Miracle-dz/UniFAR-FTUs huggingface dataset:
ALHAMBRA survey: morphological classification

Abstract The Advanced Large Homogeneous Area Medium Band Redshift Astronomical (ALHAMBRA) survey is a photometric survey designed to study systematically cosmic evolution and cosmic variance (Moles et al.2008). It employs 20 continuous medium-band filters (3500 - 9700 Å), plus JHK near-infrared (NIR) bands, which enable measurements of photometric redshifts with good accuracy. ALHAMBRA covers > 4 deg2 in eight discontinuous regions (~ 0.5 deg2 per region), of theseseven fields overlap with other extragalactic, multiwavelength surveys (DEEP2, SDSS, COSMOS, HDF-N, Groth, ELAIS-N1). We detect > 600.000 sources, reaching the depth of R(AB) ~ 25.0, and photometric accuracy of 2-4% (Husillos et al., in prep.). Photometric redshifts are measured using the Bayesian Photometric Redshift (BPZ) code (Benítez et al.2000), reaching one of the best accuracies up to date of δz/z ≤ 1.2% (Molino et al., in prep.). To deal with the morphological classification of galaxies in the ALHAMBRA survey (Pović et al., in prep.), we used the galaxy Support Vector Machine code (galSVM; Huertas-Company 2008, 2009), one of the new non-parametric methods for morphological classification, specially useful when dealing with low resolution and high-redshift data. To test the accuracy of our morphological classification we used a sample of 3000 local, visually classified galaxies (Nair & Abraham 2010), moving them to conditions typical of our ALHAMBRA data (taking into account the background, redshift and magnitude distributions, etc.), and measuring their morphology using galSVM. Finally, we measured the morphology of ALHAMBRA galaxies, obtaining for each source seven morphological parameters (two concentration indexes, asymmetry, Gini, M20 moment of light, smoothness, and elongation), probability if the source belongs to early- or late-type, and its error. Comparing ALHAMBRA morph COSMOS/ACS morphology (obtained with the same method) we expect to have qualitative separation in two main morphological types for ~ 20.000 sources in 8 ALHAMBRA fields. For early-type galaxies we expect to recover ~ 70% and 30-40% up to magnitudes 20.0 and 21.5, respectively, having the contamination of late-types of < 7%. For late-type galaxies, we expect to recover ~ 70%, 60 - 70%, and ~ 30% of sources up to magnitudes 22.0, 22.5, and 23.0, respectively, having the contamination of early-types of ≤ 10%. These data will be used to study the evolution of active and non-active galaxies respect to morphology and morphological properties of galaxies in groups and clusters.
Reexamination of the Association Between Melting Point, Buoyant Density, and Chemical Base Composition of Deoxyribonucleic Acid

The equations currently used for the calculation of the chemical base composition of deoxyribonucleic acid (DNA), expressed as moles per cent guanine plus cytosine (% GC), from either buoyant density (ρ) or midpoint of thermal denaturation (Tm) were recalculated by using only sets of data on DNA determined with the same strains. All available information from the literature was screened and supplemented by unpublished data. The results were calculated by regression and correlation analysis and treated statistically. From the data on 96 strains of bacteria, it was calculated that% GC = 2.44 (Tm – 69.4). Tm appears to be unaffected by the substitution of cytosine by hydroxymethylcytosine. This equation is also valid for nonbacterial DNA. From the data on 84 strains of bacteria, the relation% GC = 1038.47 (–1.6616) was calculated. The constants in this equation are slightly modified when data on nonbacterial DNA are included. Both correlations differ only slightly from those currently used, but now they lean on a statistically sound basis. As a control, the relation between ρ and Tm was calculated from data of 197 strains; it agrees excellently with the above two equations.
Can Hong Kong Chinese parents and their adolescent children benefit from an adapted UK parenting programme

