Miracle-dz/UniFAR-FTUs huggingface dataset:
Does a top predator suppress the abundance of an invasive mesopredator at a continental scale

Aim We examined evidence for the mesopredator release hypothesis at a subcontinental scale by investigating the relationship between indices of abundance of the dingo Canis lupus dingo (top-order predator) and the invasive red fox Vulpes vulpes (mesopredator) in three large regions across mainland Australia. The red fox is known to be one of the major threats to the persistence of small and medium-sized native vertebrates across the continent. Location Australia. Methods Indices of abundance were calculated from three independently collected datasets derived from bounty returns and field surveys. Data were analysed using univariate parametric, semi-parametric and nonparametric techniques. Results Predator abundance indices did not conform to a normal distribution and the relationships between dingo and fox abundance indices were not well described by linear functions. Semi-parametric and nonparametric techniques revealed consistently negative associations between indices of dingo and fox abundance. Main conclusions The results provide evidence that mesopredator suppression by a top predator can be exerted at very large geographical scales and suggest that relationships between the abundances of top predators and mesopredators are not linear. Our results have broad implications for the management of canid predators. First, they suggest that dingoes function ecologically to reduce the activity or abundance of red foxes and thus are likely to dampen the predatory impacts of foxes. More generally, they provide support for the notion that the mesopredator-suppressive effects of top predators could be incorporated into broad-scale biodiversity conservation programmes in many parts of the world by actively maintaining populations of top predators or restoring them in areas where they are now rare. Determining the population densities at which the interactions of top predators become ecologically effective will be a critical goal for conservation managers who aim to maintain or restore ecosystems using the ecological interactions of top predators.
Binding of cycloheximide to ribosomes from wild-type and mutant strains of Saccharomyces cerevisiae

Cycloheximide bound to cytoplasmic (80S) ribosomes of the yeast Saccharomyces cerevisiae with an association constant (Ka) of 2.0 (+/- 0.5) x 10(7) M-1. The number of binding sites found per ribosome was between 0.4 and 0.6; it was reduced by high-salt treatment of ribosomes 60S particles prepared in the presence of high salt had a lower affinity (Ka: 5.5 [+/- 0.5] x 10(6) M-1) than did 80S ribosomes, but a greater proportion of particles (0.8) were able to bind. No specific binding to 40S subunits was observed. The addition of supernatant fractions (S100, high-salt wash fraction) increased the number of binding sites found per 80S ribosome up to 0.8, leaving the association constant unchanged. In contrast, the affinity of 60S subunits was enhanced to a Ka value of 3.5 x 10(-7) M-1 by the addition of supernatant fractions, whereas the number of binding sites stayed constant. A model to explain these facts is proposed. 80S ribosomes, as well as 60S subunits of strain cy32, which is highly resistant to cycloheximide and altered in ribosomal protein L29 (18), showed a drastically reduced affinity for the drug (Ka values of 2.0 x 10(6) M-1).
1. LEG 189 SUMMARY

The Cenozoic Era is unusual in its development of major ice sheets. Progressive high-latitude cooling during the Cenozoic eventually formed major ice sheets, initially on Antarctica and later in the Northern Hemisphere. In the early 1970s, a hypothesis was proposed that climatic cooling and an Antarctic cryosphere developed as the Antarctic Circumpolar Current progressively thermally isolated the Antarctic continent. This current resulted from the opening of the Tasmanian Gateway south of Tasmania during the Paleogene and the Drake Passage during the earliest Neogene. The five Leg 189 drill sites, in 2463 to 3568 m water depths, tested, refined, and extended the above hypothesis, greatly improving understanding of Southern Ocean evolution and its relation with Antarctic climatic development. The relatively shallow region off Tasmania is one of the few places where well-preserved and almost-complete marine Cenozoic carbonate-rich sequences can be drilled in present-day latitudes of 40°–50°S and paleolatitudes of up to 70°S. The broad geological history of all the sites was comparable, although there are important differences among the three sites in the Indian Ocean and the two sites in the Pacific Ocean, as well as from north to south. In all, 4539 m of core was recovered with an excellent overall recovery of 89%, with the deepest core hole penetrating 960 m beneath the seafloor. The entire sedimentary sequence cored is marine and contains a wealth of microfossil assemblages that record marine conditions from the Late Cretaceous (Maastrichtian) to the late Quaternary and dominantly terrestrially derived sediments until the earliest Oligocene. The drill sites are on submerged continental blocks extending as far as 600 km south of Tasmania. These continental blocks were at polar latitudes in the Late Cretaceous when Australia and Antarctica were still united, although rifts had developed as slow separation and northward move1Examples of how to reference the whole or part of this volume. 2Shipboard Scientific Party addresses.
Effect of Mouse Uterine Stromal Cells on Epithelial Cell Transepithelial Resistance (TER) and TNFα and TGFβ Release in Culture1

