Miracle-dz/UniFAR-FTUs huggingface dataset:
A revision of Chara sect. Protochara, comb. et stat. nov. (Characeae: Charophyceae)

Abstract. A revision of a group of ecorticate species of Chara is presented, on the basis of fresh, pressed and spirit-preserved material. The following seven species are recognised, characterised by a very simple morphology, with few or inconspicuous accessory cells (cortication, stipulodes, bract cells, bracteoles) and large gametangia: Chara australis R.Br. , C. lucida (A.Braun) Casanova & Karol comb et. stat. nov., C. porteri Casanova, sp. nov., C. protocharoides Casanova & Karol, nom. nov. (=Protochara australis Womersley & Ophel) and C. stuartiana (Kütz.) Casanova & Karol comb. et. stat. nov. from Australia, and C. corallina Klein ex Willd. and C. wallichii A.Braun from Asia. A new section, Chara subg. Charopsis sect. Protochara (Womersley & Ophel) Casanova & Karol, comb. et stat. nov., is erected to accommodate these taxa, formerly placed in sect. Charopsis.
Long time molecular dynamic simulation on the agonist binding and activation of the β2-adrenergic receptor

β2-Adrenergic receptor (β2AR) plays a critical role in mediating the effects of catecholamine hormones. Due to the flexibility of the structure of its active state, study of agonist–β2AR is usually performed by molecular dynamic (MD) simulation. In this study we show the representative characteristics of agonist binding and activation on β2AR by MD simulation. The binding site and the conformational changes in the specific regions of β2AR are reasonable which confirmed the conclusion that agonist–β2AR reached its active-like state. We have studied the disruption of non-covalent intramolecular interactions, including the conserved DRY motif, the rotamer toggle switch and the ionic lock, the cytoplasmic ends of transmembranes 5 and 6, and some water-mediated hydrogen bond network regions. We conclude that agonist induced β2AR to its active conformation, or at least the active-like conformation.
Computational phraseology discovery in corpora with the mwetoolkit

Computer tools can help discovering new phraseological units in corpora, thanks to their ability to quickly draw statistics from large amounts of textual data. While the research community has focused on developing and evaluating original algorithms for the automatic discovery of phraseological units, little has been done to transform these sophisticated methods into usable software. In this chapter, we present a brief survey of the main approaches to computational phraseology available. Furthermore, we provide worked out examples of how to apply these methods using the mwetoolkit, a free software for the discovery and identification of multiword expressions. The usefulness of the automatically extracted units depends on various factors such as language, corpus size, target units, and available taggers and parsers. Nonetheless, the mwetoolkit allows fine-grained tuning so that this variability is taken into account, adapting the tool to the specificities of each lexicographic environmen
A new method for rapid screening of xenobiotic phloem mobility in plants

The deposition of hydrophobic polymers in the xylem of wheat grain floral axes prevents water and solute movement into grains via the xylem (xylem discontinuity). The only pathway for translocation of photo- synthate or externally applied xenobiotics into wheat grains is via the phloem. We have developed a new method based on the xylem discontinuity for rapidly screening phloem mobility of xenobiotics. By quantifying xenobiotic concentration in grains and excised plants after the compounds were applied through the cut stems, the phloem mobility can be estimated quantitatively. The phloem mobility obtained with our new grain-based method was correlated to xenobiotic chemical properties such as log Kow, pKa and electrical charge, and is consistent with pub- lished literature. Phloem mobility values determined by the grain-based assay were correlated to those from the direct phloem sap (aphid stylet exudate) assay of excised and intact plants, indicating that the grain-based assay is as reliable as the direct assay with aphid stylectomy. The new grain-based method is simple, quick, and can be scaled up for rapid screening of xenobiotic phloem mobility in plants. Similar seed (fruit)-based assay could also be developed with wide ranges of plant species that use the phloem as the only pathway for supplying water and nutrients into their seeds or fruits.
Incidence of entomophilous pollination of lowland coffee (Coffea canephora); the role of leaf cutter bees in Papua New Guinea

