade da planta, producao media por planta e teor de solidos soluveis (°Brix). Foram avaliados 53 hibridos, sendo tres testemunhas, hibridos plantados no Brasil. Apenas 12 genotipos e o hibrido comercial H9553 atendem aos criterios necessarios para tomates destinados ao processamento, com base nas caracteristicas: firmeza, concentracao de maturacao dos frutos e ausencia de indice de retencao do pedunculo. Os genotipos 1, 18 e 48 destacam-se quanto ao teor de solidos soluveis, concentracao de maturacao e firmeza dos frutos, respectivamente. A analise de divergencia genetica e agrupamentos revela que os genotipos 1 e 18 apresentam dissimilaridade dos demais genotipos. Enquanto o primeiro demonstrou maiores medias de vigor de planta, cobertura foliar do fruto, sanidade da planta e °Brix, o segundo revelou menores medias firmeza de frutos, concentracao de maturacao dos frutos e °Brix. Os hibridos 3, 6, 8, 14, 24, 37 e 48 apresentam similaridade genetica com o hibrido comercial H9553, o que os caracteriza como potenciais para serem utilizados como novas opcoes no mercado, uma vez que apresentam alta produtividade, qualidade e portanto, aceitabilidade na cadeia produtiva de tomate industrial. Ademais, por apresentarem caracteristicas favoraveis podem ser utilizados para cruzamentos futuros com genotipos de outros grupos, que tambem apresentem caracteristicas favoraveis.
Fibrosis index predicts variceal bleeding and reduces need for nonselective beta-blocker in compensated cirrhosis with initial small esophageal varices without red-color sign

Background Various non-invasive markers predicting hepatic fibrosis are poor predictors of esophageal variceal bleeding (EVB). Elastography performs well but resource-limited. Controversy for small EV prevention also exists. We aim to investigate if a non-invasive marker could predict subsequent EVB within 1 and 2 years in patients with compensated liver cirrhosis (CLC), initial small EV without red-color sign (RCS), without use of non-selective beta-blockers (NSBB) and endoscopic variceal ligation (EVL). This marker would also be tested if it could help reduce use of NSBB, thereby avoiding potential side effects and saving medical costs. Methods In this retrospective cohort study, 6,803 CLC patients fulfilling the inclusion-exclusion criteria were enrolled between 2001 and 2018, and were followed-up for 1 year, 2 years. The primary outcomes were subsequent EVB within 1 and 2 years of enrollment. Another 281 CLC patients with NSBB use were compared for additional outcome analysis. Results In total, 539 patients and 710 patients experienced EVB within 1 year and 2 years, respectively. The fibrosis index (FI) with cut-off value of 3.95 showed a negative predictive value (NPV) of 94.3% and an area under receiver operating characteristic (AUROC) of 62.95% for predicting subsequent EVB within 1 year. The EVB and mortality of patients with FI <3.95 and not taking NSBB were significantly lower than those of the other 3 groups. Similar results were demonstrated within 2 years. Conclusions In CLC patients with initial small EV and no RCS, low FI scores showed a high NPV and moderate AUROC in predicting subsequent EVB and mortalities, signifying clinically non-significant portal hypertension. Patients with low FI scores and not taking NSBB had significantly lowest EVB and mortality. The medical cost savings for cutting NSBB in these patients would be estimated at least $3 million per year in the U.S. Further randomized control trial study needed to validate this screening tool.
Effect of upright positions on the duration of first stage of labour among nulliparous mothers

