Miracle-dz/UniFAR-FTUs huggingface dataset:
The Breeding Biology of the Crescent Honeyeater Phylidonyris pyrrhoptera at Wilsons Promontory, Victoria

Summary The breeding biology of the Crescent Honey-eater Phylidonyris pyrrhoptera was studied between 1994–98 (intensively in 1996 and 1997) at Wilsons Promontory National Park. Crescent Honeyeaters commonly occurred in wet forest and dry forest habitats, but were uncommon in Saw Banksia woodland and rarely observed in closed heath-land. They were found to breed only in wet forest habitats. Pairs were present at a study site in wet forest on Mt Oberon throughout the year, whereas a pair that bred in a King Fern swamp in two successive breeding seasons appeared to abandon the site in between bouts of breeding. The breeding season, extending over three months, appears unusually short for an Australian honeyeater. Within that period some pairs were multi-brooded (i.e. re-nested after a successful breeding attempt). The breeding biology of the Crescent Honeyeater was found to be generally similar to that reported for other honeyeaters in spite of marked sexual dichromatism and dimorphism (clutch size 2.8 ± 0.4 eggs, n = 28 clutches, incubation period 13.2 ± 0.2 days, n = 5 clutches, nestling period 13.0 days, n = 9 clutches). The plumage of nestlings was found to be sexually dichromatic. Fledglings of both sexes were re-sighted at the natal site in subsequent years.
Environmental Effects on the Performance of Foliar Applied Plant Growth Regulators: A Review Focusing on Tree Fruits

ADDITIONAL INDEX WORDS. abscission, aminoethoxyvinylglycine, apples, BA, 6-benzyladenine, 2-chloroethylphos- phonic acid, Citrus, Ethrel, fruit set, fruit size, Malus ◊domestica, NAA, 1-naphthaleneacetic acid, PGR, surfac- tants, thinning SUMMARY. Plant response to foliar application of plant growth regulators (PGRs) is often variable, in part due to environmental factors. Weather prior to application is thought to infl uence cuticle development and thus PGR uptake. For example, in growth chamber studies foliar uptake of 1-naphthaleneacetic acid (NAA) is sometimes increased when fruit trees are placed in low temperature and high humidity several weeks prior to application. Environmental conditions over an extended period of time after application may infl uence PGR conversion to active form (e.g., ethephon), PGR metabolism, or metabolic factors that affect PGR activity in the plant. The effects of environmental conditions on PGR uptake have been investigated extensively in laboratory studies. In many cases, uptake is clearly increased by high temperatures immediately after application. Laboratory studies re- port a linear positive correlation between temperature and uptake and greater temperature response above 25 °C (77.0 °F). High humidity and longer drying time often are also reported to increase PGR uptake in laboratory studies. These results are consistent with many grower observations on effects of weather on chemical thinning and have been incorporated into many product labels and extension recommendations. However, relatively few fi eld experiments have been reported in which the relationship between PGR response and environmental condi- tions were assessed. Wash-off studies have demonstrated that rain shortly after application may reduce effi cacy of NAA. Several studies demonstrate environmental interaction with metabolic activity involved in PGR action. For example, shading after thinner application is reported to increase fruitlet abscission and enhance effectiveness of some thinning agents. Chemical thinning of apples (Malus ◊domestica) with ethephon is reported to correlate strongly with temperature in the days after application, while studies suggest that higher temperatures after ami- noethoxyvinylglycine (AVG) application may reduce control of preharvest drop. However, the stage of fruitlet development at apple thinning often appears to be more important than environmental conditions at the time of PGR application. In addition, fi eld experiments indicate that longer drying times at lower temperatures seem to largely compensate for greater uptake rates at higher temperatures. This paper discusses data from published and previously unpublished experiments in order to understand the effects of environment on PGR response variability.
Circulating circular RNAs as biomarkers of cancer

