Miracle-dz/UniFAR-FTUs huggingface dataset:
Activity of enzymes associated with asparagine synthesis and breakdown in wheat under biotic and abiotic stress conditions.

Asparagine synthetase activity was measured in healthy and Yellow rust (Puccinia striiformis)-infected leaves of wheat (Triticum aestivum) varieties Sappo (grown under glass) and Oakley (field-grown). Protein extraction and asparagine synthetase assay methods were developed, optimised and adapted into high-throughput methods, and asparagine produced in the assay was measured by colorimetric detection with ninhydrin ethanolic solution. Yellow rust infection caused an approximately 50% increase in asparagine synthetase activity in both glasshouseand field-grown plants.
Deep learning for natural language processing of free-text pathology reports: a comparison of learning curves

Introduction Although clinically derived information could improve patient care, its full potential remains unrealised because most of it is stored in a format unsuitable for traditional methods of analysis, free-text clinical reports. Various studies have already demonstrated the utility of natural language processing algorithms for medical text analysis. Yet, evidence on their learning efficiency is still lacking. This study aimed to compare the learning curves of various algorithms and develop an open-source framework for text mining in healthcare. Methods Deep learning and regressions-based models were developed to determine the histopathological diagnosis of patients with brain tumour based on free-text pathology reports. For each model, we characterised the learning curve and the minimal required training examples to reach the area under the curve (AUC) performance thresholds of 0.95 and 0.98. Results In total, we retrieved 7000 reports on 5242 patients with brain tumour (2316 with glioma, 1412 with meningioma and 1514 with cerebral metastasis). Conventional regression and deep learning-based models required 200–400 and 800–1500 training examples to reach the AUC performance thresholds of 0.95 and 0.98, respectively. The deep learning architecture utilised in the current study required 100 and 200 examples, respectively, corresponding to a learning capacity that is two to eight times more efficient. Conclusions This open-source framework enables the development of high-performing and fast learning natural language processing models. The steep learning curve can be valuable for contexts with limited training examples (eg, rare diseases and events or institutions with lower patient volumes). The resultant models could accelerate retrospective chart review, assemble clinical registries and facilitate a rapid learning healthcare system.
Detection and molecular characterization of vancomycin resistant Staphylococcus aureus from clinical isolates

Until now, few strains of vancomycin resistant Staphylococcus aureus (VRSA) have been reported worldwide. The disk diffusion method for determination of vancomycin sensitivity frequently misclassifies intermediately susceptible isolates to fully susceptible. However, non-automated minimum inhibitory concentration (MIC) detection methods are the gold standards. In the present study, 439 Gram positive clinical isolates were collected. Among them, 220 Staphylococcus aureus were identified. Multiplex polymerase chain reaction (PCR) detection method for vancomycin resistant S. aureus (VRSA) was developed for detection of both vanA gene (for vancomycin resistance) and nuc gene (specific for S. aureus ) in a single step PCR compared to conventional non-automated disc diffusion and MIC detection methods. Molecular typing of VRSA isolates was performed using randomly amplified polymorphic (RAPD) DNA assay technique. The results show 10 VRSA isolates detected by disc diffusion method and MIC determination. Five out of them harbored vanA gene that were detected by multiplex PCR and most of them showed low clonal diversity. Key words : Molecular characterization, multiplex polymerase chain reaction (PCR), vancomycin resistant Staphylococcus aureus (VRSA), vanA gene, nuc gene, randomly amplified polymorphic DNA (RAPD) assay technique.
The significance of protected areas for the land birds of southern Finland

