Miracle-dz/UniFAR-FTUs huggingface dataset:
Growth of sagebrush and bitterbrush following simulated winter browsing: mechanisms of tolerance

We investigated the herbivory tolerance characteristics of shrubs in a comparative study of two Great Basin shrub species with different abilities to tolerate browsing. Simulated winter browsing treatments were applied to the less tolerant species, mountain big sagebrush (Artemisia tridentata ssp. vaseyana (Rydb.) Beetle), and to the more tolerant species, bitterbrush (Purshia tridentata (Pursh) D.C.), growing in natural stands. These treatments ranged in severity from terminal bud removal to removal of 100% of current annual growth, and were applied to (1) individual branches on shrubs and (2) to entire shrubs. We measured growth responses on entire treated branches or on typical branches when treatment was to the entire shrub. We recorded the fate (long shoot, short shoot, mortality, and in Artemisia only, flowering stem) of all nodes on each measured branch and the length, node production, and estimated biomass of all new long shoots. We also estimated the proportion of resources removed by each simulated browsing treatment. Purshia compensated for the loss of tissue to a greater extent than Artemisia. In comparison to unclipped branches, Artemisia and Purshia both increased the frequency of new long shoots produced in response to simulated browsing. However, Artemisia tended toward reduced long shoot biomass with increased browsing, while Purshia was either insensitive to the severity of browsing treatment or, in one case, increased long shoots biomass after treatment. The contrasting responses were particularly evident in the most severe treatment, which resulted in death of all Artemisia branches but in biomass production equal to controls in Purshia. Additionally, node production declined in Artemisia but in Purshia was equal to or exceeded node production in control unclipped branches. In this study, neither aboveground resource availability nor bud availability fully explained differences in the abilities of Artemisia and Purshia to tolerate browsing. In addition, the results from this and related studies suggest that inherent relative growth rate was not correlated with herbivory tolerance in these species. Developmental plasticity and the resultant altered resource allocation patterns following winter browsing appear to distinguish Artemisia and Purshia in their ability to tolerate browsing.
Non-linear Bayesian joint inversion of seismic reflection coefficients

SUMMARY Inversion of seismic reflection coefficients is formulated in a Bayesian framework. Measured reflection coefficients and model parameters are assigned statistical distributions based on information known prior to the inversion, and together with the forward model uncertainties are propagated into the final result. This enables a quantification of the reliability of the inversion. Quadratic approximations to the Zoeppritz equations are used as the forward model. Compared with the linear approximations the bias is reduced and the uncertainty estimate is more reliable. The differences when using the quadratic approximations and the exact expressions are minor. The solution algorithm is sampling based, and because of the non-linear forward model, the Metropolis–Hastings algorithm is used. To achieve convergence it is important to keep strict control of the acceptance probability in the algorithm. Joint inversion using information from both reflected PP waves and converted PS waves yields smaller bias and reduced uncertainty compared to using only reflected PP waves.
Predicting patterns of post-fire germination in 35 eastern Australian Fabaceae

Germination in 35 species from 15 legume genera of southeastern Australia was promoted by a heat treatment which broke the seed coatcaused dormancy. Once the critical temperature was reached, most seeds had their dormancy broken, independent of the duration of heating. Species fell into three classes according to whether their dormancy was broken by a temperature of 40, 60 or 80°C. Highest germination in all species was achieved by heating in the temperature range 80–100°C, although long durations (120 min) at 100°C caused seed death in several species. At 120°C, seeds of most species were killed at all but one minute's duration. A proportion of seeds from 7 species (Acacia myrtifolia, Pultenaea daphnoides, P. incurvata, P. linophylla, P. polifolia, Dillwynia floribunda and Sphaerolobium vimineurn) was not killed at 120°C and had their dormancy broken. This proportion varied markedly and resultant germination levels were significantly less than those at 80 and 100°C, except in S. vimineum. Between-site variations in the 4 species tested (A. myrtifolia, A. suaveolens, A. terminalis and A. ulicifolia) were small. These variations concerned: (i) the minimum temperature required to break seed dormancy in 2 species: 60°C in one population of A. myrtifolia and A. suaveolens, and 80°C in the other; and (ii) the intensity of the germination response. Duration of heating was less important than temperature as a determinant of germination. Ordination techniques revealed that results from one duration across temperatures were comparable with data from multiple durations. This has significant applications in studying rare species, where seed may be in short supply. Predicted germination levels after a moderate intensity fire should far exceed those after a low intensity fire. Little germination was predicted for many species after a low intensity fire and for one species, A. elongata, no germination was predicted. The potential role of indicator species in relation to the maintenance of species in a community is suggested.
Development of on-the-go soil organic matter sensor

