Miracle-dz/UniFAR-FTUs huggingface dataset:
Immunological techniques : immunochromotography , enzyme-linked immunofluorescent assays and agglutination techniques

Developments and technological advances in the field of microbiological test methods have resulted in the availability of a wide range of commercial kits and new techniques for the microbiologist. More recently there has been a gradual adoption of molecular biology methods into food testing, although lack of knowledge of these methods, the perceived greater costs associated with their use compared with traditional culture methods and lack of universal acceptance, currently restricts the widespread uptake of molecular methods. By comparison immunological methods which rely on the interaction between specific antibodies to selectively capture, label and detect antigens associated with the target organism are widely used and accepted for the detection and confirmation of specific microorganisms and certain toxins. The antigen of interest may be a cellular component of the target organism, such as a specific lippopolysaccharide on the outer cell wall, a protein on the flagella of certain motile bacteria, or a product or toxin produced by the organism during growth. The choice of antigen is particularly important as this will determine the specificity of the test. Antigens present on flagella can provide greater specificity, whilst some somatic antigens can be shared by a wide range of bacteria besides the target organism. A good example of such an antigen is the somatic O-antigen of E. coli O157. Although detection of this antigen provides a convenient and relatively specific method for detecting or confirming this pathogen, other bacteria share 10
Drought tolerance of multipurpose agroforestry tree species during first and second summer droughts after transplanting

The aim of this experiment was to select suitable drought tolerant agroforestry tree species. The findings of this investigation indicated that summer drought from April to June for 25, 50 and 75 days during first and second year after transplanting adversely but differentially affected growth and physiological attributes of five tree species namely, Grewia optiva, Morus alba, Dalbergia sissoo, Acacia catechu and Populus deltoides. Plant height, collar diameter and leaf biomass were less in water stressed plants compared to unstressed plants within each tree species and within each drought level. In general, 75 days of drought exerted more pronounced effect on the performance of tree species. The minimum adverse effect of summer drought was seen on M. alba and D. sissoo, while the maximum on G. optiva and P. deltoides. Xylem water potential was significantly higher in unstressed plants compared to water stressed plants of all the five tree species. The water potential (Ψ) in water stressed plants during second summer drought was higher compared to first summer drought. The lowest potential was recorded at 75 t h day of drought. M. alba and D. sissoo maintained relatively high xylem water potential under water stress, whereas G. optiva and P. deltoides recorded the lowest values. Reduction in photosynthesis under drought over control was least in M. alba and D. sissoo, whereas maximum in stressed plants of P. deltoides up to 75 t h day of drought. Drought injury index was minimum in M. alba (40.4%), followed by D. sissoo (52.1%) up to 75 t h day. P. deltoides exhibited maximum injury index during the summer drought (83.8%).
Leaf age, seasonal and annual variations in Salvia officinalis L. var. purpurascens biochemical characteristics

Medicinal and aromatic plants (MAP’s) have gain new attention in the past years due to their content in bioactive compounds and recognized health-promoting effects. One of the most important species of MAP’s is Salvia officinalis L. , rich in several phytochemicals (essential oil, phenolic compounds) and vitamins. Besides, it has various uses and pharmacological effects (including antibacterial, antiviral, antioxidative, anti-inflammatory, antidiabetic and antitumour activities). Salvia officinalis L. has many cultivars, including Salvia officinalis L. var. purpurascens , which is currently understudied. As few is known about this specific cultivar, characterization of this plant, as well as the study of biochemical variations occurring during its development, is of great significance. Hence, in this work, young and adult leaves of Salvia officinalis L. var. purpurascens , were collected in two different seasons (June and September) and in two different years (2011 and 2013). Several biochemical traits were analyzed, namely carbohydrate content, photosynthetic pigments concentration, total phenolics, soluble proteins, as well as oxidation parameters (thiobarbituric acid reactive substances, thiols and electrolyte leakage). The Year factor significantly influenced carbohydrate content (higher in 2013 for non-structural carbohydrates and soluble sugars, but lower for starch), but also chlorophyll and carotenoid content (higher in 2011), with a similar influence recorded for the Season of harvest (higher values for starch, chlorophyll and carotenoids in September, but lower for soluble sugars). The developmental stage of leaves showed significant influence mainly in the content of photosynthetic pigments, with higher values of chlorophyll and carotenoids recorded in young leaves. The results show the biochemical variations occurring in plants of Salvia officinalis L. var. purpurascens , during developmental stages, and others associated to season of harvest and year, and their relation to climatic factors. The gathered data, besides useful for the characterization of this plant, is also valuable when aiming for the optimization of sage cultivation.
Occurrence of Listeria monocytogenes in Milk and Dairy Products Produced or Imported Into Morocco.

