Miracle-dz/UniFAR-FTUs huggingface dataset:
Alcoholic Fermentation of Orange Juice with S. Cerevisiae

Orange juice was fermented with S. cerevisiae using natural (NJ) or pasteurized (PJ) juice, at 2 pHs (3.5 or 4.0) and at 2 temperatures of fermentation (10 or 20°C) and 2 of aging (10 or 20°C). Reducing sugars (RS) and total sugars (TS), aminoN and yeast counts were determined during 4 stages: initial, fermentation, bottling and aging (4 months). Sugars and ethanol were determined as well at the end. RS and TS decreased during the fermentation for both musts as well as amino-N, later remaining almost constant. Yeast counts were 2×106/mL (NJ) and 7×106/mL (PJ). Fructose (80-90%) and glucose (<20%) were detected after bottling but not sucrose. Ethanol reached 60-80 g/L (NJ) and 80-85 g/L (PJ). Sugars and amino-N increased slightly during aging, but ethanol decreased in NJ and increased slightly in PJ. Yeast counts decreased. Yeasts metabolized almost all sugars and amino-N during the fermentation for growing; later, during ethanol production there were almost no changes up to bottling, occurring their lysis.
Mechanism Analysis and Stabilization of Three-Phase Grid-Inverter Systems Considering Frequency Coupling

Frequency coupling in the phase domain is a recently reported phenomenon for phase locked loop (PLL) based three-phase grid-inverter systems. This paper investigates the mechanism and stabilization method for the frequency coupling to the stability of grid-inverter systems. Self and accompanying admittance models are employed to represent the frequency coupling characteristics of the inverter, and a small signal equivalent circuit of a grid-inverter system is set up to reveal the mechanism of the frequency coupling to the system stability. The analysis reveals that the equivalent inverter admittance is changed due to the frequency coupling of the inverter, and the system stability is affected. In the end, retuning the bandwidth of the phase locked loop is presented to stabilize the three-phase grid-inverter system. Experimental results are given to verify the analysis and the stabilization scheme.
Cloning and in vitro Expression of N1 Neuraminidase Gene of Avian Influenza Virus A/Duck/Thailand/KU-KPS/2004(H5N1)

Avian influenza virus (AIV) can spread rapidly and causes serious disease to animals and humans so it is crucial to have effective diagnostic tools for determining its existence. The purposes of this study were first, to clone N1 neuraminidase (NA) gene of AIV A/Duck/Thailand/KU-KPS/2004 (H5N1), and second, to express recombinant N1 using baculovirus expression system. Viral RNA extracted from positive AIV allantoic fluid was reverse-transcribed to cDNA and then was amplified by PCR using N1 specific primers. The PCR products approximately 1,300 bp that encode the N1 was introduced into baculovirus vector in order to allow N1 expression in insect cell lines. Immuno-dot blot analysis of crude extract of baculovirus infected insect cells using goat-anti H5N1 AIV hyperimmune serum gave a clear immunoreactive spot. SDS-PAGE analysis showed banding patterns from the crude extract contained major protein of 54 kDa. Western blot analysis using goat-anti H5N1 hyperimmune serum and mouseantihistidine monoclonal antibody also gave a specific band approximately the same size as that of SDSPAGE. Expression analysis of this gene indicated that recombinant neuraminidase may have correct post-translation modification and folding. The recombinant neuraminidase could be very useful for the development of a test kit that can differentiate infected from vaccinated animals (DIVA).
Ground vertebrate fauna of Perth's vegetation remnants: impact of 170 years of urbanization

Ground vertebrates were surveyed on 34 vegetation remnants on the Swan Coastal Plain within the Perth metropolitan area. The remnants ranged from one hectare to nearly 340 ha and were sampled for at least 50 days during the year using pitfall traps. Six remnants were sampled in two or more successive years. Seven native, non-volant mammal, six introduced mammal, 11 amphibian and 43 reptile species were recorded. Native mammals are the most disadvantaged vertebrates in urban remnants with few species surviving the effects of long-term fragmentation. The herpetofauna is less affected, although snakes are generally rare. Marked annual variation occurred in lizard assemblages recorded on remnants sampled over consecutive years. On average, these remnants had a similarity in species composition of only 77% between years. Small remnants are important for conservation of reptile assemblages and there is a strong correlation between remnant area and species number for all reptile groups, except skinks. Remnants as small as one hectare retain viable populations of many reptiles, but need active management to exclude fire and predation. Regional biogeographic patterns are apparent in reptiles. Subregional patterns on the Swan Coastal Plain are associated with different soil types and the Swan River also creates a barrier across landforms. The diversity of reptile assemblages and variation in species trophic patterns indicate that many elements of the original food chain continue to operate in these urban environments.
Mode of larval development as a key factor to explain contrasting effects of temperature on species richness across oceans

