Miracle-dz/UniFAR-FTUs huggingface dataset:
Grass Spikelet Genetics and Duplicate Gene Comparisons

The grass spikelet contains floral organs such as stamens and carpels, as well as additional organs, glumes, lemma, palea, and lodicules that are unique to the angiosperms. Recent work is beginning to shed light onto the genes that regulate the development of spikelet organs. Many of these genes are members of multigene families. These multigene families have formed through gene duplications, some of which are specific to the grass family. I review the recent progress made in understanding the genetics of grass spikelet development. As many of these genes begin to be isolated, they will likely be compared with homologous genes from other angiosperms. Given that some of these genes will be duplicate genes, I provide a set of examples showing how orthologues and paralogues should be compared.
ANALYSIS OF THE INCLINATION INFLUENCE IN A COALESCER COLUMN FOR OIL/WATER TREATMENT VIA COMPUTATIONAL FLUID DYNAMICS

Among the equipments used in the separation of water from oil, bed coalescers stands out. Even after decades of bed coalescer development, the role of some variables, such as apparatus inclination, in its behavior remains underexplored within the field. Thus, using the ANSYS CFX 13.0 software, a modeling was proposed to determine the influence of bed coalescer inclination in the separation rate of oil from produced water. The software analyzes four inclinations relative to the horizontal axis (0°, 15°, 30° and 60°). The results from simulations identified oil accumulating zones and presence of recirculation zones. It also compared the pressure drop throughout the apparatus in all inclinations established, noting that a more favorable state occurs when the bed is at horizontal, presenting higher oil accumulation, fewer vorticity, and lower pressure drop. The less desirable scenario occurs with 60° inclination, displaying a lower separation efficiency, greater pressure drop, and higher turbulence effect.
MHD Natural Convection of a Fe3O4–Water Nanofluid within an Inside Round Diagonal Corner Square Cavity with Existence of Magnetic Source

This study concerns a numerical investigation of a magnetohydrodynamic (MHD) natural convection of a Fe3O4–water nanofluid filled within a round diagonal corner square cavity. The cavity was subjected to imposed temperatures (hot and cold walls) and one magnetic source. The nanofluid flow and heat transfer problem was mathematically modeled and its dimensionless problem was established. The finite element method was implemented in order to solve the MHD problem. The effects of the Rayleigh number, Hartmann number and round corner radius on the nanofluid flow (streamlines and velocity magnitude) and heat transfer (isotherms and temperature distribution) were evaluated. Heat transfer was assessed when the convection or the conduction dominates with regard to the nature of the flow.
Studies in the mode of action of royal jelly in honeybee development. IX. The carbohydrates and lipids in the haemolymph and the fat body of developing larvae

No qualitative difference between honeybee queens and workers was found in the haemolymph sugars during their postembryonic development. Trehalose was the chief sugar and accounted for 95% of the total carbohydrates in both castes; glucose was the only other significant sugar. Sugar concentrations varied widely both with stage of development and caste. Different caste patterns of variation in fat body glycogen, trehalose, and glucose were observed. Glycogen concentration increased in queen larvae after they were sealed in their cells. Tissue lipid concentrations were higher in queens than in workers and increased in queens after larvae were sealed in their cells. The rapid reproductive development in queens during the short pupal period may be related to their ability of accumulating large food reserves.
The mineral content of cereals, grain legumes and oilseed crops in South Australia

Samples of barley, oats, lupins, peas, rape, linseed and safflower were analysed at five growth stages for nitrogen, phosphorus, potassium, sulphur, calcium, magnesium, sodium, chlorine, silicon, copper, zinc and manganese. The results are summarized and compared with those for wheat published in a previous paper. The data are discussed in relation to nutrient removal and the effect on soil fertility.
Applying f4-Statistics and Admixture Graphs: Theory and Examples