Examination of 227 samples of milk and dairy products for Listeria monocytogenes showed that raw milk and some Moroccan traditionally made dairy products such as Iben and raib (fermented milks) and jben (fresh cheese) were contaminated with this pathogen. L. monocytogenes was the only Listeria species isolated except in one case in which it was associated with Listeria innocua . Pasteurized milk, fresh cream, and fresh and ripened cheeses (industrially made) were free from L. monocytogenes .
APICULTURE AND POLLINATOR INDUSTRY SURVEY IN THAILAND

Present study was conducted in Chiang Mai and Chiang Rai provinces are the part of this honey zone producing. This zone is the lychee and longan production in-season. Samut Songkhram province is another lychee production zone and Chanthaburi province is longan production zone in off-season. Total 22 beekeepers were selected by using snowball sampling technique. The 11 bee experts, 4 bee researchers, 9 longan and 6 lychee orchard owners were selected as respondents through purposive sampling technique. The collected data were statistically analyzed with the help of Statistical Package for Social Sciences (SPSS). Findings revealed that 4 bee species: European honeybee (Apis mellifera ligustica L.), Asian honeybee (A. cerana indica F.), giant honeybee (A. dorsata F.) and stingless bees (Tetragonula pagdeni (Schwarz) and T. laeviceps Smith) used by beekeepers in Thailand. However, the main species in the bee industry is the European honeybee with 300,000 colonies and the farm value of bee products is about 37.7 million USD and honey export value of 17.1 million USD in 2012. The key nectar crops are longan, lychee and Siam weed. The key pollen crops are corn, giant mimosa and sensitive plant. The peak activities of honeybees are within 4 months starting in December to March which coincide with the availability of the 3 main nectar crops. The biggest challenges, according to beekeepers surveyed, are food sources (25.6%) and the Tropilaelaps mite (25.6%). The bee pollination industry is most developed in the northern provinces and there is a potential to develop in other parts of Thailand. The future of apiculture industry in Thailand is still on the rise because the demand of honey and other bee products both at national and international levels is increasing and the volumes of bee products are not sufficient at present
Protective effects of Erythrina variegata and Spirulina platensis in imidacloprid intoxicated White Leg Horn cockerels

Forty two white leghorn cockerels were divided randomly and equally into six groups viz. I, II, III, IV, V and VI. Group I served as control and other groups were administered as SP @ 0.2% in II, IMI @ 50 PPM in III, SP @ 0.2% plus IMI @ 50 PPM in group IV, EVLP (1%) in group V and EVLP (1%) plus IMI @ 50 PPM in VI, respectively, for 60 days. Grossly, only kidneys and testes showed lesions in group III only. Histopathological changes such as vascular changes, swelling of the glomeruli and hypercellularity of the glomerular capillaries in kidney; vascular changes, vacuolar degeneration of the hepatocytes throughout the parenchyma and presence of mononuclear cells around congested blood vessels in liver; reduction in size of the seminiferous tubules with a single layer of germinal epithelium in testes and congestion of blood vessels, elongation of neurons, gliosis and satellitosis in brain were observed in IMI treated group. Group VI showed mild pathological lesions while there were no pathological changes in liver, kidney, testes and brain from cockerels of group IV. It was concluded that simultaneous administration of Spirulina platensis (0.2%) and Erythrina variegata (1%) in imidacloprid intoxicated (@50 ppm)white leghorn cockerels in feed for 60 days produced ameliorating effects on the toxic pathology.
Metabolism of pyrimidines in protoplasts from cultured Catharanthus roseus cells