Aim It has been proposed that the mode of larval development (MLD) could explain the exceptions to the latitudinal gradient of species richness exhibited by several groups of marine organisms. We evaluate the generality of the latitudinal patterns of species richness for different MLDs, and analyse the effects of environmental variables on species richness – explicitly considering feeding type during the larval phase – to identify the relevance of the dichotomies between feeding and non-feeding larvae and between pelagic and non-pelagic development. Location South America, from 10° to 54° S in the south-western Atlantic and from 18° to 54° S in the south-eastern Pacific. Methods Using molluscs and crustaceans in two oceans, we deconstructed latitudinal patterns of species richness for three MLDs (planktotrophic, lecithotrophic and direct development). The effects of sea water temperature, chlorophyll a concentration and shelf area on the spatial variation in species richness were analysed for each MLD. Results We found remarkably similar trends in species richness deconstructed by MLD. Planktotrophic species richness decreased polewards, and the converse pattern was observed in direct developers. In the majority of groups with lecithotrophic development, species richness increased from middle to higher latitudes. The main component explaining the variation in species richness was the spatial structure of sea water temperature. Temperature showed positive effects on planktotrophic species and negative effects in almost all lecithotrophic or direct-developing groups in both oceans and both taxa. Main conclusions The similar relationship of temperature with lecithotrophic and direct developers, which contrasts with planktotrophic species, suggests that food availability during planktonic larval development is a critical factor determining species distribution of marine invertebrates. We ruled out the cost of brooding as a single causal factor explaining the poleward increase in diversity of direct developers. Simple linear models can describe changes in the proportion of species with temperature within each MLD.
Approaches for inclusion of forest carbon cycle in life cycle assessment – a review

Forests are a significant pool of terrestrial carbon. A key feature related to forest biomass harvesting and use is the typical time difference between carbon release into and sequestration from the atmosphere. Traditionally, the use of sustainably grown biomass has been considered as carbon neutral in life cycle assessment (LCA) studies. However, various approaches to account for greenhouse gas (GHG) emissions and sinks of forest biomass acquisition and use have also been developed and applied, resulting in different conclusions on climate impacts of forest products. The aim of this study is to summarize, clarify, and assess the suitability of these approaches for LCA. A literature review is carried out, and the results are analyzed through an assessment framework. The different approaches are reviewed through their approach to the definition of reference land‐use situation, consideration of time frame and timing of carbon emissions and sequestration, substitution credits, and indicators applied to measure climate impacts. On the basis of the review, it is concluded that, to account for GHG emissions and the related climate impacts objectively, biomass carbon stored in the products and the timing of sinks and emissions should be taken into account in LCA. The reference situation for forest land use has to be defined appropriately, describing the development in the absence of the studied system. We suggest the use of some climate impact indicator that takes the timing of the emissions and sinks into consideration and enables the use of different time frames. If substitution credits are considered, they need to be transparently presented in the results. Instead of carbon stock values taken from the literature, the use of dynamic forest models is recommended.
Molecular Attributes affecting the Biofilm Formation of Listeria monocytogenes

