Miracle-dz/UniFAR-FTUs huggingface dataset:
Weed seed survival following ensiling and mesophilic anaerobic digestion in batch reactors

Westerman PR, Hildebrandt F & Gerowitt B (2012). Weed seed survival following ensiling and mesophilic anaerobic digestion in batch reactors. Weed Research52, 286–295. Summary Digestate, the semi-solid leftover after anaerobic digestion in biogas reactors, is frequently used as a crop fertiliser. The ability of seeds from various weed species to survive anaerobic digestion was tested, because surviving seeds could be spread via the digestate. Experiments were conducted in experimental mesophilic batch reactors, either with or without ensiling as a pre-treatment to simulate biomass storage in silage prior to use in reactors. The emphasis was on weed species whose seeds have a water-impermeable layer, because these may be more thermoresistant. Species with hard seeds were more likely to survive ensiling (up to 98%) and mesophilic anaerobic digestion (up to 58%) compared with species whose seeds lack a water-impermeable layer (≤1%). There was considerable variation in survival probability between and within species, and between silages and reactors. For hard-seeded species, survival depended on the proportion of hard seeds and on the ability to remain hard-seeded during treatment. Freshly harvested seeds lost their water impermeability and survived poorly. The survival of tomato seeds, an indicator species used in the sanitation of composts, was comparable with that of the best surviving species without physical dormancy, but was not comparable with that of hard-seeded species. Tomato could therefore only represent species that are not hard-seeded.
Characterizing the phylogenetic structure of communities by an additive partitioning of phylogenetic diversity

1 Analysing the phylogenetic structure of natural communities may illuminate the processes governing the assembly and coexistence of species in ecological communities. 2 Unifying previous works, we present a statistical framework to quantify the phylogenetic structure of communities in terms of average divergence time between pairs of individuals or species, sampled from different sites. This framework allows an additive partitioning of the phylogenetic signal into alpha (within‐site) and beta (among‐site) components, and is closely linked to Simpson diversity. It unifies the treatment of intraspecific (genetic) and interspecific diversity, leading to the definition of differentiation coefficients among community samples (e.g. IST, PST) analogous to classical population genetics coefficients expressing differentiation among populations (e.g. FST, NST). 3 Two coefficients which express community differentiation among sites from species identity (IST) or species phylogeny (PST) require abundance data (number of individuals per species per site), and estimators that are unbiased with respect to sample size are given. Another coefficient (ΠST) expresses the gain of the mean phylogenetic distance between species found in different sites compared with species found within sites, and requires only incidence data (presence/absence of each species in each site). 4 We present tests based on phylogenetic tree randomizations to detect community phylogenetic clustering (PST > IST or ΠST > 0) or phylogenetic overdispersion (PST < IST or ΠST < 0). In addition, we propose a novel approach to detect phylogenetic clustering or overdispersion in different clades or at different evolutionary time depths using partial randomizations. 5 I ST, PST or ΠST can also be used as distances between community samples and regressed on ecological or geographical distances, allowing us to investigate the factors responsible for the phylogenetic signal and the critical scales at which it appears. 6 We illustrate the approach on forest tree communities in Equatorial Guinea, where a phylogenetic clustering signal was probably due to phylogenetically conserved adaptations to the elevation gradient and was mostly contributed to by ancient clade subdivisions. 7 The approach presented should find applications for comparing quantitatively phylogenetic patterns of different communities, of similar communities in different regions or continents, or of populations (within species) vs. communities (among species).
A model of biogeochemical cycles of carbon, nitrogen, and phosphorus including symbiotic nitrogen fixation and phosphatase production

Global climate models have not yet considered the effects of nutrient cycles and limitation when forecasting carbon uptake by the terrestrial biosphere into the future. Using the principle of resource optimization, we here develop a new theory by which C, N, and P cycles interact. Our model is able to replicate the observed responses of net primary production to nutrient additions in N‐limited, N‐ and P‐colimited, and P‐limited terrestrial environments. Our framework identifies a new pathway by which N2 fixers can alter P availability: By investing in N‐rich, phosphorus liberation enzymes (phosphatases), fixers can greatly accelerate soil P availability and P cycling rates. This interaction is critical for the successful invasion and establishment of N2 fixers in an N‐limited environment. We conclude that our model can be used to examine nutrient limitation broadly, and thus offers promise for coupling the biogeochemical system of C, N, and P to broader climate‐system models.
A multi-marker DNA barcoding approach to save time and resources in vegetation surveys

