Miracle-dz/UniFAR-FTUs huggingface dataset:
Before 1492 The Making of the Pre-Columbian Landscape

the Ice Age. E historian Donald Worster (1992) has identified two counterposed conceptions of nature within Western tradition: the "Arcadian," or nature as harmonious and beautiful, the bountiful home of humans; and the "mechanistic," or nature as a cruel, raw and chaotic antagonist. Both perspectives see Western industrial society as having a unique power to transform and manipulate nature. The Arcadian view holds that this power should be reined in and controlled, letting nature take its course free from the corrupting influences of Western agency. The mechanists advocate the use of technology to tame the wilderness for human use. Interestingly, the modem project of ecological restoration draws on elements of both these u’aditions. Consider the following scenario, not untypical in North America: a restorationist relies on scientific knowledge and landscape-engineering technology, while working more like a gardener in an attempt to re-create an idealized landscape, conceived as the "original" Edenic wilderness thought to exist before despoliation by people. As is the case for many others in our society, this person’s conception of nature, and his or her relationship to it, is difficult to classify under Worster’s dichotomous scheme. An attempt to do so might yield "mechanistic Arcadian," an oxymoron which nonetheless characterizes the project of restoration. Though practitioners of the craft of restoration are a diverse group representing a wide range of perspectives, they all are engaged in some sense in "rehabilitating damaged ecosystems" (Cairns, 1995). In a recent textbook, John Cairns (1995:6) defines "restoration" as "the return of an ecosystem to a close approximation of its condition prior to disturbance" by humans, and elsewhere suggests that "ideally, all ecosystems should be restored to their original condition" (Cairns 1988:333). Perhaps the greatest practical and theoretical problem for the restorationist is deciding what the "original" landscape was, and when it last existed. Or simply: What is to be restored? The problem is further complicated by the fact that all landscapes inevitably change, often in unique and unpredictable ways. The natural historians of the 19th century recognized this, but the ecologists who succeeded them adopted an ahistorical view of nature based on theory developed by mathematicians and physicists to explain the workings of physical systems and machines. The resulting homeostatic ecosystem model~ epitomized in Eugene Odum’s Fundamentals of Ecology (1971)--dominated ecological theory and guided environmental management for most of this century, despite much contradictory evidence from the field. Finally in the 1970s, ecologists were no longer content to ignore the "erratic" outbreaks of forest pests, the disappointing yields of fisheries, the failure to find an ecosystem in equilibrium, or even any clear boundary to an "ecosystem. " Led by Robert May (1974), C.S. Holling (1986) and others, they began to examine the assumptions underlying the theory, and looked for alternatives to models of logistic population growth, maximum
Meiosis decreases recombination load; Mitosis increases recombination load

Chiasmata are necessary for proper chromosomal segregation, but can result in inadvertent recombination. Bernstein and Michod demonstrated that meiosis evolved as a means of error correction, not genetic mixing. Therefore meiotic recombination is not the sine qua non of sex, but is instead an epiphenomenon of imperfect meiotic error correction. By correcting against recombinant genotypes, meiosis reduces recombination load, thereby providing an unappreciated selective advantage for sex. Sex reducing recombination load should be integrated into population genetic models of multi-locus epistasis for maintenance of sex and may explain sequestration of germ lines in animals. We predict that eumetazoa have less recombination load than sexual organisms without a germ line. Mitosis largely lacks the error correction of meiosis, destroys linkage through ubiquitous mitotic recombination, and thereby increases recombination load, especially in co-adapted gene complexes. Meiosis and possibly karyogamy provide an unexpected benefit to sex, offsetting at least some of the famed costs of sex.
Effect of JUNCAO-cultivated Ganoderma lucidum spent mushroom substrate-hot water extract on immune function in mice