: Labour pain is auniversal phenomenon.The first stage of labour is longer and painful in both primiparous and multiparous mothers.A quasi-experimental study was undertaken to determine the effect of upright positions (including standing, sitting) on duration of first stage of labour among nulliparous mothers. Sixty nulliparous mothers with single live fetus in cephalic presentation,between 32-41 weeks of gestation were included. The study was carried out in Labour room of Post Graduate Institute of Medical Education and Research, Chandigarh during the period August-September 2011.After selection by purposive sampling method women were consecutively randomly allocated into study (group I) and control (group II) groups, each with 30 patients.Upright positions were given to group-I during active phase of first stage of labour. Progress of labour was assessed through partograph. The mean duration of active phase of 1st stage of labour was 4 hours in Group-I compared to 6 hours in Group-II (P value: <0.001). The mean reduction in duration of active phase of first stage of labour in Group-I was 2 hours. The results of the study concluded that maintenance of upright positions during the first stage of labour reduces the duration of first stage of labour.
Purification and properties of β-D-galactosidase from Bifidobacterium bifidum exhibiting a transgalactosylation reaction

β-D-Galactosidase was extracted by ultrasonic treatment in the presence of Triton X-100. The transgalactosylase (TGase) was separated from other β-D-galactosidases and purified 1720-fold, as measured by the TGase assay. The enzyme was shown to be homogeneous on native PAGE. The complex nature of the enzyme was demonstrated by SDS/PAGE, with four major protein bands of 163, 170, 178 and 190 kDa. The molecular mass was estimated to be 362 kDa by gel chromatography, and the pI was 5.25. The purified enzyme was stable at temperatures below 45 o C and over the pH range from 6.5-8. Lactose hydrolysis by the purified enzyme and by Bifidobacterium bifidum cells took place at the same pH and temperature, at pH 6.5 and 37 o C respectively
Transcriptome Analysis of Zones of Colonies of the ÎflbA Strain of Aspergillus niger

Wild-type colonies of Aspergillus niger grow and secrete enzymes at their periphery when they are grown on an agar medium. Inactivation of the sporulation gene flbA results in colonies that not only secrete proteins at their periphery, but also in central zones. This is accompanied by a more complex secretome, growth throughout the mycelium, and by thinner cell walls. Here, gene expression was studied at the periphery, an intermediate zone, and the centre of wild-type and ΔflbA colonies using whole genome microarrays. Heterogeneity in gene expression was not reduced in ΔflbA colonies when compared to wild-type colonies, despite decreased heterogeneity in zonal secretion, sporulation and growth. It was shown that 1152 genes had a fold change difference in expression ≥ 2, when the averaged expression profiles of the zones of the wild-type were compared with those of ΔflbA colonies. This gene set contained 13 genes predicted to be involved in reproduction, 12 genes involved in cell wall biosynthesis, modification and degradation, 345 genes encoding secreted proteins and 38 genes encoding transcriptional regulators. These genes may account for the differences between wild-type and ΔflbA colonies in zonal growth, sporulation and secretion, and the complexity of the secretome and the thickness of the cell wall. The set of differentially expressed genes, in particular, the genes encoding transcriptional regulators, may be instrumental to improve Aspergillus niger as a cell factory for the production of enzymes
Species specificity as evidenced by scanning electron microscopy of fish scales

Features engraved on the surface of fish scales (normal, regenerated and lateral line) have been elaborated using the magnifying potentials of scanning electron microscopy. An attempt has been made to define structures that can contribute towards species discrimination among four species of Labeo (L. calbasu, L. rohita, L. gonius and L. bata). Normal scale showed distinctness with regard to focus, region below focus, circuli, lepidonts and chromatophores. Distinct regeneration pattern has been observed for all considered species. Lateral line scales with central canal and associated features have also proved their worth for species characterization.
Dégâts et pertes de rendement sur la canne à sucre dûs au foreur Chilo sacchariphagus (Bojer) (Lep.: Pyralidae) dans l'île de la Réunion

Les degâts et les pertes a la recolte dus au foreur de la canne a sucre sont etudies sur la base d'une experimentation insecticide, dans deux exploitations agricoles. Les resultats montrent que ces pertes concernent principalement le rendement en poids de la canne et qu'elles proviennent des perturbations sur la croissance de la plante, en particulier sur la hauteur des cannes dites usinables. En situation de forte infestation, ces pertes peuvent atteindre 40 tonnes par hectare pour un rendement potentiel sous protection insecticide de 160 tonnes/ha. Si une baisse du poids du sucre a ete enregistree sur les parcelles experimentales, il n'a pas ete possible de detecter des pertes en qualite de sucre extrait des cannes. Ces resultats sont discutes dans le contexte particulier de la filiere canne a sucre de cette ile francaise.
T-cell recognition of mycobacterial antigens.