Abstract Recognizing that uterine stromal cells regulate several uterine epithelial cell function(s), the current study was undertaken to more fully define cell-cell communication in the uterus and to examine the role of uterine stromal cells in regulating epithelial cell monolayer integrity and cytokine release. Uterine epithelial and stromal cells from adult intact mice were isolated and cultured separately on cell culture inserts and/or in culture plates. Epithelial cells, which reach confluence as indicated by high transepithelial resistance (TER > 1000 ohms/well), preferentially release transforming growth factor-beta (TGFβ) into the basolateral chamber (≈70% > apical) and tumor necrosis factor-alpha (TNFα) into the apical compartment (≈30% > basolateral). When epithelial cells on cell culture inserts were transferred to plates containing stromal cells, coculture for 24–48 h increased epithelial cell TER (≈70% higher than control) and decreased TNFα release into both the apical and basolateral chambers (≈30%–50%). In contrast, TGFβ release was not affected by the presence of stromal cells. In other studies, the effects of stromal cells on epithelial cell TER and TNFα release persisted for 5–7 days following the removal of stromal cells and were also seen in coculture studies in which conditioned stromal media (CSM) was placed in the basolateral chamber. These studies indicate that uterine stromal cells produce a soluble factor(s) that regulates epithelial cell TER and release of TNFα without effecting TGFβ release. These results suggest that uterine stromal cells communicate with epithelial cells via a soluble factor(s) to maintain uterine integrity and epithelial secretory function.
The Evolutionary Genomics of Birds

Rapidly accumulating genome sequence information in birds, which show several unique genomic features, provides novel insights into evolutionary genomics. The avian karyotype with numerous microchromosomes has remained stable during evolution, although frequent intrachromosomal inversions have occurred. Avian sex chromosome evolution, representing the best characterized ZW system to date, follows patterns seen in other organisms but has the notable exception of incomplete dosage compensation. Recombination is unevenly distributed in the avian genome; it occurs at very high rates in microchromosomes, a consequence of an obligate crossing over in even small chromosomes, and has highly elevated rates near chromosome ends. Moreover, a heterogeneous landscape of recombination feeds significant heterogeneity in base composition via GC-biased gene conversion. A uniform molecular clock is not applicable to birds, and ample evidence for substitution rate heterogeneity both among lineages and within genomes exists.
SSDL: A High-quality Icebox Watermelon Breeding Line Resistant to Fusarium Wilt and Anthracnose

There is a continuing need for improved eating quality in watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai]. The consumption of commercially produced watermelons fell from 8.1 kg per capita during the 10 years from 1951 to 1960 to 5.8 kg (28.5% decrease) for the 1971 to 1980 period. The icebox varieties ‘Minilee’ and ‘Mickylee’ (Crall, 1986) were released in 1986 to help overcome the decline or, perhaps, to reverse the trend. They are a convenient size for the consumer, and they are well adapted to shipment in cartons to domestic and foreign markets. With the release of these and other highquality, mediumto large-size varieties, the per capita consumption has increased (Allred and Lucier, 1990). In recent years, there has been a consumer preference for diploid and triploidhybrids (Maxwell, 1992; U.S. Dept. of Agriculture, 1993). Consumer acceptance of the solid graygreen rind, characteristic of ‘Minilee’ and ‘Mickylee’, is declining (U.S. Dept. of Agriculture, 1993). Our purpose was to develop an icebox watermelon with stripes and an excellent internal quality that is suitable for use as a parent line in watermelon hybrids.
Prediction of Mechanisms of Action of Antibacterial Compounds by Gene Expression Profiling

