Miracle-dz/UniFAR-FTUs huggingface dataset:
Biogeography of the Freshwater Decapods in the La Plata Basin, South America

Abstract The distributions of freshwater fauna in the La Plata Basin, including decapods, are dynamic; their actual distributions depend on not only their movements but also on environmental fluctuations. The La Plata system has a diverse range of environments, which are colonized by crustaceans with complex evolutionary histories. Our aim was to elucidate the distribution patterns and relationships of current freshwater decapod fauna in terms of the different geo-climatic processes at work in the La Plata system. We recognized 13 zones based on their unique environmental characteristics. Species lists were assembled through field samples, examination of museum collections, and literature analysis. Faunistic similarity was evaluated using the Jaccard index and cluster analysis. A parsimony analysis of endemicity (PAE) was applied to determine the most parsimonious of all possible tree topologies. There were 69 species freshwater decapods analyzed in the La Plata Basin. The Mata Atlántica (MA), Paraná Superior (PS), and Uruguay Superior (US) zones are distinguished by their high species richness values, whereas the western and southern basin regions exhibit the lowest species richness values. The Paraguay-Pantanal (PP) and Paraguay-Pilcomayo-Bermejo (PPB) zones share some prawn taxa with the Amazon Basin. The eastern zones of the La Plata Basin were grouped by the presence of several species of the genera Parastacus, Aegla, and Trichodactylus. The northern, central, and western zones were characterized by species of the genera Dilocarcinus, Sylviocarcinus, and Zilchiopsis. According to the PAE analysis, two major zones were recognized in relation to the presence of freshwater decapods (eastern and western-central zones). In the western-central zones, three sub-areas were identified; one shares species with the Amazon basin the others have a relationship with the eastern and northern regions and represents a region that is strongly influenced by a temperate climate and therefore possesses diminished species richness values.
Contex-Based Features for Semantic Mapping of Words

It is introduced a semantic coding of words based the SVD technique for generating a semantic space in which words are then mapped. The proposed technique is based on the introduction of a link energy formula related to digrams frequency. To test the effectiveness of the porposed approach, the english translation of the set of Grimm Fairy Tales has been analyzed and a bi-dimensional visual representation has been obtained using the Sammon projection algorithm.
Further evidence for feedback regulation of gibberellin biosynthesis in pea

In shoots of the garden pea (Pisum sativum L.), the main bioactive gibberellin (GA) is GA 1, which is synthesised from GA 20 by 3I²-hydroxylation. Gibberellin A 20 is produced from GA 19, as part of the process known as GA 20-oxidation. Because these steps are thought to be negatively regulated by GA 1, we compared the metabolism of labelled GA 19 and GA 20 in mutants deficient in GA 1, with that observed in isogenic wild-type (WT) plants. There was a large and specific increase in the 3I²-hydroxylation of labelled GA 20 in the GA 1-deficient (dwarf) mutants, compared with the WT. Metabolism experiments did not provide convincing evidence for feedback regulation of 20-oxidation, possibly because GA 19 appears to be metabolised rapidly, even in WT pea shoots. Both 3I²-hydroxylase and 20-oxidase transcript levels were markedly higher in the mutants than in isogenic WT lines. The results support previous suggestions that both biosynthetic steps are feedback-regulated by GA 1 in pea.
Changes in sensitivity of Cercospora beticola populations to sterol-demethylation-inhibiting fungicides during a 4-year period in northern Greece

