Miracle-dz/UniFAR-FTUs huggingface dataset:
The shape of evolution: a comparison of real and random clades

The history of life is replete with apparent order. Much of this order may reflect the deterministic causes conventionally invoked, but we cannot be sure until we measure and subtract the order that arises in simple random systems. Consequently, we have constructed a random model that builds evolutionary trees by allowing lineages to branch and become extinct at equal probabilities. We proceed by dividing our simulated tree into clades and by comparing their sizes and shapes with the patterns exhibited by “real” clades as recorded by fossils. We regard the similarity of real and random clades as the outstanding result of this comparison. In both real and random systems, extinct clades arising after an “ecological barrel” had been filled have their maximum diversity at the midpoint of their duration; clades arising during the initial “filling” reach an earlier climax during this preequilibrial period of rapid diversification. However, some potential differences also emerge. Clades still living are much larger than extinct clades. We may attribute this to the morphological superiority of survivors, but we can also simulate it in a model that chooses the originators of clades at random. Real clades undergo greater fluctuations in diversity than do random clades, but the effect is not marked.
The Threat of Transformation: Quantifying the Vulnerability of Grasslands in South Africa

Abstract: The ability to predict which areas of conservation importance are most vulnerable to transformation and to rank the relative damage that transforming land uses could cause to biodiversity are important components of an effective and realistic conservation planning process. We used the South African grassland biome as a case study to illustrate the assessment of vulnerability to land‐use transformation through the construction of a “threat map. ” We identified the dominant transforming land uses and created suitability models based on area appropriateness for each. Land uses were scored according to their expected relative impacts on biodiversity, with a framework that included compositional, structural, and functional components. This information, once combined, resulted in a map that highlighted the areas most vulnerable to transformation in terms of the likelihood of their transformation and the impact on their biodiversity. We propose that such an analysis of the threat of transformation, in combination with species‐representation approaches, will aid the integration of conservation planning theory and decision making. This approach can be applied at any scale and in any region with a robustness and accuracy dependent on data quality, resultant suitability models, and comprehension of how land uses affect an area's biodiversity.
Nuclear Transplantation in Amphibia and the Importance of Stable Nuclear Changes in Promoting Cellular Differentiation

A diversity of results has been obtained from nuclear transfer experiments in Amphibia since the time when a satisfactory technique was first developed for transplanting living cell nuclei into enucleated eggs. This article reviews the question of whether stable changes restricting the developmental capacity of cell neclei are important in promoting the normal differentiation of somatic cells. The results of experiments with Rana and Xenopus have clearly shown that the mitotic products of some transplanted cell neclei have undergone stable changes restricting their developmental capacity. It has not yet been conclusively demonstrated that these nuclear changes arise during normal cell differentiation rather than following transplantation. If it should be found that at least some stable nuclear changes do arise during normal cell differentiation, there is at present no evidence to show whether they promote cell differentiation or arise only as a consequence of it. Other nuclear transfer experiments have shown that, at least in some cases, nuclei can support the formation of differentiated intestine cells without having lost the capacity to promote the formation of other quite different cell types. It is argued that some of these results support, and that others are consistent with, the following general conclusions: (1) that the nuclei of differentiating somatic cells do not generally undergo any restrictive changes affecting the genetic material itself; and (2) that the specialized information provided by somatic cell nuclei either results from a semistable inactivation of parts of the genetic material, or else depends solely upon the nature of the environment in which the chromosomes lie at any one time.
What's in the air? Preliminary analyses of Hawaiian airborne algae and land plant spores reveal a diverse and abundant flora