Protected areas (nature reserves) cover 0.7% of the land area in southern Finland (162,000 km2), which belongs to the south- and mid-boreal coniferous forest zones. The value of these areas in preserving land birds was studied on the basis of quantitative censuses. The numbers of bird pairs were estimated in nature reserves and in the whole of southern Finland, and the significance of the reserves was evaluated based on how large a proportion of the total population in southern Finland was found in them. Forest habitat generalists and species of coniferous forests occurred in protected areas as expected by the proportion of these areas in southern Finland. Specimens of these species groups comprise two thirds of all the country’s land birds. Species of old-growth forests and open peatlands clearly preferred protected areas, whereas species of bushes, and lush and deciduous forest were scarcer in protected areas than elsewhere in southern Finland. The latter fertile habitats are poorly represented in protected areas, even though due to their disappearance or alteration elsewhere several species confined to these habitats have declined and are even threatened. Drainage of open peatlands and clearcutting of old-growth forests has caused a decrease in the area of these habitats in southern Finland during the past decades. Therefore, protected areas have a high significance in preserving bird species preferring these habitats. Protected areas are particularly important for decreased species of old-growth forests, such as the Three-toed Woodpecker Picoides tridactylus and the Siberian Jay Perisoreus infaustus, as about 10% of their total population in southern Finland was estimated to breed in protected areas. The future protection of both old-growth and deciduous forests is important if we are to preserve bio-diversity of land birds in Finland. Las areas protegidas (reservas naturales) cubren 0.7% del area del sur de Finlandia (tamano 162.000 km2) que pertenece a las zonas de forestas de coniferas sud- y mesaboreales. Se estudio el valor de estas areas en la preservacion de aves terrestres sobre la base de sensos cuantitativos. Se estimaron los numeros de parejas de aves en las reservas naturales y en todo el sur de Finlandia, y se evaluo la importancia de las reservas basandose en la proporcion de la poblacion total del sur de Finlandia que representaban las aves que se encontraban en las reservas. Generalistas de habitats de forestas y especies de bosques de coniferas se encontraron en areas protegidas tal como era esperado en base a la proporcion de estas areas en el sur de Finlandia. Los especimenes de estos grupos de especies comprenden dos tercios de todas las aves terrestres del sur de Finlandia.
Polyphasic evaluation of Aphanizomenon issatschenkoi and Raphidiopsis mediterranea in a Mediterranean lake

Aphanizomenon issatschenkoi and Raphidiopsis mediterranea were studied in the Mediterranean Lake Doirani during a cyanobacterial bloom (August―October 2004). Aphanizomenon issatschenkoi was clearly morphologically distinct from R. mediterranea on the basis of apical cells. The two species demonstrated an almost inverse temporal distribution, consistent preference for different water depths and negative correlation between their net growth rates. Raphidiopsis mediterranea exhibited a higher net growth rate (0.17 days ―1 ) and dominated during warmer water periods, with high Z max /Z sec ratio and low but available inorganic nitrogen. Aphanizomenon issatschenkoi was more generalist, exhibiting slower net growth (0.10 days ― 1 ) and a broader distribution in relation to temperature and light, regularly forming heterocytes under low nitrogen conditions. Aphanizomenon issatschenkoi was also phylogenetically distinct from R. mediterranea on the basis of partial 16S rRNA gene sequence. The R. mediterranea typical morphotype corresponded to one phylotype in the well-defined 16S rRNA gene sequence cluster of Cylindrospermopsis raciborskii. The formation of two specialized reproductive cells in the same individual of R. mediterranea is described for the first time and may indicate unknown alternative reproductive modes and lifestyles in planktonic Cyanobacteria.
NECTAR AND NECTARY STUDIES ON SEVEN EUPHORBIA SPECIES

The nectary morphology of six Hungarian and one grown Mediterranean leafy spurge (Euphorbia) species was studied and compared. Glands with various horns were found in E. amygdaloides L. , E. cyparissias L. , E. esula L. , E. myrsinites L. and E. virgata W. et K. Nectary without horns is characteristic to E. palustris L. and E. polychroma Kern. Cuticle pattern of the glands was different and characteristic to the species. E. amygdaloides has no cuticle wrinkles. Special letter shaped wrinkles were found in the species, for example „H” shaped in E. cyparissias, E. esula, E. palustris and E. virgata. Wrinkles in E. myrsinites have several branches; they could be „Z”, „W”, „Y” and „E” shaped. The nectar of each studied plants contained fructose, glucose and sucrose. An unknown sugar was found in E. cyparissias only.
Dimers of the Neuropeptide Y (NPY) Y2 Receptor Show Asymmetry in Agonist Affinity and Association with G Proteins

In conditions precluding activation of G proteins, the binding of agonists to dimers of the neuropeptide Y (NPY) Y2 receptor shows two components of similar size, but differing in affinity. The dimers of all NPY receptors are solubilized as ∼ 180-kDa complexes containing one G protein α β γ trimer. These heteropentamers are stable to excess agonists, chelators, and alkylators. However, dispersion in the weak surfactant cholate releases ∼ 300-kDa complexes. These findings indicate that both protomers in the Y2 dimer are associated with G protein heterotrimers, but the extent of interaction depends on affinity for the agonist peptide. The G protein in contact with the first-liganded, higher-affinity protomer should have a stronger interaction with the receptor and a larger probability of activation.
Direct detection by polymerase chain reaction (PCR) of Escherichia coli in water and soft cheese and identification of enterotoxigenic strains