From 1996 to 1999, single-lesion isolates of Cercospora beticola, the cause of sugar beet leaf-spot disease, were obtained from sugar beet fields with different histories of use of the sterol-demethylation-inhibiting (DMI) fungicides, flutriafol and difenoconazole in Amyndeon, Imathia and Serres in northern Greece. Fields were sampled twice per year, before and after the within-season exposure of fungal populations to applications of DMI fungicides. The sensitivity to flutriafol and difenoconazole of 150 isolates of C. beticola per sampling site and sampling period was determined. In areas with a history of prolonged DMI use, sensitivity to both fungicides decreased gradually over the study period, suggesting directional selection on a polygenically controlled character. The size of the shift in a particular year seemed to depend on which fungicide was applied during that year in the fields, suggesting only partial cross-resistance between flutriafol and difenoconazole. Within the Serres population there was a significant correlation (r = 0·57) between sensitivities to flutriafol and difenoconazole. Decreased sensitivity was the result of the selection of less sensitive strains during the spraying periods. The frequency of such strains significantly increased through the years and finally reached values of 32% for both flutriafol and difenoconazole in the Serres population and 20 and 16%, respectively, in the Imathia population, at the end of 1999. The high frequency of less sensitive strains in the Serres population was related to a slight decline in DMI field performance in this area during that year. However, the frequency of the less sensitive strains was not stable. The sensitivity assays carried out early in each season, before the DMI spray applications, showed that the mean sensitivities of the populations were significantly higher (P < 0·05) than those of the previous autumn. These changes were mainly the result of a significant decline in frequency of the less sensitive strains, indicating that such strains have either reduced saprophytic survival ability during the overwintering period or lower competitive ability in the absence of DMI treatments.
Novel Peptide Ligands for Integrin α6β1 Selected from a Phage Display Library

: Integrin alpha 6 beta 1 is a major adhesion receptor for the basement membrane, specifically binding to laminin-1. To identify the peptide sequences recognized by alpha 6 beta 1, we screened a 15-mer phage display library by panning with alpha 6 beta 1 purified from human placenta. DNA sequencing of 73 randomly picked phage revealed that three clones were dominantly enriched after repeated panning with alpha 6 beta 1. None of the peptide sequences displayed on these phage showed significant homology to laminin-1. A synthetic peptide modeled after the sequence displayed by one of these phage, designated P3, was found to strongly inhibit the binding of laminin-1 to alpha 6 beta 1. This inhibitory effect of the P3 peptide seems to be specific for alpha 6 beta 1, since it did not affect the binding of fibronectin to integrin alpha 5 beta 1. A synthetic peptide with a scrambled P3 amino acid sequence barely inhibited the binding of laminin-1 to alpha 6 beta 1. When coated on a substratum after conjugation with bovine serum albumin, the P3 peptide was capable of promoting cell spreading in an alpha 6 beta 1-dependent manner, although the peptide with the scrambled sequence showed activity similar to that of a control peptide. These results taken together indicate that the P3 peptide is a novel ligand for integrin alpha 6 beta 1 with potent cell spreading activity.
Sodium Accumulation in Leaves of Triticum Species That Differ in Salt Tolerance

The ability to limit the accumulation of Na+ in leaves may be an important mechanism in salt tolerance because the excessive accumulation of Na+ causes the premature senescence of leaves. The objectives of this study were to test the importance of Na+ accumulation rates in determining salt tolerance and to determine whether observed genotypic differences in leaf Na+ accumulation are linked to rates of leaf expansion. Six salt-sensitive and salt-tolerant genotypes of Triticum tauschii (Coss.) Schmal. , T. aestivum L. and T. turgidum L. were grown in 150 mol m-3 NaCl and harvested at regular intervals over approximately 3 weeks. Na+ concentrations and leaf growth were measured in individual leaf blades over this time. The salt-tolerant accessions all had lower rates of Na+ accumulation than the salt-sensitive. This was not due to genotypic differences in growth rates: it was independent of the overall growth rate (vigour) of the genotypes, and the growth phase of individual leaves. In the growing leaf, the rate of Na+ accumulation was lower in salt-tolerant genotypes both during and after the phase of expansion. Leaf longevity was greater in the salt-tolerant genotypes. In one salt-sensitive genotype, the maximum Na+ concentration was much lower than that of all the other genotypes. Two mechanisms of salt tolerance appear to be operating in Triticum genotypes. One is a lower rate of Na+ accumulation which is independent of the growth of individual leaves and therefore probably regulated by some root process. The second is ion compartmentation within leaves, which enhances the ability to tolerate high concentrations of Na+ in leaves.
Fundamentals of food biotechnology

