Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogeny and molecular evolution of the DMC1 gene in the polyploid genus Leymus (Triticeae: Poaceae) and its diploid relatives

The level and pattern of nucleotide variation in duplicate genes provide important information on the evolutionary history of polyploids and divergent processes between homoeologous loci within lineages. Leymus, a group of allopolyploid species with the NsXm genomes, is a perennial genus with a diverse array of morphology, ecology, and distribution in Triticeae. To estimate the phylogeny and molecular evolution of a single‐copy DMC1 gene in Leymus and its diploid relatives, DMC1 homoeologous sequences were isolated from the sampled Leymus species and were analyzed with those from 30 diploid taxa representing 18 basic genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that: (i) different Leymus species might derive their Ns genome from different Psathyrostachys species; (ii) Pseudoroegneria has contributed to the nuclear genome of some Leymus species, which might result from recurrent hybridization or incomplete lineage sorting; (iii) the Xm genome origin of Leymus could differ among species; (iv) rapid radiation and multiple origin might account for the rich diversity, numbers of species, and wide ecological adaptation of Leymus species; and (v) the DMC1 sequence diversity of the Ns genome in Leymus species was lower than that in the Psathyrostachys diploids, while the level of DMC1 sequence diversity in Leymus was higher than that in diploid Pseudoroegneria. Our results provide new insight on the evolutionary dynamics of duplicate DMC1 genes, polyploid speciation, and the phylogeny of Leymus species.
Enhanced efficacy of mesothelin-targeted immunotoxin LMB-100 and anti–PD-1 antibody in patients with mesothelioma and mouse tumor models

Mesothelin-targeted immunotoxin LMB-100 with anti–PD-1 antibody enhanced antitumor activity in patients with mesothelioma and mouse tumor models. A setup for immunotherapy Mesothelioma is a rare but difficult-to-treat cancer, which usually recurs after chemotherapy and only occasionally responds to checkpoint inhibitor immunotherapy. During a clinical trial of an immunotoxin targeting the mesothelin protein in this cancer, Jiang et al. observed that immunotoxin-treated patients showed promising responses to immune checkpoint inhibitors, particularly if their tumors expressed the relevant checkpoint. The authors characterized the immune responses in the treated patients and also demonstrated the same phenomenon in two different mouse models of mesothelioma and lung cancer, paving the way for larger clinical trials of the therapeutic combination. LMB-100 is an immunotoxin targeting the cell surface protein mesothelin, which is highly expressed in many cancers including mesothelioma. Having observed that patients receiving pembrolizumab off protocol after LMB-100 treatment had increased tumor responses; we characterized these responses and developed animal models to study whether LMB-100 made tumors more responsive to antibodies blocking programmed cell death protein 1 (PD-1). The overall objective tumor response in the 10 patients who received PD-1 inhibitor (pembrolizumab, 9; nivolumab, 1) after progression on LMB-100 was 40%, and the median overall survival was 11.9 months. Of the seven evaluable patients, four had objective tumor responses, including one complete response and three partial responses, and the overall survival for these patients was 39.0+, 27.7, 32.6+, and 13.8 months. When stratified with regard to programmed death ligand 1 (PD-L1) expression, four of five patients with tumor PD-L1 expression had objective tumor response. Patients with positive tumor PD-L1 expression also had increased progression-free survival (11.3 versus 2.1 months, P = 0.0018) compared with those lacking PD-L1 expression. There was no statistically significant difference in overall survival (27.7 versus 6.8 months, P = 0.1). LMB-100 caused a systemic inflammatory response and recruitment of CD8+ T cells in patients’ tumors. The enhanced antitumor effects with LMB-100 plus anti–PD-1 antibody were also observed in a human peripheral blood mononuclear cell–engrafted mesothelioma mouse model and a human mesothelin–expressing syngeneic lung adenocarcinoma mouse model. LMB-100 plus pembrolizumab is now being evaluated in a prospective clinical trial for patients with mesothelioma.
Flow regulation, geomorphology, and Colorado River marsh development in the Grand Canyon, Arizona