Circular RNA (circRNA) is a kind of novel non-coding RNA, which is widely present in eukaryotes and has a special circular structure formed by 3'- and 5'-ends linking covalently. CircRNA has many features, including high stability, conservation, etc. Since the discovery of circRNA, it has been considered a “by-product” of gene expression. In recent years, many studies have confirmed that circRNAs play an essential role in the pathogenesis of many diseases. CircRNA is involved in various cancer processes including the regulation of cell growth, proliferation, invasion, metastasis, etc., and is differentially expressed in tumor tissues and even in the circulation of patients. Because of these characteristics, circRNA has become a competitive candidate in being a novel biomarker of cancer. This article reviews the role of circulating circRNA in cancer and its diagnostic significance.
Discovery of potential cyclooxygenase inhibitors using in silico docking studies

This study deals with the evaluation of the cyclooxygenase inhibitory activity of flavonoids (tangeritin, morin, rhamnetin, theaflavin, pachypodol, eriodictyol, homoeriodictyol, aromadedrin, okanin) using in silico docking studies. In silico docking studies were carried out using AutoDock 4.2. Three important parameters like binding energy, inhibition constant and intermolecular energy were determined. The results showed that all the selected flavonoids showed binding energy ranging between -8.77 kcalmol -1 to -6.10 kcalmol -1 when compared with that of the standard (-8.30 kcalmol -1 ). Intermolecular energy (-10.56 kcalmol -1 to -7.89 kcalmol -1 ) and inhibition constant (373.91 nM to 34.03 µM) of the ligands also coincide with the binding energy. All the selected flavonoids contributed cyclooxygenase inhibitory activity because of its structural parameters. These molecular docking analyses could lead to the further development of potent cyclooxygenase inhibitors.
Limits of high density, low-force pressure contacts

The prosaic pressure contact is a source of unreliability not only in completed systems but more seriously in testing of ICs prior to packaging. Using a custom-built apparatus, pressure contacts are characterized with applied forces down to a few nN and contact areas down to 10/sup -11/ cm/sup 2/. Nominally clean gold-gold and iridium-gold contacts in air exhibit resistivities higher than that predicted from a simple model based on the plastic deformation of the gold. Interfacial films appear to be a source of unreliability. The surface film on gold in air appears to disrupt conduction to a similar degree. <<ETX>>
Construction of Substring Indices Using Sequence BDDs

In sequence data mining, it is a fundamental task to compactly represent large sequence data and process efficiently on computer. There are demands for efficient substring index data structures for storing all substrings of a given text. Suffix trees and DAWGs (Directed Acyclic Word Graph) are examples of substring indices, but lack operations to manipulate sets of strings. The novel data structure Sequence Binary Decision Diagram (SeqBDD) by E. Loekito, J. Bailey, and J. Pei in 2009 is a new type of Binary Decision Diagram (BDD) and represents sets of sequences. This study focuses largely on two issues: (a) compact substring indices based on SeqBDD, called Suffix Decision Diagram (SuffixDD), making it possible to represent the set of all substrings efficiently with various operations inherited from Zero-suppressed Binary Decision Diagram (ZDD); (b) methods to build SuffixDD, beginning with the empty string and repeatedly updated if a new letter is read. This paper presents an efficient algorithm for constructing SuffixDD of a given text only by the primitive SeqBDD operations, together with a proof of correctness and some notes about BDD families, and discusses why the new data structure appears to have an advantage over existing substring indices. Upper bound on the running time is also obtained. It is hoped that proposition of this data structure to a wider audience at this time will help to promote useful discussion of the important issues.
Selective Enhancement of Expression of Class-Mu Glutathione S-Transferase Genes during Involution of Rat Ventral Prostate Induced by Androgen Withdrawal

cDNA clones encoding class-Mu subunits (Yb1, Yb2 and Yb3) of glutathione Stransferases were isolated from a cDNA library of a rat ventral prostate. The mRNA levels of Yb1, Yb2 and Yb3 were significantly elevated in the prostate of androgenablated rats. The enhancement of gene expression was characteristic for class-Mu subunits, since the relative abundance of mRNAs for class-Alpha and class-Pi was not affected by castration. The up-regulation of transcripts was repressed by immediate administration of testosterone propionate after castration.
Characterization of NF-κΒ/IκΒ Proteins in Zebra Fish and Their Involvement in Notochord Development