Vegetation surveys have a long tradition in ecological studies, but several limitations in the morphological identification of species have been recognized. The objective of this study was to evaluate the effectiveness of DNA barcoding in plant species identification to save field technicians time and resources. Vegetation surveys were performed in four plots of semi-dry grassland in the Italian subalpine region of Lombardy. Two identification approaches were employed: a conventional morphological identification and a molecular multi-marker DNA barcoding method. Results showed that morphological identification of 49 species collected from the study area (five field inspections) required a substantial amount of time to complete relative to the molecular method. The same 49 samples were analysed using the following DNA multi-marker barcodes: rbcL, matK and trnH-psbA. rbcL showed 100% amplification success with standard primers, but low interspecific genetic variability. matK demonstrated some amplification problems with standard primers; however, consistent genetic diversity was observed. Finally, the trnH-psbA spacer region exhibited reliable amplification success and the highest molecular variability. In a comparison with publicly available databases, trnH-psbA and matK returned the highest proportion of identified samples, whereas rbcL returned several misidentifications. The DNA barcoding approach is a powerful tool in vegetation surveys and may significantly reduce the time and cost spent for species identification. However, to effectively apply DNA barcoding in vegetation surveys, exhaustive local or regional molecular databases must be defined. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169, 518-529. ADDITIONAL KEYWORDS: integrated taxonomy - matK - plastid DNA markers - rbcL - trnH-psbA - vegetation plot.
Population structure, growth, and sexual maturation of short-finned squid (Illex illecebrosus) at Newfoundland

Nous presentons ici la taille a l'âge, la croissance et la structure de populations d'encornet nordique (Illex illecebrosus) vivant dans les eaux de Terre-Neuve au cours de l'annee 1990. Les âges ont ete estimes a partir du nombre d'increments de statolithes et ont ensuite ete utilises pour calculer les dates d'eclosion. Les eclosions ont eu lieu entre decembre et juin, le plus grand nombre etant cependant survenu entre mars et mai. Un echange constant d'individus parmi la population cotiere etait evident, puisque le mois modal d'eclosion est passe de mars pour l'echantillon le plus precoce juillet) a mai pour l'echantillon le plus tardif (novembre). Compte tenu de la gamme de longueurs du manteau, la croissance etait bien exprimee par un modele lineaire. La croissance des femelles etait plus rapide que celle des mâles et, en ce qui concerne les eclosions survenues entre mars et mai, la taille a l'âge et le taux de croissance augmentaient selon le mois d'eclosion. Cet effet positif de l'eclosion tardive s'est egalement fait sentir dans la prise de poids, le developpement des gonades et la maturation sexuelle.
Conservation of Brazilian Amphibians

Abstract: Brazil is the world leader in amphibian diversity, with 765 species, most of which have been described in the last 40 years. The Brazilian Official List of Threatened Species and the results of a workshop for the Global Amphibian Assessment indicate that 26 species are threatened. The majority of these occur in the Atlantic Forest, one of the world's biodiversity hotspots. The main threat to amphibians is the destruction of their habitats through deforestation, conversion into agricultural land, mining, wildfires, and infrastructure development and urbanization. In Brazil little is known about other causes of amphibian decline observed worldwide, such as pesticides, infectious diseases, climate change, invasive species, or wildlife trade. Brazilian conservation policies include such important legal instruments as the Official List of Threatened Species and the selection of priority areas for conservation measures in all of Brazil's major biomes. Although there is little information on geographic distributions and the natural history and ecology of the large majority of the currently recognized species, a number of important regional studies for amphibian conservation are under way. New species are discovered each year.
Evaluating the Barrier Assessment Technique Derived from FishXing Software and the Upstream Movement of Brook Trout through Road Culverts