New, productive fluvial marshes may develop along regulated canyon rivers through reduction in flood frequency, thereby increasing diversity, production, and wildlife habitat availability. Few fluvial marshes occurred along the eddy-dominated Colorado River in the Grand Canyon prior to construction of Glen Canyon Dam in 1963. Reduction of flooding after 1963 permitted widespread marsh development. Fluvial marshes exhibited low stability but high resilience, quickly redeveloping after scouring by high flows between 1983 and 1986. In 1991, 253 fluvial wet marshes (cattail/reed and horseweed/Bermuda- grass) and 850 dry marshes (horsetail/willow) occupied 25.0 ha (1%) of the 363 km main- stream riparian corridor between Lees Ferry and Diamond Creek, Arizona. Fluvial marsh development and composition varied in relation to local and reach-based geomorphology, and microsite gradients in inundation frequency and soil texture. Colorado River marsh density (number/kM2) increased with distance downstream, and marshes were larger and more abundant in wide reaches. Wet marsh cattail/reed stands developed on silty loam soils in low velocity depositional environments that were inundated 54% of the days from 1986 to 1991, whereas dry horsetail/willow marshes occupied less frequently inun- dated sites with sandy soils. Mean marsh standing mass (641 g C/M2) was comparable with values from regulated alluvial river marshes, but litter retention appeared limited by flow variability in both regulated and unregulated fluvial marshes. We discuss implications of flow management on the four marsh assemblages, and the need for consensus on priorities for management of regulated fluvial wetlands.
Presence of Red Fire Ants (Solenopsis invicta Buren) in Broad-Snouted Caiman (Caiman latirostris) Nests

Abstract The presence of Solenopsis invicta in Caiman latirostris nests is suspected to be a possible cause of death in caiman hatchlings, but this has not been documented within the native distribution of this ant. In crocodilian ranching programs, wild eggs are collected from the field, and delays between collection and transportation to incubators are usually minimized in the hope of maximizing embryo survival. We analyzed nests harvested during five consecutive nesting seasons of C. latirostris to determine the phenology of S. invicta colonization of caiman nests. The percentages of colonized caiman nests for each season were calculated. Densities of S. invicta mounds built on bare ground were assessed to determine potential relationships between density and the proportion of caiman nests colonized by the end of nesting season. We also evaluated whether S. invicta preferred certain habitats to establish their mounds. We found no relationship between S. invicta mound densities and the percentage of C. latirostris nests with Red Fire Ants. The presence of S. invicta mounds among years was similar between different habitats at the beginning of each season. We found that S. invicta can colonize C. latirostris nests during the breeding period and that colonization of nests is higher than 50% in seasons where rainfall was 200 mm at the beginning of the season (December and January). In contrast, during years in which rainfall was below 200 mm, caiman nest colonization was reduced.
Pre-migratory and migratory movements of Swallows Hirundo rustica in Britain and Ireland

Previous published information on the migratory and pre-migratory movements of Swallows Hirundo rustica in Britain and Ireland was based on 191 birds ringed up to 1965 and found within the same autumn. By 1988, this number had increased to 3337. In view of recent interest in the migratory strategies and conservation of Swallows in Britain, this expanded data base has now been analysed. Particular attention is paid to the speed, distance, direction and timing of movements shown by 468 ringed birds which were found between July and November within 10 days of ringing at least 5 km from the ringing site. First-year birds showed pronouned non-directional wandering during August, but became increasingly oriented to the south-east from September onwards. Movements to the north and west were, on average, 25–38 km within 10 days, but some were up to 270 km. Eight out of 20 adult movements were also westward or northwards for up to 43 km. Data from all birds combined showed evidence that birds from easterly regions.
The Magical Number Five in Art Appreciation