The metabolism of [2-14C]thymine, [2-14C]thymidine, [2-14C]uracil and [14C]uridine was investigated in protoplasts obtained from suspension cultures of Catharanthus roseus. Most of the exogenously supplied thymine, thymidine and uracil was degraded, and salvage of these pyrimidines accounted for 5–36 per cent of the total amount of 14C-labelled precursors which was metabolized. However, more than 80 per cent of the labelled uridine was utilized for the biosynthesis of nucleotides and nucleic acids, and the rest was degraded. In contrast to the results from protoplasts of sugar cane cells in suspension culture, the data indicate that protoplasts possess a pathway for the degradation of pyrimidines, and that the overall metabolism of these pyrimidines in protoplasts is very similar to the metabolism in the intact cells.
Genetic characteristics of broodstock and offspring of the seven-band grouper (Hyporthodus septemfasciatus) using fluorescent-AFLP markers

Seven-band grouper (Hyporthodus septemfasciatus) is a commercial rocky reef fish in East Asia that has been regarded as a promising species for aquaculture. To investigate the broodstock contributions to offspring for the sustainability of fry production, 62 individuals of H. septemfasciatus from two broodstocks and one offspring population were analysed using fluorescent-AFLP. A total of 602 bands were amplified and 70.10% of them were polymorphic. The numbers of polymorphic loci were 308 (P broodstock I = 55.50%) and 356 (P broodstock II = 63.12%) in the two broodstocks, and 294 (P offspring = 52.88%) in the offspring, respectively. The average values of Shannon diversity index (I) and expected heterozygosity (H) were higher in the broodstock (I broodstock I = 0.281, I broodstock II = 0.244, H broodstock I = 0.185, H broodstock II = 0.161) than those in the offspring (I offspring = 0.243, H offspring = 0.161). AMOVA and FST analyses showed that significant genetic differentiation between broodstock and offspring populations, and limited effective broodstock population size has contributed to the offspring. Both STRUCTURE and Principal Coordinates Analysis (PCoA) also showed the three populations composed of two stocks and most offspring individuals (95.0%) only originated from 44.0% of the individuals of broodstock I, which may have negative effects on sustainable fry production. Therefore, genetic variation between broodstock and offspring should be monitored, and large effective size of broodstock should be employed to ensure the success of commercial breeding programmes. Our data provide a useful genetic basis for future planning of sustainable culture and management of H. septemfasciatus.
HMGA1 knock-down induces autophagy through regulation of ULK gene expression in cancer cells

High Mobility Group A1 (HMGA1) is a chromatinic protein whose overexpression is a feature of malignant neoplasias. Many studies support its causal role in cell transformation and cancer progression. Indeed, HMGA1 is an architectural transcriptional factor that regulates, by binding DNA and interacting with various transcriptional regulators, the expression of several genes involved in critical biological processes, such as cell proliferation, apoptosis and migration. Autophagy is a self-degradative process that, providing energy sources, removing damaged organelles and misfolded or aggregated proteins, allows cell survival in stress conditions or, when iper-activated, leads to non-apoptotic programmed cell death. Autophagy is often deregulated in cancer cells in which plays an important and complex role, being mainly oncogenic during cancer initiation, and tumor-suppressive during cancer progression. Studying the effects of HMGA1 knock-down in skin cancer cells SCC-13, I have found that it increases autophagy, as assessed by both western blot and immunofluorescence analysis of several autophagic markers, such as pS6, LC3 and SQSTM1/p62. Interestingly, the ability of HMGA1 depletion to increase autophagy is not restricted to skin cancer cells, since similar results have been achieved also silencing HMGA1 expression in HeLa cells, and mouse embryonic fibroblasts null for Hmga1 are more susceptible than the wild-type counterpart to undergo autophagy after starvation or treatment with rapamycin. Consistently, silencing of HMGA1 upregulates the two autophagy-initiating kinases Unc-51-like kinase 1 (ULK1) and Unc-51-like kinase 2 (ULK2), and functional experiments demonstrate that HMGA1 binds their promoter regions and negatively regulates their transcription. Accordingly, the block of ULK1 expression reduces the pro-autophagic effects induced by HMGA1 silencing indicating that they are, at least in part, mediated by ULK1. Taken together, these results clearly indicate that HMGA1 protects cancer cells from autophagy, thus suggesting, on one hand, a new mechanism through which HMGA1 can contribute to cancer progression and, on the other hand, a mechanism through which autophagy can be deregulated in cancer cells.
Imaging from temporal data via spiking convolutional neural networks