AbstractAnthropogenic barriers to fish passage, such as culverts and dams, are major factors impeding the persistence and recovery of aquatic species. Considerable work has focused on mitigating these impacts; however, activities associated with measuring and restoring connectivity of aquatic ecosystems often face challenges in determining the passability of barriers by aquatic species. Hydrological modeling software that incorporates biological aspects of a focal species is often used as a relatively inexpensive method for assessing barrier passability for restoration decisions. However, the biological relevance of these approaches remains to be rigorously tested. We assessed passage rates of PIT-tagged Brook Trout Salvelinus fontinalis through four road culverts and adjacent reference sites (unaltered areas of the streams) on the island of Newfoundland to determine whether upstream passage through road culverts was more restrictive than unaltered reference areas of the stream. Next, we examined the usef.
Myoendothelial Differentiation of Human Umbilical Cord Blood–Derived Stem Cells in Ischemic Limb Tissues

Abstract— Human umbilical cord blood (UCB) contains high numbers of endothelial progenitors cells (EPCs) characterized by coexpression of CD34 and CD133 markers. Prior studies have shown that CD34+/CD133+ EPCs from the cord or peripheral blood (PB) can give rise to endothelial cells and induce angiogenesis in ischemic tissues. In the present study, it is shown that freshly isolated human cord blood CD34+ cells injected into ischemic adductor muscles gave rise to endothelial and, unexpectedly, to skeletal muscle cells in mice. In fact, the treated limbs exhibited enhanced arteriole length density and regenerating muscle fiber density. Under similar experimental conditions, CD34− cells did not enhance the formation of new arterioles and regenerating muscle fibers. In nonischemic limbs CD34+ cells increased arteriole length density but did not promote formation of new muscle fibers. Endothelial and myogenic differentiation ability was maintained in CD34+ cells after ex vivo expansion. Myogenic conversion of human cord blood CD34+ cells was also observed in vitro by coculture onto mouse myoblasts. These results show that human cord blood CD34+ cells differentiate into endothelial and skeletal muscle cells, thus providing an indication of human EPCs plasticity. The full text of this article is available online at http://www.circresaha. org.
CHIR-265 is a potent selective inhibitor of c-Raf/B-Raf/mutB-Raf that effectively inhibits proliferation and survival of cancer cell lines with Ras/Raf pathway mutations

4855 The Ras/Raf/MEK/ERK signal transduction cascade is a very compelling pathway to disrupt in several cancer types because of its role as a vital mediator of cell proliferation, survival and other aspects of cellular behavior that contribute to the transformed phenotype. The Raf serine/threonine kinases are central to this signaling pathway and the fact that activating mutations often occur in B-Raf (melanoma, low-grade ovarian, papillary thyroid) underscores the importance of this target in cancer. CHIR-265 is an orally-bioavailable, selective, potent inhibitor of C-Raf, wild type B-Raf and mutant (V600E) B-Raf (IC 50 range from 3 to 60 nM). Concentrations of CHIR-265 that effectively block phosphorylation of Raf’s downstream substrates MEK and ERK in cells, also kill melanoma and colorectal cancer cell lines harboring B-Raf mutations independent of PTEN mutation status. EC 50 values for p-ERK inhibition range from 140 to 300 nM in SK-MEL-28 (human melanoma, mut B-Raf V600E , PTEN +, P53 -), Malme-3M (human melanoma, mut B-Raf V600E , PTEN +, P53 wt), and A375M (human melanoma, mut B-Raf V600E , PTEN -, P53 wt). Raf kinase inhibition by CHIR-265 in mutant B-Raf melanoma cell lines causes cell cycle arrest and induces apoptosis, mimicking the effect of Raf RNAi in these cells. Additionally, CHIR-265 inhibits vascular endothelial growth factor receptor type 2 (VEGFR-2). Potent inhibition of phosphorylation of VEGFR-2 and proliferation of VEGF-stimulated hMVEC (EC 50 = 30 &20 nM) indicate that CHIR-265 is a potent inhibitor of both Raf and the pro-angiogenic kinase, VEGFR. Consistent with its in vitro activity, CHIR-265 causes tumor regression and dose-dependent tumor growth inhibition in B-Raf-driven human melanoma xenograft model. The demonstration that CHIR-265 is very effective ( in vitro and in vivo ) in inhibiting Raf enzymes, key kinases for cancer cell growth and survival, suggests that this compound is an excellent clinical candidate to treat Raf driven cancer such as malignant melanoma.
Enzymatic hydrolysis of Nile tilapia (Oreochromus niloticus) myofibrillar proteins: effects on nutritional and hydrophilic properties