Lowland ‘robusta’ type coffee, (Coffea canephora), is a cash‐crop in many tropical countries, and is reported in the literature as primarily wind‐pollinated. The floral characteristics seem to refute this, and our evidence shows that in Papua New Guinea the flowers are classically entomophilous, being pollinated primarily by bees and flies. By far the most important and consistent visitors are solitary bees, especially Creightonella frontalis which nests within the plantations. The activity patterns and nesting biology of this bee are closely tied in with the success of the coffee bushes. Measures to improve pollination and fruit set in the coffee plantations are therefore suggested.
Demand-driven solutions to reduce aggression between pigs

Aggression between unfamiliar pigs at mixing is a major animal welfare problem in commercial farming. It has been studied since the 1970s and remains an important topic in animal welfare research. Methods to reduce pig aggression at mixing have been reviewed previously, but there has been little translation of the advocated techniques and building designs into practice. As a result, the problem persists on many commercial units. A similar situation exists for many other animal welfare issues. This article takes a new approach in not only reviewing the recent scientific literature, but also reviewing the evidence of uptake in industry. Firstly, the current state of aggression mitigation research is reviewed; including the most successful recent developments in breeding against aggression, early life socialisation, the use of pheromones and nutrition. Secondly, information is extracted from both peer reviewed and industry literature to establish the extent to which these strategies have been transferred from research to practice. Finally, we discuss why in spite of the amount of research on reducing aggression at mixing the problem has not reduced in intensive farming systems. The limited uptake in practice appears to be due to low prioritisation of the problem, the practicalities of implementation, lack of information on cost-effectiveness and ineffective communication of research to the farming community. To bridge this gap, industry must be involved in the design of practical solutions and the cost-effectiveness of these must be quantified. This approach should also be considered for other animal welfare issues under investigation. We recommend a better alignment between research questions and industry interests to increase the success of research efforts to improve animal welfare in practice.
Distributed Consensus Control for Nonlinear Multiagent Systems Under Directed Graphs of Dynamic Frequency Switches

This article focuses on distributed consensus control for nonlinear multiagent systems under directed graphs of dynamic frequency switches. The agents exchange information with each other through directed graphs that are switched based on a new general switching law. Not all graphs contain a spanning tree with the leader as the root. Under this condition, a novel distributed switched observer is constructed for each follower, and it can accurately estimate the state information of the leader by means of the switching law. Subsequently, a unified distributed controller is designed for each follower with the observer. Based on the Lyapunov stability theory, it is strictly proved that all agents can achieve a consensus with the controller. More importantly, our proposed algorithm can render the number of switches of the graphs to grow faster than an affine function of the length of a time interval, which greatly reduces the conservativeness on graphs switches. Moreover, the consensus algorithm has a wide application prospect in cooperative control. Finally, the effectiveness of theoretical results is illustrated by making numerical simulations.
Ecological characterization of three different phylogenetic groups belonging to the cellulolytic bacterial species Fibrobacter succinogenes in the rumen

To study the group-dependent ecology of Fibrobacter succinogenes in the rumen, real-time polymerase chain reaction assays for two phylogenetic groups (groups 2 and 3) of F. succinogenes were newly established and applied to rumen samples. Both the assays targeting the bacterial 16S rDNA were sensitive and accurate, showing wide quantifiable ranges (104−109 and 102−109 copies of 16S rDNA) and high recoveries of known amounts of added DNA (96.9 and 98.0%). The quantity of group 1 was confirmed to be numerable by subtracting assay values of groups 2 and 3 from that of F. succinogenes species (groups 1–3). By using the developed assays and the above subtractive calculation, the quantities of all three groups were evaluated in solid and liquid fractions of the rumen content and also on hay stems. In the solid fraction, groups 1 and 2 were abundantly present, compared with group 3 (P < 0.05). On untreated hay stems, group 1 was dominant throughout 48 h. In addition, group 1 showed growth even on the cellulase-treated hay stems, unlike the other two groups. These results suggest that F. succinogenes group 1 greatly contributes to rumen fiber digestion, even for less degradable materials.
Clinical Significance of Higher Cutoffs for Myositis Autoantibody Positivity Using the Euroimmun Research Line Blot: Comment on the Article by Mecoli et al