Summary Sixty-five parents joined seven semi-structured group interviews sharing their experience of joining an adapted parenting programme for Hong Kong Chinese parents. The aim of the research was to explore parents’ outcome, parent–adolescent outcome of the parenting programme, as well as any culturally sensitive parenting strategies that were acceptable to Hong Kong Chinese parents. Findings The results indicate that Hong Kong Chinese parents perceived that the parenting programme was useful in improving communication with their adolescents, reducing conflict as well as supporting them to become confident parents of adolescents. Applications This study further illustrates the possible culturally sensitive elements of the Hong Kong Chinese parenting programme. It should focus on helping parents to reflect on their own parenting and help parents to learn granting autonomy to their adolescents, communication skills and conflict resolution skills.
Genetic Variability and Heritability in Sugarcane

Thirty-two genotypes were evaluated in a replicated trial at Sugarcane Research Program, Jitpur, Bara, Nepal in 2000-2001 to estimate phenotypic and genotypic coefficients of variation, heritability and genetic advance for seven stalk characters in sugarcane ( Saccharum officinarum L). Analysis of variance revealed highly significant differences between genotypes for all the characters studied. Genotypic variance was higher than environmental one for cane yield, millable cane number, single cane weight, stalk diameter and stalk length. A single cane weight, germination at 45 days after planting and millable cane number had high genotypic and phenotypic coefficients of variation. High heritability estimates were recorded for millable cane number, stalk diameter and single cane weight. Maximum genetic gain as percent of mean was observed for single cane weight and millable cane number. Key words: Genetic advance; Genetic variability; Heritability; Sugarcane DOI: http://dx.doi. org/10.3126/narj.v4i0. 4870 Nepal Agriculture Research Journal Vol. 4&5, 2001/2002 Page: 56-59 Uploaded date : 9 June, 2011
What best explains vigilance in elk: characteristics of prey, predators, or the environment?

We quantified the vigilance levels of elk (Cervus elaphus) preyed on by wolves (Canis lupus) in Yellowstone National Park, between January and May in 2005 and 2006, and used Akaike's information criterion to compare a set of 38 regression models for vigilance levels. These models combined up to 9 predictor variables of 3 types: characteristics of the prey group (herd size and composition), characteristics of the predator (wolf pack size, distance away, and the presence/absence of a kill), and characteristics of the local environment (distance to woodland edges, snow depth, and snow cover). The set of models spanned a range of complexity from simple univariate models to complex combinations with up to 3 variables of each type. Complex models incorporating the characteristics of the wolf pack, the structure of the elk herd, and the environmental conditions had higher information content than simple models. Although univariate models of vigilance detect significant relationships, they have low information content relative to multivariate models. These results show that elk assesses factors of several types when assessing risk and deciding how much time to allocate to vigilance. In particular, we found that all well-supported models of vigilance included several "prey" variables and several "predator" variables. This result highlights the need to consider information about predators when trying to explain variation in vigilance levels in prey. Copyright 2008, Oxford University Press.
In vitro assays for bioactivity-guided isolation of antisalmonella and antioxidant compounds in Thonningia sanguinea flowers

Bioguided fractionation of the aqueous extract of Thonningia sanguinea flowers, used traditionally in the treatment of microbial diseases, led to the isolation of two phenolic compounds. The structure of these compounds was elucidated by 1H, 13C 1D NMR and mass spectrometry experiments. The antibacterial activity against Salmonella strains and antioxidant activity of the crude extract, fractions and isolated compounds was evaluated using the DPPH method. The isolated compounds identified as brevifolin carboxylic acid and gallic acid demonstrates moderate antibacterial activity against Salmonella enteritidis, Salmonella typhimurium, and Salmonella abony. The results indicated that the two isolated compounds, gallic acid (IC50 = 13.5 iM) and brevifolin carboxylic acid (IC50 = 18.0 iM) were mainly responsible for the good scavenging activity of the aqueous extract.
Batf defines a differentiation checkpoint limiting hematopoietic stem cell self renewal in response to DNA damage