ii Dedication.v Acknowledgments.vi Vita.vii Field of Study.vii List of Tables.xi List of Figures.xii Chapter 1: Literature Review.1 1.1 Listeria monocytogenes.1 1.1.1. General characteristics.1 1.1.2 Listeria species and serotyping.2 1.1.3 Listeria genome.2 1.2 Listeriosis and its outbreak.2 1.2. 1 Listeriosis characteristics.2 1.2. 2 Listeriosis outbreaks.3 1.3 Listeria monocytogenes pathogenesis.4 1.3. 1 Listeria pathogenicity island.5 1.3. 1.1 Positive regulatory factor A (prfA). 6 1.3. 1.2 The internalin family--key attachment and internalization proteins.9 1.3. 1.3 Listeriolysin O (LLO). 14 1.3. 1.4 Phospholipase C and metalloprotease.16 1.3. 1.5 Actin Assembly gene.18 1.3. 1.6 Hexose phosphate transporter (HptA). 20 1.4. Biofilms.20 1.4. 1 Quorum sensing.22 1.4. 2 L. monocytogenes biofilms.23 1.4. 3 L. monocytogenes in mixed culture biofilms.25 1.4. 4 Molecular attributes of biofilms.26
APEC: improved acknowledgement prioritization through erasure coding in bufferless NoCs

Bufferless NoCs have been proposed as they come with a decreased silicon area footprint and a reduced power consumption, when compared to buffered NoCs. However, while known for their inherent simplicity, they suffer from early saturation and depend on additional measures to ensure reliable packet delivery, such as control protocols based on ACKs or NACKs. In this paper, we propose APEC, a novel concept for bufferless NoCs that allows to prioritize ACKs and NACKs over single payload flits of colliding packets by discarding the latter. Lightweight heuristic erasure codes are used to compensate for discarded payload flits. By trading off the erasure code overhead for packet retransmissions, a more efficient network operation is achieved. For ACK-based networks, APEC saturates at 2.1x and 2.875x higher generation rates than a conventional ACK-based bufferless NoC for packets between 5 and 17 flits. For NACK-based networks, APEC does not require concepts such as deflection routing or circuit-switched overlay NACK-networks, as prior work does. Therefore, it can simplify the network implementation compared to prior work while achieving similar performance.
Redefinition of cell size classification of phytoplankton – a potential tool for improving the quality and assurance of data interpretation

To date, p hytoplankton cell size classification is based on linear metrics (nano: 2-20 μm; micro: 20-200 μm; macro: >200 μm) although three-dimensional metrics are used for cell or body size descriptions of all terrestrial and aquatic organisms. This study proposes a redefinition of phytoplankton size classification expressed in terms of cell volume (μm 3 ) metrics by analyzing statistically a data set of 397 species from three major groups of eukaryotic taxa (diatoms, dinoflagellates, coccolithophores). The three size classes based on cell volume metrics are nanoplankton (10-10 3 μm 3 ), microplankton (10 3 -10 6 μm 3 ) and macroplankton (10 6 -10 9 μm 3 ). Size spectra of cell volume frequencies, species richness-cell size and cell abundance-cell size relationships were evaluated with the use of cell volume (μm 3 ) metrics while fitting of the relevant equations significantly accounted for the data. The analysis of size classes versus taxonomic composition based on cell volume metrics revealed taxonomic group (diatoms, dinoflagellates, coccolithophores) differentiations in nano-micro-macro size classes, thus providing an accurate size classification within and among taxa. This classification offers more precise information on the taxon-size relationships, which are valuable for phytoplankton community structure studies and useful for further development of the remote sensing models designed for differentiating phytoplankton taxa by satellite. Normal 0 false false false EL X-NONE X-NONE
Mitochondrial Cytochrome b Sequences Support Recognition of Two Cryptic Species of Plains Killifish, Fundulus zebrinus and Fundulus kansae

Abstract The current literature treats the plains killifish as a single species (Fundulus zebrinus). However, a recent range-wide survey of genetic variation detected two distinct groups. The presence of the two groups suggests that the plains killifish may actually represent two species (F. zebrinus and F. kansae), as has been proposed in prior taxonomic treatments. Previous molecular studies within the genus Fundulus have relied upon the mitochondrial cytochrome b gene. I generated a set of cytochrome b sequences in order to compare the phylogenetic support for the putative species F. zebrinus and F. kansae with that found in other accepted sister species of Fundulus. Both neighbor-joining and maximum parsimony analyses recovered two clades of plains killifish that were strongly supported by a variety of measures including branch lengths, decay indices and bootstrap proportions. The strength of support for the putative F. kansae and F. zebrinus clades was comparable to, or better than, similar measures for six other sister species pairs of Fundulus. While the molecular data supported the recognition of two species of plains killifish, the groups recognized were not in agreement with the range descriptions previously proposed for the two species.
The In Vitro Antioxidant and Anti-Proliferative Effect and Induction of Phase II Enzymes by a Mistletoe (Viscum Album ) Extract