ABSTRACT Although largely involved in innate and adaptive immunity, NF-κB plays an important role in vertebrate development. In chicks, the inactivation of the NF-κΒ pathway induces functional alterations of the apical ectodermal ridge, which mediates limb outgrowth. In mice, the complete absence of NF-κB activity leads to prenatal death and neural tube defects. Here, we report the cloning and characterization of NF-κΒ/IκB proteins in zebra fish. Despite being ubiquitously expressed among the embryonic tissues, NF-κΒ/IκB members present distinct patterns of gene expression during the early zebra fish development. Biochemical assays indicate that zebra fish NF-κΒ proteins are able to bind consensus DNA-binding (κB) sites and inhibitory IκBα proteins from mammals. We show that zebra fish IκBαs are degraded in a time-dependent manner after induction of transduced murine embryo fibroblasts (MEFs) and that these proteins are able to rescue NF-κΒ activity in IκBα−/− MEFs. Expression of a dominant-negative form of the murine IκBα (mIκBαM), which is able to block NF-κΒ in zebra fish cells, interferes with the notochord differentiation, generating no tail (ntl)-like embryos. This phenotype can be rescued by coinjection of the T-box gene ntl (Brachyury homologue), which is typically required for the formation of posterior mesoderm and axial development, suggesting that ntl lies downstream of NF-κΒ. We further show that ntl and Brachyury promoter regions contain functional κB sites and NF-κΒ can directly modulate ntl expression. Our study illustrates the conservation and compatibility of NF-κΒ/IκB proteins among vertebrates and the importance of NF-κΒ pathway in mesoderm formation during early embryogenesis.
Temporal changes in benthic macroinvertebrates and their interactions with fish predators after restoration in the Cheonggyecheon, a downtown stream in Seoul, Korea

The Cheonggyecheon (Cheonggye stream), a downtown stream in Seoul, Korea, was restored by the historic Cheonggyecheon Restoration Project (2003–2005), and its discharge and other environmental conditions are artificially regulated throughout the year. The aim of this study was to assess temporal changes in benthic macroinvertebrates and their interactions with fish predators in the Cheonggyecheon. Sampling was conducted twice a year (spring and autumn) at three sections of the stream from 2006 to 2010 using a Surber sampler (50 × 50 cm) for benthic macroinvertebrates and a cast net (mesh size, 10 × 10 mm) and a kick net (mesh size, 5 × 5 mm) for fishes. Analyses of annual precipitation and most water quality parameters showed no significant differences across the study period (P > 0.05). The species richness and density of benthic macroinvertebrates and fishes varied across the sampling period. Analyses of functional feeding groups and trophic guilds showed distinct trends, such as an increase in the number of insectivorous fish in the absence of invertebrate predators. Correlation and regression analyses for five major groups of benthic macroinvertebrates and fishes demonstrated that the density of certain groups of benthic macroinvertebrates (e.g. Tubificidae, Erpobdellidae, Baetidae, and Chironomidae) and insectivorous fishes (e.g. Gobioninae, Leuciscinae, Danioninae, and Gobiidae) were negatively correlated. In conclusion, in an artificially regulated stream like the restored Cheonggyecheon, where physical environments are nearly unchanged, fish predation can be a major factor controlling benthic macroinvertebrate communities.
Macrophysiology – progress and prospects

Summary Macrophysiology is the investigation of variation in physiological traits over large geographic and temporal scales and the ecological implications of this variation. It has now been undertaken, as a defined field, for a decade. Here, we overview its conceptual foundations, methodological approaches and insights, together with challenges the field is facing currently. Macrophysiology builds on approaches that investigate the ecological and evolutionary significance of physiological trait variation and feedbacks in these processes. One of its key strengths is its ability to provide a basis for examining interactions among the intraspecific, interspecific and assemblage levels. Macrophysiology is distinct from and typically concerns larger spatial and temporal scales than conservation physiology, whereas it is in several respects similar to, but antecedes, functional biogeography. Contrary to some claims, macrophysiology is not concerned only with the implications for geographic ranges of physiological trait variation. Several insights, which would not otherwise have been achieved, have arisen from the field, notably the understanding of variation in global patterns of upper and lower lethal temperature limits and organism performance, which have important implications for forecasting the impacts of climate change. Ten major challenges are identified for the field of macroecology, including better integration of approaches and information for plants and animals. Nonetheless, the prospects for macrophysiology as a significant way to understand our world remain bright.
Dry-matter intake of Hereford and first-cross cows measured by controlled release of chromic oxide on three pasture systems

