Miracle-dz/UniFAR-FTUs huggingface dataset:
Is there association between APOE e4 genotype and structural brain ageing phenotypes, and does that association increase in older age in UK Biobank? (N = 8,395)

Apolipoprotein (APOE) e4 genotype is a purported risk factor for accelerated cognitive ageing and dementia, though its neurostructural substrates are unclear. The deleterious effects of this genotype on brain structure may increase in magnitude into older age. This study aimed to investigate in UK Biobank the association between APOE e4 allele presence vs. absence and brain imaging variables that have been associated with worse cognitive abilities; and whether this association varies by cross-sectional age. We used brain magnetic resonance imaging (MRI) and genetic data from a general-population cohort: the UK Biobank (N=8,395). We adjusted for the covariates of age in years, sex, Townsend social deprivation scores, smoking history and cardiometabolic diseases. There was a statistically significant association between APOE e4 genotype and increased (i.e. worse) white matter (WM) hyperintensity volumes (standardised beta = 0.088, 95 confidence intervals = 0.036 to 0.139, P = 0.001), a marker of poorer cerebrovascular health. There were no associations with left or right hippocampal, total grey matter (GM) or WM volumes, or WM tract integrity indexed by fractional anisotropy (FA) and mean diffusivity (MD). There were no statistically significant interactions with age. Future research in UK Biobank utilising intermediate phenotypes and longitudinal imaging hold significant promise for this area, particularly pertaining to APOE e4’s potential link with cerebrovascular contributions to cognitive ageing.
PHYTOCHEMICAL COMPOSITION AND LARVICIDAL ACTIVITY OF ESSENTIAL OIL FROM THE LEAVES OF PLEIOSPERMIUM ALATUM (WALL. EX WT. & ARN) SWINGLE (RUTACEAE) AGAINST AEDES AEGYPTI, ANOPHELES STEPHENSI AND CULEX QUINQUEFASCIATUS (DIPTERA: CULICIDAE)

The present study was conducted to evaluate the essential oil from the leaves of Pleiospermium alatum (Wall. ex Wt. & Arn) Swingle (Rutaceae) was evaluated for mosquito larvicidal activity against the larvae of Aedes aegypti, Anopheles stephensi and Culex quinquefasciatus . GC and GC- MS analyses revealed that the essential oil contain fourteen compounds. D-Limonene (34.02%) was identified as a major chemical compounds followed by Elemol (18.04%) and γ –Terpinene (11.83%). The larval mortality was observed after 12 and 24 hours of exposure periods. The results revealed that essential oil potential larvicidal activity against the 4 th instar larvae of A. aegypti, A. stephensi and C. quinquefasciatus . After 12 h of exposure period the larvicidal activities were LC 50 =95.2 and LC 90 =366.7 ppm ( A. aegypti ), LC 50 =72.6 and LC 90 =305.2 ppm ( A.stephensi ) and LC 50 =104.4 and LC 90 =373.6 ppm ( C. quinquefasciatus ) and the larvicidal activities after 24 h of exposure period was LC 50 =53.8 and LC 90 =251.0 ppm ( A.aegypti ), LC 50 =44.4 and LC 90 =213.8 ppm (A. stephensi) , and LC 50 =143.3 and LC 90 =375.5 ppm ( C. quinquefasciatus ). The present study showed the leaves of the essential oil from the P. alatum and its D-Limonene major compound may have potential for use in control of A . aegypti , A. stephensi and C. quinquefasciatus and could be useful in search of new, safe, inexpensive and more effective control of vector mosquitoes. Key Words: Pleiospermium alatum. GC-MS. Aedes aegypti. Anopheles stephensi . Culex quinquefasciatus
Effects of strain and sex on the behaviour of free-range slow-growing chickens raised in a hot environment

ABSTRACT Behaviour is a good indicator of the well-being of chickens. The objective of the study was to compare foraging behaviour in males and females of three indigenous chicken strains under generally hot free-range conditions. Behavioural activities were monitored in 21-wk-old Potchefstroom Koekoek (PK), Ovambo (OV) and Naked Neck (NN) chickens. Birds were separated by sex and allocated to four pens of Chloris gayana. Three birds per pen were randomly chosen and marked with paint 20 min before observation. Temperature humidity index (THI) was calculated and main effects analysed using the general linear models procedure. Naked Necks spent more time walking than OV and PK. Strain did not affect other behaviours. Females spent more time foraging, while males dominated standing and walking. There was negative correlation between THI and time spent foraging. There was interaction between strain and sex on time spent standing. Foraging and drinking behaviours were more prominent in the morning (07:00 h) and late afternoon (17:00 h) compared to the 12:00-h period, whereas preening and dust-bathing were dominant around mid-day. Strain, sex and THI influence behaviour in free-range chickens. Breeding programmes should be cognizant of these attributes in order to produce hardier birds in view of worsening climatic uncertainties.
Long-read sequence capture elucidates the evolution of the hemoglobin gene clusters in codfishes

Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. This approach does not capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. In this study, we demonstrate the power of combining targeted sequence capture with long-read sequencing technology, leading to the successful sequencing and assembling of the two hemoglobin (Hb) gene clusters LA (~100kb) and MN (~200kb) across eight species of codfishes that are separated by up to 70 million years of evolution. The highly continuous assemblies – capturing both intergenic and coding sequences – revealed overall conserved genetic organization and synteny of the Hb genes within this lineage, yet with several, lineage-specific gene duplications. Moreover, for some of the species examined we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. Taken together, our study highlights the efficiency of targeted long-read capture for comparative genomic studies by shedding light on the evolutionary history of the Hb gene family across the highly divergent group of codfishes.
Environmental factors determining the establishment of the African Long‐legged Buzzard Buteo rufinus cirtensis in Western Europe

Winters have become warmer under the impact of climate change, which has modified the phenology of birds and also their distribution ranges. The African Long-legged Buzzard Buteo rufinus cirtensis has recently colonized Europe via the Strait of Gibraltar. We aim to explain the native distribution of this species and to predict favourable areas in newly colonized parts of Europe using geospatial modelling to identify the most influential factors in this process. We applied the favourability function, a generalized linear model describing environmental favourability, for the presence/absence of breeding areas in northern Morocco and the southern Iberian Peninsula, according to a set of variables describing climate, topography, human activity, vegetation and purely spatial trends. A model was built using some known breeding sites in northern Morocco, and was used to forecast future suitable breeding areas in Europe. A second model was built with the available data for northern Morocco and Europe in order to explain the current distribution of breeding sites. Both models were assessed according to discrimination, calibration and parsimony criteria, and the influence of each factor was analysed using variation partitioning. We conclude that the Iberian Peninsula could provide new suitable areas for the species and facilitate its northward expansion. This result, together with the increasing number of records available, suggests that this species could soon spread throughout Europe. Steady temperatures and abundant but seasonally distributed precipitation showed the strongest predictive power in the models. This indicates a close relationship between the species’ distribution and climate in the study area, and suggests that this species finds its most favourable environments in the Mediterranean biome. Topography and vegetation, specifically cliffs and woods near hunting zones, point to a fine-scale habitat selection for breeding. As the case of the African Long-legged Buzzard is not a unique event, our results may be useful to determine whether a northward expansion of the Mediterranean biome could be followed by distribution shifts of bird species that have so far been restricted to Africa. This article is protected by copyright. All rights reserved.
Construction of New Genetically Engineered Vaccine Strain for O-type Foot-and-Mouth Disease of Pig

Foot-and-mouth disease is an acute and highly contagious viral infectious disease. Although the foot and mouthdisease vaccine has been applied in some parts of the world since the beginning of the 20th century, the currentepidemic of foot and mouth disease in the world is still serious and constitutes an obstacle to the trade of animal andanimal products in the world. The porcine pseudorabies virus gene deletion strain PRV TK-/ gE-/ LacZ +, which isconstructed by our laboratory, has the advantages of good safety, large capacity and high recombination effi ciency. Inthis study, the artifi cial O-type foot-and-mouth disease P1 gene as an antigen gene, UbiP1 fused with ubiquitin (Ub)as another antigen gene to enhance cellular immunity, and then shRNA designed for FMD 3B gene and porcine IFN-[gamma] with antiviral and immune-regulatory eff ects. The two functional genes were constructed in turn to constructa transfer vector with four functional genes. The transfer vector was transfected into TK-/ gE- / LacZ+ cells with PRVdeletion vector, and the plasmids were purifi ed and identifi ed. The recombinant pseudorabies virus, which containsthe six functional genes of P1 gene, UbiP1, shRNA and IFN-γ, was obtained, which laid the foundation for furtherconstruction of new genetically engineered vaccine.
Soil microbes and successful invasions of an exotic weed Eupatorium adenophorum L.

The effects of soil microbes collected from the two invasive species Eupatorium adenophorum and E. odoratum and the two native species E. japonicum and E. chinense on the growth and biomass of E. adenophorum was examined to explore a possible link between soil microbes and successful invasions of the weed species E. adenophorum. In most cases, plant height, stem diameter, root number and root length were significantly enhanced when E. adenophorum was grown in sterilized soils compared with those when one was grown in non-sterilized soils collected from the rhizosphere of E. adenophorum, E. japonicum and E. chinense. In contrast, the growth and biomass of E. adenophorum were apparently inhibited when grown in soils collected from the rhizosphere of E. odoratum. Plant height, stem diameter, leaf area per plant and root length of E. adenophorum was greater when it was grown in soils collected from the rhizosphere of E. adenophorum compared with those when it was grown in soils collected from the rhizosphere of E. odoratum, but the enhancement considerably greater when it was grown in soils collected from the rhizosphere of E. japonicum and E. chinense compared with those when it was grown in soils collected from the rhizosphere of E. adenophorum. In addition, the biomass allocation of E. adenophorum was not significantly affected by soil microbes and soil sources. These results suggest that although the competitive advantage of the invasive weed E. adenophorum is not achieved solely by soil microbes, successful invasions of E. adenophorum may result partly from its release from the harmful soil microbes in its native range and the positive feedbacks of soil microbes from itself and the native species in its invading range.
Genetic diversity assessment in Jasminum species using Amplified Fragment Length Polymorphism