Soil organic matter (OM) greatly influences soil quality and productivity. Conventional soil OM analysis is expensive, time consuming and laborious. To practice precision farming, one important step is to describe the variability of a farm and the conventional analysis is always delayed. Quick ground sensor or on-the-go sensor can help to achieve this need. With the development of a new technology, the soil OM information can be gathered in a real time basis by using Soil Organic Matter Sense (SOMSENSE) with the integration of software developed using MATLAB. A model of soil OM estimation based on Red, Green, and Blue (RGB) scales showed significant findings when plotting on 1:1 line. This technique will help farmers or farm managers to determine their field variability quickly to practice precision farming based on OM variability map.
Isolation and characterization of microsatellite loci from Larix kaempferi

Microsatellites were isolated and characterized for Japanese larch, Larix kaempferi, a conifer species distributed in Japan. A larch genomic DNA library enriched for (AG)n repeats was screened using the colony polymerase chain reaction method and 145 unique microsatellite containing sequences were obtained. Seventy-two primer pairs were designed and 30 produced single-locus products, and 19 of them were polymorphic. The expected heterozygosity ranged from 0.566 to 0.951. These 19 polymorphic microsatellite loci should be valuable markers for genetic studies on Japanese larch.
Generation of nucleotide sugars for biomass formation in plants

Nucleotide sugars are activated forms of monosaccharides and serve as glycosyl donors for glycosyltransferases in the synthesis of cell wall polysaccharides. Since they affect the amounts and architecture of cell wall polysaccharides in plants, the levels of nucleotide sugars, as well as the levels of the glycosyltransferases, at least partially, regulate the production of plant cellulosic biomass. Nucleotide sugars are principally generated through de novo pathways, in which various UDP- and GDP-sugars are produced through sequential interconversions from starting substrates such as UDP-glucose. The salvage pathway is an alternative route to synthesize nucleotide sugars. In the salvage pathway, free monosaccharides released during the metabolism of polysaccharides and glycoconjugates are first phosphorylated by monosaccharide kinases, and then converted to nucleotide sugars by nucleotide sugar pyrophosphorylases in the presence of the respective nucleotide triphosphates as co-substrates. In this review, we focus on the recent progress in our understanding of the mechanism for the generation of nucleotide sugars through the salvage pathway for free monosaccharides in higher plants.
Caenorhabditis elegans as an Experimental Model Organism to Study Parkinson's Disease-Related Genes

Parkinson’s disease (PD) is the second most common neurodegenerative disorder, mainly characterized by motor dysfunctions resulting from massive and selective loss of dopaminergic neurons. Mutations in the human parkin gene, which encodes an E3 ubiquitin ligase, are the most frequent causes of hereditary PD, leading to autosomal-recessive juvenile Parkinsonism. However, the cell biological role of Parkin and the molecular pathogenic mechanisms by which mutations cause PD are unclear. In this study, the Caenorhabditis elegans parkin ortholog, pdr-1, was identified and characterized in detail. PDR-1 is functionally conserved, since it physically associates and cooperates with enzymes of the ubiquitylation/degradation system to mediate ubiquitin conjugation. Strikingly, in contrast to pdr-1 loss-of-function mutants, the in-frame deletion mutant protein PDR-1(delaa24-247) still interacts with its co-enzymes, and moreover, the corresponding mutant pdr-1(lg103) is hypersensitive towards misfolded protein conditions. In this mutant, both cytosolic stress conferred by overexpression of mutant human alpha-synuclein, a gene linked to autosomal-dominant forms of PD, as well as endoplasmatic reticulum (ER)-derived folding stress result in severe developmental defects and lethality. Although expression of pdr-1 is regulated by all three activators of the unfolded protein response (UPR), IRE-1, PEK-1, and ATF-6, genetic analyses established a function of PDR-1 in parallel to IRE-1 signalling. Therefore, PDR-1/Parkin plays an essential role in the regulation of different proteotoxic stress pathways: it contributes to the ER-specific UPR, but also participates in the cytosolic detoxification of protein aggregates, including alpha-synuclein. The truncated protein PDR-1(delaa24-247) seems to mediate a toxic misfunction by sequestering critical components of the protein folding/degradation machinery, which is related to the stress hypersensitivity in the pdr-1(lg103) mutant. In this study, an experimental animal system was established which is well suited to identify modifiers of toxicity and relevant compounds. Such studies might allow to dissect the molecular and cellular pathways involved in the pathogenesis of PD and to identify potential therapeutic drug targets.
Functional Analysis of the Yku Complex in Telomere Length Regulation