f-statistics (Patterson et al., 2012; Reich, Thangaraj, Patterson, Price, & Singh, 2009) are a widely used toolkit for making inferences about phylogeny and admixture from population genetic data, particularly in humans. The statistics measure correlations in allele frequencies among sets of two, three or four populations. Observed values reflect degrees of shared ancestry and can serve as a means for testing hypotheses regarding population split orders and past gene flow events under historical models. As compared to some other common methods in population genetics, f-statistics are quite simple and flexible, but interpreting them is not always straightforward. Additionally, one of the primary applications of f-statistics is in building admixture graphs (i.e., phylogenetic trees augmented with admixture events) with more than four populations, which introduces a greater level of complexity. In this note, I hope to clarify some of these potential difficulties and provide a range of tips for practitioners. Some of the topics have been addressed previously but are covered here as well for the sake of completeness. 2 | f-STATISTIC S AND ADMIX TURE
Binding Activity of 5α-Reduced Gestagens to the Progestin Receptor from African Elephant (Loxodonta africana)

Abstract Recent findings in the African elephant (Loxodonta africana) indicate that the major progestins contained within and biosynthesized by corpora lutea are 5α-reduced metabolites and that progesterone is quantitatively of minor importance. The specific gestagenic action within the reproductive tract of elephants was determined by measurement of relative binding affinity of the respective progestins to the gestagen receptor extracted from elephant endometrium. The cytosol was incubated with 40 nmol/liter [3H]ORG-2058 and increasing concentrations of the tested progestin. Progesterone (P4), 5α-pregnane-3,20-dione (DHP), and 5α-pregnane-3α-ol-20-one (5α-P-3OH) were used. The competition for binding sites on the progestin receptor was shown by decreasing counts measured after extraction with scintillation fluid. The progestin concentration which induced a 50% reduction of measured counts was estimated (C50) and relative binding affinity of progesterone to other progestins was calculated (RBA = C50progestin/C50p4). The relative binding affinity of DHP to P4at the gestagen receptor of elephant endometrium was equivalent. The other 5α-reduced progestin (5α-P-3OH) showed no competition to the [3H]ORG-2058 receptor binding. We conclude that the biological significance of P4and DHP at the receptor level is very similar. The higher quantitative levels of DHP in corpus luteum and serum support the hypothesis that this progestin is the major gestagen in the elephants, whereas 5α-P-3OH is an inactive metabolite.
DNA LIBRARIES FOR SEQUENCING THE GENOME OF OSTREOCOCCUS TAURI (CHLOROPHYTA, PRASINOPHYCEAE): THE SMALLEST FREE‐LIVING EUKARYOTIC CELL 1

Ostreococcus tauri is a marine photosynthetic picoeukaryote presenting a minimal cellular organization with one nucleus, one chloroplast, and one mitochondrion. It has the smallest genome described among free‐living eukaryotic cells, and we showed by pulsed‐field gel electrophoresis (PFGE) that it is divided between 15 bands ranging from 1.2 to 0.15 Mb, giving a total size of 9.7 Mb. A Bacterial Artificial Chromosome (BAC) library was prepared from genomic DNA extracted from a culture of O. tauri. A total of 2457 clones was obtained with an average insert size of around 70 kb, representing an 18‐fold coverage of the genome. The library was spotted on high density filters, and several probes of coding sequences were hybridized to both the high density BAC library filters and directly to the dried PFGE gels of the O. tauri genomic DNA. These hybridizations allowed a preliminary organization of the library and the localization of several markers on the chromosomes. Randomly selected fragments were also sequenced, representing 12% of the O. tauri genome. Many sequences showed significant similarities in data banks, mainly with plant and algae sequences. About 1000 coding sequences could be identified. These data confirmed the position of O. tauri in the green lineage and the hypothesis of a very compact organization of its genome.
Effect of presoaking on extraction of hemicellulosic sugars and flavonoids from switchgrass (Panicum virgatum) leaves and stems.