ABSTRACT We have generated a database of expression profiles carrying the transcriptional responses of the model organism Bacillus subtilis following treatment with 37 well-characterized antibacterial compounds of different classes. The database was used to build a predictor for the assignment of the mechanisms of action (MoAs) of antibacterial compounds by the use of support vector machines. This predictor was able to correctly classify the MoA class for most compounds tested. Furthermore, we provide evidence that the in vivo MoA of hexachlorophene does not match the MoA predicted from in vitro data, a situation frequently faced in drug discovery. A database of this kind may facilitate the prioritization of novel antibacterial entities in drug discovery programs. Potential applications and limitations are discussed.
Specific Differentiation betweenMycobacterium bovis BCG and Virulent Strains of theMycobacterium tuberculosis Complex

ABSTRACT A PCR procedure based on the intergenic region (IR) separating two genes encoding a recently identified mycobacterial two-component system, named SenX3-RegX3, was developed and was shown to be suitable for identifying Mycobacterium bovis BCG. ThesenX3-regX3 IR contains a novel type of repetitive sequence, called mycobacterial interspersed repetitive units (MIRUs). All tested BCG strains exclusively contained 77-bp MIRUs within the senX3-regX3 IR, whereas all non-BCGM. tuberculosis complex strains contained a 53-bp MIRU, in addition to the 77-bp MIRUs. All 148 strains analyzed so far could be divided into eight different groups according to the copy numbers of the 77-bp MIRU and to the presence or absence of the 53-bp MIRU. BCG strains contained either one, two, or three 77-bp MIRUs. The other strains contained one to five 77-bp MIRUs invariably followed by a 53-bp MIRU. The consistent absence of the 53-bp MIRU in BCG strains and its presence in virulent strains allowed us to develop an enzyme-linked immunosorbent assay using specific capture oligonucleotide probes to distinguish between BCG and other M. tuberculosis complex strains.
Comparing the Therapeutic Effects of Vitamin C and CoQ10 in Reducing the Number of Damaged Cells in Mice Hippocampus Following Ischemia-Reperfusion

Background and purpose: Vitamin C and CoQ10 are known as two potent antioxidants. We studied the protective role of CoQ10 and ascorbic acid against ischemia-reperfusion. Also, we compared the therapeutic effect of these two antioxidants. Materials and methods: In this study 35 male balb-C were divided into five groups: intact, ischemic control, sham control and treatment groups with CoQ10 and ascorbic acid. In treatment groups, the mice were treated with CoQ10 and vitC as pre-treatment for a week. Then, ischemia induced by Common Carotid artery ligation and the mice were post-treated with CoQ10and ascorbic acid for a week. Nissl staining was applied to count the necrotic cells of hippocampus. TUNNEL kit was used to quantify apoptotic cell death and to measure short term memory we applied y-maze and shuttle box tests. Results: High rate of apoptosis was seen in ischemic group. In the treatment groups using these antioxidants resulted in lower rate of apoptosis compared with that of the control group. Furthermore, less neuronal death was seen in the group treated with CoQ10 compared with those treated with ascorbic acid. Conclusion: According to the results, the intake of ascorbic acid and CoQ10 significantly reduced apoptosis and decreased memory loss. But the antioxidant effect of CoQ10 was stronger than vitamin C in this zone of brain.
Use of 16S rRNA, 23S rRNA, and gyrB Gene Sequence Analysis To Determine Phylogenetic Relationships of Bacillus cereus Group Microorganisms

