Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of irrigation regimes on carbon isotope discrimination, yield and irrigation water productivity of wheat

The present research study was carried out during the years 2009-2010 and 2010-2011 to identify the relationship between carbon isotope discrimination (δ) of grain and leaf, yield of winter wheat, and irrigation water productivity (IWP) under different water conditions in a semiarid climate. The field experiments were conducted with four different irrigation treatments (I1: rainfed: I2: irrigate when calculated soil water depletion is 60 mm below field capacity (full irrigation); I3: two irrigations maximum, one at tillering and another at grain filling; I4: no irrigation after establishment until heading, after which irrigate when soil water depletion is 60 mm below field capacity). The leaf (δL) and the grain (δG) carbon isotope discriminations, biomass, and grain yield (GY) were measured in the experiments and the harvest index (HI) and IWP were calculated. At the end of the study, taking a 2-year average, GY and HI were found to be 3.35 t ha-1, 4.53 t ha-1, 4.13 t ha-1, and 4.37 t ha-1 and 29%, 31%, 31%, and 32%, respectively, according to the treatments. The results showed a significant positive linear correlation between δ and GY. These results highlight that grain δ at the pre-anthesis stage could be beneficial for predicting yield under well-irrigated conditions. The highest IWP value was obtained from I4 treatment. δ-IWP and GY-IWP were negatively correlated. IWP can be indicated as an advantage in deciding about limited irrigation regimes for wheat production in arid areas. The results of the present study show that full irrigation treatment (I2) could be recommended in areas with no water shortage conditions. Moreover, limited irrigation such as treatment I4 at 4.8% level produced only optimum yield reduction and had the potential for saving approximately 50% of irrigation water.
EFFECT OF DIETARY OF PALM POLLEN AND GINSENG SUPPLEMENTATION ON PRODUCTIVE, REPRODUCTIVE TRAITS AND SOME PHSIOLOGICAL PAMETERS OF LAYING JAPANESE QUAILS.

A total number of 108 Japanese quail birds (72 females and 36 males) at 6 weeks old was used to evaluate the supplementation of either Palm Pollen(PP) or Panax Ginseng (PG) or their mixture to the diets of laying quail on productive, reproductive traits and some physiological parameters. Quails were weighed individually, randomly (201.97gm ± 1.13 body weight) distributed into four experimental groups. Each group contained 27 birds (18 hens and 9 males). The first group was fed the basal diet as control group (without any supplementation), the second group was fed the basal diet and supplemented with 5 g PP/kg diet, the third group was supplemented with 0.5 g PG/kg diet and the fourth group was supplemented with 5g PP +0.5g PG /kg diet during the experimental period from 7 to 22 weeks of age. Each group was divided into three replicates of 6 females and 3 males in each. The results indicated that quails fed either Palm Pollen or Panax Ginseng or their mixed had significant (P<0.01) increased live body weight change (weight gain), egg production percentage and egg mass as well as improved(P<0.01) feed conversion ratio (g feed/g egg mass) as compared with control group. However, percentage of fertility and hatchability of egg sets had significant (P<0.01) increased. Sperm motility (% ) and sperm-cell concentration (x10 9 /ml) of quails treated with supplemented of PP and PG significantly (P<0.01) increased compared with the other treatment groups, while dead spermatozoa (%), sperm abnormalities (%) and acrosomal damage (%) of quails treated with PP or PG and their 718 WESAM IBRAHIM et al. mixture significantly (P<0.01) decreased compared with the control group. Fertility, and hatchability of egg sets laying were significantly (P<0.01) increased compared with control group. Total protein increased significantly (P<0.01) However, blood serum tri-glycerides, cholesterol and glucose concentration decreased significantly (P<0.01). The histological findings in testes of male treated with either PP or PG or their mixture showed an improvement of the cellular activity and spermatogenesis in the testicular sections. Conclusively, supplementing of Palm Pollen 5 g PP/kg diet or Panax Ginseng (0.5 g PG/kg diet) and their mixture to the diet of laying quails can be used safely significantly increasing appease productive and reproductive performance of quails.
Soil Extracellular Enzyme Activities and Uptake of N by Oilseed Rape Depending on Fertilization and Seaweed Biostimulant Application

