Miracle-dz/UniFAR-FTUs huggingface dataset:
Antioxidant Activities of Plants Used in Traditional Medicine in Turkey

Ethanol extracts from 6 species representing six different families, used in traditional medicine in Turkey were evaluated for their antioxidant activities. The inhibition of superoxide anion formation and lipid peroxidation levels of Ononis spinosa, Centranthus longiflorus, Lythrum salicaria, Plantago major, Juglans regia and Teucrium polium extracts were tested using in vitro standard procedures and IC50 values were determined. In vitro tests included superoxide anion radical scavenging activity and lipid peroxidation. All ethanol extracts of plants showed concentration-dependent superoxide anion radical scavenging activity. The results of the superoxide anion formation assay showed that the ethanol extract of Centranthus longiflorus was found to be most potent inhibitor (IC50 0.77 mg/ml) and followed by Plantago major (IC50 1.21 mg/ml), Juglans regia (IC50 1.39 mg/ml), Ononis spinosa (IC50 1.35 mg/ml), Teucrium polium (IC50 3.10 mg/ml) and Lythrum salicaria (IC50 5.00 mg/ml). All the extracts, excluding Ononis spinosa and Teucrium polium, showed concentration-dependent inhibitory effect on lipid peroxidation. IC50 values of the effective ethanol extracts of plants on lipid peroxidation were as follows: Juglans regia (IC50 3.3 mg/ml), Plantago major (IC50 3.4 mg/ml), Centranthus longiflorus (IC50 3.9 mg/ml) and Lythrum salicaria (IC50 5.3 mg/ml). The results showed that Centranthus longiflorus, Plantago major and Juglans regia extracts had the highest antioxidant capacities among the six species examined.
Palaeofloristic assemblages and palaeoecology of the Lower Oligocene Bembridge Marls, Hamstead Ledge, Isle of Wight

A sequence of nine, plant-macrofossil-bearing horizons has been recognized in the Lower Oligocene from the Isle of Wight, England. The plant fossils are contained in finely laminated, olive-brown to black silty-clays and clays. Some horizons exhibit rhythmic alternation of sediment couplets; others show evidence of bioturbation and rootlet penetration. These horizons are included within a sequence of finely laminated greenish grey silty-clays and clays, largely devoid of plant macrofossil material. The plant-bearing horizons contain abundant fruits, seeds, fern sporangia, Azolla megaspores, and rare leaves. The nearest living relatives of the fossils all inhabit an aquatic or marginal aquatic environment. The associated fossil fauna includes lake bottom and lake margin species. The palynoflora of the plant-bearing and immediately underlying horizons includes large numbers of planktonic algae and limited representatives of a forest vegetation. It shows a strong relationship between the occurrences of Sparganiaceaepollenites pollen and of Typha macrofossils. Palaeoecological interpretations of this plant-fossil-bearing sequence are discussed with particular reference to modern environments. One new genus and three new species are described. Emendations are presented for four other species. Stratiotes leaf margin teeth are described.
Follicular dynamics, corpus luteum growth and regression in lactating dairy cattle

Ultrasound imaging and progesterone (P4) profiles were used to characterize follicular and corpus luteum (CL) growth and regression in 10 cycling dairy cows. Thirteen of sixteen cycles were characterized by two waves of follicular growth, the second wave giving rise to the ovulatory follicle. The remaining three cycles had three waves. There was no difference between two- and three-wave cycles with regard to the day of emergence of the first or second dominant follicle (day 2.5 ± 0.9 vs. day 2.4 ± 1.2 and day 12.4 ± 1.6 vs. day 12.0 ± 2.0, respectively) or the onset of regression of the first dominant follicle (day 12.5 ± 1.5 vs. day 12.3 ± 1.5). In two wave cycles, estrous cycle length was shorter (20.8 ± 1.7 d vs. 29.7 ± 4.9 d), the first day of decline in P4 (day 16.2 ± 1.5 vs. day 23.7 ± 5.5) and the onset of CL regression (day 17.1 ± 1.3 vs. day 24.3 ± 5.5) was earlier. It is concluded that two waves of follicular growth in an estrous cycle is the norm in lactating dairy cows. The presence of an addi.
Emission of methane from chalk streams has potential implications for agricultural practices