Jasmines (Jasminum sp.), a native of tropical and subtropical region, are esteemed for their attractive fragrant flowers and essential oil. However, very meagre information is available on the genetic relatedness among species and cultivars of jasmine. This study analyzed genetic relatedness of 48 genotypes across 26 species using Amplified Fragment Length Polymorphism markers. Of the ten sets of primers screened, four sets were selected for the present investigation on genetic diversity. A total of 212 bands were scored, of which 90.5% were polymorphic. The relationship among genotypes was analyzed using Unweighted Pair Group method of cluster analysis. Among 48 genotypes J. auriculatum formed a separate node while rest of the 47 genotypes formed two major clusters with two sub clusters in each. Cluster I comprised of 28 genotypes and cluster II had 19 genotypes. It was difficult to classify the genotypes either based on geographical region or based on their cultivation since there was assortment of wild and cultivated species. However the results reflect a high level polymorphism suggesting occurrence of genotypes of diverse genetic background that will be useful in breeding programmes.
Morphometric characteristics of Sycamore maple (Acer pseudoplatanus L.) fruits in Novi Sad urban populations

This paper shows the results of the analysis of the fruit morphometric characteristics of 29 trees of sycamore maple (Acer pseudoplatanus L.) and red-leaf sycamore maple (Acer pseudoplatanus 'Atropurpureum' Spath.) in Novi Sad area. Based on the test trees, it can be concluded that the analyzed secondary population of sycamore maple has a high level of intra - populations variability, based on different degrees of variability of measured parameters and statistically significant differences of all analyzed parameters within the analysed genotypes. The results indicate that there are certain differences between fruit of sycamore maple and its red - leaf variety. Given that there is no statistically significant difference between sites and different urban spaces, it can be concluded that stress factors caused by a high degree of urbanity do not affect the morphometric characteristics of fruits in the analyzed test trees. Testing the symmetry of fruits indicates a high level of genetic variability within the analyzed population.
ClassificaIO: machine learning for classification graphical user interface

Machine learning methods are being used routinely by scientists in many research areas, typically requiring significant statistical and programing knowledge. Here we present ClassificaIO, an open-source Python graphical user interface for machine learning classification for the scikit-learn Python library. ClassificaIO provides an interactive way to train, validate, and test data on a range of classification algorithms. The software enables fast comparisons within and across classifiers, and facilitates uploading and exporting of trained models, and both validation and testing data results. ClassificaIO aims to provide not only a research utility, but also an educational tool that can enable biomedical and other researchers with minimal machine learning background to apply machine learning algorithms to their research in an interactive point-and-click way. The ClassificaIO package is available for download and installation through the Python Package Index (PyPI) (http://pypi.python.org/pypi/ClassificaIO) and it can be deployed using the “import” function in Python once the package is installed. The application is distributed under an MIT license and the source code is publicly available for download (for Mac OS X, Linux and Microsoft Windows) through PyPI and GitHub (http://github.com/gmiaslab/ClassificaIO, and https://doi.org/10.5281/zenodo.1320465).
Contribution to identify the causal agents of Dutch elm disease in the Czech Republic

Dvořák M. , Tomšovský M. , Jankovský L. , Novotný D. (2007): Contribution to identify the causal agents of Dutch elm disease in the Czech Republic. Plant Protect. Sci., 43: 142–145. This study provides new data on Dutch elm disease in the Czech Republic. Ophiostoma novo-ulmi is reported for the first time in the area of the Czech Republic, as well as both subspecies ssp. novo-ulmi (indigenous in the area of the Ukraine and Moldavia), and ssp. americana indigenous in North America. The majority of the recorded strains belonged to O. n. -u. ssp. novo-ulmi, while O. n. -u. ssp. americana and hybrids of these two subspecies were found less frequently. On the other hand, Ophiostoma ulmi was not found at all in the investigated samples. Identification on the subspecies level was performed by methods of molecular biology, i.e. PCR and RFLP of gene regions cu and col1.
The brown bear Ursus arctos population in Lar Wildlife Refuge, northern Iran