We read with interest the article ''Myositis Autoantibodies: A Comparison of Results from the Oklahoma Medical Research Foundation Myositis Panel to the Euroimmun Research Line Blot'' by Mecoli et al.1 . The study showed that, by using the Euroimmun panel for myositis-specific autoantibodies (MSA), different cut-offs should apply for all specificities tested in order to determine a true positive antibody status.
Cryptophyte bloom in a Mediterranean estuary: High abundance of Plagioselmis cf. prolonga in the Krka River estuary (eastern Adriatic Sea)

During the June 2010 survey of phytoplankton and physicochemical parameters in the Krka River estuary (eastern Adriatic Sea), a cryptophyte bloom was observed. High abundance of cryptophytes (maximum 7.9×106 cells l–1) and high concentrations of the class-specific biomarker pigment alloxanthine (maximum 2312 ng l–1) were detected in the surface layer and at the halocline in the lower reach of the estuary. Taxonomical analysis revealed that the blooming species was Plagioselmis cf. prolonga. Analysis of the environmental parameters in the estuary suggested that the bloom was supported by the slower river flow as well as the increased orthophosphate and ammonium concentrations. The first record of a cryptophyte bloom in the Krka River estuary may indicate that large-scale changes are taking place in the phytoplankton community. Such changes could have a major impact on the natural ecosystem dynamics and the mariculture production in the area.
Application of a genetic algorithm for multi-item inventory lot-sizing with supplier selection under quantity discount and lead time

This study presents an application of genetic algorithm (GA) for solving the multi-item inventory lot-sizing problem with supplier selection under discounts and lead time constraints. A mixed-integer linear programming (MILP) model is developed for proposed problem. To solve the problem, a genetic algorithm (GA) with two additional operations is proposed for handling the effect of the problem size. An adaptor for adjusting a chromosome data before the evaluation process and a penalty step for deterring an infeasible solution are developed. Finally, numerical examples are generated to evaluate the performance of the proposed GA, and the comparison with MILP approach about the solution quality and time is presented.
Inhibition of Rhizobium trifolii by Yeast Extracts or Glycine is Prevented by Calcium

Summary: Several yeast water preparations and commercial yeast extracts varied in their toxicity to two strains of Rhizobium trifolii. Strains of R. japonicum and R. leguminosarum were also susceptible to yeast extract, while strains of R. meliloti were resistant. An interaction between glycine and monovalent cations was the main cause of yeast extract toxicity. Divalent cations, notably Ca2+, added to inhibitory media prevented the toxicity and enhanced growth with increased concentrations of yeast extract.
Evidence that the N-terminal extension of the vicieae convicilin genes evolved by intragenic duplications and trinucleotide expansions.

This study was aimed to identify lentil (Lens culinaris subsp. culinaris) convicilin genes and to carry out a comparative analysis of these genes in the tribe Vicieae. Convicilins differ from vicilins, a related group of plant seed storage proteins, mainly by the presence of an additional sequence of amino acids in the sequence corresponding to the first exon, referred as the N-terminal extension. A single gene for convicilin, a component of legume seed storage pro - teins, was identified in the cultivated lentil. In this species, the N-terminal extension is formed by a stretch of 126 amino acids of which 59.2% are charged amino acids: 29.6% glutamic acid, 3.2% aspartic acid, 14.4% arginine, 8.8% lysine, and 3.2% histidine. This lentil convicilin sequence is similar to the sequence of convicilins in other species of the tribe Vicieae. However, the size of the N-terminal extension clearly differs among convicilins. Sequence comparison and phylogenetic analyses including convicilin and vicilin of Vicieae species indicated that the differentiation between vicilins and convicilins predated the differentiation of the two vicilin gene families (47- and 50-kDa vicilins), and that the N-terminal extension evolved mainly by a series of duplications of short internal sequences and triplet expansions, the predominant one being GAA.
Comparison of serological and culture plate methods for detecting species of Phytophthora, Pythium, and Rhizoctonia in ornamental plants.