Part 1 Underlining principles of biochemistry, microbiology, and biochemical engineering: principles of biochemistry principles of microbiology principles of biochemical engineering. Part 2 Applications of biotechnology to food products: yeast-based processes and products bacteria-based processes and products other microorganism-based processes and products. Part 3 Other potential applications of the new technology: plant biotechnology animal biotechnology biosensors for biological monitoring of foods waste management and food processing food safety and new biotechnologies.
Germination of Hymenachne amplexicaulis and H. acutigluma under contrasting light, temperature and nitrate regimes

A laboratory experiment compared germination of the invasive exotic grass Hymenachne amplexicaulis (Rudge) Nees and the native H. acutigluma (Steud.) Gilliland. Seeds of both species were exposed to combinations of light (constant dark, alternating dark/light or constant light), temperature (constant or alternating) and nitrate regimes (with or without the addition of KNO3). Three seed lots of H. amplexicaulis (fresh, two adn four months old) and one of H. acutigluma (fresh seed) were tested. A significant temperature x light x nitrate x seed lot interaction occured. At a constant temperature very few seeds of either H. amplexicaulis or H. acutigluma germinated, regardless of the light regime or addition of KNO3. Generally, maximum germination occurred under a combination of alternating temperature, the presence of light (either constant or alternating) and the addition of KNO3. The exception was four month stored H. amplexicaulis seed, which reached maximum germinaction without the need for KNO3. Fresh seed of both H. amplexicaulis and H. acutigluma exhibited similar germination requirements. These findings suggest that conditions that buffer seeds from light and/or temperature fluctuations could reduce germination and possibly extend the life of seed banks of both H. amplexicaulis and H. acutigluma. Conversely, for land managers trying to control the exotic H. amplexicaulis, activities that create more favourable conditions for germination may help deplete seed banks faster.
Automatic Security Protocol Analysis with Tamarin-Prover

In the face of attacks against cryptographic protocols both of practical and theoretical kind and with increasing frequency, we are interested in improving the trustworthiness of security proofs. This part of security analyses is prone to human error to a special degree because mistakes in mathematical proofs are often oblique and thus hard to spot. Moreover, the sheer complexity of protocols and their extensions and the consequential length of security proofs are severe bottlenecks. This motivates the use of automated security analysis tools and proof assistants as a solution to this problem. We focus on an evaluation of Tamarin-Prover while working towards an automatic security analysis of the Internet Key Exchange version 2 which is used in IPsec.
Morphological and genetic differences in ecologically distinct populations of Petrosia (Porifera, Demospongiae)

The taxonomic status of two sponge tnorphotypes living sympatrically in Mediterranean caves and usually ascribed to Petrosia ficiformis was elucidated on the basis of morphological, morphometric and genetic features. The two morphotypes, spherical and cylindrical, showed differences in the shape and size of spicules and in the morphology of the aquiferous system. Electrophoretic analyses demonstrated that the two morphotypes are reproductively independent and so they should be considered as distinct biological species. The spicular features allow attribution of the cylindrical morphotype to P.ficiformis and the spherical one to P. clavata. For these two species parasympatric speciation is proposed.
Overexpression of Oshsp16.9 Gene Encoding Small Heat Shock Protein Enhances Tolerance to Abiotic Stresses in Rice

Plants have adapted the ability to respond to various abiotic stresses such as high salinity, osmotic stress, high and low temperatures, and drought in order to survive. Small heat shock proteins (sHsps) play important and extensive roles in plant defenses against abiotic stresses. Herein, we cloned an sHsp gene from the rice, which we named Oshsp16.9 based on the molecular weight of the protein. Real-time PCR analysis showed that expression of the Oshsp16.9 gene was rapidly and strongly induced by stresses including high-salinity (250 mM NaCl), osmotic stress (300 mM mannitol), 100 μM ABA, cold (4°C) and heat (45°C). Subcellular localization assay indicated that Oshsp16.9 was localized specifically in the cytoplasm. In addition, overexpression of Oshsp16.9 in rice conferred tolerance of transgenic plants to salt and drought stress. Taken together, these results suggest that the Oshsp16.9 gene is an important determinant of stress response in plants.
Seasonal population fluctuations of the diamondback moth, Plutella xylostella (L.) (Lep.: Plutellidae) on different cauliflower cultivars