A new approach for imaging that is solely based on the time of flight of photons coming from the entire imaged scene, combined with a novel machine learning algorithm for image reconstruction: a spiking convolutional neural network (SCNN) named Spike-SPI (Spiking - Single Pixel Imager). The approach uses a single point detector and the corresponding time-counting electronics, which provide the arrival time of photons in the form of spikes distributed over time. This data is transformed into a temporal histogram containing the number of photons per arrival time. A SCNN that converts the 1D temporal histograms into a 3D image (2D image with depth map) by exploiting the feature extraction capabilities of convolutional neural networks (CNNs), the high dimensional compressed latent space representations of a variational encoder-decoder network structure, and the asynchronous processing capabilities of a spiking neural network (SNN). The performance of the proposed SCNN is analysed to demonstrate the state-of-the-art feature extraction capabilities of CNNs and the low latency asynchronous processing of SNNs that offer both higher throughput and higher accuracy in image reconstruction from the ToF data, when compared to standard ANNs. The results of Spike-SPI show an increase in spatial accuracy of 15% over then ANN, using the Intersection of Union (IoU) for the objects in the scene. While also delivering a 100% increase over then ANN in object reconstruction signal to noise ratio (RSNR) from ~3dB to ~6dB. These results are also consistent across a range of IRF (Instrument Response Functions) values and photo counts, highlighting the robust nature of the new network structure. Moreover, the asynchronous processing nature of the spiking neurons allow for a faster throughput and less computational overhead, benefiting from the operational sparsity in the single point sensor.
Genetic Improvement of the Pentose-Fermenting Yeast Pachysolen tannophilus for Fermentation of Lignocellulosic Substrates

GENETIC IMPROVEMENT OF THE PENTOSE-FERMENTING YEAST PACHYSOLEN TANNOPHILUS FOR FERMENTATION OF LIGNOCELLULOSIC SUBSTRATES Nicole Krystyna Harner Co-Advisors: University of Guelph, 2015 Dr. H. Lee and Dr. J.T. Trevors An efficient lignocellulosic bioconversion process requires robust inhibitortolerant yeast strains capable of fermenting all sugars in non-detoxified lignocellulosic hydrolysates to desired product(s). Pentose-fermenting yeasts such as Pachysolen tannophilus can ferment both glucose and xylose to ethanol, but performs poorly in the presence of hydrolysate inhibitors. We initiated a strain development program to improve the properties of P. tannophilus by non-recombinant means. A blend of random mutagenesis coupled with genome shuffling was used to obtain improved strains of P. tannophilus with enhanced ethanol production and tolerance to inhibitors in hardwood spent sulfite liquor (HW SSL). Genome shuffled strains (GHW301, GHW302 and GHW303) grew at higher concentrations of HW SSL (80 % v/v) compared to HW SSLtolerant (UHW301, UHW303 and UHW303) UV mutants (60 and 70 % v/v) and the wild-type (WT) strain (50 % v/v). In defined media containing acetic acid (0.70–0.90 % w/v), GHW301, GHW302 and GHW303 exhibited a shorter lag compared to acetic acidtolerant (UAA301, UAA302 and UAA303) UV mutants, while the WT did not grow. Genome shuffled strains produced more ethanol than the WT at higher concentrations of HW SSL and an aspen hydrolysate. To identify the genetic basis of inhibitor tolerance, whole genome sequencing was carried out on GHW301, GHW302 and GHW303 and compared to the WT strain. Sixty single nucleotide variations were identified that were common to all three genome shuffled strains. Of these, 40 were in gene sequences and 20 were within 5 bp–1 kb either up or downstream of protein encoding genes. Based on the mutated gene products, mutations were grouped into functional categories and affected a variety of cellular functions, demonstrating the complexity of inhibitor tolerance in yeast. Sequence analysis of UV mutants (UAA302 and UHW303) from which GHW301, GHW302 and GHW303 were derived, confirmed the success of our cross-mating based genome shuffling strategy. Whole-genome sequencing analysis allowed identification of potential gene targets for tolerance to inhibitors in lignocellulosic hydrolysates, and this information can guide engineering strategies aimed at developing strains for efficient bioethanol production.
Notes on Thymus L. (Labiatae) in Europe. III.