In order to establish the baseline quantities of key fermentable sugars, switchgrass (Panicum virgatum L., var. Alamo) stems and leaves were pretreated with dilute acid, and the release of sugars was compared to that reported in the U.S. DOE biomass feedstock composition and property database. Switchgrass was planted in the spring of 2008 and harvested in the spring of 2009. The feedstock was separated into leaves and stems and ground to particle sizes of 0.34 and 0.37 mm, respectively. Dilute acid pretreatment of the material (130°C in 0.98% H2SO4 for 25 min) yielded xylose recoveries of 76% and 61% for leaves and stems, respectively. Recoveries were calculated by dividing the recovered sugar by the values reported in the DOE feedstock database. Coupling a 2 h 85°C hot water presoaking step to the 25 min 130°C in 0.98% H2SO4 pretreatment increased the xylose recovery by 23% and 5% for leaves and stems, respectively. These results demonstrate that a presoaking step increases the sugar release without escalating the severity of the pretreatment. Moreover, the 85°C presoaking water contained the flavonoid quercetin, which is a documented antioxidant. The presoaking water from leaves and stems displayed yields of 0.14 and 0.12 mg of quercetin per g of dry switchgrass, respectively. Thus, the presoaking step not only increases monosacchride recovery, but provides a slipstream that could be processed into a value-added revenue-generating stream for the biorefinery.
The physics and biology of fluorescence microscopy in the life sciences

The last decade has seen a renaissance in the use of fluorescence microscopy in biology. This development was fuelled by the discovery of autofluorescent proteins that, through simple genetic conjugation to virtually any protein of interest, allowed their investigation of living cells. Importantly, this also prompted the introduction of advanced fluorescence microscopy techniques of ever increasing sophistication that exploit the possibilities of this new labelling technique. The microscope became an analytical instrument, images became rich sources of quantitative information, and we obtained an unprecedented insight into the working of the molecular machines that operate in living cells. This new field is positioned at the interface between biology and physics. This review will provide an historic overview of this process, describing some of the most exciting developments, and mainly focusing on one of the most informative imaging techniques for the elucidation of the chemistry of life; Förster Resonance Energy Transfer microscopy.
Photosynthetic characteristics of planktonic blue-green algae: The response of twenty strains grown under high and low light

The relationship between photosynthetic rate and irradiance was measured for 20 strains of blue-green algae from the genera Anabaena, Aphanizomenon and Oscillatoria. Cells were grown at 20°C under 6:18 light-dark at 30 or 150 µE m-2 s-1. Under high light the mean light saturated rate of photosynthesis (P max) of the Oscillatoria cultures was 14·8 mg O2 mg Chl a -1 h-1, but under low light this was depressed by 42%. Anabaena and Aphanizomenon cultures showed a similar mean P max under high light (13·8 mg O2 mg Chl a -1 h-1), but only a 13% depression of this value under low light. Oscillatoria cultures were more efficient than Anabaena and Aphanizomenon cultures at harvesting low irradiances, as measured by the initial slope of the photosynthesis-irradiance plot. The efficiency of light harvesting at low irradiances increased in Anabaena and Aphanizomenon cultures grown under low light. Oscillatoria cultures on the other hand showed little increase in efficiency when grown under low light. Mainly due to th.
Tasks, occupations and wages in OECD countries

This paper investigates the relationships between earnings, human capital, and job tasks, exploiting internationally comparable information from the OECD Survey of Adult Skills. We use the theoretical framework presented in Autor and Handel (2013) and extend their empirical results to 20 OECD countries. Our data allow for a richer characterisation of worker’s human capital, by including both educational attainment and a measure of cognitive skills. We are able to confirm the predictive power of job tasks in explaining wage differences both between and within occupations, and to provide empirical support for the model’s prediction in the vast majority of countries.
Gene Expression Profiling of Plants under Salt Stress