Summary Faecal output of 287 beef cows consisting of Hereford (H × H), Simmental × Hereford (S × H), Friesian × Hereford (F × H) and Brahman × Hereford (B × H) breeding was estimated using controlled release of chromic oxide (Cr2O3). All cows were from 6 to 10 years of age and had grazed on one of three pasture systems in the subtropics of New South Wales since they were 7–8 months of age. These pastures were designated as being of high, medium and low nutritive value. Faecal organic matter output (FOMO) was estimated in each of four periods (early lactation, mid lactation, late lactation, and non-lactating) during one annual production cycle. Herbage mass exceeded 2 t/ha on all pasture systems, but estimates of organic-matter digestibility, nitrogen content and pasture composition indicated large differences in pasture quality (high > medium > low). Live weight of cows averaged 604, 488 and 393 kg live weight on the high, medium and low pastures, respectively. There were significant differences in live weight between genotypes on the medium (B × H > F × H and H × H) and low (S × H ≡ F × H ≡ B × H > H × H) pastures but not on the high pasture). FOMO and dry-matter intake (DMI) differed significantly between genotypes among lactating cows on all pasture systems. Rankings on high pastures were reasonably consistent in all periods: S × H ≡ F × H ≥ B × H ≥ H × H, as were those on low pastures, B × H ≥ S × H ≡ F × H ≥ H × H. Differences on medium pastures were significant only during mid-lactation when B × H ≡ S × H ≡ F × H > H × H. Significant differences between genotypes were observed among non-lactating cows on high pastures only, where H × H ≡ S × H ≡ F × H > B × H. Lactating females had significantly higher FOMO and DMI than non-lactating females when compared across genotypes during early lactation on all pastures.
Development of a multiphase reaction system for integrated synthesis of isomaltose with a new glucosyltransferase variant

Abstract A new genetically derived variant of the glucosyltransferase from Streptococcus oralis has been characterized physicochemically and kinetically. Compared with the industrially used glucosyltransferase from Leuconostoc mesenteroides, the enzyme variant GTF-R S628D possesses 25 times higher affinity for the specific glucosylation of glucose. For a concept of integrated reaction and product isolation, a fluidized bed reactor with in situ product removal was applied. The technical feasibility and the applicability of the kinetic models for reaction and adsorption could be demonstrated. The immobilized enzyme was stable (20% activity loss after 192 h) and product could be obtained with 90% purity. A bioprocess model was generated which allowed the integral assessment of the enzymatic synthesis and in situ product adsorption. The model is a powerful tool which assists with the localization of optimal process parameters. It was applied for the process evaluation of other glucosyltransferases and demonstrated key characteristics of each enzymatic system.
Musk Thistle (Nodding Thistle)

Economic damage. Musk thistle invades pastures, rangeland, and forest lands, and areas along roadsides, railroad right-of-ways, waste areas, and stream banks. In agricultural systems, the invasive nature and prolific seed production of musk thistle result in large populations of the weed, which compete with crops for space, nutrients, and light. Thus, infestations may reduce productivity of pasture and rangeland by suppressing growth of desirable forage plants, as well as preventing livestock from eating plants growing in the vicinity of thistles due to the sharp spines on their stems, leaf margins and blooms (Trumble and Kok, 1982; Desrochers et al., 1988a). In the northeastern United States, the highest economic losses due to musk thistle infestations occur on fertile soils formed over limestone. Ecological damage. Musk thistle generally does not pose a great threat to high-quality natural areas, although it has been known to invade native and restored grasslands despite the presence of dense, native prairie vegetation. Musk thistle may retard natural secondary succession processes. Because musk thistle is unpalatable to wildlife and livestock, selective grazing leads to severe degradation of native meadows and grasslands as grazing animals focus their foraging on other plants, giving musk thistle a competitive advantage. Successful biological control of musk thistle (Kok and Surles, 1975) is often accompanied by increased growth and coverage of pasture grasses such as fescue (Festuca arundinaria Schreb.) and orchard grass (Dactylis glomerata L.), or less desirable plants such as spotted knapweed (Kok and Mays, 1991). Extent of losses. The rate of expansion of musk thistle populations in North America has been very rapid since the mid-1950s, when it was first recognized as a weed (Dunn, 1976). A single musk thistle per 1.49 m2 can reduce pasture yields by 23%. In Canada, stands of 150,000/ha have been observed (Desrochers et al., 1988a). Direct losses are difficult to quantify due to lack of long-term monitoring programs and data.
Invasive plants as catalysts for the spread of human parasites