SUMMARY 1. The emission of biogenic gases, particularly methane, is usually associated with wetlands rather than clean streams. Here, we investigated methane production from a southern English chalk stream, where increased sedimentation, compounded by extensive macrophyte growth, may have altered ecosystem function. 2. Cover of the channel by the dominant macrophyte, Ranunculus penicillatus, peaked in August, when plant beds were associated with low water velocity and the accumulation of sediment ( 90%) of the methane flux is transported to the atmosphere through the Ranunculus stems. 5. Although the total flux of methane from U.K. chalk streams is probably relatively modest (estimated at 3.2 · 10 )6 Tg CH4 year )1 ), this phenomenon changes our perception of the health of these ecosystems and indicates another deleterious side effect of agriculture.
An evaluation of National and State policy and procedures for the prevention of the importation of weeds into Australian rangelands

Australia’s rangelands are under pressure from many sources, not the least of which is exotic plants often intentionally introduced as pasture or fodder crops. Before being intentionally introduced into Australia, a plant must pass a weed risk assessment administered by Biosecurity Australia. In addition, there are checks by Australian Quarantine and Inspection Service of shipments and international mail before it is allowed entry into Australia, restricting the unintentional and illegal introduction of plants. However, there are many ways in which plants can bypass these procedures and once inside Australia there is little to prevent these plants moving from state to state. Closing these gaps at the international borders and developing effective policies to deal with interstate movement of plants is essential to reduce the impacts of weeds on biodiversity, pastoral activities and other uses of Australian rangelands. This paper highlights these issues and provides recommendations to correct the problems.
Stem biomass and volume models of selected tropical tree species in West Africa

Estimating tree volume and biomass constitutes an essential part of the forest resources assessment and the evaluation of the climate change mitigation potential of forests through biomass accumulation and carbon sequestration. This research article provides stem volume and biomass equations applicable to five tree species, namely Afzelia africana Sm. (Caesalpiniaceae), Anogeissus leiocarpa (DC.) Guill. and Perr. (Combretaceae), Ceiba pentandra (L.) Gaertn. (Bombacaceae), Dialium guineense Willd. (Caesalpiniaceae), Diospyros mespiliformis Hochst. ex A.DC. (Ebenaceae) in natural protected tropical forests and, in addition, Tectona grandis L.f. (Verbenaceae) in plantations. In addition to the tree species specific equations, basic wood density, as well as carbon, nitrogen, organic matter and ash content were determined for these tree species in tropical conditions in West Africa. One hundred and sixty-two sample trees were measured through non-destructive sampling and analysed for volume and biomass. Stem biomass and stem volume were modelled as a function of diameter (at breast height; Dbh) and stem height (height to the crown base). Logarithmic models are presented that utilise Dbh and height data to predict tree component biomass and stem volumes. Alternative models are given that afford prediction based on Dbh data alone, assuming height data to be unavailable. Models that include height are preferred, having better predictive capabilities. Ranges in carbon, nitrogen and ash contents are given as well. The successful development of predictive models through the use of non-destructive methods in this study provide valuable data and tools for use in determining the contribution of these major African rainforest tree species to global carbon stocks, while ensuring the preservation of this valued African resource. This study needs to be expanded to further regions and tree species to complete a full inventory of all tree species, emphasising the relevance of African trees to carbon stocks at a global scale.
Implications of redox processes for the rehabilitation of an urban lake, Onondaga Lake, New York