Soil salinity is among the leading environmental stresses affecting global agriculture, causing billions of dollars in crop damages every year. Regardless of the cause, ion toxicity, water deficit, or nutritional imbalance, high salinity in the root zone severely impedes normal plant growth and development, resulting in reduced crop productivity or crop failure. Development of salt-tolerant cultivars is an attractive and economical approach to solving this problem. Although several salt-tolerant plant genotypes have been developed through transgenic approaches, often they have failed or exhibited limited success under field saline conditions. This is due to several reasons, including the fact that plant growth and development under saline conditions in the field is often influenced by cumulative effects of multiple environmental stresses and genetic factors, which may not have been considered during the development of salt-tolerant transgenic plants. Adoption of inappropriate screening techniques or selection criteria may also lead to selection of genotypes that may not be stress tolerant in a real sense. In most plant species, salt tolerance is a genetically complex trait, often modulated by multiple biosynthetic and signaling pathways. Cross-talks among various stress-controlling pathways have been observed under salt stress, many of which are regulated by transcription factors. Thus, a comprehensive knowledge of the up- and downregulating genes under salt-stress is necessary, which would provide a better understanding of the interactions among pathways in response to salt stress. Attaining such knowledge is a good step toward successful development of salt-tolerant crop cultivars. To this end, DNA microarray technology has been employed to study expression profiles in different plant species and at varying developmental stages in response to salt stress. As a result, large-scale gene expression profiles under salt stress are now available for many plant species, including Arabidopsis, rice, barley, and ice plant. Examinations of such gene expression profiles will help understand the complex regulatory pathways affecting plant salt tolerance and potentially functional characterization of unknown genes, which may be good candidates for developing plants with field salt tolerance. In this article, we review and discuss the current knowledge of plant salt tolerance and the extent to which expression profiling has helped, or will help, a better understanding of the genetic basis of plant salt tolerance. We also discuss possible approaches to improving plant salt tolerance using various tools of biotechnology.
Abaxial Anthocyanin Layer in Leaves of Tropical Rain Forest Plants: Enhancer of Light Capture in Deep Shade

The permanent pigmentation of the leaves of tropical rain forest herbs with anthocyanin has traditionally been viewed as a mechanism for enhancing transpiration by increased heat absorption. We report measurements to ? +0.1? 0C on four Indo-malesian forest species polymorphic with respect to color. There were no detectable differences in temperature between cyanic and green leaves. In deeply shaded habitats, any temperature difference would arise from black-body infrared radiation which all leaves absorb and to which anthocyanins are transparent. Reflectance spectra of the lower leaf surfaces of these species revealed increased reflectance around 650-750 nm for cyanic leaves compared with green leaves of the same species. In all species anthocyanin was located in a single layer of cells immediately below the photosynthetic tissue. These observations provide empirical evidence that the cyanic layer can improve photosynthetic energy capture by back-scattering additional light through the photosynthetic tissue.
Effects of genetic, managemental and dietary factors on the efficacy of exogenous microbial phytase in broiler nutrition

test, counter-active phytase and phosphorus dosages, caging, above-average mortality, anticoccidial, maize as cereal base and added fat on the nutritional responses of broilers to exogenous microbial phytases (Rosen, 2002). The next objective was to investigate the effects of ration contents of cereal grains, supplementary oils and fats, dietary nutrients and different phytase products. All available, unselected, unique data sets from 311 controlled tests were computer filed and statistically analysed by standard methods of applied regression analysis (Draper and Smith, 1981) in order to relate start-to-finish feed intake and liveweight gain effects to independent variables, in best-fit, statistically-significant regressions, having minimum standard deviation (SD), maximum multiple regression coefficient square and statisticallysignificant partial regression coefficients, excluding aberrant responses (residuals > 3SD). The notations used in this research were:
THE EFFECT OF SODIUM BICARBONATE, CEMENT KILN DUST AND AMMONIUM PERCHLORATE ON THE GROWTH OF LAMBS

Two experiments were conducted in which 20-kg feeder lambs were fed diets supplemented with sodium bicarbonate, cement kiln dust or ammonium perchlorate, or control diet in combination with long timothy hay until they reached a market weight of 40 kg. Lambs fed sodium bicarbonate or cement kiln dust grew faster (P < 0.05) than the control group and showed equal or superior feed efficiency. Cement kiln dust in the diet produced a higher fecal pH (P < 0.01) thus demonstrating a buffering effect in the lower digestive tract. Sodium bicarbonate or cement kiln dust had no effect on rumen pH. The control and ammonium perchlorate groups grew at the same rate but the control animals showed better feed efficiency.
Biochar and Ash Fertilization Alter the Chemical Properties of Basket Willow (Salix viminalis L.) and Giant Miscanthus (Miscanthus x giganteus)

