Miracle-dz/UniFAR-FTUs huggingface dataset:
A conceptual framework for the modelling and simulation of social systems

This paper presents a conceptual framework for the modelling and simulation of properties, interactions and processes of social systems based on computational templates using discrete event system specification (DEVS) formalism and OMG Systems Modelling Language (SysML) diagrams. No antecedents of this combination were found in the literature, and so this is one of the contributions of this paper. Additionally, this article explains how the principles and rules of SysML can be applied to the analysis of social systems. An example of the proposed framework based on a basic Agent_Zero model is shown. The conceptual framework was built based on a critical literature review, and included new additional elements to create a complete but simple conceptual framework. The codes for the simulations were written in Python 3.
Shared use of flowers leads to horizontal pathogen transmission

Plant–pollinator interactions are based on mutual benefits; the plant gains fertilization and the pollinator gains food resources. But aside from providing rewards, flowers can be risky places to visit, for example if a predator ambushes during the feeding/pollination process. Here, we show that pollination may also involve the transmission of pathogens for the pollinators. Experimental evidence is given that a trypanosome parasite, Crithidia bombi, can be horizontally transmitted within populations of its hosts, the bumblebees Bombus spp. , through the shared use of flowers. Important floral characteristics such as nectar availability or inflorescence architecture may also affect transmission rate. Therefore, in addition to energetic considerations, pollinator strategies could also be governed by the risk of contracting pathogens.
Definition of unique traits of human CD4− CD8−αβ T cells

We have studied the nature of human CD4− CD8− (double negative) αβ T cells to determine whether they possess unique characteristics which could further differentiate them from conventional CD4+ or CD8+ (single positive) T cells. We observed that double negative TCR αβ+ T cells differ from single positive T cells in the following respects: (i) their T cell receptor (TCR) repertoire is different, as revealed by the analysis of 47 clones derived from three individuals and by analysis of peripheral blood lymphocytes (PBL) prior to in vitro manipulation; (ii) their in vivo CD3:TCR expression is lower before in vitro manipulation and expansion; (iii) their direct proliferative response to IL‐3, which is not mediated by secondary release of other T cell growth factors. These characteristics have also been recently ascribed to murine double negative αβ T cells, which develop extrathymically and are considered to be a distinct T cell lineage. Our data suggest that, like their murine counterparts, human double negative αβ T cells may represent a distinct T cell lineage which might develop extrathymically.
Induction of the SOS response in Escherichia coli by 4‐quinolone antimicrobial agents

Abstract The induction of the RecA protein in strains of Escherichia coli was demonstrated for five 4-quinolone compounds. Using a recA ∷ lac fusion, the expression of the recA gene was quantified for each agent. Induction was shown to be time and concentration-dependent. At a certain concentration (dependent on each 4-quinolone) maximum induction was observed. Above this concentration, reduced induction was observed with an increase in 4-quinolone concentration. The inducing concentration of each 4-quinolone correlated well with the antibacterial activity of each agent.
The Unpredictability of the Marine Phytoplankton

The focus of this paper is on what appears to be a large and partly inherent measure of unpredictability in marine phytoplankton species. Thus, if a species is frequently abundant and occasionally undetectable or if instead it is frequently undetectable and occasionally abundant, it behaves unpredictably in its occasional failure or in its occasional success. The option of "abundant or unabundant or below detection," with resolution to just one of these at any given place, results in the close juxtaposition of abundances of a given species (>3.0 cells/cm3) with unabundances or undetectable amounts (the last <0.03 cells/cm3), often under conditions of excess nutrient, and attests to its fast-growing but unpredictable behavior. Such species occur in the Slope Water off the coast of southern New England. Farther away, in the mid-Atlantic, a different lot of predictable but slowly growing species occurs. In terms of a single midocean species an appropriate formula is: "if it is a predictable species, then it is a slow grower" implying "if it is not a slow grower, then it is not a predictable species," with the parts before and after "implying" reversed for a single Slope Water species. One purpose of this paper is application of a philosophical explanation of an observed concentra- tion of a given species. Such an observation is a resolution of "abundant or unabundant or below detection" to just one of these. A second purpose is clarification of scientific explanation (Hempel 1970), wherein theory formation is considered to be a suppositional process, as in the if-then sequences of the above formula.
Analytical, Nutritional and Clinical Methods Evaluation of the phenolic content, antioxidant activity and colour of Slovenian honey