Purpose: To evaluate the effect of JUNCAO-cultivated Ganoderma lucidum spent mushroom substratehot water extract (SMSG-HWE) on murine immunity. Methods: Five groups of mice (n = 10) received water with 0.00, 0.14, 0.28, 0.84, or 1.68 g/kg of SWSG-HWE, respectively, orally for 30 days. Various biochemical parameters of serum and tissues, including spleen and thymus indices, were determined were determined for the mice Results: The following markers were significantly higher in the 0.84 g/kg SMSG-HWE group than in the control group (all p < 0.05): splenic lymphocyte proliferation, a marker of cell-mediate immunity; dinitrofluorobenzene-induced delayed hypersensitivity; and the number of haemolytic plaque-forming cells, as a marker of humoral immunity. Phagocytic rate, which evaluates mononuclear-macrophage function as a marker of innate immunity, was significantly higher in both the 0.84 g/kg HWE and 1.68 g/kg SWSG-HWE groups, while phagocytic index was significantly higher in the 0.28 g/kg SWSG-HWE group, compared to the control group (all p < 0.05). Natural killer cell activity also was significantly enhanced in the 0.84 g/kg and 1.68 g/kg SWSG-HWE groups (p < 0.05). Conclusion: These findings indicate that SWSG-HWE enhances murine immune function, and may be suitable as a potential additive in animal feed. Keywords: Hot water extract, Cell-mediated immune function, Concanavalin A, Mononuclearmacrophage function, Haemolytic plaque, Humoral immunity, Innate immunity, Animal feed additive
Characterization of factors influencing the regulation of dietary folic acid deposition in the eggs

The enrichment of eggs with folate is a viable option for supplying the general population of a food product rich in natural folates. However, attempts to increase the concentration of folate in egg beyond the achieved level of enrichment had been unsuccessful because egg folate reached a maximum plateau when folic acid (FA) was increased in the diet. Thus, experiments were conducted to determine the factors regulating the deposition of dietary FA into the eggs. In the first study, the effect of feeding equimolar intakes of FA or 5-methyltetrahydrofolate (5-methylTHF), the biologically active form of folate on egg folate concentrations, indices of folate status, and activities of folate-dependent enzymes were evaluated. Folic acid and 5-methylTHF demonstrated equivalent effects in enhancing the egg folate concentrations and improving the indices of folate status in the laying hen. The activities of folate-dependent enzymes were similar between the two forms of folate except for hepatic dihydrofolate reductase (DHFR) activity which increased in FA-fed birds compared to 5-methylTHF-fed birds. However, this demonstrated the inherent ability of the laying hen to metabolically convert FA into its biologically active forms. Therefore, the influence of intestinal FA absorption in the regulation of dietary FA deposition in the egg was subsequently evaluated using the in vitro intestinal everted sac technique. Folic acid was absorbed in all regions of the intestine. Absorption was maximum at acidic pH 6.0, and was increased in the duodenum and jejunum compared to the ileum and cecum. The rate of FA absorption in the jejunum diminished at higher FA concentrations, resembling a pattern similar to egg folate concentration when dietary FA supplementation was increased. Therefore, further study was conducted to determine the regulation of FA absorption when levels of FA in the
Minimizing spurious features in 16S rRNA gene amplicon sequencing

The 16S rRNA gene amplicon sequencing is a widely used high-throughput method for the taxonomic inference in microbial communities. Many data analysis pipelines have been developed to enhance the accuracy in reflecting the real taxonomy, in order to better guide the downstream identification, isolation and mechanistic studies. Though rigorous quality filtration steps were adopted in these pipelines, with well-designed mock and simulated data sets, we found that there were still a widely divergent number of spurious features due to the “pseudo sequences” artificially generated during the PCR and sequencing process. These pseudo sequences were in low abundances, and were unreliable determined through a weighted re-sampling test. To minimize their influences on the characterization of taxonomy, we proposed an approach that contains two steps, an abundance filtering (AF) step and the subsequent AF-based OTU picking and remapping (AOR) step, which can efficiently decrease the spurious OTUs, sequences or oligotyping features, and improve Matthew's Correlation Coefficient (MCC) values in OTU clustering. The approach can be easily integrated with the popularly-used 16S rRNA sequencing data analysis pipelines, to make the number of OTUs, alpha and beta diversities from divergent pipelines more consistent with the real structure of microbial communities.
Risk assessment and prevention of surface subsidence in deep multiple coal seam mining under dense above-ground buildings: Case study