To a degree not widely recognized, some naturalized and invasive plants increase the risks to human health by enhancing the proliferation of vectors of virulent human parasites. These potential risks are restricted by neither ecosystem nor geography. The dense, floating mats of the tropical South American invasive macrophyte Eichhornia crassipes (water hyacinth) creates habitat for larvae of the dipteran vectors of Plasmodium spp. , the causative agents of malaria, and other parasites. In Africa, the South American shrub Lantana camara (lantana) provides suitable habitat in otherwise treeless areas for dipteran vectors (Glossina spp.) of protozoans (Trypanosoma spp.) that cause trypanosomiasis. In the eastern United States, proliferation of the invasive Berberis thunbergii provides questing sites for the blacklegged ticks that carry the spirochete Borrelia burgdorferi, the causative agent of Lyme disease. Unanticipated health consequences will likely continue to emerge from new plant introductions. Hantaviruses are rodent-borne parasites that cause lethal hemorrhagic fevers in humans. Populations of rodent Hantavirus vectors in South America increase rapidly in response to fruit availability among masting, native bamboos. In the United States the omnivorous deer mouse Peromyscus maniculatus also carries Hantavirus (Sin Nombre Virus). The on-going escape of Asian frost-tolerant bamboos from cultivation raises the possibility of their becoming invaders - several have already become naturalized - and in turn providing a temporary food source for populations of infected native rodents. Proposed introductions of floating aquatic vascular species, species with masting reproduction and species that could occupy an unfilled niche in a new range deserve careful evaluation as catalysts of unintended species interactions, especially of human parasites.
Variations in the biomass of Antarctic krill (Euphausia superba) around the South Shetland Islands, 1996–2006

The time-series of acoustically surveyed Antarctic krill (Euphausia superba) biomass near the South Shetland Islands (SSI) between 1996 and 2006 is re-estimated using a validated physics-based model of target strength (TS), and a species-discrimination algorithm based on the length-range of krill in plankton samples to identify krill acoustically, derived from TS-model predictions. The SSI area is surveyed each austral summer by the US Antarctic Marine Living Resources Program, and the acoustic data are used to examine trends in krill biomass and to assess the potential impact of fishing to the reproductive success of land-based predators (seals and penguins). The time-series of recomputed biomass densities varies greatly from that computed using an empirical log-linear TS-model and fixedranges of differences in volume –backscattering strengths (DSv), conventionally used to identify krill acoustically. The new acoustic estimates of biomass are significantly correlated with both proportional recruitment and krill abundance estimated from zooplankton samples. Two distinct peaks in biomass (1996 and 2003) are in accord with recruitment events shown by net-based krill time-series. The foundation for the new TS-model and the associated krill-discrimination algorithm, coupled with the agreement between acoustic- and net-survey results, provides strong support for the use of the new analytical technique. Variable biases in the re-estimated krill biomass have been greatly reduced. However, survey variability increased as a result of the increased rejection of acoustic backscatter previously attributed to krill. Management of Southern Ocean krill stocks based on a precautionary approach may therefore result in decreased allocations of krill, given its dependence on the variability of survey estimates.
Automatic three-dimensional mesh generation by the finite octree technique

An octree-based fully automatic three-dimensional mesh generator is presented. The mesh generator is capable of meshing non-manifold models of arbitrary geometric complexity through the explicit tracking and enforcement of geometric compatibility and geometric similarity at each step of the meshing process. The resulting procedure demonstrates a linear growth rate with respect to the number of elements and can be easily integrated with any geometric modeller through a set of geometric operators.