villous-hirsute indumentum, but slightly revolute When the account of the genus was prepared leaf marginS( and generally longer calyx (up to for Flora Europaea (Jalas 1971, 1972), the g 5 mm) and ^ teeth ( tQ ^ mm) author's knowledge of the variation pattern In thg area q{ pangeon 0ros> Eastern Macedo, within the so-called cherlerwides-group (Jalas & ni Greece> the twQ sub ies are connected Kaleva 1970) of the section Pseudothymbra was fay t intermediates. simply too fragmentary to allow any thorough Stojanov et al. (1967: 933) consider T. nei revision of the taxa concerned. During subse- ceffU to bg synonymous with T_ perinicus> a quent studies of a fairly large number of speci- yiew hardly tenable in the ligM of the material mens, representing different parts of the distri- studied 0n the other hand> the possibiiity can. bution area of the group and including most nQt fae disregarded that subsp. neiceffii may be of the pertinent types, it became apparent that, a more Qr less stabilized hybrid derivative from m the Balkan Peninsula, this group consists of earlier crosses between T leucotrichus and at least half a dozen different taxa, which are y thracicus relatively well defined and show interesting dis tributional peculiarities. The present paper will be restricted to two of these, whose taxonomical Thymus perinicus (Velen.) Jalas, comb, et stat. value was clearly underestimated by Ronniger nov. (1930) and most subsequent authors.
Functional implications of changes in seagrass species composition in two shallow coastal lagoons

While the consequences of losing seagrass meadows are well known, there is less information on the functional implications of changes in seagrass species composition. In this study, we use data from a long-term monitoring project in shallow lagoons on the Florida Gulf Coast to assess changes in the functional attributes of seagrass beds during a shift in seagrass species composition. We compare seagrass beds in 2 neighboring lagoons with different trends: one where the composition changed from 100% Halodule wrightii to a mixed bed with up to 60% Ruppia maritima, and one where the species composition remained unchanged. Our results indicate that the partial replacement of H. wrightii by R. maritima did not alter seagrass biomass m−2, detrital biomass m−2, benthic gross primary production, or benthic respiration. However, there was a small positive effect on benthic net primary production. While seagrass biomass m−2 declined at both sites, the emergence of R. maritima increased the amount of available habitat through rapid expansion. Overall, our data suggest that shifts between 2 seagrass species with similar mor phology, but different ecological strategies, may have little impact on the ecosystem services of seagrass beds in shallow coastal lagoons.
Extra-Pair Copulation and Extra-Range Movements in Flammulated Owls

We report an extra-pair copulation (EPC) in the Flammulated Owl (Otus flammeolus), the first in strigiforms, and document 21 cases of extra-range movements (ERMs) in this species. Extra-range movements occurred throughout nesting with both sexes participating: males anytime during nesting and females only after their young fledged. Males appear to make ERMs to gain EPCs and later to evaluate resources and the status of males in other areas, whereas females may be assessing the success of nests in adjacent ranges to judge the quality of potential future mates.
Proteolysis and production of biogenic amines in Toma Piemontese PDO cheese during ripening

Proteolysis of Toma Piemontese PDO cheese (large/long-ripened cheese and small/short-ripened cheese types) during ripening was studied by monitoring changes in nitrogenous compounds (protein content, SDS-PAGE, pH 4.6 soluble-nitrogen and ripening index). Changes in the concentration of four biogenic amines and their precursor amino acids were also determined, showing the presence of histamine and tyramine (up to a total concentration of 145 mg kg') in long-ripened cheese. The total concentration of biogenic amines in the commercial samples analyzed did not exceed 219 mg kg -1 . In comparison to short-ripened Toma, long-ripened Toma had a higher level of proteolysis (ripening index up to 20.8% after 64 days ripening) with the characteristic disappearance of the α s1 -casein band in the electrophoresis profiles. The increase in proteolysis during ripening was confirmed by PCA, showing the possibility of using this technique to assess the age of unknown cheese samples. The main variables contributing to the first principal component were ripening index, % soluble N, phenylalanine and α s1 -casein.