ABSTRACT Recently, solid waste backfill mining has rapidly developed, finding application in the control of surface subsidence and reduction of accumulated solid wastes. However, with the mining depth, the technique faces a number of other problems, in regard to the source of backfill materials, transportation costs, and control of the surface subsidence in deep multiple coal mining. In this article, an integrated system comprising deep mining, coal-gangue dressing, and underground backfill mining is proposed on the basis field-work. Analysis of the type, construction, and protection standards of the buildings resulted in the elaboration of numerical model aimed at studying the surface subsidence and deformation. Research results demonstrate that backfill mining of the coal seam group leads to a gradual increase in maximum surface subsidence, horizontal movement, inclination, and horizontal deformation, whereas the key index to control is the compression ratio of backfill materials. The results of surface subsidence prediction and measurements in the Tangshan Coal Mine show that the solid waste backfill mining technique can effectively control the surface subsidence, deformation, and safety of buildings. This study is highly instrumental in sustained deep mining and environmental protection.
Red jasmine rice extract suppresses genes associated with cartilage degradation in IL-1β-stimulated chondrosarcoma (SW1353) via blocking NF-κB pathway

Objective This study aimed to evaluate the chondroprotective potential of red jasmine rice crudeextract (RRE) against an expression of genes associated with cartilage degradation stimulated byIL-1 β in a human chondrosarcoma cell line, SW1353, culture model.Methods SW1353 cells were pre-incubated with 1 ng/mL of recombinant human interleukin-1 β(IL-1 β) followed by the addition of RRE in a range of concentrations from of 0 to 100 μg/mL. After24 hours of incubation, cells were harvested and expression of genes associated with cartilagedegradation was measured using real-time RT-PCR. The culture media were evaluated for MMP-13levels using an ELISA kit. Upregulation of the signaling pathway which promotes the in flammatorycascade, nuclear factor kappa B (NF-κB), was determined by Western blot analysis.Results Cytokine IL-1 β significantly upregulated the expression of the proinflammatory mediatorsIL-1 β, IL-6, TNF-α, and COX-2 as well as enzymes involved in osteoarthritis such as MMP-13, ADAMTS-4, and ZIP-8. The results showed that RRE at a concentration of 100 μg/mL signi fi cantly suppressed IL-1 β-induced expression of these genes. Moreover, the effect of IL-1 β on NF-κB signalingpathway activation was suppressed by RRE via decreased phosphorylated form of IKKα/β, IκBα,and NF-κB p65.Conclusion RRE has chondroprotective potential through reduction of the gene upregulatingeffect of IL-1 β which involve cartilage degradation via suppression of the NF-κB signaling pathway.Development of RRE has for alternative use potential in treating degenerative joint diseases.
Bacillus cereus HS24 Suppresses Conidia Germination of Magnaporthe oryzae by Inhibiting the Ca2+ Signaling Pathway

Rice yield is greatly reduced due to rice blast, a worldwide multi-cycle fungal disease caused by the ascomycete Magnaporthe oryzae. Previously, Bacillus cereus HS24 was isolated from rice growing area, which showed a strong bio-control effect on M. oryzae. In order to better exploit it as a bio-control agent, HS24 has been studied for its mechanism of controlling rice blast. Our results showed that conidial germination of M. oryzae was significantly inhibited by HS24 suspension, n and the inhibition rate reached to 97.83% at the concentration of 10 CFU/ml. The transcriptional level of CAMKII, PMC1 and CCH1, which are key genes involved in Ca2+ signaling pathway, were significantly decreased in HS24-treated conidia. The treatment of M. oryzae with Ca2+ signaling pathway inhibitors KN-93, Verapamil, and cyclopiazonic acid (CPA) significantly reduced conidial germination rate and inhibited germ tube elongation. This inhibition effect was found to be concentration-dependent, similar to the HS24 treatment. By quantifying free Ca2+ in M. oryzae conidia, a significant reduction of intracellular free Ca2+ concentration in HS24-treated conidia in comparison to sterile water-treated conidia was found. The addition of exogenous Ca2+ did not abolish the inhibitory effect of HS24 on the reduction of intracellular free Ca2+ concentration and conidial germination. In conclusion, B. cereus HS24 can inhibit conidial germination by suppressing Ca2+ signaling in M. oryzae, and thus offers a great potential as a bio-control agent in rice blast management. Importance In the bio-control of rice blast, most of researches focused on the inhibitory effect of bio-control agents on development of M. oryzae, including inhibition of conidia germination, germ tube deformity, mycelium growth inhibition, etc, while little work has elucidated the molecular mechanisms underlying the various phenotypic change in M. oryzae. In order to better exploit HS24 as a potential bio-control agent, we studied the molecular mechanisms underlying the suppression of B. cereus HS24 on M. oryzae Guy11, and draw the conclusion that HS24 may inhibit conidia germination and germ tube elongation through inhibiting the Ca2+ signaling pathway. In this study, we characterized the morphological and physiological changes of M. oryzae when interacting with B. cereus HS24, and further investgated the responses of M. oryzae Ca2+ signallig pathway to HS24 treatment. Thus we have provided one more piece for the B. cereus / M. oryzae supression puzzle at the molecular level.
The application of genetic indicators in wild populations: Potential and pitfalls for genetic monitoring [Chapter 15]

