Miracle-dz/UniFAR-FTUs huggingface dataset:
Amplification of c-myc Locus is Independently Associated with the Deletions of Chromosome 8p in Breast Carcinoma

Abstract Attempts have been made in this study is to find out the mechanism of c-myc gene activation in breast carcinoma (CaBr) by analyzing alterations (rearrangement/amplification) in the ~580 Kb surroundings of this gene. The alteration in the c-myc locus was correlated with the deletions in chromosome (chr.) 8p to find if there is any association between the two phenomenons. The c-myc locus alteration was analyzed by Southern hybridization using the pal-1/ c-myc/ mlvi-4 probes. Overall, amplification in the c-myc locus was seen in 26% of the samples with 22% in the pal-1 region, 19% in the c-myc gene and 7% in the mlvi-4 region. This indicates that the c-myc gene activation may occur due to the amplification in the pal-1 region located 550 Kb 5’ and mlvi-4 region located 20 Kb 3’ of c-myc. About 42% of the samples showed loss of heterozygosity (LOH) in ≥ 40% of the microsatellite markers tested. Atleast 21% of the samples showed co-alterations in both arms of chr.8. No significant association was observed between the amplification in the c-myc locus and deletions in chr.8p. Thus the deletions in chr.8p and the amplification in the c-myc locus are independently associated with the development of CaBr.
Chemical Screening of Medicinal Plants used in the Traditional Pharmacopoeia of Niger

AbstractThe demand for inexpensive treatment methods to meet primary health care needs in Niger has increased interest in traditional medicine. A survey of plants used by traditional healers was under taken. A total of 185 plant samples from 59 species (31 families) were screened for chemical compo sition. The following constituent distribution was observed (number of samples): flavonoids (79); steroids (78); tannins (61); alkaloids (41); quinones (34); cyanoglucosides (4).
Ecology and Control of Russian Thistle (Salsola Iberica) after Spring Wheat Harvest

Abstract Russian thistle is the most problematic broadleaf weed for spring-sown crops in the low-precipitation (< 340 mm yr−1) region of the inland Pacific Northwest of the United States. A 6-yr field experiment was conducted at Lind, WA, to evaluate three postharvest control strategies for Russian thistle in continuous annual spring wheat. Postharvest treatments were (1) tillage with low-disturbance overlapping undercutter V-blade sweeps; (2) paraquat + diuron at the labeled rate, which is widely used by farmers; and (3) an untreated check (letting Russian thistle grow unhindered). The undercutter V-sweep consistently killed all Russian thistle with essentially no residue burial, and no seed was produced. In contrast, the paraquat + diuron treatment halted Russian thistle dry biomass production, but plants continued to extract soil water and produce an average of 310 seeds m−2 on the lower branches. In the check, Russian thistle produced an average of 700 kg ha−1 postharvest dry biomass and 5,670 seeds m−2. The undercutter V-sweep treatment had significantly more water in the 180-cm soil profile at time of wheat harvest, after a killing frost in October, and in mid March as well as greater spring wheat grain yield compared with the herbicide and check treatments. Results show that postharvest tillage with an undercutter V-sweep consistently achieved 100% control, retained ample wheat residue on the surface to control erosion, and was by far the most effective treatment in this experiment. Nomenclature: Diuron, paraquat, Salsola iberica Sennen & Pau SASKA, wheat, Triticum aestivum L
The Correlation Between Biofilm Formation and Drug Resistance in Nosocomial Isolates of Acinetobacter baumannii