Abstract T-cells play a dominant role in the immune response to mycobacterial infections. Most recognized mycobacterial antigens have been identified by monoclonal antibody techniques and, subsequently, sequenced and isolated by molecular cloning. Both CD4+ and CD8+ alpha beta T-cells, as well as gamma delta T-cells have been shown to participate in anti-mycobacterial host responses. The antigens recognized by CD4+ T-cells have been studied in most detail, with particular interest on proteins actively secreted by tubercle bacilli, on lipoproteins and on heat shock or stress proteins. Peptide mapping of T-cell epitopes of several mycobacterial proteins has suggested that many of their epitopes are recognized permissively in the context of multiple human and mouse major histocompatibility complex (MHC) class II alleles. This finding is encouraging for the development of subunit vaccines and diagnostic reagents.
Proximate analysis, mineral composition, phytochemical contents, antioxidant and antimicrobial activities and GC-MS investigation of various solvent extracts of cactus cladode

Abstract Cladodes Powder Extracts (CPE) are known for their medicinal properties such as being an auxiliary treatment for obesity and gastrointestinal or cardiovascular disorders as well as lowering cholesterol levels. The presented results proved that CPE was found to be a rich source of carbohydrate, ash, moisture and minerals namely Magnesium, Calcium and Zinc which highlighted its good nutritional value. Moreover, the solvent extracts displayed appreciable level of polyphenols, flavonoids and tannins contents compounds which may explain their higher and varied antioxidant and antimicrobial properties. The time-kill assay revealed that the bactericidal concentration required for cladode to kill M. luteus should be less than 3.12 mg/mL (2MIC). Interestingly, GC-MS analyses of ethyl acetate CPE demonstrate the presence of six compounds. The overall data emphasize the nutritional potential of CP as a promising natural preservative and a substitute to the synthetic counterparts and therefore to be consumed in a healthy diet.
The application of probiotics and flaxseed promotes metabolism of n-3 polyunsaturated fatty acids in pigs

ABSTRACT The effect of combining probiotics (Lactobacillus plantarum and Lactobacillus fermentum) with flaxseed (a source of n-3 PUFAs) on the lipid metabolism and long-chain fatty acid profile of conventional piglets after weaning was studied. The levels of total lipids and high-density lipoproteins cholesterol decreased from Day 7 post-weaning, whereas levels of low-density lipoproteins cholesterol, total cholesterol and triglycerides did not change significantly in piglets with supplemented diet. The levels of alpha-linolenic acid (ALA), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) increased seven days post-weaning; however, the levels of dihomogamma-linolenic acid and arachidonic acid (AA) were lower and linoleic acid (LA) higher in synbioticsfed piglets compared with controls. This study demonstrates the efficacy of conversion of ALA to EPA and DHA, where delta-6-desaturase was predominantly used for n-3 polyunsaturated fatty acid synthesis from ALA at the expense of n-6 PUFAs from LA, which caused rapid increase in EPA/AA ratio on Day 14 after weaning. Combination of probiotic cheese and flaxseed is a good dietary supplement for piglets before weaning, helping them to adapt to change in diet more easily by regulating changes in lipid metabolism and vitality, and reducing the likelihood of chronic diseases.
Genera Pleurothallidinarum: an updated phylogenetic overview of Pleurothallidinae