Protein concentrate (PC) was prepared from eviscerated and mechanically deboned fish. The pulp was washed sequentially with 0.05 M NaCl and 4 g l−1 NaHCO3 solutions, with cold ethanol and then with hot (50 °C) ethanol. Subsequently, it was dried (40 °C) and ground to 60 mesh. Enzyme (Flavourzime®) hydrolysates were prepared with a degree of hydrolysis (DH) ranging from 3.5 to 45%. The PC was characterized for proximate composition, amino acid profile, physical and functional properties. The influence of DH on functional and nutritional properties was evaluated. Hygroscopicity increased in all hydrolysates for environmental relative humidities above 40% and solubility increased rapidly for DH above 7%. Water retention, water absorption and oil absorption all decreased as a function of DH. The pH (3 to 9) influenced the water and oil absorption of the hydrolysate with 7% DH. A pH near the isoelectric point tends to decrease water absorption but increase oil absorption capacity. The insoluble fraction (IF) of the hydrolysates presented a better amino acid profile than the soluble fraction (SF). The nutritional indexes determined for the IF did not differ from the total hydrolysate, but they were consistently higher than those for the SF. Copyright © 2003 Society of Chemical Industry
Abundance and dominance become less predictable as species richness decreases

Aim: To test the hypothesis that communities with higher diversity have more predictable properties by examining patterns of community structure along a species richness gradient. Location: Trinidad and Tobago (11°00 N, 61°00 W), on the South American continental shelf, opposite the Orinoco River delta, north-east Venezuela. Methods: We used quantile regressions to investigate how three total abundance, absolute and relative dominance measures – numerical abundance, biomass and energy use, respectively – change across a species richness gradient. We investigated which allocation rule best mimics community assembly in this species richness gradient by examining the abundance of the dominant species and comparing it with predictions of niche apportionment models. Results: All measures of total abundance increase on average across the gradient, but the upper limit remains constant. On average, absolute dominance is constant, but the distance between the upper and lower limits decreases along the gradient. Relative dominance decreases with species richness. Observed dominance patterns are best described by Tokeshi's random fraction model. Main conclusions: Our results show that both total abundance and absolute dominance become increasingly variable as biodiversity decreases. Consequently, our study suggests that ecosystem properties are less predictable when biodiversity is lower.
A genecological investigation of the annual rhythm of Pinus contorta Dougl. and a comparison with Pinus silvestris L.

In a material of 27 provenances of two-year-old Pinuss contorta it was found that the annual rhythm, illustrated by degree of lignification, colour of the bark on the terminal shoot, dry/fresh weight of needles, shoot extension, budsetting and electrical resistance, was related to the geographic and climatic parameters of seed source. Regression analyses showed that the rhythm was most closely correlated with the mean January daily temperature and latitude. The analyses also showed how latitude and altitude interact. Budsetting was found to have a pattern of geographic variation that was different from the other expressions of rhythm. A comparison between P. contorta and P, silvestris with reference to lignification, laboratory frost resistance and field hardiness, indicated that the Canadian pine, which withstands a Scandinavian climate far north of its seed source, presumably manages to do so in spite of a relatively low degree of winter adjustment in late September.
Intraspecific Differentiation in the Japanese Brown Frog Rana japonica Inferred from Mitochondrial DNA Sequences of the Cytochrome b Gene

Abstract Intraspecific differentiation of the Japanese brown frog Rana japonica was investigated by analyzing nucleotide sequences of the mitochondrial cytochrome b (cyt b) gene in order to clarify phylogenetic relationships among three population groups known to exist in this species. The nucleotide sequences of 447 base pair (bp) segments were determined by the PCR-direct sequencing method on 31 individuals from 14 populations of R. japonica from Honshu, and phylogenetic trees were constructed by the UPGMA and NJ methods using Rana catesbeiana as an outgroup. A sequence alignment provided 92 variable sites (15 corresponded to the first codon position, three to the second, and 74 to the third), and 19 haplotypes were identified from 31 frogs. The sequence divergences were 0.22∼2.50% (x̄ = 0.65%) within populations, 0.22∼12.02% (x̄ = 7.34%) between populations, and 23.59∼27.89% (x̄ = 26.19%) between R. japonica and R. catesbeiana. Although many nucleotide substitutions were silent mutations, 12 amino acid replacements were found to occur within R. japonica. A high frequency of transitions relative to transversions was observed within R. japonica. The present nucleotide sequence data showed that the eastern and western groups of R. japonica was considerably differentiated to each other, and that the Akita population of the northwestern group was evidently derived from the eastern group, but the Nakajo and Izumozaki populations of the northwestern group diverged considerably from each of the eastern and the western groups.
Tolerance of identity preserved soybean cultivars to preemergence herbicides