Background: Acinetobacter baumannii has become a major cause of hospital-acquired infections due to its resistance to common antibacterial agents. Biofilm formation is a well-known pathogenic mechanism involved in A. baumannii infections. Objectives: The aim of this study was to determine the association between biofilm formation and antibiotic resistance, production of AmpC and Extended-Spectrum β-lactamases (ESBL) in clinical isolates of A. baumannii collected from two hospitals of Tehran. Materials and Methods: Sixty isolates of A. baumannii were employed of which, 30 were burn and 30 were non-burn isolates. Biofilm formation was measured by the microtiter plate assay. The production of AmpC was detected by the AmpC disc test with cloxacillin, and ESBL production was determined using the double disc synergy test. Results: Biofilm production occurred in 61.7% of the isolates among which, non-burn isolates (59.5%) produced more biofilm compared to the burn strains (40.5%). Multidrug resistance was observed in both biofilm positive and negative strains. However, the non-burn isolates were significantly more resistant to meropenem and tobramycin regardless of their potential to form biofilm. Interestingly, biofilmproducing non-burn isolates were significantly more resistant to amikacin, gentamicin, tobramycin and meropenem. Production of AmpC was also significantly higher in biofilm-producing non-burn isolates. Conversely, ESBL production was significantly higher in burn isolates. There was an association between biofilm formation and AmpC but not ESBL-production among non-burn isolates. Conclusions: The potential to form biofilm correlated with antibiotic resistance and AmpC production in non-burn burn isolates of A. baumannii. On the other hand, the burn strains produced significantly higher amounts of ESBL yet biofilm production was unrelated to antibiotic resistance or ESBL-production.
Polychaetes associated to calcareous sediments from Venezuela: Scolecida

One hundred eighty-eight (188) polychaete specimens were examined, being collected in calcareous sediments from coral reefs at the National Park Archipielago Los Roques, Venezuela. The samples were obtained in seven stations, between 2009 and 2012, using a PVC corer. A total of 9 species were identified, belonging to the clade Scolecida: 4 species of Capitellidae, 2 species of Orbiniidae, and 1 species for Maldanidae, Paraonidae and Opheliidae; from these 9 species, 3 are considered as new records for Venezuela. These results increase our knowledge about the marine biodiversity at the continental shelf in Venezuela and the southern Caribbean Sea, which is poorly known, especially in this group.
Regulation of the interfacial activation within the Candida rugosa lipase family

The fungus Candida rugosa produces several lipase isoenzymes and the 3D structure of three was solved (Lip1, Lip2 and Lip3). In an aqueous solution, the hydrophobic catalytic cavity of these lipases is buried under a flap that blocks the entrance of the substrate. In the hydrolysis of triacetin, the limiting step of the catalytic process was the activation of the enzyme and only the existence of the highly hydrophobic interface provided by hexane was able to shift the equilibrium towards the open conformation. In the case of Lip1, the hexane interface was crucial and once the open conformation was stabilised, Lip1 was as efficient as Lip3 for the hydrolysis of triacetin. Lip2 isoenzyme behaves more similarly to mLip3 reinforcing the higher structural and functional similarity between these isoenzymes. Inhibition experiments carried out under non-kinetic conditions allowed to correlate the higher flexibility of the closed flap and the higher hydrophobicity of the catalytic pocket of mLip3 with the greater facility of this isoenzyme to become activated by interfaces of different chemical nature. Both factors might allow a more intense penetration of mLip3 into the interfaces. In these systems, we observed a unique behaviour of Lip2, enzyme that although in a monomeric state and provide with an analogous flap structure to that of Lip1 or Lip3 underwent a very fast activation even in the absence of supramicellar concentrations of surfactants. We determined that the inhibitor itself forms micelles and hypothesised that they might provide an adequate interface for Lip2 activation. Copyright © 2009 John Wiley & Sons, Ltd.
Listeria monocytogenes in refrigerated and frozen chicken parts

The incidence of Listeria monocytogenes in refrigerated and frozen chicken parts was investigated, using the Mini-Vidas™ system (bioMerieux). Two hundred and eigthy chicken parts were tested: 40 skin samples from the breast and leg, 120 samples from refrigerated wings, breasts and legs and 120 samples from frozen wings, breasts and legs (40 of each). The 219 samples tested positive (78.21%). The parts with the highest incidence were frozen breasts (100%) and wings (95%). In frozen legs, the values were lower (60%). In refrigerated parts, the incidence was higher in breasts (85%) and in wings (80%). In legs samples, similarly to the frozen ones, the incidence was lower (50%). In the skin of the breasts and legs, the incidence was 77.50%. Statistical evaluation demonstrated that there are no differences between frozen breasts and wings but there are differences between similar refrigerated parts. The refrigerated and frozen legs are the only parts that are statistically equal. The percentages that were dete.
Co‐existence of divergent communities at natural boundaries: spider (Arachnida: Araneae) diversity across an alpine timberline