Abstract: The airborne algae of Oahu, Hawaii was studied along a transect crossing from the leeward to the windward side of the Koolau Mountain Range in summer 2013. Algae were collected on agarized medium in petri dishes from a car window as the vehicle drove from Honolulu to Kailua, Oahu, through an elevation gradient of > 360 m and a rainfall gradient of c. 900–3150 mm yr−1. Light microscopy and molecular methods [18S ribosomal (r)RNA gene, 16S rRNA gene, and UPA sequences] were used to characterize a total of 97 operational taxonomic units from the transect. The airborne algal flora of the transect was dominated by cyanobacteria, followed by chlorophycean green algae, diatoms, and ferns and liverworts. This study is the first in Hawaii to incorporate molecular techniques into the identification of airborne algae.
Impacts of climate change and land-use on the potential distribution of an invasive weed: a case study of Lantana camara in Australia

Taylor S, Kumar L & Reid N (2012). Impacts of climate change and land-use on the potential distribution of an invasive weed: a case study of Lantana camara in Australia. Weed Research.52, 391–401. Summary Lantana camara (lantana) is an extremely invasive species in many countries, including Australia. Biosecurity agencies will benefit from prior knowledge of the potential distribution of L. camara, under current and future climate scenarios. A process-based niche model for this species was developed using the CLIMEX modelling package. The potential distribution generated from this model was refined by incorporating existing land-use data in a Geographical Information System (GIS). The potential distribution of L. camara under current climate indicated that L. camara occupies almost the full extent of climatically suitable habitat available to it in Australia. Under future climate scenarios, L. camara range expands into new areas in Victoria, South Australia and Tasmania, while the northern parts of the continent become climatically unsuitable. This trend continued with the inclusion of land-use data, although with a more restricted distri-bution, as locations with suitable climate but unsuitable land-use were excluded. Weed control authorities in the new areas at risk of invasion under climate change need to be alerted to this emerging threat, so that effective response measures can be taken.
Investigating lethal and sublethal effects of the trace metals cadmium, cobalt, lead, nickel and zinc on the anemone Aiptasia pulchella, a cnidarian representative for ecotoxicology in tropical marine environments

The zooxanthellate sea anemone Aiptasia pulchella is found throughout the tropical and subtropical oceans of the Indo-Pacific and is easily maintained in aquaria, posing potential suitability as a standard tropical marine test organism for use in ecotoxicology. To gain an understanding of the sensitivity of A. pulchella to trace metals, 96-h static-renewal toxicity tests were conducted. Values of 96-h LC50 between 946 and 1196 µg L–1 were estimated for cadmium, between 595 and 1146 µg L–1 for zinc, 8060 and 12 352 µg L–1 for lead and 2209 and 5751 µg L–1 for nickel. In addition, preliminary assessment of rapid tentacle retraction was made. Six-hour EC50 values of 355 and 979 µg L–1 for cadmium, between 384 and 493 µg L–1 for zinc, between 2340 and 2584 µg L–1 for nickel, and 2610 µg L–1 for lead, were estimated for ‘severe’ tentacle retraction. Cobalt concentrations up to 1547 µg L–1 caused extreme zooxanthellae loss, but no more than 10% mortality and no rapid ‘severe’ tentacle retraction. The present study has provided important baseline information, enabling comparison of the acute sensitivity of A. pulchella to trace metals with other marine invertebrates, and guiding the development of sublethal endpoints.
Comparing entire colour patterns as birds see them

Colour patterns and their visual backgrounds consist of a mosaic of patches that vary in colour, brightness, size, shape and position. Most studies of crypsis, aposematism, sexual selection, or other forms of signalling concentrate on one or two patch classes (colours), either ignoring the rest of the colour pattern, or analysing the patches separately. We summarize methods of comparing colour patterns making use of known properties of bird eyes. The methods are easily modifiable for other animal visual systems. We present a new statistical method to compare entire colour patterns rather than comparing multiple pairs of patches. Unlike previous methods, the new method detects differences in the relationships among the colours, not just differences in colours. We present tests of the method's ability to detect a variety of kinds of differences between natural colour patterns and provide suggestions for analysis.
Iron Status and Coronary Risk in Rheumatic Heart Children