In order to determine if variations in rRNA sequence could be used for discrimination of the members of the Bacillus cereus group, we analyzed 183 16S rRNA and 74 23S rRNA sequences for all species in the B. cereus group. We also analyzed 30 gyrB sequences for B. cereus group strains with published 16S rRNA sequences. Our findings indicated that the three most common species of the B. cereus group, B. cereus, Bacillus thuringiensis, and Bacillus mycoides, were each heterogeneous in all three gene sequences, while all analyzed strains of Bacillus anthracis were found to be homogeneous. Based on analysis of 16S and 23S rRNA sequence variations, the microorganisms within the B. cereus group were divided into seven subgroups, Anthracis, Cereus A and B, Thuringiensis A and B, and Mycoides A and B, and these seven subgroups were further organized into two distinct clusters. This classification of the B. cereus group conflicts with current taxonomic groupings, which are based on phenotypic traits. The presence of B. cereus strains in six of the seven subgroups and the presence of B. thuringiensis strains in three of the subgroups do not support the proposed unification of B. cereus and B. thuringiensis into one species. Analysis of the available phenotypic data for the strains included in this study revealed phenotypic traits that may be characteristic of several of the subgroups. Finally, our results demonstrated that rRNA and gyrB sequences may be used for discriminating B. anthracis from other microorganisms in the B. cereus group.
Nitrogen use efficiency in corn (Zea mays L) genotypes under different conditions of nitrogen and seeding date

Many factors can contribute the nitrogen use efficiency in corn (Zea mays L) genotypes, like weather and soil, for instance. This present study aimed to identify efficient genotype using nitrogen across three seeding date and two covered nitrogen level at Tocantins-Brazil, during the season 2009/2010. The assessment characteristic were through: ear of corn yield and grain yield (kg ha-1), they were correct for 13% of humidity; agronomic nitrogen use efficiency (NUEA), partial by Moll et al and Low N index by Fischer et al. It was done through analysis of variance, considering the fixed genotype effect and the other random. Significant genotype, seeding date, covered nitrogen level, genotype x seeding date and genotype x covered nitrogen level were observed for ear of corn yield, grain yield, NUEA. The NUEA was significantly lower at LN than at HN for all genotypes. At LN the genotypes showed an average of 206 kg of produced grains for each N kg applied (kg kg-1). At HN they showed an average of 39 kg kg-1. The genotypes GEN 03, GEN 10 and GEN 16 were the most efficient that used the nitrogen, in both assessments methods above. It could be concluded that the choice of the methodology may be function of the study purpose, nitrogen level or seeding date effect.
Diel changes in phagotrophy by Cryptomonas in Lake Biwa

Diel changes in bacterial ingestion by a mixotrophic flagellate, Cryptomonas sp. , and heterotrophic nanoflagellates (HNF) were examined in situ at 4‐h intervals for 2 d in the epilimnion and metalimnion of Lake Biwa using bacteria‐sized fluorescent microspheres as a tracer food. Clearance rates of HNF for the microspheres ranged between 1.3 and 4.5 nl cell−1 h−1, but the average rate did not differ between day and night. In contrast, clear diel changes were observed in the clearance rate of Cryptomonas sp. in the epilimnion from <0.5 nl cell−1 h−1 at midnight to >3 nl cell−1 h−1 at noon. In the metalimnion where light intensity was lower, however, the clearance rate of Cryptomonas sp. was always <0.5 nl cell−1 h−1 through the study period. Thus, bacterial ingestion of Cryptomonas sp. is not to acquire supplementary energy or carbon at low phototrophic activities. During the study period, both inorganic phosphorus and nitrogen concentrations were less than or close to the detection limits (10 nM P and 1 µM N) in the epilimnion, but much higher in the metalimnion. The results strongly support the idea that Cryptomonas sp. utilizes N and P from bacteria as substitutable nutrients when photosynthesis takes place under conditions of nutrient depletion. To assess the grazing effect of mixotrophic algae on bacterial populations, it is essential to consider diel changes in their phagotrophic mode of nutrition that are induced by light regime and nutrient concentrations in ambient water.
Effects of sea surface warming on the production and composition of dissolved organic matter during phytoplankton blooms: results from a mesocosm study