Abstract. 1 Habitat boundaries can contain high biodiversity because they potentially combine species from two habitat types plus additional boundary specialists. However, most research on animal communities is focused on uniform habitats. 2 Here, we assessed the degree to which the community change at a habitat edge is determined by the broad‐scale spatial transition from one habitat to the other, or by fine‐scale environmental influences. We compared the distribution of ground‐dwelling spider species from open land to forest with the distribution around stand‐alone trees at the boundary, the alpine timberline (Grisons, Switzerland). 3 Our results showed that spiders were more strongly influenced by local environmental conditions (40% of explained variation) than by the spatial position within the ecotone (24.5% of explained variation, with 15.6% overlap between the two). Spider communities differentiated according to light availability and corresponding changes in the ground vegetation. 4 Since the small area around a single tree at the studied timberline offered a similar broad spectrum of environmental conditions as the open land and forest together, it provided both habitats for species from the adjoining open land and forest as well as for some possible timberline specialists. 5 Accordingly, natural habitat boundaries may maintain very contrasting communities by providing a wide range of habitat conditions.
Habitat Overlap and Facilitation in Tamarisk and Box Elder Stands: Implications for Tamarisk Control Using Native Plants

Invasive plants are typically managed using top‐down control techniques that focus on the removal of the target organism. Bottom‐up control limits the resources available to the undesired species by manipulating disturbance, competition, and successional processes, and thus may prevent reinvasion. Tamarisk species (Tamarix sp.) have invaded riparian areas throughout western North America, resulting in expansive control efforts. A companion study has shown that a native competitor, Box elder (Acer negundo), is capable of outcompeting and killing established Tamarisk through light interception in canyons of Dinosaur National Monument (DNM), Colorado. The goal of this study was to determine the feasibility of using Box elder as a bottom‐up control agent by (1) determining the distributional overlap of the two species in DNM; (2) determining if Tamarisk facilitates Box elder establishment; and (3) analyzing Box elder seedling survival across a range of physical gradients. The distribution of Tamarisk and Box elder overlapped considerably throughout the study area. Box elder seedlings were planted under Tamarisk canopies or areas with the canopy removed. Survival was significantly higher under Tamarisk canopies, indicating that Tamarisk facilitates Box elder seedling survival. Box elder seedling survival was tested across soil texture, litter depth, groundwater depth, and shade intensities indicative of conditions found in the canyons of DNM, and survival was high for all treatments. The manipulation of competitive and successional processes through the promotion of Box elder and other native tree establishment is suggested as a means of bottom‐up Tamarisk control to complement traditional control techniques.
Determination of Nutritive Value of Poa trivialis Using in vitro Methods, Gas Production and Nylon Bag

This study was conducted to determine the chemical composition, metabolizable energy, digestibility and ability of gas production of Poa trivialis. Samples was collected at three phenological stages including: vegetative growth, flowering and seedling on two different elevations of 1300 to 1500 m and 2000 to 1800 m asl in Neor and Hir region as the first and second sites, respectively. Testing of gas production was performed using Semi-automatic gas producers machine WT-Binder 87532 Model (made ​​in Germany). Fistulated castrated male sheeps were used for preparation of required rumen fluid. Results show that more crude protein and less cell wall were in the vegetative growth stage. Gas production was higher in the first stage in comparison with other growing stages. The amounts of gas production of soluble and insoluble structures at the first and second sites were 75.63 and 81.50 mL, respectively. Metabolizabe energy of Poa triviali was2.38 in the first site and in the second site 2.48 Mcal/kg DM in the vegetative growth stage. Collected samples from the second site had more metabolizabe energy, digestibility, degradability and gas production in comparison with the results of the first site.
Sexually dimorphic melanin‐based colour polymorphism, feather melanin content, and wing feather structure in the barn owl (Tyto alba)