The increasing interest for phytochemical antioxidants, found in many medicinal plants, is demonstrated experimentally by epidemiological and in vitro studies which show their positive effects on human health. Mistletoe contains therapeutically active ingredients which incubated with several human cancer cell lines revealed cytotoxicity for the cancer cells, but no evidence is available for their chemoprotective properties. We investigated in vitro the potential of extracts from Viscum album growing on Mallus domestica (VAM) to modulate the activity of phase II detoxifying enzymes using the gluthatione S-transferase (GST) and quinone oxidoreductase (QR) assays and to inhibition of adherent epithelial human ovarian tumor cells A2780 proliferation using the MTT assay. We found that different concentrations of VaM extract had inhibitory effects on the growth of adherent epithelial human ovarian tumor cells A2780 (IC50 = 120.62 µg/ml, after 48 h treatment). Also, this extract is a good antioxidant source (total phenol content of 91.51 mg gallic acid equivalents /g dry weight), having a radical scavenging ability and a reducing potential proportional to the dose used (from 0.312 to 5 mg/ml) in vitro. At 120 µg/ml, this extract increased, significantly, the activity of GST and QR, as well the level of GSH.
Binding Mode Identification for 7-keto-8-Aminopelargonic Acid Synthase (AtKAPAS) Inhibitors

In this study, we determined the 3D structure of Arabidopsis thaliana KAPAS by homology modeling. We then investigated the binding mode of compounds obtained from the in-house library using computational docking methods. From the flexible docking study, we achieved high dock scores for the active compounds denoted in this study as compound 3 and compound 4. Thus, we highlight the flexibility of specific residues, Lys 312 and Phe 172, when used in active sites. result of several flexible docking processes, this study emphasizes the flexibility of several residues. Noticeably higher
Effect of different cooking methods on the antioxidant activity of some vegetables from Pakistan

Summary The effects of different cooking methods (boiling, frying and microwave cooking) on the antioxidant activity of some selected vegetables (peas, carrot, spinach, cabbage, cauliflower, yellow turnip and white turnip) were assessed by measuring the total phenolic contents (TPC), reducing power and percentage inhibition in linoleic acid system. TPC (gallic acid equivalents g/100 g of dry weight) and reducing power of the methanolic extracts of raw-, microwaved-, boiled- and fried vegetables ranged 0.333–2.97, 0.52–2.68, 0.48–2.08, 1.00–2.02 and 0.391–2.24, 0.822–1.10, 0.547–1.16, 0.910–4.07, respectively. The level of inhibition of peroxidation ranged 71.4–89.0, 66.4–87.3, 73.2–89.2 and 77.4–91.3%, respectively. Antioxidant activity of the vegetables examined was appreciably affected because of varying cooking treatments. TPC of vegetables, generally, decreased by boiling, frying and microwave cooking. There was a significant (P < 0.05) increase in reducing power as a result of frying. However, boiling and microwave cooking did not affect reducing power. Inhibition of peroxidation increased by boiling and frying, whereas, in contrast it was decreased by microwave cooking. The results of the present investigation showed that all the cooking methods affected the antioxidant properties of the vegetables; however, microwave treatment exhibited more deleterious effects when compared with those of other treatments. Thus an appropriate method might be sought for the processing of such vegetables to retain their antioxidant components at maximum level.
Classification of Green Pitcher Plant (Sarracenia oreophila (Kearney) Wherry) Communities in the Little River Canyon National Preserve, Alabama