To describe differences in art appreciation between children of different ages, between children and adults, and between adults with different educational backgrounds, five components of aesthetic judgment were defined. These were named: “Attraction,” “Representation and realism,” “Emotional expression,” “Style and form,” and “Interpretation. ” In a review of six studies with participants ranging from primary and secondary school children to various adult groups, it was investigated in which amount the five components characterized each group. For that purpose, explanations for art preferences in these studies were analyzed. The results indicate that individuals or groups can be characterized with respect to their art appreciation as showing a particular “profile” of the five aesthetic components. Also, it seems justified to distinguish one stage-like transition in aesthetic development, in early adolescence. This is seen as a transition from a chiefly semantic (content-related) to a mainly aesthetic (style-, emotion-, and interpretation-related) orientation.
Resistance Mechanisms to an Acetolactate Synthase (ALS) Inhibitor in Water Starwort (Myosoton aquaticum) Populations from China

Abstract Overreliance on tribenuron has resulted in resistance evolution in water starwort. This study investigates the resistance mechanisms to tribenuron in water starwort populations from China. The cytochrome P450 monooxygenase (P450) inhibitor malathion increased tribenuron sensitivity in all populations. The decrease in the amount of herbicide dose that causes 50% growth reduction (GR50) for the sensitive (S) population JS24 and the resistant (R) populations JS16 and JS17 were 2.3-, 2.5-, and 4.1-fold, respectively. However, the GR50 values for the R populations were still much higher than those of the S population. This observation indicates that P450-mediated enhanced metabolism is one mechanism for resistance in water starwort. The glutathione-S-transferase (GST) activity could be induced by tribenuron for all tested populations. In particular, the GST activity of JS16 is inherently greater and is more rapidly induced than that of JS17 or JS24. Resistance attributed to mutant acetolactate synthase (ALS) alleles was identified by sequence analysis for each population. Pro197Ser substitution was detected in JS16 and JS17. Molecular markers were also developed to rapidly identify resistance as well as individuals carrying the specific Pro197Ser mutation in water starwort populations. The resistance patterns experiment revealed that the R populations exhibited different levels of resistance to pyrithiobac sodium salt, florasulam, pyroxsulam, and flucarbazone-Na; however, R populations were sensitive to imazethapyr, fluroxypyr-meptyl, 2,4-D butylate, isoproturon, and diflufenican. This study establishes that either one or at least two resistance mechanisms are involved in herbicide resistance in water starwort. Moreover, these mechanisms might contribute to the different levels of resistance to tribenuron among water starwort populations. Nomenclature: 2,4-D butylate; diflufenican; florasulam; flucarbazone-Na; fluroxypyr-meptyl; imazethapyr; isoproturon; pyrithiobac sodium salt; pyroxsulam; tribenuron; water starwort, Myosoton aquaticum (L.) Moench.
Correlation between Fitness and Genetic Diversity

Abstract: Genetic diversity is one of the three forms of biodiversity recognized by the World Conservation Union ( IUCN ) as deserving conservation. The need to conserve genetic diversity within populations is based on two arguments: the necessity of genetic diversity for evolution to occur, and the expected relationship between heterozygosity and population fitness. Because loss of genetic diversity is related to inbreeding, and inbreeding reduces reproductive fitness, a correlation is expected between heterozygosity and population fitness. Long‐term effective population size, which determines rates of inbreeding, should also be correlated with fitness. However, other theoretical considerations and empirical observations suggest that the correlation between fitness and heterozygosity may be weak or nonexistent. We used all the data sets we could locate (34 ) to perform a meta‐analysis and resolve the issue. Data sets were included in the study, provided that fitness, or a component of fitness, was measured for three or more populations along with heterozygosity, heritability, and/or population size. The mean weighted correlation between measures of genetic diversity, at the population level, and population fitness was 0.4323. The correlation was highly significant and explained 19% of the variation in fitness. Our study strengthens concerns that the loss of heterozygosity has a deleterious effect on population fitness and supports the IUCN designation of genetic diversity as worthy of conservation.
The impact of illiquidity risk for the Nordic markets

ABSTRACT In this study, we propose a new measure of illiquidity for small, open stock markets; dollar zero-returns. Compared with other commonly used measures of illiquidity, the dollar zero-return produces the highest anomalous return across all four Nordic markets. In testing the pricing implication of the proxies of illiquidity, we use liquidity adjusted asset pricing models suggested in the literature for a panel of 25 size-related portfolios for the Nordic markets. Our results show that the only illiquidity measure that gives a significant positive effect across all Nordic markets is the dollar zero-return. Our results also show that the illiquidity mimicking portfolio factor, constructed through dollar zero-return, is the only factor showing a significant premium across different specifications, and its pricing remain significant also when the effect of the level of illiquidity (constructed through all measure of illiquidity) and of size is netted out.
The effects of quantity and duration of simulated pollutant nitrogen deposition on root‐surface phosphatase activities in calcareous and acid grasslands: a bioassay approach