Abstract Basic information about an animal population is essential to produce management and conservation strategies. Little is known about the brown bears Ursus arctos in Asia, and especially in Iran, and camera traps can be useful to provide information needed for creating conservation programs. The brown bear population and its diel activity patterns in Lar Wildlife Refuge (LWR) in the southern part of Alborz Mountains, northern Iran, were estimated from June 2013 to August 2014 for a total of 2783 camera-trap nights. Seven individuals were identified in November and December 2013, which were the only months bears were documented during the survey. Their peak diel activity was during late evening between 16:00 and 17:00. The results suggested that there were few brown bears in the LWR, that they are not resident in the Refuge, and that they come from an adjacent protected area, Central Alborz Protected Area (CAPA), perhaps to feed on spawning brown trout Salmo trutta.
Mitigation of sodium chloride toxicity in Solanum lycopersicum L. by supplementation of jasmonic acid and nitric oxide

ABSTRACT We investigated the effects of exogenous application of jasmonic acid (JA) and nitric oxide (NO) on growth, antioxidant metabolism, physio-biochemical attributes and metabolite accumulation, in tomato (Solanum lycopersicum L.) plants exposed to salt stress. Treating the plants with NaCl (200 mM) resulted in considerable growth inhibition in terms of biomass, relative water content, and chlorophyll content, all of which were significantly improved upon application of JA and NO under both normal and NaCl-stress treatments. Salt treatment particularly 200 mM NaCl caused an apparent increase in electrolyte leakage, lipid peroxidation, and hydrogen peroxide production, which were reduced by exogenous application of JA and NO. Salt treatment triggered the induction of antioxidant system by enhancing the activities of antioxidant enzymes like superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), and glutathione reductase (GR). Application of JA and NO separately as well as in combination caused a significant improvement in activities of SOD, CAT, APX, and GR activities. JA and NO either applied individually or in combination boosted the flavonoid, proline and glycine betaine synthesis under NaCl treatments. In conclusion, the exogenous application of JA and NO protected tomato plants from NaCl-induced damage by up-regulating the antioxidant metabolism, osmolyte synthesis, and metabolite accumulation.
Detection of environmental glucocorticoids and investigation of their effects using the zebrafish embryo as a model

Synthetic glucocorticoids (GCs) are widely used anti-inflammatory drugs. They mimic cortisol, the natural stress hormone in humans and in fish. Cortisol binds and activates the glucocorticoid receptor (GR), which regulates genes governing development, immune response, osmoregulation, and behavior. Therefore, the presence of GCs in the aquatic environment may cause endocrine disruption through impairing these essential physiological processes in fish. The aim of this thesis was to assess the effects of environmentally relevant concentrations of GCs in teleost fish, focusing on the inflammatory response and molecular mechanisms of GC action on different levels, from mRNA to proteins to metabolites. To confirm the environmental presence of GCs, GC activity was determined along a Swiss freshwater stream impacted by a wastewater treatment plant, using effect-directed analysis. The effluent samples showed the highest potency to activate the GR, as determined by the GR-CALUX® assay. The chemical analysis found clobetasol propionate (CP), a highly potent GC, to be responsible for 63% of the total GR activity in the sample. CP was selected as a model chemical to study GC effects in fish. Embryos of zebrafish (Danio rerio) aged until 5 days post fertilization (dpf) were used as a model organism; working with embryonic stages is a refinement of animal experiments. We demonstrated that CP is readily taken up by the embryos. Bacterial lipopolysaccharides (LPS) induce one of the main inflammatory cascades. As observed in LPS challenge assays, the inflammatory response of the embryos was significantly reduced after exposure to ? 0.1 nM CP. We showed that mRNA expression of several LPS mechanism- and GC action-related genes was regulated by CP. Among them, Annexin a1b (anxa1b) was significantly down-regulated after exposure to ? 0.05 nM CP. Sensitive regulation of anxa1b by the non-steroidal anti-inflammatory drug diclofenac (DCF) suggested that this gene product is a potential biomarker of steroidal and non-steroidal immunosuppressive effects. An LC-MS/MS-based targeted proteomics technique was developed to measure proteins, as it is these molecules that actually carry out cellular functions. 12 out of 40 GC action-related protein targets were detectable in control embryo digests and were subsequently monitored after CP, DCF and grab water sample exposures. We found that the muscle protein Myhz2 was regulated only after DCF exposure, while I? B? , an anti-inflammatory protein, was regulated only by CP, in agreement with mRNA level data. Global and targeted metabolomics analyses were performed in zebrafish embryos exposed to CP from 4 to 5 dpf, in collaboration with M. Lamoree (VU Amsterdam). Several of the detected compounds showed significant response to CP: lysine, nicotinamide, choline, hypoxanthine, tyrosine and tryptophan. To conclude, this thesis demonstrates that GCs are present in the aquatic environment and may suppress the inflammatory response of fish at environmentally relevant concentrations.