The Ku protein from Saccharomyces cerevisiae (Yku) forms, like its human homologue hKu, a heterodimer comprised of a 70kD and an 80 kD subunit. In yeast and mammals, the Ku heterodimer is required for the repair of DNA double strand breaks (DSBs) via nonhomologous end-joining (NHEJ). Interestingly, Ku has been shown to bind to the native chromosome ends. It contributes to the maintenance of wild type telomere length and, moreover, has been implicated in the protection of the telomeres from end-to-end fusions. Telomere-bound Yku delocalizes from telomeric foci in response to DNA damage and accumulates at the sites of a DNA break. This thesis aimed to further characterize the Yku heterodimer and its function at DSBs and the native chromosome ends. In a genetic screen for mutations that - in combination with a yku deletion - lead to cell death, a novel mutation in the yeast telomerase subunit CDC13/EST4 has been identified earlier in the laboratory. Cdc13p binds to the single stranded DNA overhang at telomeres and is required to recruit the yeast telomerase to chromosome ends. The results presented here suggest that the mutant protein, Cdc13-4p, can still bind to the telomere and does interact with the telomerase subunit Est1p in vivo. A model is proposed in which the mutant Cdc13p is altered in its binding to a regulatory protein, thereby modulating telomerase access to the chromosome ends. The lethal effect in yku mutants is discussed to result from the loss of additional telomere sequences at the already very short telomeres of yku mutants. In order to fulfill its opposite functions at the ‘different’ DNA ends, Yku might depend on larger protein networks. Putative Yku interacting proteins have been identified in a two hybrid screen. One interactor, Sir4p, has previously been implicated in NHEJ. The Sir4p domain identified could be shown to interact with the Yku heterodimer via the Yku80p subunit. Experiments that allowed the separation of phenotypes caused by the loss of the Sir4 protein itself and phenotypes induced by a de-repression of silencing in sir4 mutants revealed no direct involvement of Sir4p in the repair of DSBs. In contrast to Cdc13p, Sir4p acts epistatic with Yku at the telomeres, indicating that the protein-protein interaction detected by two hybrid criteria might take place at telomeres. Besides defects in DNA repair and telomere protection, mice deficient for Ku have been reported to exhibit phenotypes indicative of premature aging. Loss of yku70 or overexpression of the Yku heterodimer effects life span in yeast. Experiments presented here rise the possibility that the premature aging is correlated with Ku’s function at the telomere.
Factors Affecting Tracking of Coronary Heart Disease Risk Factors in Children a

The public health implications of reducing or preventing the excess increase in blood pressure and the acquisition of obesity during childhood years are important. Many children with high blood pressure, particularly those who are initially obese or become obese as young adults and those with excess left ventricular mass for body size, become adults with high blood pressure. Although blood pressure and cholesterol have been shown to track during childhood and from childhood into the adult years, the use of repeated determinations along with measures of obesity and information concerning family history of diabetes and coronary heart disease can significantly add to the prediction of future elevated levels.
Strength Development and Pore Structure Characterisation of Binary Alkali-activated Binder Based on Tungsten Mining Waste