Honey samples from the seven most common honey types in Slovenia were screened for total phenolic content by the modified Folin– Ciocalteu method, for potential antioxidant activity using the ferric reducing antioxidant power (FRAP) assay and by the 1,1-diphenyl-2picrylhydrazyl (DPPH) method for antiradical activity. In addition the colour characteristics of honey samples were analysed. The results of the study showed that total phenolic content, antioxidant activity and colour parameters differ widely among different honey types. Phenolic content expressed as gallic acid equivalent ranged from 44.8 mg/kg in acacia honey to 241.4 mg/kg in fir honey. Antioxidant activity was the lowest in the brightest acacia and lime honeys and the highest in darker honeys, namely fir, spruce and forest. The colour of the Slovenian honeys, analysed in this study was very variable and ranged from pale yellow to dark brown. Correlations between the parameters analysed were found to be statistically significant (p < 0.05). 2007 Elsevier Ltd. All rights reserved.
Geographic signatures of North American West Coast estuaries

West Coast estuaries are geologically young and composed of a variety of geomorphological types. These estuaries range from large fjords to shallow lagoons; from large to low freshwater flows. Natural hazards include E1 Niños, strong Pacific storms, and active tectonic activity. West Coast estuaries support a wide range of living resources: five salmon species, harvestable shellfish, waterfowl and marine birds, marine mammals, and a variety of algae and plants. Although populations of many of these living resources have declined (salmonids), others have increased (marine mammals). West Coast estuaries are also centers of commerce and increasingly large shipping traffic. The West Coast human population is rising faster than most other areas of the U.S. and Canada, and is distributed heavily in southern California, the San Francisco Bay area, around Puget Sound, and the Fraser River estuary. While water pollution is a problem in many of the urbanized estuaries, most estuaries do not suffer from poor water quality. Primary estuarine problems include habitat alterations, degradation, and loss; diverted freshwater flows; marine sediment contamination; and exotic species introductions. The growing West Coast economy and population are in part related to the quality of life, which is dependent on the use and enjoyment of abundant coastal natural resources.
The anti-arrhythmic effects of pomegranate (Punica granatum) are mainly mediated by nitric oxide

BACKGROUND: Pomegranate juice (PJ) contains strong antioxidant polyphenols, and cardiovascular beneficial effects have been reported for the fruit. OBJECTIVE: Using a Langendorff’s model, we hypothesized that PJ has antiarrhythmic effects on isolated rat hearts. METHODS: The hearts in the control group (n = 10) were perfused with Krebs solution. The test groups (n = 10, each) were further perfused with PJ, L-NAME (L), or both (PJL). Following 30 min stabilization, all hearts experienced 30 min global ischemia and 120 min reperfusion. The hearts were monitored for the occurrence of single and salvo arrhythmias, ventricular tachycardia (VT), and ventricular fibrillation (VF). The cardiac release of creatine kinase-MB (CK-MB), lactate dehydrogenase (LDH), and nitrite were measured. In addition, the markers of oxidative stress including superoxide dismutase (SOD), glutathione peroxidase (GPX), catalase (CAT), and malondialdehyde (MDA) were assayed in the homogenates of the hearts. RESULTS: The PJ group showed a significant reduction in the occurrence of arrhythmias, an improvement in redox markers, and a rise in nitrite release, compared to the control. Simultaneous treatment with L-NAME significantly reduced, but not fully abolished, these effects. CONCLUSIONS: The current study suggests strong anti-arrhythmic effects for PJ, which are mainly mediated by nitric oxide.
Water- and temperature-dependence of DNA damage and repair in the fruticose lichen Cladonia arbuscula ssp mitis exposed to UV-B radiation