The diamondback moth, Plutella xylostella (L.) (Lep.: Plutellidae) is one of the most important pests of cruciferous plants throughout the world. In recent years, it has been identified as a serious pest of the cauliflower fields in Tehran province. Resistance of P. xylostella to all main groups of insecticides has been recorded and it is ranked in the 20 most resistant pest species reported until now. According to many researchers, to solve the problem of pest resistance to chemical pesticides, an integrated pest management programme should be used. Despite this condition, it seems that the use of resistant cauliflower cultivars is an appropriate policy for integrated control of the pest in the field. In order to identify the most resistant cultivar in the field, eight cauliflower cultivars in a completely randomised design with five replicates were planted at the Shahed University research field (south of Tehran). Density of eggs, larvae and pupae of P. xylostella were measured every 10 days in these cultivars. The results showed that there is no significant difference between numbers of eggs per plant on different cultivars. But number of larvae and pupae per plant were significantly different among different cultivars. Smilla and Snow mystique cultivars had the highest number of larvae and pupae. On the other hand, Buris and Snow crown cultivars had the lowest number of pupae and Snow crown and SG cultivars had the lowest number of larvae per plant. According to the results, the Buris and Snow crown cultivars had the lowest infestation and had a kind of resistance to pest.
The rye genome in wheat breeding

Merker, A. 1984. The rye genome in wheat breeding. —Hereditas 100: 183–191. Lund, Sweden. ISSN 0018–0661. Received June 10, 1983 Five different BC1F3-populations from the cross (hexaploid triticale × bread wheat) bread wheat× were cytologically analysed for the presence of rye chromatin by means of a Giemsa C-banding technique. The populations contained from 13 to 30 per cent plants with detectable rye transfers. Different rye chromosomes appeared in different frequencies. IR being the most frequent and 7R the least. 5R and 7R appeared only in monosomic dose, the others in disomic also. The populations had high frequencies of aneupioids. Of the plants with rye transfers. 60 per cent were aneuploid and. of those without, 47 per cent were aneuploid. Average fertility for the group with rye transfers was lower than for the group without. Fertile disomic substitution lines with the rye chromosomes IR. 2R. 3R and 6R have been isolated from the material. The results are discussed in relation to the extension of the gene pool of bread wheat and in relation to wheat breeding.
Control of herpes simplex virus type 1 latency in human trigeminal ganglia

Herpes simplex virus type 1 (HSV-1) is a double-stranded DNA virus that infects humans and, after a primary lytic infection, establishes lifelong latency in the sensory neurons of the trigeminal ganglia (TG). HSV 1 latency is accompanied by a chronic immune cell infiltration of the TG, the infiltrate being mainly composed of CD8+ T cells. These T cells are believed to control viral latency, but cellular and viral factors like viral microRNAs are also considered to play a crucial role in the establishment and maintenance of viral latency. In the present work, it was investigated whether the tissue-infiltrating T cells are clonally expanded, which would indicate that these T cells are activated by antigen. By applying complementarity determining region 3 (CDR3) spectratyping and immunohistochemistry, several clonal expansions were identified in the TG-resident T cells. In addition, several T cells were present that seemed to be unspecific bystander T cells. Strikingly, some expanded T cell clones were present in the right and left TG of the same individual. This strongly suggests that similar antigens are present in both TG and that the infiltration of immune cells to the TG is driven by antigen. The morphology of the TG was investigated by immunohistochemistry and in situ hybridiza¬tion. Analysis of the distribution of T cells throughout the TG provided puzzling results: unexpectedly, most neurons surrounded by T cells did not harbour the only known prominent transcript during latency, the latency associated transcript (LAT). Whether these neurons do actually harbour latent virus was addressed by a combination of LAT in situ hybridisation, T cell immunohistochemistry, and single cell analysis of laser microdissected sensory neurons by PCR. This analysis revealed that only LAT+ neurons were harbouring HSV 1 DNA and viral microRNAs. Also, mRNA for a viral gene product was only detected in LAT+ neurons. All analysed LAT– neurons were devoid of viral microRNAs and DNA of HSV 1. DNA of HSV 2 or varicella-zoster virus (VZV) was not detected in any of the excised neurons. Alto¬gether this indicates that in the vast majority of infected human neurons, HSV 1 latency is not directly controlled by T cells, but rather by cellular or viral factors like the miRNAs. Our data suggest that CD8+ T cells only come into action if these mechanisms are overrun.
Outcome, Hemodynamic and Genetic Assessment in Patients with Functionally Univentricular Hearts after the Fontan Operation at Young Age