1. Genetic diversity is the foundation of all biodiversity but is seldom considered in studies of biodiversity surrogates. 2. Genetic monitoring may soon be more tractable than many traditional ecological approaches. 3. Genetic indicators are influenced by multiple ecological and evolutionary processes. 4. Genetic indicators can be difficult to interpret. 5. A priori criteria and/or thresholds for interpreting indicators are important to define.
Juices enriched with phenolic extracts from grapes

The paper describes the preparation and evaluation of phenolic extracts from waste materials – pomace (grape marc), seeds and press oil cake of the white grape variety Irsai Oliver (Vitis vinifera L.) and their addition to apple and grape juices to increase the nutritional properties. The waste samples were extracted using 50 or 80% ethanol (v/v). Some of the samples were extracted for 60 min at boiling temperature under reflux; the remainder were processed for 24 h on a shaker at room temperature. The highest antioxidant capacity (as measured using DPPH (758 ± 28 mM Trolox/kg of extracted matter)) and content of total polyphenols (74 ± 0.7 g gallic acid/kg of extracted matter) were found in the extract of the seeds obtained through extraction using 50% ethanol (v/v) at boiling temperature for 60 minutes. The press oil cake extract obtained by means of 80% ethanol (v/v) at boiling temperature for 60 min was evaluated as the best for enriching the sensory quality of apple and grape juices. The addition of 1 g of freeze-dried press oil cake extract to 1 l of juice increased the antioxidant capacity and total polyphenol content two-fold
The ecological genetics of Pseudomonas syringae in the kiwifruit phyllosphere : a thesis submitted in partial fulfilment of the requirements for the degree of Ph.D. in Evolutionary Genetics, New Zealand Institute for Advanced Study at Massey University, Auckland, New Zealand

The impact of disease-causing bacteria on their hosts is shaped by interactions with co-occurring microbes, but such interactions are rarely studied. Pseudomonas syringae is a ubiquitous and significant plant pathogen infecting a wide range of plants, often of agricultural importance. The community context of P. syringae in infected plant hosts has been little explored. I determined the population structure and genetic diversity of Pseudomonas syringae strains collected from infected and uninfected orchards over the course of a growing season during the current outbreak of bacterial canker of kiwifruit (P. syringae pv. actinidiae, Psa) in New Zealand. A total of 148 strains comprising Phylogroups 1, 2, 3 and 5 were characterised by Multi Locus Sequence Typing (MLST). The overall population structure was clonal, but with a low level of recombination for single housekeeping genes within phylogroups. More than half of the isolates belonged to a new Phylogroup 3 clade (PG3a) that was also commonly found on kiwifruit leaves in China and previously reported from kiwifruit leaves in Japan. To understand the ecological basis of the co-occurrence of PG3a and PG1 (Psa) I looked for evidence of niche specialisation by performing reciprocal invasion from rare assays of a selected representative from each lineage both in vitro and in planta. P. syringae G33C (PG3a) demonstrates antagonistic behaviour towards Psa NZ54, whereas Psa NZ54 exhibits a beneficial effect on growth of P. syringae G33C; an effect that could not be attributed to virulence activity encoded by the Type 3 Secretion System. Given this antagonistic
A framework for identifying and characterising coral reef “oases” against a backdrop of degradation