PCR was used to develop a method to detect Escherichia coli in surface water and soft cheese, which does not require cultivation of bacteria. DNA sequences from the ma/B operon of E. coli were amplified to specifically detect this bacterium. Samples of surface water and soft cheese naturally contaminated with E. coli from less than 100 cells per g up to several times 105cells per g were analysed by both the classical culture method and the PCR assay. Comparable results were obtained with both methods. Soft cheese samples artificially contaminated with various levels of enterotoxigenic E. coli were analysed with a second PCR test specific for the heat‐labile enterotoxin type I (LTI) of E. coli. The detection limit was about 1000 bacteria per g of soft cheese. In addition, two soft cheese samples naturally contaminated with 2 times 105and 6 times 105E. coli per g as determined by the culture method were analysed by LTI‐PCR and found to contain low levels of enterotoxigenic E. coli.
PRELIMINARY PHYTOCHEMICAL SCREENING AND EVALUATION OF ANTIBACTERIAL ACTIVITY OF DIFFERENT SOLVENT EXTRACTS OF PLECTRANTHUS BOURNEAE GAMBLE (LAMIACEAE)

Objective: The aim was to investigate the antibacterial activity of Plectranthus bourneae Gamble (Lamiaceae) using different solvents. Methods: Petroleum ether, chloroform, acetone, ethanol and aqueous leaves extracts at different concentration (25, 50, 75, 100 µg/ml) were evaluated for antibacterial activity using disc diffusion method against some Gram-positive species namely Bacillus subtilis, Clostridium sporogenes, Staphylococcus aureus, Streptococcus mutans, Streptococcus mitis and Gram-negative species Salmonella typhi, Klebsilla pneumoniae, Entrobactor aerogenes, Citrobactor freundii, Escherichia coli. The minimum inhibitory concentration (MIC) and minimum bacterial concentrations (MBC) were determined by serial dilution method. Results: The antibacterial activity results of ethanol extract (50 µg/ml) showed maximum zone of inhibition (26 mm) against S. aureus and MIC value of 0.78 µg/ml and MBC of 1.56 µg/ml whereas aqueous extract was least effective on all the strains. The Gram-positive strains of S. aureus and S. mutans were found to be the most sensitive and resistance on all the extracts. Except S. typhi, Gram-negative bacteria used were less inhibitory effect to all the extracts. Conclusion: The present study concluded that the ethanolic extracts of P. bourneae possess potential antibacterial activities against certain microorganisms.
Predictability of Pedigree Indexes for Bulls from Two, Three, and Four Generations

Abstract Pedigree indexes were calculated from two, three, and four generations for subsets of 380 Holstein bulls that had been progeny tested. Traits indexed were milk, fat, and type. Only male ancestors were considered. Regression coefficients of Predicted Difference and contemporary deviation on pedigree index usually were highest for pedigree index from three generations for milk and fat. Rank correlations of pedigree indexes from two and three generations were . 95 to . 98 but from three and four generations were . 99 to 1.00. Maternal great-grandsires had detectable influence on genetic merit of bulls even though contribution was small as expected. Maternal great-great-grandsires did not contribute to predictability of pedigree indexes.
Differential expression of soluble pyrophosphatase isoforms in Arabidopsis upon external stimuli