Abstract A synthesis of the impacts of domestic and industrial wastes on oxygen resources and redox conditions of polluted Onondaga Lake, Syracuse, N.Y. , is presented based on a long-term (1978–2005) monitoring program. Insights from this retrospective analysis are used to evaluate management alternatives for the remediation of oxygen resources and redox conditions. Reduced byproducts of anaerobic metabolism accumulated annually in the hypolimnion, causing low dissolved oxygen (DO) concentrations in the upper waters during fall turnover. The high natural sulfate (SO4 2−) concentration of the lake promoted DO depletion and the production of methylmercury (CH3Hg+). Severe depletions of DO occurred annually in the upper waters during fall mixing, representing violations of water quality standards for extended intervals from 1978 to 1996. Depletions of DO during fall were less severe from 1997 to 2004. The improvement is reported to be in response to: (1) more routine occurrence of spring turnover following closure of an industry; (2) reduction in primary productivity; (3) return of large bodied Daphnia from closure of the industry; (4) satisfaction of historic debt from earlier higher primary production levels; and (5) year-round nitrification at a contributing domestic wastewater facility. Additional improvements in oxygen resources and decreases in SO4 2− reduction are anticipated based on mandated future upgrades of phosphorus and ammonia treatment at the wastewater facility. Prevailing DO conditions during fall turnover, particularly within the context of anticipated improvements from the mandated upgrades, indicate hypolimnetic aeration or oxygenation is not required to meet water quality goals. Amendments to the hypolimnetic pool of NO3 − are recommended instead of aeration or oxygenation to inhibit production of CH3Hg+ by SO4 2− reducing bacteria.
Comparison of free range broiler chicken strains raised in confined or semi-confined systems

The present study was carried out to compare the growth curve, performance and carcass yield of two broiler strains, Paraiso Pedres (PP) and ISA Label (ISA), raised in confined or semi-confined systems. It was used a completely randomized design with five replicates, consisting of 20 and 29 birds in semi-confined and confined systems, respectively. Semi-confined birds had free access to pasture at 28 days of age. Performance data were recorded weekly by building growth curves as well as calculating the growth rate. After reaching the recommended body weight (2.5 kg), male birds were slaughtered for physicochemical analysis of carcass, parts and organs. Semi-confined PP and ISA birds showed higher growth potential, higher weight gain, lower feed intake and better feed-to-gain ratio than confined birds. No interactions were observed for carcass yield and meat quality characteristics. Males presented higher yields of feet, drumstick, thigh, drumstick + thigh, and heart, while females presented higher breast and abdominal fat yield. Breast meat from ISA Label birds was more yellowish than from PP, whereas less soft meat was observed in semi-confined birds.
Genotypic variation for tolerance to phosphorus deficiency in rice and the potential for its exploitation in rice improvement

Deficiency in phosphorus (P) can severely limit rice yields. Developing cultivars with tolerance to P deficiency may represent a more sustainable solution than sole reliance on fertilizer application. To assess genotypic variation for tolerance to P deficiency the P uptake of 30 genotypes was measured on P-deficient soil. Variation for P uptake was high, ranging from 0.6 to 12.9 mg P/plant. Traditional varieties were superior to modern varieties. A major quantitative trait locus for P uptake had previously been identified in a population developed by crossing the modern variety ‘Nipponbare’ with the P deficiency-tolerant landrace ‘Kasalath’. This quantitative trait locus was transferred to ‘Nipponbare’ by three backcrosses. Under P deficiency this improved line surpassed ‘Nipponbare’ in P uptake by 170% and in grain yield by 250%. These results show that the genotypic variation for tolerance to P deficiency in rice can be used successfully in rice improvement. By combining high P uptake of the donor variety ‘Kasalath’ with a high harvest-index characteristic of modern varieties it was possible to more than triple the grain yield of ‘Nipponbare’ under P deficiency.
Reconstructing Extinct Plant Water Use for Understanding Vegetation–Climate Feedbacks: Methods, Synthesis, and a Case Study Using the Paleozoic-Era Medullosan Seed Ferns