The mineralogical properties of tungsten mining waste mud (TMWM) make its valorisation and re-usage as an alumino-silicate source material to produce an alkali-activated binder without calcination is a challenge. Moreover, the dissolution of silicate and alumina species from TMWM is very slow. Despite the crystallinity of TMWM, this study demonstrates that its combination with other sources of the alumino-silicate source was the materials–such as red clay brick waste(RCBW),ground granulated blast furnace slag (GGBFS) and electric arc furnace slag (EAFS) – improved the compressive strength and the pore structure of the alkali-activated matrix.Thecombinedprecursors (90 vt.%TMWM+10 vt.%RCBW, 90 vt.%TMWM+10 vt.%GGBFS, and 90 vt.%TMWM+10 vt.%EAFS) were activated using a combination of alkaline activator solutions (sodium silicate and sodium hydroxide) with the ratio of 1:3(66.6wt.%sodiumsilicatecombined with 33.33 wt.% of NaOH 10M). The results show that the compressive strength increased from11.23MPa at 28 days to reach 24.98MPawhentheTMWMwaspartially replacedby10vt. %RCBW. In addition,this study shows that the interconnected porosity decreased where the critical pore size was reduced from 21.28 µm to 0.55 µm for the tungsten mining waste-based alkali-activated binder and the binary alkali-activated binder based on TMWM and RCBW. Keywords: Mining Waste, Alkali-activated, Microstructure, MIP, Metakaolin
Two cases of haplo-lethal deficiency in Ustilago bullata operative against saprophytism.

The smut fungi have been considered as incompletely facultative saprophytes, since in the majority of cases the haploid mycelium and sporidia have been found to be the only stage of these organisms capable of a saprophytic existence, while the dikaryon mycelium is obligately parasitic. Ordinarily no difficulty is experienced in culturing the smut fungi, and the literature shows that many species have been successfully grown on artificial media, these cultures usually being represented by pedigreed haplonts of two or more sexes, depending upon the species concerned. However, during the course of extensive cultural studies of Ustilago bullata Berk.2 the writer has encountered a phenomenon which apparently is unparalleled in the records of previous studies of the smut fungi.
Growth response of two varieties of slash pine seedlings to chronic ozone exposures

Two geographical varieties of Pinus elliottii (Engelm.) seedlings, elliottii and densa, were exposed continuously to two daily peak exposure profiles of ozone having 7-h (0900–1600) seasonal means of 0.104 and 0.076 ppm and charcoal-filtered air over a 112-day period. The profiles represented a daily rise and decline of hourly ozone concentration. They were constructed with a daily hourly maximum, which for one profile (0.126 μL/L) exceeded the current ozone standard daily; the standard was not exceeded for the other profile (0.094 μL/L). Destructive harvests at 7-day intervals over the exposure period were employed to assess visible injury and to construct growth curves for stem diameter, plant height, top and root dry weight, and needle number and length. The visible injury was slight, yet all the growth parameters decreased significantly with time and ozone concentration; root growth was the most severely impacted. The observed growth response and visible injury of the two varieties were similar. Seed .
Clinical Implications of the Expression of Estrogen Receptor-α and -β in Primary and Metastatic Lesions of Uterine Endometrial Cancers

Novel human estrogen receptor (ER)-β was identified in cDNA libraries from human testes. ER-β specifically expresses in the testis, ovary, thymus, spleen, osteoblasts, fetus and uterine endometrium. ER-β might not conserve the same physiological functions as does ER-α. Therefore, expressions of ER-α and ER-β mRNAs in primary and metastatic lesions of uterine endometrial cancers were investigated. The levels of ER-β mRNA were significantly lower than those of ER-α mRNA in uterine endometrial cancers and in normal uterine endometria. The ratio of ER-β to ER-α mRNA in most primary uterine endometrial cancers was similar to that in normal uterine endometria (<0.4% of ER-β mRNA to ER-α mRNA). On the other hand, in 14 of the 20 lymph node metastasis-positive cases of uterine endometrial cancers, the ratio in the metastatic lesion was significantly higher than that in the primary lesion of the corresponding case, and patient prognosis in these cases was extremely poor. Therefore, it is suggested that the intact synchronized expression of ER-β interacting with ER-α might be disrupted, especially in most metastases of uterine endometrial cancers, leading to poor patient prognosis related to estrogen refractoriness.
Synthesis Method for Chebyshev Dual-Band Microwave Filters