1. Human activities have led to widespread ecological decline; however, the severity of degradation is spatially heterogeneous due to some locations resisting, escaping, or rebounding from disturbances.2. We developed a framework for identifying oases within coral reef regions using long-term monitoring data. We calculated standardised estimates of coral cover (z-scores) to distinguish sites that deviated positively from regional means. We also used the coefficient of variation (CV) of coral cover to quantify how oases varied temporally, and to distinguish among types of oases. We estimated "coral calcification capacity" (CCC), a measure of the coral community's ability to produce calcium carbonate structures and tested for an association between this metric and z-scores of coral cover.3. We illustrated our z-score approach within a modelling framework by extracting z-scores and CVs from simulated data based on four generalized trajectories of coral cover. We then applied the approach to time-series data from long-term reef monitoring programmes in four focal regions in the Pacific (the main Hawaiian Islands and Mo'orea, French Polynesia) and western Atlantic (the Florida Keys and St. John, US Virgin Islands). Among the 123 sites analysed, 38 had positive z-scores for median coral cover and were categorised as oases.4. Synthesis and applications. Our framework provides ecosystem managers with a valuable tool for conservation by identifying "oases" within degraded areas. By evaluating trajectories of change in state (e.g., coral cover) among oases, our approach may help in identifying the mechanisms responsible for spatial variability in ecosystem condition. Increased mechanistic understanding can guide whether management of a particular location should emphasise protection, mitigation or restoration. Analysis of the empirical data suggest that the majority of our coral reef oases originated by either escaping or resisting disturbances, although some sites showed a high capacity for recovery, while others were candidates for restoration. Finally, our measure of reef condition (i.e., median z-scores of coral cover) correlated positively with coral calcification capacity suggesting that our approach identified oases that are also exceptional for one critical component of ecological function.
Critical multifunctional role of the betaine aldehyde dehydrogenase gene in plants

ABSTRACT The betaine aldehyde dehydrogenase (BADH) gene plays a multifunctional role in plants. It is an important factor in fragrance production, abiotic stresses and antibiotic-free selection of transgenic plants. Molecular studies have presented a new picture of this critical factor involved in abiotic stress responses via the MAPK (mitogen-activated protein kinase) signalling pathway in numerous plants. Besides BADH, glycine betaine performs an important function in plant tolerance to environmental stresses. The presence of glycine betaine can help maintain the integrity of cell membranes against unexpected environmental stresses. BADH leads to production of glycine betaine through the oxidation of betaine aldehyde. Hence, BADH is considered a key regulator for glycine betaine formation. Consequently, by providing glycine betaine as a chemical interface, there is a critical role of BADH in enhancing the tolerance in an extensive range of plants subjected to different destructive abiotic stresses. The present article reviews the significant multifunctional role of the BADH gene in various plants, and also particularly argues how this important gene plays a responsive function to different destructive abiotic stresses, and its potential use in crop improvement using advanced technologies. Consequently, cloning of more BADH genes, specially from stress-tolerant plants, discovering their responsive signalling roles under environmental stresses, and validating such candidates for their potential are very helpful, and can open new windows to generate new stress-resistant crop cultivars.
Assessing Nitric Oxide (NO) in Higher Plants: An Outline

Nitric oxide (NO) is a free radical and a component of the N-cycle. Nevertheless, NO is likewise endogenously produced inside plant cells where it participates in a myriad of physiological functions, as well as in the mechanism of response against abiotic and biotic stresses. At biochemical level, NO has a family of derived molecules designated as reactive nitrogen species (RNS) which finally can interact with different bio-macromolecules including proteins, lipids, and nucleic acids affecting their functions. The present review has the goal to provide a comprehensive and quick overview of the relevance of NO in higher plants, especially for those researchers who are not familiar in this research area in higher plants.