—Vegetation affects feedbacks in Earth’s hydrologic system, but is constrained by physiological adaptations. In extant ecosystems, the mechanisms controlling plant water used can be measured experimentally; for extinct plants in the recent geological past, water use can be inferred from nearest living relatives, assuming minimal evolutionary change. In deep time, where no close living relatives exist, fossil material provides the only information for inferring plant water use. However, mechanistic models for extinct plant water use must be built on first principles and tested on extant plants. Plants serve as a conduit for water movement from the soil to the atmosphere, constrained by tissue-level construction and gross architecture. No single feature, such as stomata or veins, encompasses enough of the complexity underpinning water-use physiology to serve as the basis of a model of functional water use in all (or perhaps any) extinct plants. Rather, a “functional whole plant” model must be used. To understand the interplay between plant and atmosphere, water use in relation to environmental conditions is investigated in an extinct plant, the seed fern Medullosa ((Division Pteridospermatophyta), by reviewing methods for reconstructing physiological variables such as leaf and stem hydraulic capacity, photosynthetic rate, transpiration rate, stomatal conductance, and albedo. Medullosans had the potential for extremely high photosynthetic and assimilation rates, water transport, stomatal conductance, and transpiration—rates comparable to later angiosperms. When these high growth and gas exchange rates of medullosans are combined with the unique atmospheric gas composition of the late Paleozoic atmosphere, complex vegetation-environmental feedbacks are expected despite their basal phylogenetic position relative to post-Paleozoic seed plants.
CHEMICAL COMPOSITION AND ANTIOXIDANT ACTIVITY OF APIS MELLIFERA BEE POLLEN FROM NORTHWEST ALGERIA

The aim of this study was to assess the nutritional compositionand antioxidant activity of bee pollen produced in the North western region of Algeria.The content of total phenolic compounds,flavonoids, and antioxidant activity using the molybdate ion reductionmethod were determined. The meancontents of phenolic compounds and total flavonoids were 30.46 ± 8.22 mgof GAE.g –1 pollen and 8.92 ± 5.5 mg of RE.g –1 pollen, respectively. Highantioxidant activities were found for the molybdate ion reductionmethod, with values that ranged from 71.95 to 101. 5μg of GAE.g –1 pollen. The bee pollen ofBoufarikshowed high antioxidant activity probably due to the high contentof phenolic compounds present in pollen.
Biodiversity conservation in dynamic landscapes: trade-offs between number, connectivity and turnover of habitat patches

1. Many species are adapted to landscapes with characteristic dynamics generated by ongoing habitat destruction and creation. Climate change and human land use, however, may change the dynamics of these landscapes. Studies have repeatedly shown that many species are not able to cope with such changes in landscape dynamics. Conservation policies must, therefore, explicitly address this threat. The way in which management should be modified when formerly static landscapes become dynamic or when landscape dynamics change is unclear. 2. Using an analytical formula for the rapid assessment of metapopulation lifetime in dynamic landscapes, we investigate if and how changes in one landscape attribute may be compensated by changes in another attribute to maintain species viability. We study such trade-offs considering both spatial (number, connectivity of patches) and temporal (patch destruction and creation rates) landscape attributes. 3. We show that increasing patch destruction can be compensated to a certain extent by improvements in other spatial and/or temporal landscape attributes. Focusing on trade-offs between management options reveals two key factors essential for management decisions: First, the trade-offs are generally nonlinear irrespective of considering spatial or temporal landscape attributes. Secondly, species can be grouped according to their response to particular management options. 4. Synthesis and applications. We demonstrate the usefulness of an analytical formula for calculating trade-offs between landscape attributes for a variety of landscapes and species. Two practical and robust management recommendations can be derived: (i) The nonlinearity of trade-offs implies that the effectiveness of conservation measures depends explicitly on the current level of landscape attributes. It must, therefore, be taken into account in conservation decision making. In particular, the existing level of patch turnover is decisive: if it is already high, improvements in other landscape attributes are ineffective in maintaining species viability. Thus, monitoring the current level of landscape attributes is indispensable for effective biodiversity conservation. (ii) Compensation of increased patch destruction by increased patch creation is only suitable for species with high dispersal propensity adapted to variable environments (aside from habitat patch turnover). This implies that conservation policies which rely on such compensation, like offsetting and conservation banking, are feasible only for this type of species.
COMBINING KNOWLEDGE GRAPHS AND ONTOLOGIES FOR DYNAMIC APPS

In a recent article about knowledge graphs I noted that I tend to use the KG term interchangeably with the term ‘ontology‘. While this interchangeability is generally true when ontologies are used to model instance and class knowledge, in other words for knowledge representation (KR), it does overlook important cases when ontologies are themselves a specification for aspects such as access control, applications, or user interfaces. In these cases the ontology is less related to knowledge and more related to specifications or control. In such cases it is probably best to retain the distinction of an ontology from a knowledge graph (which I tend to think of as more oriented to content). I elaborate further on this distinction in this article.
A statistical approach to mutation detection in zebrafish with next‐generation sequencing