Subtribe Pleurothallidinae with just over 5000 species is possibly the most species-rich of all orchids. It has been growing steadily for more than two centuries, but the last three decades have been especially active in terms of systematic and phylogenetic studies in the group. The growth in species numbers has been accompanied by the marked increase in generic and infrageneric concepts. Nevertheless, Pleurothallidinae are plagued with cases of convergent and divergent morphology, and phylogenetic relatedness is not always apparent. This opens the door to controversial changes in generic circumscriptions that are considered too inclusive by some and too exclusive by others. A grave consequence of these disagreements is the difficulty of assessing which and how many species actually belong to each genus. Here an attempt is made to place generic names among their close relatives as a first step to re-evaluating the whole subtribe .
Estudos sobre dois peixes migratorios do baixo Tocantins, antes do fechamento da barragem de Tucurui

Migratory fish species are generally the most important species for the fishing industry as well as for artesanal fishing. In the lower Tocantins, two species of migratory fish dominate the captures: the mapara (Hypophtlzalmus nzarginatus) and the curimata (Prochilodus nign'cans). These two species were studied before the daming of this river by the Tucurui hydroelectric dam as part of a larger study of commercial fisheries encompassing the Tocantins basin fromthe mouth to Maraba (Para). Based principally on landing records, this study describes the migration cycles of the two species. A classical and simple pattern of migration can be recognized: an upstream movement of immature and adults in the upper part of the distribution area, and then, the reverse or downstream movement of larvae and adults in a dispersion phase. The main difference between these two species lies in the size of distribution area. The mapara is limited to part of the river downstream from the hydroelectric dam of Tucurui, and so, would not be affected by its presence. The curimata has a much larger geographic range ia the Tocantins basin. "lie part of population living downstream will probably be profundly pertubed by the dam due to the blockage of its migratory route. %% Y:.
Çocuk gelişimi

Özel eğitim ile ilgili temel kavramlar, özel eğitimin genel amacı, özel eğitimin önemi, özel eğitim ilkeleri, özel eğitim kurumları ve özellikleri, engele neden olan faktörler, engeli önleme ve erken tanı, özel eğitim alanını sınıflandırma, yaygınlık oranları, dünyada özel eğitim Türkiye’de özel eğitim, görme engellileri tanıma ve sınıflandırma, görme engelliliğin nedenleri, görme engelini önleme ve erken tanı, görme engellilerin eğitimleri, işitme engellileri tanılama ve sınıflandırma, işitme engellilik nedenleri, işitme engelini önleme ve erken tanı, işitme engellilerin eğitimleri, dil ve konuşma güçlüğünü tanılama ve sınıflama, dil ve konuşma güçlüğü nedenleri, dil ve konuşma güçlüğünü önleme ve erken tanı, dil ve konuşma yetersizliği olan çocukların eğitimleri
Understanding the role of Epstein-Barr virus in T- and NK-cell disorders

Epstein-Barr virus (EBV) is associated with B- and epithelial cell malignancies. It is also associated with lymphoproliferations and malignancies of T- and natural killer (NK) cells. The global impact of these conditions is significant, and although rare, they are aggressive and are often resistant to treatment. Diagnosis is often delayed, and evidence-based treatment strategies are limited due to their rarity. Viral gene expression in extranodal T- and NK-cell lymphoma (ENKTL), chronic active Epstein-Barr virus (CAEBV) and haemophagocytic lymphohistiocytosis (HLH) is limited. The viral latent membrane proteins LMP1, LMP2A and LMP2B-TR-TR have growth-transforming properties in B- and epithelial cells. Their effects on cellular gene expression in primary NK cells included pathways involved in cell cycle and stress responses. LMP1 and LMP2B-TR expression by ENKTL and CAEBV cell lines is associated with increased survival in the absence of relevant growth factors, but also with increased susceptibility to apoptosis. This cannot be fully explained by variation in the expression of proteins involved in the intrinsic apoptotic pathway. Finally, we describe PrimeFlow RNA, a new protocol for identification of the EBV-infected lymphocyte subset. Importantly, this technique means that we can begin to identify druggable targets on the EBV-infected cells directly from patient blood samples.