Belfry, K. D. , Soltani, N. , Brown, L. R. and Sikkema, P. H. 2015. Tolerance of identity preserved soybean cultivars to preemergence herbicides. Can. J. Plant Sci. 95: 719–726. Six field trials were conducted over a 3-yr period (2011 to 2013) near Exeter and Ridgetown, Ontario, Canada, to assess the tolerance of seven identity-preserved (IP) soybean cultivars to preemergence (PRE) herbicides applied at 2×the recommended dose. All cultivars demonstrated excellent tolerance to dimethenamid-P, pyroxasulfone, S-metolachlor, chlorimuron-ethyl, clomazone, cloransulam-methyl, flumetsulam and imazethapyr, showing 5% or less injury. At Exeter, linuron caused as much as 13 and 18% injury at 2 and 4 wk after soybean emergence, while injury due to metribuzin was as high as 22 and 47% for the same dates, respectively. At Exeter, linuron, metribuzin and S-metolachlor plus metribuzin reduced soybean height up to 17, 41 and 24%, respectively; soybean height was generally not affected at the Ridgetown sites. At Exeter, met.
Toxicokinetics and Biotransformation of As(III) and As(V) in Eisenia fetida

ABSTRACT Earthworms, Eisenia fetida, were exposed to soils spiked with As(III) and As(V), to understand the response of earthworms to As in terms of both toxicity and accumulation using toxicokinetics, and to explain As metabolism and bioavailability. As(III) showed higher toxicity than As(V), in all toxicity endpoints of burrowing time, survival, growth, and cocoon production. Bioconcentration occurred at both As(III) and As(V) treatments during 28-d exposure. Worms did not show the elimination of As for consecutive 28 d of exposure to clean soils. Biotransformation of As was characterized using HPLC-ICP-MS and XANES, showing the reduction of As in worms regardless of the As species to which worms were exposed. Metabolism of As in worms that formed As-thiol complex is thought to limit the excretion of As, and thus induce bioconcentration in worms. Uptake rates by one-compartment model indicated that pore water was the bioaccessible pool of As, and directly controlled the uptake of As by worms. The study suggests that higher uptake rate and bioaccumulation of As(III) than of As(V) are among the factors that make As(III) more toxic than As(V).
Strain and sex effects on ascites development in commercial broiler chickens

Summary The objective of this study was to assess the importance of strain and sex and their interaction effect on broiler chickens’ performance and susceptibility to ascites. Chicks from three strains (Ross 308, Cobb 500 and Arian, labeled as A, B and C respectively) were obtained from the same age breeder and sexed when one-day-old. Each crosses’ sex was assigned to four pens of 60 broilers each. Body weight gain (BWG), feed intake, feed conversion ratio (FCR) and ascites mortality were determined. At the age of 28 and 49 d haematocrit values, arterial pressure index (API = right ventricular/total ventricular weight ratio), the values of plasma thyroid hormone concentration (thyroxin, T4 and triiodothyronine, T3) and metabolic lung weight (lung weight/body weight (0.75) ) were determined. Strain B had the highest BWG but an equal incidence of ascites as strain A, which had low BWG and ascites mortality. Ascites mortality was not correlated with BWG and FCR. A significant strain interaction by sex on feed conversion (P<0.01) and final weight (P<0.05) was found. The sex effect was significant only in strain C on feed conversion and final weight. Strains B and C had lower thyroid hormones and reduced metabolic lung weights compared with strain A. The sex effect was not significant on the parameters associated with ascites syndrome and its incidence.