This study aimed at clarifying the relationship between iron status and atherogenic lipid profile in normal and chronic rheumatic heart as well as congenital heart defect children. The study included 31 children, 16 cases with chronic rheumatic heart disease (10 males and 6 females) and 6 with congenital heart disease. Nine children with normal hearts were taken as the control. Serum iron and total iron binding capacity were higher in both chronic rheumatic and congenital heart disease children than in the controls; but the increase was only significant in the second case. Serum low-density lipoprotein cholesterol (LDL-ch) and high-density lipoprotein-cholesterol (HDL-ch) were not significantly changed in either disease. In relation to sex, no significant changes were noticed in iron status of chronic rheumatic heart children. Serum LDL-ch and LDL-ch to HDL-ch ratio were significantly higher in females than in males. A correlation study was also done between lipid profile and iron status.
Phosphorylation of human chromosome maintenance 1 mediates association with 14-3-3 proteins

Abstract Human chromosome maintenance 1 (CRM1) was originally cloned based on homology to a yeast gene. CRM1, which belongs to the family of importin β-related nuclear transport receptors, directly and specifically associates with nuclear export signals (NESs) and mediates nuclear export of proteins containing leucine-rich NESs. We present evidence that CRM1 associates with a 22-kDa 14-3-3 scaffolding protein that is a principal structural and regulatory component of Human embryonic kidney (HEK 293) cells. We found a potential 14-3-3-binding motif (1049KHKRQMSVPG1058) in the CRM1 C-terminal domain that depended on serine 1055 phosphorylation by Protein Kinase A (PKA). We demonstrated that CRM1 is a PKA substrate using an in vitro assay. Using a pull-down approach and co-immunoprecipitation, we found that CRM1 interacted with the 14-3-3 motif in vivo and in vitro. We also detected colocalization of CRM1 and 14-3-3 proteins using confocal microscopy. Nuclear pore localization of CRM1 was disrupted by treatment with a PKA activator or inhibitor or by a S1055D/S1055A mutation in the CRM1 14-3-3-binding motif. Transient transfection assays showed that the apoptosis rate of cells with the S1055D construct was twice that of cells with wild type (WT) or S1055A construct. Our observations indicated that phosphorylation on the serine 1055 residue of CRM1 by PKA promoted 14-3-3 binding and cytoplasmic localization, resulting in enhancement of cell apoptosis.
A hierarchical model for analysing the stability of vegetation patterns created by grazing in temperate pastures

Questions: Does vegetation structure display any stability over the grazing season and in two successive years, and is there any correlation between the stability of these spatial patterns and local sward composition? Location: An upland grassland in the French Massif Central. Method: The mosaic of short and tall vegetation stands considered as grazed and ungrazed patches respectively is modeled as the realization of a Boolean process. This method does not require any arbitrarily set sward-height thresholds to discriminate between grazed and ungrazed areas, or the use of additional variables such as defoliation indexes. The model was validated by comparing empirical and simulated sward-height distributions and semi-variograms. Results: The model discriminated between grazed and ungrazed patches at both a fine (1 m2) and a larger (500 m2) scale. Selective grazing on legumes and forbs and avoidance of reproductive grass could partly explain the stability of fine-scale grazing patterns in lightly grazed plots. In these plots, the model revealed an inter-annual stability of large-scale grazing patterns at the time peak biomass occurred. At the end of the grazing season, lightly grazed plots showed fluctuating patch boundaries while heavily grazed plots showed a certain degree of patch stability. Conclusion: The model presented here reveals that selective grazing at the bite scale could lead to the creation of relatively stable patches within the pasture. Locally maintaining short cover heights would result in divergent within-plot vegetation dynamics, and thus favor the functional diversity of vegetation.
A ictiofauna do Parque Estadual do Cantão, Estado do Tocantins, Brasil