When the pathogens were present in roots at levels that yielded ELISA reactions > 0.3 absorbance units above the test threshold, there was good agreement between the two methods, particularly for detection of Phytophthora spp. (.)In greenhouse experiments, there was no significant difference between ELISA and culture plating in detection of P. cryptogea in inoculated sage roots(.)
GUSTATORY DISCRIMINATION BETWEEN LIQUIDS BY THE APHID MYZUS PERSICAE (SULZER)

The relative acceptability of different fluids to Myzus persicae (Sulzer) was compared using simple choice‐chambers in which the aphids had equal access to two fluids via a membrane of stretched Parafilm “M”(R). Sucrose solutions were markedly preferred to water. Sucrose solutions containing a mixture of 6 L amino acids (asparagine, leucine, lysine, methionine, threonine and valine, each at 0.1%) were considerably more acceptable than a solution of sucrose only. A solution of the amino acids alone was not discriminated from water. Solutions containing 0.1% neutral red were less acceptable than those without this dye. The results indicate the applicability of the method for rapidly demonstrating the effects of stimulatory and inhibitory substances.
Morphophysiological responses of Aechmea blanchetiana (Bromeliaceae) to excess copper during in vitro culture

Abstract The use of plants as bioindicators can be effective for environmental monitoring, mainly related to heavy metals such as copper (Cu). In vitro conditions are more easily controlled, to enable isolating the stress factors that can interfere in plants’ responses. The aim was to investigate the morphophysiological responses of Aechmea blanchetiana submitted to excess Cu, and to verify the degree of tolerance and potential as a bioindicator of this species. Previously cultured shoots of A. blanchetiana were transferred to agar-solidified MS medium. After 60 days, the tank system was recreated, with the addition of stationary liquid MS medium with different concentrations of Cu (0, 25, 50 and 100 μM). After 90 days with excess Cu, anatomical analysis along with quantification of the contents of nutrients, photosynthetic pigments and chlorophyll a fluorescence were carried out. Alterations in the stomatal density and chlorenchyma thickness were observed in the plants grown with excess Cu. There was an increase in the Cu content in the plants in function of the Cu levels. However, the adjustments in the content of the other nutrients were essential for tolerance to excess Cu. Aechmea blanchetiana tolerates high Cu concentrations and has potential for use as a bioindicator.
Influence of production and prices on optimum culling rates and annualized net revenue.

Abstract Dynamic programming was used to make optimum insemination and culling decisions for a dairy enterprise. Monthly costs and revenues for cows were calculated from milk and fat yields, calf values, feed costs, veterinary costs, housing and equipment costs, and interest. Cows were described in the dynamic programming model by lactation number, month in lactation, milk production during the present and previous lactations, and time of conception. The model considered variation in milk yield, replacement heifer costs, carcass values, involuntary culling, genetic improvement, conception rates, semen costs, and interest. Prices and parameters were chosen to represent the Holstein population in the US. Optimum average yearly culling rate was about 25% (optimum average herd life was 47.8 mo) and the yearly annuity of net revenue for a replacement heifer over a 15-yr planning horizon was $443 in the base situation. Various average mature equivalent yields, replacement heifer prices, milk prices, and feed prices were used in a sensitivity analysis. The yearly annuity of net revenue was sensitive to changes in all these parameters. Milk yield, milk prices, and feed prices had major effects on yearly annuity. Optimum culling decisions were sensitive to changes in replacement heifer prices. Average mature equivalent milk yield, milk price, and feed price had small effects on culling.
The intergenerational transmission of loneliness between parents and their adult children