Feathers confer protection against biophysical agents and determine flying ability. The geometry and arrangement of the barbs, together with the keratin and pigments deposited in the feathers, determine the mechanical stability of the vane, and its stiffness and resistance to abrasive agents. In colour-polymorphic species, individuals display alternative colour morphs, which can be associated with different foraging strategies. Each morph may therefore require specific flying abilities, and their feathers may be exposed to different abrasive agents. Feathers of differently coloured individuals may thus have a specific structure, and colour pigments may help resist abrasive agents and improve stiffness. We examined these predictions in the barn owl (Tyto alba), a species for which the ventral body side varies from white to dark reddish pheomelanic, and in the number and size of black spots located at the tip of the feathers. White and reddish birds show different foraging strategies, and the size of black feather spots is associated with several phenotypic attributes. We found that birds displaying a darker reddish coloration on the ventral body side deposit more melanin pigments in their remiges, which also have fewer barbs. This suggests that wear resistance increases with darkness, whereas feathers of lighter coloured birds may bend less easily. Accordingly, individuals displaying a lighter reddish coloration on the ventral body side, and those displaying larger black spots, displayed more black transverse bars on their remiges: as larger-spotted individuals are heavier and longer-winged birds also have more transverse bars, these bars may reduce feather bending when flying. We conclude that differently coloured individuals produce wing feathers of different strengths to adopt alternative behavioural and life history strategies. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109, 562‐573.
Primary Structure, sequence analysis, and expression of the thermostable D - hydantoinase from Bacillus stearothermophilus SD1

The gene coding for the thermostable D-hy- dantoinase from the thermophilic bacterium Bacillus stearothermophilus SD1 was cloned and its nucleotide sequence was completely determined. The D-hydantoi- nase protein showed considerable amino acid sequence homology (20-28%) with other hydantoinases and functionally related allantoinases and dihydroorotases. Strikingly the sequence of the enzyme from B. stear- othermophilus SD1 exhibited greater than 89% identity with hydantoinases from thermophilic bacteria. Despite the extremely high amino acid homology among the hydantoinases from thermophiles, the C-terminal re- gions of the enzymes were completely diAerent in both sequence and predicted secondary structure, implying that the C-terminal region plays an important role in determining the biochemical properties of the enzymes. Alignment of the sequence of the D-hydantoinase from B. stearothermophilus SD1 with those of other func- tionally related enzymes revealed four conserved re- gions, and five histidines and an acidic residue were found to be conserved, suggesting a close evolutionary relationship between all these enzymes.
A Complete Public Domain Family Genomics Dataset

Background The availability of open access genomic data is essential for the personal genomics field. Public genomic data allow comparative analyses, testing of new tools and genotype-phenotype association studies. Personal genomics data of unrelated individuals are available in the public domain, notably the Personal Genome Project; however, to date genomics family data and metadata are severely lacking, mainly due to cost, privacy concerns or restricted access to Next Generation Sequencing (NGS) technology. Family data have a lot to offer as they allow the study of heritability, something which is impossible to do just by using unrelated individuals. Findings A whole family from Southern Spain decided to genotype, sequence and analyse their personal genomes making them publicly available under a Creative Commons 0 license (CC0; commonly denominated as public domain). These data include a) five 23andMe SNP chip genotype bed files, b) four raw exomes with their assorted bam files and VCF files, c) a metagenomic raw sequencing data file and d) derived data of likely phenotypes using SNPedia-derived tools. Conclusions To our knowledge this is the first CC0 released set of genomic, phenotypic and metagenomic data for a whole family. This dataset is also unique in that it was obtained through direct-to-consumer genetic tests. Hence any ordinary citizen with enough budget and samples should be able to reproduce this experiment. We envisage this dataset to be a useful resource for a variety of applications in the personal genomics field as a) negative control data for trait association discovery, b) testing data for development of new software and c) sample data for heritability studies. We encourage prospective users to share with us derived results so that they can be added to our existing collection.
The potential additive and non-additive benefits of mate choice in the threespine stickleback (Gasterosteus aculeatus)