A synthesis method for symmetric and asymmetric dual-band microwave filters is presented. The proposed method is based on the frequency transformation technique, and the poles and zeros of a desired dual-band filter can be determined by the low-pass prototype filter. To simplify the filter design, an analytical method based on iterations is introduced to eliminate the redundant transmission zeros. The remaining transmission zeros can be rearranged to improve the frequency selectivity. To validate this method, a microstrip open-loop symmetric dual-band filter has been designed and fabricated. The measured results are in good agreement with the simulated ones.
Evidence of Effects of Endemic Chytridiomycosis on Host Survival, Behavior, and Emigration: Reply to Schmidt

[Extract] In our recent publication (Murray et al. 2009), we documented a marked disease-associated reduction in apparent survival of threatened frogs infected with the pathogen Batrachochytrium dendrobatidis (Bd), despite a long period since its invasion. This result raises concern for hundreds of species of amphibians globally because it demonstrates that endemic chytridiomycosis can remain virulent for long periods, potentially placing ongoing pressure on amphibian populations that may elevate extinction risk. In response, Schmidt claims "the apparent monthly survival estimates of Murray et al. are likely confounded with permanent emigration from the study site… . If infected and uninfected frogs have different emigration probabilities, then one would obtain different apparent survival estimates from the mark-recapture analysis for Bd-positive and Bd-negative frogs. " Schmidt concludes, "I believe that most of the difference [in survival rate between infected and uninfected animals] is caused by permanent emigration from the study site. "
Bioinformática estrutural aplicada ao estudo de proteínas alvo do genoma do Mycobacterium tuberculosis

The large-scale genome sequencing are providing us with several information about hundreds of organisms. Understanding of different protein functions expressed by genes obtained in the sequencing projects, lead us to the post-genomic era, with characterization of protein 3D structure. The determination of protein structure, is not always possible, due to limitations in X-ray crystallography and NMR techniques. This fact makes the utilization of comparative modeling very useful. The main interest in the study of metabolic pathways is the fact that some of these pathways are not present in human, which make them selective targets for drug design, decreasing the impact of drugs in humans. DBMODELING is a relational database, created to highlight the importance of molecular modeling methods applied in the Mycobacterium tuberculosis genome. The motivation of this work is the fact that M. tuberculosis is the cause of the deaths of milions of people in the world, thus the protein target structural characterization to propose new drugs became essential. There are currently in the database more than 260 protein models of the M. tuberculosis genome, and other genomes of interest will be added. This database contains a detailed description of reaction catalized, of gene and structural quality of each protein, and their atomic coordinates are available to download, can be accessed at http://www.biocristalografia. df.ibilce. unesp.br/tools. This work increase the conviction that comparative modeling is an useful tool in structural bioinfomatics, once that we have not access to the experimentally structures
Vascular transport and soybean nodule function: II. A role for phloem supply in product export

Abstract The ureide content of soybean (Glycine max (L.) Merr. ) nodules was unaffected by variations in the transpirational rate, while whole plant manipulations designed to decrease phloem supply to nodules resulted in lower rates of nitrogenase activity and an increase in the ureide content of the nodules. The rate of ureide export from the nodule was estimated from the exponential rate of decrease in the pool size of ureides in nodules, following exposure to an N2-free atmosphere (Ar:O2). Export was greatly reduced under treatments which reduced phloem supply to the nodule. A water budget for nodules suggested that the delivery of water to the nodule via mass flow in the phloem was comparable to that required for export of ureides from the nodule in the xylem from the nodule. Therefore, we suggest that xylem export from nodules is related to the phloem supply to the nodule rather than to the transpirational flux in the parent root. This suggestion is related to the reported decreases in nodule permeability to gases under conditions of phloem deprivation.