Abstract Pitcher plant bogs of the Little River Canyon National Preserve in northern Alabama contain the federally endangered green pitcher plant (Sarracenia oreophila (Kearney) Wherry). Multivariate analysis of the bog vegetation and environmental variables revealed three communities with unique species compositions and soil characteristics. The significant soil characteristics were percent A-horizon sand and A-horizon depth. A blackgum (Nyssa sylvatica Marsh.)-yellow-poplar (Liriodendron tulipifera L.)-azalea (Rhododendron canescens (Michx.) Sweet) type was found on sites bisected by ephemeral streams with a closed canopy. A scarlet oak (Quercus coccinea Muenchh.)-flowering dogwood (Cornus florida L.)-sweet goldenrod (Solidago speciosa Nutt. var. erecta (Pursh) MacM. ) type was found on upland sites close to the canyon rim and along perennial streams sites. A smooth yellow false foxglove (Aureolaria flava (L.) Farw. )-pale-spike lobelia (Lobelia spicata Lam.)-violet lespedeza (Lespedeza violacea (L.) Pers. type was found on relatively flat sites away from the canyon rim. The results can be used to locate potential sites for restoration of green pitcher plant bogs. Survival of the bogs is threatened by encroachment of over and midstory vegetation.
Reconstructing the phylogenetic relationships of nematodes using draft genomes and transcriptomes

Nematoda is a very diverse animal phylum. Within Nematoda, species display a multitude of life styles, different reproductive strategies and parasitism has arisen independently several times. Furthermore, morphological conservation and a high rate of homoplasy have impeded the resolution of nematode systematics. To address these issues, single gene (usually the nuclear ribosomal small subunit gene) and mitochondrial gene phylogenies have been used, but the information contained within the sequence of these genes is not enough to resolve the topological relationships between clades that emerged during rapid cladogenesis. Next generation sequencing data have been shown to produce high quality genomic and transcriptomic assemblies at low cost, as a result more and more nematode species are being sequenced. Sequences were gathered or generated for 53 nematode species from ESTs, gene predictions from full genome assemblies and transcripts from RNA-Seq experiments. These sequences were screened for orthologous gene clusters, which were concatenated into a supermatrix with thousands of aminoacid sites. The analysis of the supermatrix with maximum likelihood and Bayesian inference methods sheds light into the early splitting clades of the phylogenetic tree of nematodes and the derived clades III, IV and V. Furthermore, the phylogenetic relationships within the parastitic family Onchocercidae were resolved, unveiling the evolutionary history of these important taxa. Finally, data produced in this work will be useful for subsequent evolutionary studies of the phylum Nematoda.
Ultrastructure of tracheid cell walls in radiata pine (Pinus radiata) mild compression wood

The structure of tracheid cell walls in mild compression wood of Pinus radiata D. Don was examined by confocal laser scanning fluorescence microscopy (CLSM) and transmission electron microscopy (TEM). Fluorescence microscopy using lignin autofluorescence revealed cell to cell variations in lignification of the cell corner middle lamella (CCML) and outer S2 (S2L) regions supporting observations made at higher resolution with TEM. The mild compression wood sample examined lacked the characteristic intercellular spaces of most grades of compression wood and thus represents the least severe grade of compression wood. TEM observations revealed evidence for radial striations in the S2 region probably representing regions of alternating high and low lignin concentration, which may be the precursor to the helical cavities found in severe compression wood. These radial striations typically showed a sinuous and branched structure, extending partly into the S2L region, where the orientation of lignin lamellae was pr.
Gear-independent patterns of variation in catch of juvenile Atlantic cod (Gadus morhua) in coastal habitats

Habitat and size of juvenile Atlantic cod (Gadus morhua) change substantially during the first 3 years after settlement, and hence, cohort size cannot be followed using a single gear. We investigated whether catch could be calibrated across gear types by deploying pairs of gears repeatedly in the same habitat. As expected, size selectivity differed substantially among gears. Trawls and seines generally collected individuals 150 mm. Size modes, corresponding to age-classes, were common to catches of most gears. Highest catches were taken by trawls and seines. Gillnet catches were orders of magnitude lower. Standardized catches could not be calibrated across pairs of gears deployed in the same habitat at approximately the same time. However, it was possible to identify spatial depth gradients and diel changes in catch that were independent of gear. Consistent spatial and temporal patterns across gears were interpreted as characteristic of fish populations, not just of gears. Density in coastal habitats was higher at night and was higher at 4n7 m than at greater depths. These results, in conjunction with other studies, establish that coastal depths of 4n7 m represent the centre, and not the edge, of the distribution of age 0 cod in Newfoundland during autumn. Hence nursery areas during the early 1990s, a time of historically low spawning stock biomass, must be identified as the coastal zone, not offshore.