A field and laboratory based bioassay has been developed to investigate the effects of the quantity and duration of simulated pollutant nitrogen (N) deposition on root-surface phosphomonoesterase (PME) activities in calcareous and acid grasslands. Seedlings of Plantago lanceolata were transplanted to a calcareous grassland and Agrostis capillaris seedlings were grown in microcosms containing soil from an acid grassland that had received either 7 yr (long-term) N additions or 18 months (short-term) N and phosphorus (P) additions. The bioassay revealed that short-term N treatments had little effect on the enzyme activity, whereas long-term N additions significantly increased PME activity within 7 d of transplanting into the field plots. Root-surface PME activity of A. capillaris was significantly reduced in soil that received additions of P. In the plots receiving long-term additions of N, a strong relationship was observed between extractable soil ammonium and root-surface PME activity. Soil ammonium concentrations accounted for 67% of the variation in PME activity of P. lanceolata in the calcareous grassland, and 86% of the variation in PME activity of A. capillaris in the acid grassland. These results provide evidence that N deposition may have considerable effects on the demand and turnover of P in ecosystems that are approaching or have reached N saturation.
Tamarindus indica (Cesalpiniaceae), and Syzygium cumini (Myrtaceae) Seed Extracts can Kill Multidrug Resistant Streptococcus mutans in Biofilm

Extracts of Emblica officinalis seeds prepared by Microwave Assisted Extraction (MAE) method were evaluated for their antimicrobial property against planktonic form of certain human/plant pathogenic microbes. Additionally, seed extracts of E. officinalis, Tamarindus indica, Manilkara zapota, Phoenix sylvestris, Syzygium cumini, and selected phytocompounds were tested against multi-drug resistant Streptococcus mutans (a major pathogen associated with human dental caries) in its planktonic as well as biofilm form. Ability of these extracts to eradicate and kill S. mutans biofilm was investigated. E. officinalis extracts exerted bactericidal action against S. mutans , Pseudomonas aeruginosa , and Vibrio cholerae . Acetone extract of S. cumini , and curcumin were able to inhibit S. mutans at appreciably low concentrations of 50 μg/mL and 20 μg/mL respectively. T. indica and S. cumini seed extracts were able to kill ≥80% cells of S. mutans in biofilm, in the concentration range of 500-1000 μg/mL. These extracts were able to achieve ≥95% killing of S. mutans biofilm at concentrations ranging from 600-2000 μg/mL. Ability of the potent extracts to kill S. mutans biofilm did not seem to be much dependent on eradication of the biofilm. Extraction efficiency was found to have a good correlation with antibacterial activity.
Diet and reproductive success of an Arctic generalist predator: Interplay between variations in prey abundance, nest site location, and intraguild predation

ABSTRACT Under varying prey abundance, generalist consumers should be less affected than specialists due to their more diverse diet. Nonetheless, when prey availability declines, interspecific competition among consumers should increase and could lead to increased intraguild predation. We examined these potential effects in a generalist predator of the tundra, the Glaucous Gull (Larus hyperboreus), over a 7-yr period characterized by large fluctuations in lemming abundance, a potential prey item for gulls. We studied diet by analyzing regurgitated pellets collected at nests and blood nitrogen and carbon stable isotopes, and we monitored annual nesting density and reproductive success on Bylot Island, Nunavut, Canada. Stable isotopes revealed a relatively similar contribution of terrestrial and marine food sources to the gull diet, although the terrestrial contribution increased in the year of high lemming abundance. According to analysis of pellets, diet during incubation was dominated by geese and lemmings, whereas geese were the main prey during chick-rearing. As expected for a generalist predator, annual variation in diet during incubation reflected overall lemming abundance, and the increased consumption of geese during chick-rearing was associated with an influx of goose families into the study area at that time. Gull nest density, laying date, clutch size, and mass gain of chicks did not vary with lemming population fluctuations. Hatching success, on the other hand, was positively related to lemming abundance and was greater for nests located on islets than for those along the shores of ponds and lakes. Intraguild predation on gull eggs by predators such as Arctic foxes, which primarily feed on lemmings during the summer, was probably the main cause of nest failure. Although a generalist predator like the Glaucous Gull has a diversified diet and may feed only opportunistically on lemmings, our results suggest that large cyclical fluctuations in lemming abundance may still affect gull reproductive success through intraguild predation.
Annual and spatial variation for macroinvertebrates in the Upper Mississippi River near Cape Girardeau, Missouri