This article presents the results of a two-year study investigating the effects of the fertilization of soil, with biochar and ash from plant biomass, on selected properties of the pyrolysis products obtained from basket willow (Salix viminalis L.) and giant miscanthus (Miscanthus x giganteus). The study was designed to determine whether soil enrichment through the use of organic fertilizers (ash added at the rate of 1.5 t ha−1, biochar added at the rate of 11.5 t ha−1 and a combination of them) in the cultivation of energy crops would affect the quality of pyrolysates obtained from these plants. The research goal was to use biochar and biomass ash to produce high-quality pyrolysates with fertilizing potential. The aboveground parts of the plants were subjected to the pyrolysis process, which was carried out in constant conditions, i.e., a temperature of 500 °C and duration of 10 min. The pyrolysates obtained were examined for their pH value, the content of absorbable forms of phosphorus (P2O5), potassium (K2O) and magnesium (Mg), as well as total carbon and the total content of selected macro- and micro-elements. The results of the current study show the beneficial effects of these soil fertilizers, reflected by the high quality and enhanced mineral contents of the biochars obtained. The highest total increase in the contents of absorbable forms of P, K and Mg was found in the pyrolysis products from basket willow fertilized with ash alone, amounting to 21.6% in relation to the pyrolysates from the control sample. As for the pyrolysates from the biomass of giant miscanthus, the greatest total increase in the contents of the elements, amounting to 44.4%, was identified when biochar and ash were used in combination. Soil amendments such as biochar and ash used for growing bioenergy crops can alter the aboveground plant quality. The subsequent pyrolysates created from these plants may be enriched and can be an alternative to mineral fertilizers. Natural amendment, such as high-quality pyrolysates, can be used in the cultivation of many plants. Additionally, conversion of plant biomass into pyrolysates is important for the environment, affecting the balance of carbon in the atmosphere through its capture and storage in a stable form outside the atmosphere, e.g., in soil.
Stomach Flushing Vs. Fecal Analysis: The Example of Phrynops rufipes (Testudines: Chelidae)

Abstract The following is a study of the trophic niche of Phrynops rufipes revealed by an investigation of stomach flushing and fecal samplings. We successfully stomach flushed all 31 adult turtles captured and collected feces from ten of the flushed turtles. Our results show that only an integrated approach using both techniques is able to provide a comprehensive picture of P. rufipes diet. Trichoptera larvae were the most eaten item in numeric terms and in frequency of occurrence, but shrimp contributed the greatest volume of invertebrates. The seeds of most kinds of palm trees common around streams in the area were eaten. Due to the limitations of stomach-flushing technique, palm fruits were underestimated, but they still contributed the highest volume of material flushed from the stomachs and found in the feces. Our findings alter the conclusions concerning the food habits of P. rufipes: it is an omnivore species that feeds in an opportunistic way on a greater quantity of benthonic macro-invertebrates and fishes than was evident from previous studies based on fecal sampling alone.
IdeoKar: an ideogram constructing and karyotype analyzing software

Ideograms are diagrammatic or idealized representations of chromosomes, showing their relative size, homologous groups and cytogenetic landmarks. Chromosomal analysis of cytological preparations involves calculation of karyotypic parameters and generation of ideograms. We generated IdeoKar, a free and user-friendly karyotype analysis software that facilitates data collection from different digital images of metaphase chromosome spreads and calculates a wide variety of chromosomal and karyotypic parameters along with the related standard errors which can be saved as a Microsoft Excel file. This software is also capable of drawing ideograms of both diploid and allopolyploid species in a single image file. IdeoKar is designed to fast and efficient karyotype analysis and ideogram generation. It can be used with personal computers without any specific hardware. This software and related documentation is freely available at the website of the University of Kurdistan at: http://agri.uok. ac.ir/ideokar/index.html.