There is growing evidence that the accumulation of DNA damage and telomere dysfunction contributes to declines in stem cell function and tissue maintenance during aging and in response to chronic disease. Checkpoint responses that mediate the decline in stem cell function in response to DNA damage remain yet to be delineated. Here we conducted a functional genomic in vivo screen to identify genes impairing the function of hematopoietic stem cells in the context of chronic DNA damage induced by telomere dysfunction. Screening a shRNA library of 1000 cancer related genes revealed that shRNA mediated knock down of the transcription factor Batf was most potent to rescue the function of telomere dysfunctional stem cells. Specifically, Batf knockdown was 500fold enriched in telomere dysfunctional HSCs compared to wildtype HSCs when transplanted into lethally irradiated recipients. Our study shows that Batf is strongly upregulated in HSCs in response to telomere dysfunction or gamma-irradiation induced DNA damage and during mouse aging. Upregulation of Batf in HSCs in response to DNA damage was G-CSF/Stat3 dependent. shRNA-mediated knockdown of Batf rescued the repopulation capacity of telomere dysfunctional stem cells in transplanted recipients. This rescue in HSC function was associated with impaired induction of lymphocyte differentiation markers, cell cycle inhibitors (p53, p21, p16), and apoptosis in telomere dysfunctional or gamma-irradiated HSCs. Irradiation experiments revealed that lymphoid competent HSCs (CD150lowCD34-KSL) were most sensitive to DNA damage induced stem cell depletion, which was rescued by shRNA mediated knockdown of Batf. Together, this study provides the first experimental evidence that DNA damage leads to induction of a Batf-dependent differentiation checkpoint limiting the repopulation capacity of HSCs and the self-renewal of lymphoid
Functional analysis of the SWI/SNF family protein LSH

Methylation of the carbon-5 position of cytosine is the major covalent modification of DNA found in multicellular organisms and is involved in a diverse range of biological processes in mammals, plants and fungi. In mammals, this modification plays a number of diverse roles in development and cellular differentiation. These include transcriptional gene silencing, chromosomal integrity, repression of transposable elements, parental imprinting and X chromosome inactivation (Bird, 2002). Patterns of DNA methylation are established and maintained by proteins of the DNA methyltransferase (DNMT) family (Bestor, 2000a; Bird, 2002). Interestingly, genetic studies in A. thaliana and mouse have identified a protein from a functionally distinct family that is also required for high levels of DNA methylation. This protein, termed DDM1 in plants (deficient in DNA methylation 1) or Lsh in mouse (lymphoid specific helicase), belongs to the SNF2 chromatin remodelling family of ATPases (Dennis et al., 2001; Jeddeloh et al., 1999; Vongs et al., 1993). SNF2 enzymes have a variety of chromatin related functions that are based upon the ability to disrupt DNA:histone contacts in an ATP dependant manner (Narlikar et al., 2002). Despite the genetic characterisation of Lsh, little is known about its molecular function. Cytological studies and experiments with ES cells have shown that although Lsh co localises with Dnrntl at replication foci during late S phase, it is not required for maintenance methylation of satellite DNA or on replicating episomal plasmids. Lsh has also been shown to be required for de novo methylation and to co-immunoprecipitate with Dnmt3a and Dnmt3b (Zhu et al., 2006). Taken together these studies indicate that the primary role of Lsh is in de novo methylation and it is dispensable for maintaining methylation during DNA
Fragmentation and Pollination Crisis in the Self-Incompatible Iris Bismarckiana (IRIDACEAE), with Implications for Conservation

Recent evidence suggests that fragmentation effects on pollinators may drive plant species to extinction even if their immediate habitats are not affected. We hypothesize that species at high risk of suffering this "pollination crisis" are characterized by the following set of traits: self-incompatibility with synchronous flowering; reliance on a small number of pollinator species whose pollinators are specialists; and the existence of only a few, sparse populations. Iris bismarckiana fits this description perfectly. We studied two populations separated by recent urban development in order to (a) determine if the species is suffering a "pollination crisis", (b) assess which stage of the process limits reproductive success, and (c) evaluate artificial pollination as a viable conservation means for this species. We performed pollination experiments in two populations of I. bismarckiana. The overall natural fruit-set of open-pollinated inflorescences was around 13%, while supplementary cross-pollination by p.
What limits a rare alpine plant species? Comparative demography of three endemic species of Myosotis (Boraginaceae)