textabstractThe incidence of CHD is about 0.8%, meaning 12.5 cases per 1000 life births. Errors in the morphogenesis of a normal four-chambered heart result in congenital heart disease (CHD), the most common form of birth defects. Heart formation is a complex morphogenetic process that requires correct function of 1) various embryological developmental regions (including the heart fields and the neural crest); 2) complex looping patterns resulting from selective growth and cell death, and 3) numerous regulatory and structural genes. Disruption of these processes cumulates in various forms of CHD. In the minority of cases of CHD, there is a chromosomal or monogenetic defect. The majority of cases of CHD, however, are of multifactorial origin, meaning a complex interplay of genetic and environmental factors (i.e. a polygenic model). Up until now, several candidate genes have been identified in patients with defects of cardiac septation, conotruncal anomalies and/or underdevelopment of one of the ventricles. In patients with a so called functionally univentricular heart, all these defects can be combined in one heart. Data on the embryological development of univentricular lesions are scarce, as
Correlation of Visual Quality Grading and SPAD Reading of Green-Leaved Foliage Plants

Abstract Green-leaved foliage plants are valued for their leaf forms and sizes but mainly for their foliar greenness. Evaluation of the quality of these plants has been based primarily on visual grading, which often brings biases, depending on the appraisers. The objective of this study was to evaluate the possibility of using the SPAD-502 as an instrument for estimating plant quality. Ten green-leaved foliage plant species were grown in shaded greenhouses and treated with either a water-soluble fertilizer or a controlled-release fertilizer, each at four nitrogen (N) rates. Six months later, mature leaf thickness was measured and visual quality graded. After the greenness of the mature leaves was measured with the SPAD-502 meter, leaf chlorophyll was extracted using dimethyl sulphoxide, and chlorophyll content was determined. Results showed that leaf thickness ranged from 0.19–0.66 mm among the 10 species but had no apparent effect on either SPAD readings or chlorophyll content. Visual-quality grades of the plants were closely correlated with the SPAD readings (r ≥ 0.84). Highly significant linear relationships (r 2 ≥ 0.87) were found between SPAD readings and chlorophyll a, b, or total chlorophyll content. Thus, the SPAD-502 could be used as an instrument to provide quick, nondestructive, and objective estimation of quality for green-leaved foliage plants.
Real-time PCR in microfluidic devices

A central method in a standard biochemical laboratory is represented by the polymerase chain reaction (PCR), therefore many attempts have been performed so far to implement this technique in lab-on-a-chip (LOC) devices. PCR is an ideal candidate for miniaturization because of a reduction of assay time and decreased costs for expensive bio-chemicals. In case of the “classical” PCR, detection is done by identification of DNA fragments electrophoretically separated in agarose gels. This method is meanwhile frequently replaced by the so-called Real-Time-PCR because here the exponential increase of amplificates can be observed directly by measurement of DNA interacting fluorescent dyes. Two main methods for on-chip PCRs are available: traditional “batch” PCR in chambers on a chip using thermal cycling, requiring about 30 minutes for a typical PCR protocol and continuous-flow PCR, where the liquid is guided over stationary temperature zones. In the latter case, the PCR protocol can be as fast as 5 minutes. In the presented work, a proof of concept is demonstrated for a real-time-detection of PCR products in microfluidic systems.