The induction of cyclobutane pyrimidine dimers (CPDs) by ultraviolet-B radiation (UV-B, 280-315 nm) and repair mechanisms were studied in the lichen Cladonia arbuscula ssp. mitis exposed to different temperatures and water status conditions. In addition, the development and repair of CPDs were studied in relation to the different developmental stages of the lichen thallus podetial branches. Air-dried lichen thalli exposed to UV-B radiation combined with relatively high visible light (HL, 800 mumol m(-2) s(-1); 400-700 nm) for 7 days showed a progressive increase of CPDs with no substantial repair, although HL was present during and after irradiation with UV-B. Fully hydrated lichen thalli, that had not been previously exposed to UV-B radiation for 7 days, were given short-term UV-B radiation treatment at 25degreesC, and accumulated DNA lesions in the form of CPDs, with repair occurring when they were exposed to photoreactivating conditions (2 h of 300 mumol m(-2)s(-1), 400-700 nm). A different pattern was observed when fully hydrated thalli were exposed to short-term UV-B radiation at 2degreesC, in comparison with exposure at 25degreesC. High levels of CPDs were induced at 2degreesC under UV-B irradiation, without significant repair under subsequent photoreactivating light. Likewise, when PAR (300 mumol m(-2)s(-1) ) and UV-B radiation were given simultaneously, the CPD levels were not lowered. Throughout all experiments the youngest, less differentiated parts of the lichen thallus - namely 'tips', according to our arbitrary subdivision - were the parts showing the highest levels of CPD accumulation and the lowest levels of repair in comparison with the older thallus tissue ('stems'). Thus the experiments showed that Cladonia arbuscula ssp. mitis is sensitive to UV-B irradiation in the air-dried state and is not able to completely repair the damage caused by the radiation. Furthermore, temperature plays a role in the DNA damage repairing capacity of this lichen, since even when fully hydrated, C. arbuscula ssp. mitis did not repair DNA damage at the low temperatures. (Less)
A method for the rapid measurement of thermal tolerance traits in studies of small insects

Abstract A technique for rapidly measuring non‐lethal thermal tolerance traits in small insects and terrestrial arthropods of similar size is described. Single or multiple individuals are heated or cooled in an arena milled into a temperature‐controlled aluminium block and their behaviour recorded continuously using a digital video camera. Data are collected retrospectively by playback of the stored images. To illustrate this technique measurement of six thermal tolerance traits using this method is described using first instar nymphs (body length = 0.66 mm) of the aphid Myzus persicae. These traits are high and low temperatures at which individual aphids cease walking, high and low temperatures at which aphids move for the final time, the temperature at which aphids begin to recover from chill coma, and the temperature at which they begin to walk again. The method is validated by comparing the results of multiple low temperature assays. No significant differences are detected between assays. Potential applications, limitations and technical problems are discussed.
Protocol of Aerobic Exercise and Cognitive Health (REACH): A Pilot Study

A growing body of evidence supports that aerobic exercise can decrease the risk of future cognitive impairment and Alzheimer’s disease (AD). There is a pressing need to rigorously determine whether cognitively normal yet at-risk individuals stand to benefit from the protective effects of exercise. The present study will test the feasibility of an aerobic exercise intervention in such a population and inform the design of a larger-scale randomized, controlled trial examining the effect of aerobic exercise on biomarkers of AD in late-middle-aged, at-risk individuals. This was a single-site, 1 : 1 block-randomized, parallel, two-arm trial. Cognitively normal participants aged 45–80 with documentation of familial and genetic AD risk factors were randomly assigned to one of two interventions. The Usual Physical Activity group was provided educational materials about exercise. The Enhanced Physical Activity intervention delivered 26 weeks of individualized and supervised aerobic exercise. Exercise duration and intensity were incrementally increased to 150 min/week and 70–80% of heart rate reserve, respectively. Retention and adherence were measured to assess study feasibility. In addition, pre- and post- intervention differences between the two arms were evaluated for cardiorespiratory fitness, physical activity, brain glucose metabolism, cerebral structure, vascular health, memory, executive function, and mood. Data from randomized controlled trials of exercise training are needed to identify the proper exercise prescription for reducing accumulation of AD biomarkers in cognitively normal individuals. The current trial will contribute to filling that gap while informing the design of large-scale trials.
Elevated CO2 enhances plant growth in droughted N2-fixing alfalfa without improving water status