We sampled macroinvertebrates at four sites in the Open River section of the Upper Mississippi River near Cape Girardeau, Missouri (Rkm 106-114). In 1999, 2000, and 2002 - 2004, macroinvertebrates were sampled in the fine sediments downstream of four wing dikes with a Ponar dredge. In 1999 and 2001, macroinver- tebrates on rocks were sampled on the upstream face of those same wing dikes with rock baskets. We identified 68 taxa in the fine sediments and 50 taxa on the rocks, with only 27 taxa being found in both. In both habitats, annual variability in population densities and community structure exceeded spatial variability. Macroinvertebrate densities in the fine sediments ranged from approximately 3700 to 11,700 individuals/m 2 with oligochaetes com- prising 77- 95 % of total density. Non-metric Multidimensional Scaling ordination suggests that annual differ- ences in the fine sediment assemblage reflect variation in hydrological conditions (high spring flow and low an- nual flow). Macroinvertebrate density on the rocks ranged from approximately 57,800 to 163,000 individuals/m 2 with hydropsychid caddisflies (Hydropsyche bidens/orris and Potamyia flava) comprising 82 - 97 % of total den- sity. This dominance of oligochaetes in fine bottom substrates and caddisflies on hard substrates is consistent with many other studies on big rivers in the Mississippi River Basin (e. g., Upper and Lower Mississippi, Ohio, Il- linois, and Missouri Rivers), and may be the current "reference condition" for these big rivers. This makes tradi- tional water quality monitoring and assessment efforts using macroinvertebrates more difficult because increased dominance by more pollution tolerant taxa is perceived as evidence of water or habitat degradation. However, macroinvertebrate assemblages in our study reach seem less stressed than other big rivers known to be impaired. Specifically, densities of the pollution-sensitive mayfly Hexagenia indicate that conditions in our study reach have improved markedly since the 1960's.
Isolation, Production, and Characterization of Protease from Bacillus subtilis IB No. 11

A potent protein degrading bacterium was isolated from soil samples of different environments. Polyphasic taxonomic studies and phylogenetic 16S rRNA sequence analyses led to identify the isolate IB No. 11 as a strain of Bacillus subtilis. The isolated strain was recognized to produce protease constitutively, and the maximum production (1.64 units/ml) was attained in a shake flask culture when the isolate was grown at 40 , for 32 h in basal medium supplemented with starch (0.25%) and gelatin (1.25%) as sole carbon and nitrogen source, respectively. The optimum pH and temperature for the protease activity were determined to be pH 7.0 and 50 , respectively. Ca 2+ and Mn 2+ enhanced remarkably the protease activity but neither showed positive effect on the protease's thermal stability. In addition, it was observed that the protease was fairly stable in the pH range of 6.5-8.0 and at temperatures below 50 , and it could be a good candidate for an animal feed additive. The inhibition profile of the protease by various inhibitors indicated that the enzyme is a member of serine-proteases. A combination of UV irradiation and NTG mutagenesis allowed to develop a protease hyper-producing mutant strain coded as IB No. 11-4. This mutant strain produced approximately 3.23-fold higher protease activity (6.74 units/mg) than the parent strain IB No. 11 when grown at 40 for 32h in the production medium. The protease production profile of the selected mutants was also confirmed by the zymography analysis. (Key words : Protease, Bacillus subtilis IB No. 11, Isolation, Characterization)