The Parque Estadual do Cantao is a protected area in the Araguaia River. In a survey carried out during a complete hydrological cycle, 271 species of fish, belonging to 183 genera, 41 families and 12 orders were captured. Characidae was the most diverse family with 89 species (32.6% of the total), followed by Loricariidae with 23 species (8.4%) and Cichlidae with 21 species (7.7%), ten families were represented by only one species. The results showed that the PE Cantao is an area with high diversity of fish species, and that the assemblies are still well preserved, so the existence and maintenance of this Park is of high interest for the preservation of the Araguaia River fish fauna.
Production of biogenic amines by lactic acid bacteria and bifidobacteria isolated from dairy products and beer

Summary The aim was to monitor production of eight biogenic amines (BAs) (histamine, tyramine (TYR), tryptamine, putrescine, cadaverine (CAD), phenylethylamine, spermine and spermidine) by selected 81 lactic acid bacteria (LAB) strains: Lactobacillus, Lactococcus, Leuconostoc, Enterococcus, Pediococcus, Tetragenococcus and Bifidobacterium. The tested LAB and bifidobacteria were isolated from dairy products and beer. The decarboxylase activity of the micro-organisms was studied in growth medium after cultivation. The activity was monitored by HPLC after the pre-column derivatisation with dansylchloride. Fifty LAB showed decarboxylase activity. Thirty-one strains produced low concentrations of CAD (≤10 mg L−1). Almost 70% of beer isolates generated higher amounts of TYR (≤3000 mg L−1). Most of the tested LAB demonstrated decarboxylase activity. The above micro-organisms can contribute to the increase of content of BAs in dairy products or beer and thereby threaten food safety and health of consumers. Production of BAs even by the representatives of some probiotic strains (Bifidobacterium and Lactobacillus rhamnosus) was detected in this research. This study has also proved that contaminating LAB can act as sources of higher amounts of CAD and TYR in beer.
Diversity Partitioning of Wild Bee Assemblages (Hymenoptera: Apoidea, Apiformes) and Species Preferences for Three Types of Refuge Habitats in an Agricultural Landscape in Poland

Abstract Patterns in bee assemblages consisting of 52 core (most abundant) species in farmland in the Wielkopolska region of W Poland were analysed. The entomological material was assessed during earlier research in 1978-1993 from 18 plots in three habitat types: shelterbelts, roadsides and forest patches. At the scale of the refuge habitat size analysed here, an increase in area only slightly enhanced bee species richness. The bee assemblage structures of roadsides and forest patches differ significantly, but their indicator species do not form any well-defined ecological groups. In non-linear forest patches, the bee community structure was more homogeneous than on roadsides. These two habitat types differed significantly in their species composition. Nine significant indicator species were found, but they did not share any ecological characteristics. Three factors were found to affect significantly the responses of individual bee species in the agricultural landscape: the degree of isolation of the refuge habitat, the edge ratio, and roadsides as a refuge habitat type. A large part of the regional diversity is due to the heterogeneity of habitats within the landscape. Habitat area has little influence on the diversity of wild bees, at least within the size range analysed here. We concluded from this study that, regardless of the habitat type, the density of bees from the summer phenological period is affected by the number of food plant species. Point forest patches are habitats where summer species from the genus Andrena and the cleptoparasitic genera Nomada and Sphecodes achieve their highest abundances. Roadsides negatively affected abundances of wild bees and there were no characteristic species for this type of habitat. We hypothesised that this might be related to the specific ecological part played by this type of habitat.
(1→3)‐β‐ D‐glucan may contribute to pollen sensitivity

The amount of (1→3)‐β‐ D‐glucan in pollen from different plants was evaluated using the Limulus assay with a specific lysate. The amount ranged from 79 to 1800 ng/106 pollen. A calculation of the inhaled dose suggests that the amount of (1→3)‐β‐ D‐glucan present during periods with a high pollen content in the air exceeds levels that cause airways inflammation.
Macrosemimimus, gen. nov. (Actinopterygii, Semionotiformes), from the Late Jurassic of Germany, England, and France