The long-term interaction between elevated CO2 and soil water deficit was analysed in N2-fixing alfalfa plants in order to assess the possible drought tolerance effect of CO2. Elevated CO2 could delay the onset of drought stress by decreasing transpiration rates, but this effect was avoided by subjecting plants to the same soil water content. Nodulated alfalfa plants subjected to ambient (400 μmol mol−1) or elevated (700 μmol mol−1) CO2 were either well watered or partially watered by restricting water to obtain 30% of the water content at field capacity (ampproximately 0.55 g water cm−3). The negative effects of soil water deficit on plant growth were counterbalanced by elevated CO2. In droughted plants, elevated CO2 stimulated carbon fixation and, as a result, biomass production was even greater than in well-watered plants grown in ambient CO2. Below-ground production was preferentially stimulated by elevated CO2 in droughted plants, increasing nodule biomass production and the availability of photosynthates to the nodules. As a result, total nitrogen content in droughted plants was higher than in well-watered plants grown in ambient CO2. The beneficial effect of elevated CO2 was not correlated with a better plant water status. It is concluded that elevated CO2 enhances growth of droughted plants by stimulating carbon fixation, preferentially increasing the availability of photosynthates to below-ground production (roots and nodules) without improving water status. This means that elevated CO2 enhances the ability to produce more biomass in N2-fixing alfalfa under given soil water stress, improving drought tolerance.
Degradation of the lignocellulose complex in wood

Degradation of the lignocellulose complex in wood varies depending on the microorganism causing decay. The degradative processes of white-, brown-, and soft-rot fungi as well as different forms of bacterial degradation are presented. Ultrastructural methods were used to elucidate cell-wall alterations that occurred during the various stages of decay. In wood inoculated with the white-rot fungus Ceriporiopsis subvermispora, changes in the cell wall, such as electron-dense zones after staining with uranyl acetate, were evident during incipient stages of decay. The ratio of syringyl:guaiacyl lignin of different woods, different cell types, and even the different layers within a cell wall influenced the type and extent of decay by white-rot fungi. Soft rots caused unique changes in the lignocellulose matrix. The type of wood substrate governed the form (type I or type II) of soft rot that occurred. Brown-rot fungi depolymerized cellulose early in the decay process and degraded cellulose without prior removal .
Urban coyotes are genetically distinct from coyotes in natural habitats

Urbanization is increasing throughout the world, transforming natural habitats. Coyotes (Canis latrans) are found in highly urban, suburban, rural and undeveloped mountainous habitats, making them an exemplary model organism to investigate the effects of urbanization on animals. We hypothesized that coyotes in natural habitats are more genetically related to distant coyotes in similar natural habitats and less related to coyotes in urban areas due to natal habitat-biased dispersal. We also hypothesized that increasing urbanization would result in decreased genetic diversity due to habitat fragmentation, dispersal barriers and genetic drift. We analyzed 10 microsatellite genetic markers from 125 individual coyotes sampled across a spectrum of highly urban to highly natural areas in southern California. Most coyotes clustered into four distinct genetic populations, whereas others appeared to have admixed ancestry. Three genetic populations were associated primarily with urban habitats in Los Angeles and Orange Counties. In contrast, the remaining population was associated with more naturally vegetated land near the surrounding mountains. Coyotes living in natural areas formed a genetically distinct cluster despite long geographic distances separating them. Genetic diversity was negatively associated with urban/suburban land cover and local road density, and positively associated with the relative amount of natural vegetation. These results indicate that genetic differentiation and loss of genetic diversity coincided with the extremely rapid expansion of Greater Los Angeles throughout the 1900s. Thus, urbanization reduces gene flow and erodes genetic diversity even in a habitat generalist thought to be minimally impacted by land development.
Genetics of Growth and Reproduction in the Turkey 5. Selection for Increased Body Weight Alone and in Combination with Increased Egg Production