Establishing what are the underlying causes of species range limits is of fundamental interest in ecology. We followed the fate of individually mapped plants of three endemic New Zealand high-alpine species of Myosotis, over a period of 9 years. The species provide contrasts in their geographical range and their demography. Myosotis oreophila Petrie is rare and extremely localized (c. 0.5 ha extent), Myosotis cheesemanii Petrie is regionally endemic, and Myosotis pulvinaris Hook. f. is more widespread. All three occur on the Dunstan Mountains, Central Otago, South Island, New Zealand within a 1-km radius, and individual plants were followed in four permanent plots. The three species differed in their longevity and in population variability, with the most widespread species (M. pulvinaris) having the lowest survival (61% per year), the fewest old plants (only 3% of plants present in 1993 surviving until 2001), no increase in survival rates with age, and the most variability in total numbers across years. Both of the rare species, M. oreophila and M. cheesemanii, had higher survival (75% and 88%, respectively, per year) especially for older plants, many older plants (20% and 59%, respectively, of 1993 plants surviving until 2001), and lower variability in total numbers across years. These results are consistent with other studies showing that rare plant species tend to have higher inertia than more common congeners. The range limits of M. oreophila showed a high level of spatial constancy on a scale of metres over the 9 years, despite 80% turnover in plants during that time. The M. oreophila population showed lower mean densities of plants near to the population boundaries, identical age-specific survival rates, but lower flowering probabilities, than the core of the population. We were unable to detect any abiotic differences between inside and outside the M. oreophila range in terms of topography, soil parent materials, microclimate or through manipulation of snow cover. Disturbance may be a factor affecting the distribution of M. cheesemanii but limiting factors for M. oreophila and M. pulvinaris are likely to be biotic (competition, seed limitation, dispersal capacity) and/or historic. Further experimentation is recommended.
The effectiveness of combination Mahogany (Swietenia mahogany) seed and Sour Sup (Annona muricata) leaf pesticide to the time of stop feeding and LC50 Mortality on Armyworm (Spodoptera litura F.)

Spodoptera litura Fabr. is one of polyphagous insect that attacks lot of crop species. Integrated Pest Management (IPM) is a effort to suppress insect pest population. Utilization of plant materials as ingredients insecticide is considered necessary because biodegradable, relatively safe for human, animal, non-target as well as agricultural production. This study uses a combination of Sour Sup (Annona muricata) and Mahogany seed (Swietenia mahogany) as a botanical pesticide. The purpose of this study was to determine the effect of single and combined Mahogany seed (MS) and Sour Sup (SS) leaf extracts against Time stop-feeding and mortality. In this study, concentrations applied to armyworm larvae are control, 100 g/l, 150 g/l, 200 g/l, 250 g/l, 300 g/l and a combination both of them (150 SS + 150 MS; 250 SS + 50 MS; 50 SS + 250 MS; 200 SS + 100 MS; and 100 SS + 200 MS g/l). The results showed that the use of extracts of Sour Sup leaf and Mahogany seed as insecticide either alone or in combination against pests S. litura causing stop eating, causing larval mortality, the ability of larvae to pupae, as well as the ability to imago. However, the the most effective concentration is combination of pesticides obtained in MS 200 and SS 100 g/l with mortality as much as 53.33% at the 72nd hour after application.
Corals of the genus Porites are a locally abundant component of the epibiont community on mangrove prop roots at Calabash Caye, Turneffe Atoll, Belize

Version Accepted manuscript Citation (published version): John Finnerty, Zachary Bengtsson, Kirsten Kuhn, Anya Battaglino, Allen Li, Matthew Talbot, Marzie Wafapoor, Calder Atta, Michael Kowalski, Sarah Margolis, Ekaterina Rar, Elizabeth Burmester, Kathryn Lesneski, Karina Scavo Lord, Leslie Kaufman, Nathan Stewart. "Corals of the genus Porites are a locally abundant component of the epibiont community on mangrove prop roots at Calabash Caye, Turneffe Atoll, Belize. " Caribbean Naturalist, Volume 2019, Issue 67, pp. 1 16.
Chromosomes and DNA of Anguilla anguilla: a study with restriction endonucleases