ABSTRACT We describe a new semionotiform genus, which was recognized while studying Macrosemimimus fegerti, gen. et sp. nov., from the Late Jurassic Solnhofen Archipelago, Germany. Macrosemimimus (Lepidotes) lennieri from the early Kimmeridgian of Cap de la Hève, France, including Lepidotes toombsi from the Lower Kimmeridge Clay in Cambridgeshire, England, as a junior synonym, also belong to the new genus. Though different species, the presence of the same fish genus in different biodiversity zones suggests that semionotiforms might have been less sensible to the ecological and physical factors that caused the endemisms recognized in the invertebrate faunas. Macrosemimimus is mainly distinguished by the peculiar shape of the antorbital portion of the frontal bones, a single pair of extrascapular bones that do not reach the dorsal midline, anteriorly open circumborbital ring, only two suborbital bones, edentulous maxilla, a large quadratojugal involved in the jaw articulation, four postcleithra, and the pectoral fins placed very low and joining ventrally. The two included species differ in the ornamentation of the skull bones, the morphology of the scales, the relative size and position of the extrascapular bones, the dorsal extension of the preoperculum, and the kind of dentition. Although the phylogenetic relationships of Macrosemimimus are not yet established, the particular shape of the antorbital portion of the frontals and the patterns of the extrascapular and suborbital bones indicate possible systematic affinity with the macrosemiids, “Lepidotes” gloriae from the Oxfordian of Cuba, and “Lepidotes” microrhis and “Lepidotes” tanyrhis from the Barremian of Las Hoyas, Spain.
Observing gravitational-wave transient GW150914 with minimal assumptions

The gravitational-wave signal GW150914 was first identified on Sept 14 2015 by searches for short-duration gravitational-wave transients. These searches identify time-correlated transients in multiple detectors with minimal assumptions aboutthe signal morphology, allowing them to be sensitive to gravitational waves emitted by a wide range of sources including binary black-hole mergers. Over the observational period from September 12th to October 20th 2015, these transient searches were sensitive to binary black-hole mergers similar to GW150914 to an average distance of $\sim 600$ Mpc. In this paper, we describe the analyses that first detected GW150914 as well as the parameter estimation and waveform reconstruction techniques that initially identified GW150914 as the merger of two black holes. We find that the reconstructed waveform is consistent with the signal from a binary black-hole merger with a chirp mass of $\sim 30 \, M_\odot$ and a total mass before merger of $\sim 70 \, M_\odot$ in the detector frame.
Suppression of Shade- or Heat-induced Leaf Senescence in Creeping Bentgrass through Transformation with the ipt Gene for Cytokinin Synthesis

Cytokinins have been associated with delaying or suppressing leaf senescence in plants. The objectives of this study were to determine whether the expression of theiptgene that encodes adenine isopentenyltransferase would delay leaf senescence induced by shade or heat stress in a perennial grass species. Creeping bentgrass (Agrostis stolonifera cv. Penncross) was transformed with ipt isolated from agrobacterium (Agrobacterium tumefaciens) using two gene constructs (SAG12-ipt and HSP18-ipt) designed to activate cytokinin synthesis during shade or heat stress. Whole plants of nine SAG12-ipt transgenic lines and the nontransgenic control plants were incubated in darkness at 20 8C for 20 days. Chlorophyll content of all transgenic lines and the control line decreased after dark treatment, but the decline was less pronounced in transgenic lines. All transgenic lines had higher isopentenyladenine (iP/iPA) content than the control line after 20 days of treatment. In six of the transgenic lines, iP/iPA content remained the same or higher after dark treatment. Whole plants of nine HSP18-ipt transgenic lines and the control plants were incubated at 35 8C for 7 days. Chlorophyll and iP/iPA content declined in the control plants, but the nine transgenic lines had asignificantly higherconcentration of iP/iPAand were ableto maintainchlorophyll contentat the prestress level. Our results suggest that expression of SAG12-ipt or HSP18-ipt in creeping bentgrass resulted in increases in cytokinin production, which may have led to the delay and suppression of leaf senescence induced by shade or heat stress.