Hypothesis: The genetic benefits of female mating preferences can be additive (good alleles’), non-additive (‘compatible alleles’) or both, and the importance of each may be population dependent. Organism: Threespine stickleback (Gasterosteus aculeatus) from two independent natural populations. Location: Two adjacent sites in Scotland, one a pond with high stickleback density and high parasite prevalence, the other a river with low stickleback density and fish predators. Methods: In vitro fertilizations in a North Carolina Type II breeding design to estimate the contribution of additive and non-additive genetic variation to early offspring survival. Results: In both populations we detected significant additive maternal effects. These effects were largely explained by variance in egg size, though not entirely so. In the pond population there were significant male additive genetic effects on offspring survival, implicating a role for ‘good alleles’, but not non-additive effects. In the river population there were significant additive and non-additive effects, implicating a role both for ‘good alleles’ and genetic compatibility. Different populations of the same species may vary in the mechanism by which sexual selection operates.
IFN-β-Mediated Up-Regulation of CD1d in Bacteria-Infected APCs1

The expression of CD1d molecules is essential for the selection and activation of a unique subset of T cells, invariant NKT cells, which express limited TCR diversity and have been demonstrated to function in both regulatory and antimicrobial immune responses. Although it has been reported that the levels of CD1d expression can be modulated during infection, the mechanisms that mediate this effect are poorly defined. In this study, we show that infection of dendritic cells and macrophages both in vitro and in vivo with the intracellular pathogen Listeria monocytogenes leads to up-regulation of CD1d. IFN-β is required to mediate this up-regulation in L. monocytogenes infection, as well as being sufficient to up-regulate CD1d expression in vitro. Unlike MHC class I molecules, the increased surface expression of CD1d by IFN-β is not regulated at the transcriptional level. Confocal microscopy and metabolic labeling experiments show that the total pool of CD1d protein is increased in IFN-β-treated cells and that increased surface expression of CD1d is not due to the redistribution of the intracellular pool of CD1d. IFN-β treatment increases the de novo synthesis of CD1d. This change in surface CD1d expression was functionally relevant, as IFN-β-treated dendritic cells are more efficient in stimulating invariant NKT cells than untreated controls. Taken together, these data support a role for early IFN-β-mediated up-regulation of CD1d in NKT cell activation during infection.
Habitat Associations of Dusky-footed Woodrats (Neotoma fuscipes) in Mixed-conifer Forest of the Northern Sierra Nevada

Abstract Dusky-footed woodrats (Neotoma fuscipes) are important components of forest communities, including serving as a primary prey of the California spotted owl (Strix occidentalis occidentalis), a species of concern in California. We examined habitat associations of the dusky-footed woodrat at 4 study sites in mixed-conifer forest of the northern Sierra Nevada, California, during 2003–2005. We investigated the importance of California black oak (Quercus kelloggii) as a macrohabitat component for woodrats, and we examined microhabitat association at 2 levels, house location and house use, by comparing house-site (n = 144) characteristics to random sites (n = 144) and characteristics of used and unused houses, respectively. Woodrat density was positively related to density of large (≥33-cm-diameter at breast height) oaks, probably because large oaks are valuable food resources. Location of woodrat houses was strongly influenced by the presence of large (≥30-cm-mean diameter) logs and large (≥30-cm-diameter at root collar) stumps, but also by steeper slopes, and lack of bare ground and mat-forming shrub cover. We found little evidence that adult woodrats distinguished among houses with respect to microhabitat, suggesting that woodrats make decisions about microhabitat suitability when the house is built. In 2005, adults chose larger houses that were characterized by more logs and less poletimber than those of subadults, but we detected no such differences in 2004. Dusky-footed woodrats in the northern Sierra Nevada would benefit from management techniques that promote the growth and retention of large California black oaks and create large logs and stumps within a stand.