In plants, pyrophosphate (PPi), generated in a wide range of reversible anabolic reactions, is hydrolyzed by pyrophosphatases. The presence of tonoplast- and Golgi-integral H+-translocating pyrophosphatases in plants led to the conclusion that plant cytosol has no soluble pyrophosphatase activity. However, the Arabidopsis thaliana (L.) Heynh. Genome also encodes five soluble pyrophosphatase isoforms (Ppas). There are almost no data in the literature on their redundancy in plant metabolism; therefore, we performed expression analyses of A. Thaliana soluble pyrophosphatase isoforms in response to external stimuli including carbohydrate status, hormone action, and stress exposure. The results revealed pronounced specificity for each isoform. Interestingly, one isoform (PPa3; At2g46860) was specifically induced during seedling etiolation, and in the presence of the nonmetabolizable sugar 3-O-methylglucose. Based on quantitative PCR analyses, PPa1 (At1g01050) and PPa4 (At3g53620) appeared to be regulated by sugars. Quantitative PCR analyses indicated isoform- and tissue-dependent responses of Ppa isoforms to ABA, salt, and cold stresses. PPa2 (At2g18230) and PPa5 (At4g01480) responded differentially to salinity, cold treatment, and ABA. We conclude that plant cytosolic pyrophosphatases perform multiple, so far overlooked functions during plant development and stress exposure.
Characteristics of dairy farms in the North-Eastern part of Italy: rations, milk yield and nutrients excretion

Abstract This survey was aimed to evaluate the characteristics of dairy farms in the North-Eastern part of Po valley in terms of ration composition, milk yield and N and P excretions. Eighty-nine farms, with Italian Holstein Friesian cows, were selected in order to cover different situations in term of farm size and milk yield (MY). MY and quality were obtained from the national database of functional controls. Each farm was visited in order to collect information about ingredients and chemical composition of rations used. Farms were classified in four groups differing for dietary crude protein density (Lcp<15.3% DM; Hcp>15.3% DM) and for MY (Lmy>30 kg/d; Hmy<30 kg/d). N and P excretions were quantified by following a mass balance approach. Dietary crude protein content (CP) was not correlated to milk yield (MY) and quality. The estimated amounts of N excreted, discounted for 28% of N losses in atmosphere, were 78.5, 78.2, 87.2 and 89.1 kg/cow/year, and P excreted were 20.2, 18.6, 18.7 and 19.8 kg/cow/year for the LcpLmy, LcpHmy, HcpLmy, HcpHmy groups, respectively. On corn silage and cereals based rations, a dietary CP of 14.3% DM can support 31 kg MY/cow/day.
Genetic improvement of cotton tolerance to salinity stress

Soil salinity is a great threat to cotton production worldwide. Plant adaptation to environmental stresses involves the expression of specific stress-related genes. Consequently, engineering genes that protect and maintain the function and structure of cellular components can enhance tolerance to salinity stress. Engineered cotton plants have been reported to perform much better than their wilt plants either in greenhouse or field conditions under salinity stress. However, engineered cotton with improved salt-tolerance is still far behind the requirements of commercial production due to its limited salinity tolerance or poor agronomic performance. This review highlights recent advances in genetic improvement, particularly molecular breeding for salinity tolerance of cotton. It is suggested that future research should focus on the development of specific cotton cultivars with high salt tolerance through a combination of traditional breeding and molecular technology.
Domains Necessary for Gα12 Binding and Stimulation of Protein Phosphatase-2A (PP2A): Is Gα12 a Novel Regulatory Subunit of PP2A?

Many cellular signaling pathways share regulation by protein phosphatase-2A (PP2A), a widely expressed serine/threonine phosphatase, and the heterotrimeric G protein Gα12. PP2A activity is altered in carcinogenesis and in some neurodegenerative diseases. We have identified binding of Gα12 with the Aα subunit of PP2A, a trimeric enzyme composed of A (scaffolding), B (regulatory), and C (catalytic) subunits and demonstrated that Gα12 stimulated phosphatase activity (J Biol Chem 279: 54983–54986, 2004). We now show in substrate-velocity analysis using purified PP2A that Vmax was stimulated 3- to 4-fold by glutathione transferase (GST)-Gα12 with little effect on Km values. To identify the binding domains mediating the Aα-Gα12 interaction, an extensive mutational analysis was performed. Well-characterized mutations of Aα were expressed in vitro and tested for binding to GST-Gα12 in pull-down assays. Gα12 binds to Aα along repeats 7 to 10, and PP2A B subunits are not necessary for binding. To identify where Aα binds to Gα12, a series of 61 Gα12 mutants were engineered to contain the sequence Asn-Ala-Ala-Ile-Arg-Ser (NAAIRS) in place of 6 consecutive amino acids. Mutant Gα12 proteins were individually expressed in human embryonic kidney cells and analyzed for interaction with GST or GST-Aα in pull-down assays. The Aα binding sites were localized to regions near the N and C termini of Gα12. The expression of constitutively activated Gα12 (QLα12) in Madin Darby canine kidney cells stimulated PP2A activity as determined by decreased phosphorylation of tyrosine 307 on the catalytic subunit. Based on crystal structures of Gα12 and PP2A Aα, a model describing the binding surfaces and potential mechanisms of Gα12-mediated PP2A activation is presented.
Tachinidae (Diptera) collected in traps used for mass-trapping of Bactrocera oleae (Rossi) (Diptera: Tephritidae) in olive groves in Central Spain