Abstract Selection for increased 16-week body weight alone resulted in a large increase in body weight and a major reduction in egg production over nine generations of selection. The realized heritability estimates for 16-week body weight were . 31 ± . 04 and . 30 ± . 03, respectively, for males and females. The realized genetic correlation between female 16-week body weight and egg production was −. 4 2 ± . 12. Large negative realized genetic correlations (−.50 to −.63) were observed between female 16-week body weight and intensity of lay traits (average clutch length, maximum clutch length and rate of lay), while generally only small non-significant positive correlations were found between body weight and broodiness traits (number of broody periods, length of broody period, and total days lost from broodiness). No significant correlations with egg weight, percent fertility or hatchability of fertile eggs were observed. Gains in 16-week body weight of from approximately 1/4 to 1/2 of those observed when selecting for body weight alone were achieved in another line without any reduction in egg production by the use of a selection index which gave three times the emphasis on 16-week body weight as on 180-day egg production. The realized heritability of 16-week body weight and the realized genetic correlations with egg production, intensity of lay traits and broodiness traits were similar in this line to those estimated in the line selected only for increased 16-week body weight.
Fecundity and mortality in populations of Salicornia europaea agg. at Skallingen, Denmark

Seedlings of the annual, Salicornia europaea (sensu stricto), germinated in the outer marsh sand flats at Skallingen in early May, and the relative growth rates of root and shoot were high during the establishment phase. Mortality of plants, which was not density-dependent, was greater than 70% in most plots from early May to early October, as a result of wave action, desiccation and the presence of algal mats. Salicornia ramosissima was present in the outer and inner marshes mixed with Puccinellia maritima. Seedling densities of this annual were high, and in early May growth rates were lower than those for Salicornia europaea. Overall mortality of plants from early May to early October was density-independent. Mortality of S. ramosissima in the inner marsh was only 50% from May to October, whereas the mortality of S. ramosissima in the outer marsh was 95% in the same period. Different levels of seed production per plant, which reflected differences in plant architecture, were evident between the two micro-species. Reciprocal transplants from the inner marsh failed to survive on the outer marsh sand-flat. Mean seed production per plant in plants transplanted from the outer marsh sand-flat to the inner marsh was only 10% of the value of the control populations. The distances of seed dispersal were different in the outer and inner marsh. Low recruitment occurred in areas cleared of Salicornia plants in the inner marsh, unlike the situation in the outer marsh sand-flat where tides dispersed seed.
Emergence of suppression of root-knot nematodes in sweet potato cropping systems treated with Pasteuria penetrans

Reproduction of root-knot nematodes and plant damage to the sweet potato cropping system treated with Pasteuria penetrans, a parasitic bacterium of nematodes, were examined in a field plot test. Bacterial cultures were applied to nematode-infested soil at a concentration of 7 × 10 9 endospores / 9 m 2 plot, and sweet potato cropping systems were conducted during an eight-year period. In a consecutive cropping system with Kokei 14, a susceptible cultivar, significantly higher density of the P. penetrans endospores was observed in the soil at the end of the fourth year. In this system, population densities of the second-stage juvenile of Meloidogyne spp. in the soil had been lower than in the system without bacterial application since the third year. In this system, a yield of marketable storage root was obtained comparable to that treated with 1,3-dichloropropene (92% a.i., 20 l / 10 a) fumigation in the fifth and sixth year. In a rotational cropping system using Beniotome, a cultivar which has resistance, suppressive effects of P. penetrans