Objective: This study examined the relationship between loneliness in parents and in their adult children, and took into account the role of gender differences in the intergenerational transmission of loneliness. Background: Although it is well documented that loneliness has negative effects on a person’s physical and mental health, only a relatively small number of empirical studies have investigated the intergenerational transmission of loneliness between parents and their children, including the potential long-term effects of transmission processes. Moreover, the findings of the few existing studies have been inconsistent and contradictory, particularly with regard to gender differences. Method: The statistical analysis drew on data from the German Socio-Economic Panel Study (SOEP). Based on data from 2013 and 2017, stepwise multilevel linear regression models were estimated for 4,457 respondents between the ages of 18 and 40 and their parents. Results: Significant associations were found between loneliness in parents and in their adult children. The analysis also revealed that the relationship between loneliness in mothers and in their children did not depend on whether mothers and children were living in the same household. However, no significant differences were found between same-sex and opposite-sex parent-child dyads. Conclusion: This study provided moderate evidence for the intergenerational transmission of loneliness between parents and their adult children, as well as indirect evidence for the long-term effects of transmission processes between mothers and children.
Vegetation responses to long-term alkaline cement dust pollution inPinus sylvestris-dominated boreal forests - niche breadth along the soil pH gradient

Questions How resilient is boreal forest vegetation growing on acidic podzols to the environmental change caused by alkaline kiln dust pollution? How adaptive is the vegetation, when species pool and time for dispersal do not limit? How constant is the species niche breadth along the soil pH gradient? Location Region of 30 km around the Kunda cement plant, northern Estonia (59°30′ N, 26°32′ E), which has been continuously polluted last 140 years. Methods We sampled 20 forest stands on sandy gleyic podzols at various distances from the pollution source, leeward and windward of prevailing winds. Data processing: principal components analysis for gradient generalization, indicator species analysis for grouping species along the pollution gradient and generalized linear model analyses to estimate species reaction to pollution, considering covariates. Results The impact of alkaline dust accumulated over a century persisted despite resolute reductions of pollution. Forest soil conditions changed 10 km leeward and 5 km windward from the source: the litter pH level changed from 3.6 to 4.5 in unpolluted forests to 7.1–7.4 in the heavily polluted forests, and soil Ca content increased ten-fold. Soil alkalization has induced a remarkable succession from typical boreal vegetation toward vegetation of boreo-nemoral or calcareous habitats. We detected a linear increase of species richness from habitats on acidic soils (unpolluted) to newly formed alkaline soils (polluted habitats), reflecting the species pool composition and size, which is known to be large for calcicolous species. The establishment of several endangered calcicolous species shows the lack of dispersal limitation and points on their narrow soil pH niche. The niche breadth of species along the pH gradient varied among species, but only a few species appeared to be pH generalists. Conclusions Species ranking along the pH and/or Ca gradients indicates (1) the existence of different ecological guilds in terms of ecological niche use, and (2) the formation of a new community is dictated by the tolerance level of each species. This supports the individualistic community assembly rule suggested by Gleason. We find that such polluted regions with disturbed communities have high scientific value as long-term ecological experiments, but this might lead to conflict between the peculiar biodiversity complex and human well-being.
Avian recolonization of eastern Canadian bogs after peat mining

To evaluate the potential of bog ecosystems to recover following peat mining, we compared bird species richness,abundance, and assemblages and vegetation among naturally revegetated and undisturbed bog sites in southeastern Quebec.Based on mining history, we selected 28 sites (12 natural, 9 abandoned after blockcut extraction, and 7 abandoned after vacuumextraction) in 15 bogs. We estimated percent cover for six vegetation strata in 106 plots with 100 m radius, on which bird pointcounts were conducted in 1993 and 1996. Vegetation structure differed significantly between natural, post-blockcut andpost-vacuum sites. While vegetation cover was almost complete in natural sites, abandoned sites, especially post vacuum, wereless vegetated, even after 20 years. Bird species richness and abundance were similar in natural and post-blockcut sites andboth were higher than in post-vacuum sites. Ten of the 28 species studied in detail responded to site perturbation. Among them,the Palm Warbler was most closely associa.