We have studied fixed chromosomes and purified DNA of Anguilla anguilla L. after digestion with HaeIII, AluI, MboI, and DdeI restriction endonucleases. Our data demonstrated (i) confirmation of the heteromorphic nature of NORs, (ii) absence of detectable sex chromosomes, and (iii) presence of discrete intercalary domains in this species. Our data also permitted us to hypothesize the existence of highly repetitive DNAs, localized in specific heterochromatic regions of A. anguilla chromosomes.Key words: fish, chromosomes, DNA, restriction enzymes.
Effect of phosphorus and zinc nutrition of wheat (Triticum aestivum) in soils of sub-humid southern plains of Rajasthan

A field experiment was conducted to study the individual and interactive effect of P and Zn on yield, nutrient composition and uptake of nutrients in wheat (Tn'ticurn aestivum L. emend. Fiori & Paol.). The grain and straw yields increased significantly with increasing doses of P and Zn. The interaction between P and Zn also had significantly beneficial effect on the yields of wheat. The content and uptake of N by wheat grain and straw increased significantly with P and Zn application. The content of P in grain and straw decreased but its uptake increased with applied Zn. There was adverse effect of higher level of Zn on P uptake and vice-versa. The content and uptake of Zn increased significantly with increasing levels of Zn. Variation of P : Zn ratio due to increasing level of P also indicated the reduction in Zn content in grain and straw.
Assembling the Angiosperm Tree of Life: Progress and Future Prospects

Abstract Over the past two decades there has been remarkable progress in resolving angiosperm phylogeny and patterns of evolution. Analyses of large, primarily plastid molecular data sets have revealed new insights into numerous historically contentious problems of deep-level angiosperm phylogeny, including relationships among “basal angiosperms” (not members of either the eudicot or monocot clades), among clades of Mesangiospermae, and among major clades of eudicots. The same large data sets also have provided evidence for numerous rapid radiations throughout the evolution of angiosperms. The five lineages of Mesangiospermae, as well as most major core eudicot lineages, each likely arose within a narrow range of just a few million years. The rapid radiations in rosids (Rosidae) gave rise to angiosperm-dominated forests, which are also associated with the diversification of ants, beetles, hemipterans, amphibians, and most extant ferns. Ongoing phylogenetic analyses now routinely construct phylogenetic hypotheses encompassing thousands of taxa. Such trees enable us to take a broad phylogenetic perspective on character evolution, community assembly, and conservation. While the wealth of new sequence data continues to transform the study of angiosperm evolution, it also presents major computational and informatic challenges associated with the management and analysis of enormous data sets.
RNAi-Based Functional Genomics in Caenorhabditis elegans

Characterizing the functions of the many genes discovered by the sequencing projects is now the primary focus of genome-scale studies. Although sequence or structure-based comparisons are helping to generate hypotheses on the biochemical functions of many gene products, determining the in vivo role(s) for large sets of genes remains a critical objective. RNA interference (RNAi) offers a rapid way to gain a first look at loss-of-function phenotypes associated with specific genes. So far RNAi has been used to test the function of a third of the predicted genes in the Caenorhabditis elegans (C. elegans) genome, and it can be expected that a first pass survey of the entire genome will soon be completed. From the current body of work an initial estimate of the power and challenges of using RNAi for genome-wide analyses can be made. A comparison of results obtained from independent large-scale RNAi studies reveals that despite a high degree of congruence, no single study is likely to achieve a comprehensive RNAi-based phenotypic "map" of the C. elegans genome; instead a more accurate picture will be assembled from a composite of independent results for the same genes. RNAi analysis, together with other functional genomic approaches such as expression profiling and protein interaction mapping, is transforming C. elegans into a premier model system for the development and integration of functional genomic approaches in a metazoan.