Summary The zebrafish is an excellent model organism for forward-genetics, with attributes such as small size, rapid development and straightforward imaging enabling mutagenesis screens for a wide variety of phenotypes. For the majority of these screens over the last few decades, the mutations were mapped using bulk segregant analysis (BSA) to establish approximate chromosomal locations, followed by fine mapping using microsatellite markers on hundreds (or thousands) of embryos. This process is very time consuming despite the large clutch sizes of the zebrafish. Next-generation sequencing (NGS) technologies have drastically improved the speed of this process, but there is no consensus on the best method for performing the BSA and fine-mapping analysis on NGS data. Here we describe a simple statistical approach to this problem using difference-in-homozygosity as a single variable with a normal distribution. This approach was used to accurately map and identify the causative mutation in a zebrafish line with a recessive mineralization disorder.
Revisiting the phylogeny of Ranunculeae: Implications for divergence time estimation and historical biogeography

Previous studies based on different molecular datasets have generated conflicting topologies for Ranunculeae. Here, we revisit the phylogeny of Ranunculeae by analyzing the individual matK/trnK, psbJ‐petA, and internal transcribed spacer (ITS) data, the combined matK/trnK, psbJ‐petA, and ITS dataset, and the combined rbcL, trnL‐F, matK/trnK, psbJ‐petA, and ITS dataset. Based on the tree‐based comparisons, BLAST searches against NCBI of the sequences, and close examination of the alignment, we found that 10 psbJ‐petA sequences previously used were questionable (erroneous or problematic) and responsible for previous conflicting topologies. After omitting these questionable sequences, we provide a new phylogeny for Ranunculeae, in which Beckwithia–Cyrtorhyncha, Kumlienia, and Peltocalathos were replaced. These new replacements are supported by corresponding morphological characters. Moreover, three previously proposed intercontinental disjunct distributions within Ranunculus were also refuted. In our framework, our divergence time and biogeographic analyses indicate that divergence time estimates and the ancestral areas reconstructed for 10 of the 15 nodes in the genus‐level phylogeny were influenced by elimination of the questionable sequences. The most recent common ancestor of Ranunculeae was inferred to be present in Europe and North America during the late Eocene. Clades I and II began to diversify in Europe and North America, respectively, and subsequently migrated to other continents. This study shows that it is necessary to analyze individual chloroplast DNA region datasets separately to detect questionable sequences early in the study. The combined dataset including the questionable sequences resulted in an erroneous phylogenetic tree, and the use of this tree subsequently affected age estimates and biogeographic analyses.
Effects of the Addition of Probiotic Containing both Bacteria and Yeast or an Antibiotic on Performance Parameters, Mortality Rate and Antibiotic Residue in Broilers

The experiment was conducted to investigate the effects of supplementing a commercially available probiotic (an Active Elements®; AE) containing Lactobacillus plantarum and Saccharomyces cerevisiae, an antibiotic; Chlortetracycline (CTC), and the probiotic plus antibiotic, via the drinking water on broiler production performance, mortality rate and the antibiotic residue in meat. Four hundred one-day-old male Cobb broiler chicks were randomly allocated to 4 treatments; a non-treated control, a 0.05% CTC, a 1:500 AE, and a combination of CTC and AE. Chicks were fed with a commercial broiler diet ad libitum. They were reared under an environmentally controlled house for 6 weeks. The data revealed that supplementation with probiotic (group 3-4) resulted in significantly higher accumulated body weight gain during the first two weeks. The final body weight, final body weight gain, feed intake and FCR were not significantly different among treatments. The mortality rate was highest in the combination group, followed by control and the AE-treated group. The antibiotic residues in the breast tissue sampling at the 6th week of age were less than 50 μg/kg tissue. The gross and histological examinations revealed no obvious pathological lesions in any treatment. In conclusion, this study indicated that administration of this probiotic to broiler chickens early in life had beneficial effects on weight gain. The FCR and antibiotic residues of the probiotic-supplemented birds were similar to antibiotic-supplemented birds. The percentage mortality was less than the non-treated group. Therefore, this probiotic may be used as an alternative to replace the adverse effect of antibiotic.