An experimental study was conducted to test the effects of projected sea surface warming (according to the IPPC scenarios) on the accumulation and composition of dissolved organic matter (DOM) during marine phytoplankton blooms in cold seas (<4°C). Eight mesocosms (∼1400 L) were filled with natural seawater, and two replicate mesocosms each were incubated by raising temperature by +0, +2, +4 and +6°C, respectively. The enclosed water was initially fertilized with inorganic nutrients to induce the development of phytoplankton blooms, which were then dominated by diatoms. Over a 4-week period, dissolved combined carbohydrates (DCCHO) and dissolved amino acids (DAA) were determined as major components of freshly produced, labile to semi-labile DOM. In all mesocosms, the increase in DCCHO concentration occurred sharply after the peak of chlorophyll a concentration, when nutrients became depleted. Rising temperature resulted in an earlier, faster and higher accumulation of DCCHO and of combined glucose predominantly. DCCHO yielded a maximum percentage of 35, 40, 49 and 59% of total combined carbohydrates in the +0, +2, +4 and +6°C treatments, respectively. Accumulation of DAA occurred more continuously and at an average rate of 0.79 ± 0.20 nmol L−1 h−1, but was not affected by rising temperature. Owing to the higher accumulation of DCCHO, the C:N ratio of DOM increased strongly during the course of the bloom, with higher ratios in the warmer treatments. Our study suggests that warming increases the extracellular release of carbohydrates from phytoplankton and, therefore, may affect the bottom-up control of the microbial loop in cold seas in the future.
Encrypted Blockchain Databases

Blockchain databases are storage systems that combine properties of blockchains and databases like decentralization, tamperproofness, low query latency and support for complex queries. Blockchain databases are an emerging and important class of blockchain technology that is critical to the development of non-trivial smart contracts, distributed applications and decentralized marketplaces. In this work, we consider the problem of designing end-to-end encrypted blockchain databases to support the development of decentralized applications that need to store and query sensitive data. In particular, we show how to design what we call blockchain encrypted multi-maps (EMM) which can be used to instantiate various kinds of NoSQL blockchain databases like key-value stores or document databases. We propose three blockchain EMM constructions, each of which achieves different tradeoffs between query, add and delete efficiency. All of our constructions are legacy-friendly in the sense that they can be implemented on top of any existing blockchain. This is particularly challenging since blockchains do not support data deletion. We implemented our schemes on the Algorand blockchain and evaluated their concrete efficiency empirically. Our experiments show that they are practical.
The bystander effect in rats

In rats as in humans, nonhelping bystanders suppress helping whereas naive bystanders boost helping above individual levels. To investigate whether the classic bystander effect is unique to humans, the effect of bystanders on rat helping was studied. In the presence of rats rendered incompetent to help through pharmacological treatment, rats were less likely to help due to a reduction in reinforcement rather than to a lack of initial interest. Only incompetent helpers of a strain familiar to the helper rat exerted a detrimental effect on helping; rats helped at near control levels in the presence of incompetent helpers from an unfamiliar strain. Duos and trios of potential helper rats helped at superadditive rates, demonstrating that rats act nonindependently with helping facilitated by the presence of competent-to-help bystanders. Furthermore, helping was facilitated in rats that had previously observed other rats’ helping and were then tested individually. In sum, the influence of bystanders on helping behavior in rats features characteristics that closely resemble those observed in humans.
Yeast VSM1 Encodes a v-SNARE Binding Protein That May Act as a Negative Regulator of Constitutive Exocytosis

ABSTRACT We have screened for proteins that interact with v-SNAREs of the late secretory pathway in the yeast Saccharomyces cerevisiae. A novel protein, designated Vsm1, binds tightly to the Snc2 v-SNARE in the two-hybrid system and can be coimmunoprecipitated with Snc1 or Snc2 from solubilized yeast cell extracts. Disruption of the VSM1 gene results in an increase of proteins secreted into the medium but does not affect the processing or secretion of invertase. In contrast,VSM1 overexpression in cells which bear a temperature-sensitive mutation in the Sec9 t-SNARE (sec9-4cells) results in the accumulation of non-invertase-containing low-density secretory vesicles, inhibits cell growth and the secretion of proteins into the medium, and blocks rescue of the temperature-sensitive phenotype by SNC1 overexpression. Yet, VSM1 overexpression does not affect yeast bearing asec9-7 allele which, in contrast to sec9-4, encodes a t-SNARE protein capable of forming a stable SNARE complex in vitro at restrictive temperatures. On the basis of these results, we propose that Vsm1 is a novel v-SNARE-interacting protein that appears to act as negative regulator of constitutive exocytosis. Moreover, this regulation appears specific to one of two parallel exocytic paths which are operant in yeast cells.