Tachinid flies are important for biological control of pests, because most species are parasitoids of insects. The objectives of this work were 1) to describe the species of tachinid flies captured by mass trapping devices against the olive fruit fly, Bactrocera oleae , in olive groves in Central Spain, and 2) to report on the selectivity of the different devices for this important group of insects. The study was carried out in two olive groves in the province of Madrid during 2005 and 2008. The number of trapping devices was five in 2005 and twelve in 2008. A total of 66 species of tachinid flies was captured. Comments on some of them are provided because of their special interest. Three tachinid species ( Clemelis massilia , Schembria meridionalis and Ceromya flaviseta ) are recorded from the Iberian Peninsula for the first time. It is remarkable that captures of C. massilia accounted for 72.3% in 2008. Comparison of the different mass-trapping devices indicates that none of them is selective for this important family of parasitoids. Numbers of tachinid flies captured per trap and season ranged between 1 and 13 in 2005, and 24 and 283 in 2008. This is the first study carried out in Spain on tachinids captured by mass-trapping devices and it reports the abundance and species diversity of this group of insects in olive groves as well as the poor selectivity of mass-trapping on them
A water-borne sex pheromone and trail following in the apple snail, Pomacea canaliculata

We investigated whether individuals of the apple snail Pomacea canaliculata were attracted by conspecifics or follow mucus trails of other individuals. The snails’ behaviour was studied by a series of choice experiments in a T-maze and in Petri dishes. Both males and females chose the side with a snail of the opposite sex significantly more frequently than the control side without a snail. Males were attracted by water conditioned with females more frequently than unconditioned water, whereas females did not show a preference for male-conditioned water. Moreover, juveniles were not attracted by water conditioned with a male, a female and a juvenile. These data indicate that males were attracted by female odour, which contains one or more water-borne sex pheromones. In addition, both males and females follow mucus trails of snails of the opposite sex. Since females also followed trails of females, the function of trail following is not necessarily related to reproduction. In these experiments P. canaliculata did not distinguish the direction of the trail.
Competition between the bush fly and a dung beetle in dung of differing characteristics

A range of densities of bush fly (Musca vetustissima) eggs and dung beetle (Onthophagus binodis) adults were placed on either nutritious spring or poor summer dung in the laboratory at 25 °C. Intra‐ and interspecific competition were greater for flies in summer dung than in spring dung, and intra‐ and interspecific competition were greater for dung beetles in spring dung than in summer dung. In summer dung fly size and survival were influenced by both beetle and fly densities. Flies in summer dung were smaller, and below a headwidth of about 2.0 mm there was a correlation between size and survival. Mortality was probably due largely to death of larvae. Also beetles produced very few brood balls, and shredded this dung, particularly at high densities. In spring dung, beetle brood ball production which was greater was reduced by both beetle and fly densities, and beetles left the pads earlier at high fly densities. Fly survival was influenced by beetle density, but less than in summer dung, and not by fly density. Mortality was probably caused by death of eggs. These data support field observations that dung beetles cause higher fly mortality in summer dung than spring dung.
IRRIGATION OF SORGHUM CROP WITH WASTE STABILIZATION POND EFFLUENT: GROWTH AND YIELD RESPONSES

The effect of treated wastewater and equivalent basal fertilizer on growth, yield and nutrient quality of sorghum (Sorghum bicolor (L.) Moench) was investigated under field conditions. Treated wastewater significantly increased plant height, stem thickness, number of grain/panicle, grain weight/panicle and 1000 grain weight of sorghum, while basal fertilizer only elevated grain weight/panicle compared to controls. Among the nutrient quality parameters only total sugar content was significantly increased by the treated wastewater over the controls. Other nutrient quality parameters including crude proteins, nitrogen free extract, ether extract and crude ash remained unchanged following the treatments. These results are discussed in the light of previous studies and the potential of wastewater resource in irrigated agriculture is discussed.