The present study has aimed at enhancing the insufficient knowledge of functional soil enzymes properties influenced by inorganic fertilization and biostimulant application to increase the uptake of nitrogen affecting the winter oilseed rape yield. Field experiments were conducted in Poland (53° N, 18° E) in Alfisol (USDA). In this experiment, the NPK rates applied were as follows: high 180 N, 70 P and 160 K 132 N (kg ha−1) or low 144 N, 35 P and 66 K (kg ha−1); fertilization with elemental S 36 or 0 (kg ha−1); and the seaweed biostimulant Kelpak was applied or there was no such treatment. Due to low NPK fertilization rates, the activity of dehydrogenases, peroxidases, and catalase increased in subsistent generative development stages from flowering to ripening. At the ripening stage, the activity of these enzymes, as well as nitroreductase activity, were inhibited by high NPK fertilizer rates. The seaweed biostimulant application and S fertilization increased N accumulation in plants of oilseed rape in generative development, by 16% and 13%, respectively, as compared with the lack of these treatments. The application of S increased the uptake of nitrogen in shoots and in whole oilseed rape plants only after application of higher rates of NPK.
Measuring Tree Height with Remote Sensing—A Comparison of Photogrammetric and LiDAR Data with Different Field Measurements

We contribute to a better understanding of different remote sensing techniques for tree height estimation by comparing several techniques to both direct and indirect field measurements. From these comparisons, factors influencing the accuracy of reliable tree height measurements were identified. Different remote sensing methods were applied on the same test site, varying the factors sensor type, platform, and flight parameters. We implemented light detection and ranging (LiDAR) and photogrammetric aerial images received from unmanned aerial vehicles (UAV), gyrocopter, and aircraft. Field measurements were carried out indirectly using a Vertex clinometer and directly after felling using a tape measure on tree trunks. Indirect measurements resulted in an RMSE of 1.02 m and tend to underestimate tree height with a systematic error of −0.66 m. For the derivation of tree height, the results varied from an RMSE of 0.36 m for UAV-LiDAR data to 2.89 m for photogrammetric data acquired by an aircraft. Measurements derived from LiDAR data resulted in higher tree heights, while measurements from photogrammetric data tended to be lower than field measurements. When absolute orientation was appropriate, measurements from UAV-Camera were as reliable as those from UAV-LiDAR. With low flight altitudes, small camera lens angles, and an accurate orientation, higher accuracies for the estimation of individual tree heights could be achieved. The study showed that remote sensing measurements of tree height can be more accurate than traditional triangulation techniques if the aforementioned conditions are fulfilled.
Allelopathic Activity of Spearmint (Mentha spicata L.) and Peppermint (Mentha × piperita L.) Reduces Yield, Growth, and Photosynthetic Rate in a Succeeding Crop of Maize (Zea mays L.)

The inclusion of species with allelopathic activity in crop rotation systems may have benefits for crop management such as weed control, but less is understood about their wider impacts on succeeding crops. The main objective of this study was to investigate the effects of two allelopathic species (spearmint and peppermint) on growth, physiological characteristics, and yield of a following maize crop. Thus, field experiments were carried out at two sites, according to a randomized complete block design, while the examined treatments were: (a) fallow–fallow–maize crop rotation system (FFM), (b) spearmint–spearmint–maize crop rotation system (SSM), and (c) peppermint–peppermint–maize crop rotation system (PPM). Our results indicated that the inclusion of spearmint or peppermint in crop rotation systems negatively affect the growth of maize plants. The highest plant height was recorded for FFM rotation system where no allelopathic species were used. At both sites and for four sampling dates, the aboveground dry biomass was also affected by the implemented crop rotation system. In particular, dry biomass was significantly lower in the PPM and SSM crop rotation systems comparing to the FFM system, whereas there were no significant differences between these two crop rotation systems. Similar to the maize biomass, the highest values of photosynthetic rate, stomatal conductance, and relative chlorophyll content were observed for the FFM rotation system. Additionally, differences in grain yield were observed among the tested crop rotation systems. Grain yield ranged from 10,200 to 13,346 kg ha−1 and from 11,773 to 14,106 kg ha−1 at site A and B, respectively, while it was reduced by 16.54–23.58% and 12.16–17.83% in the SSP and PPM rotation systems comparing to the FFM system. In conclusion, our results indicate that the inclusion of peppermint or spearmint in crop rotation may inhibit plant growth and reduce grain yield of maize as successive crop, an effect that could be attributed to the allelopathic activity of spearmint and peppermint.
Planet-Disc Interactions and Early Evolution of Planetary Systems

The great diversity of extrasolar planetary systems has challenged our understanding of how planets form, and how their orbits evolve as they form. Among the various processes that may account for this diversity, the gravitational interaction between planets and their parent protoplanetary disc plays a prominent role in shaping young planetary systems. Planet-disc forces are large, and the characteristic times for the evolution of planets orbital elements are much shorter than the lifetime of protoplanetary discs. The determination of such forces is challenging, because it involves many physical mechanisms and it requires a detailed knowledge of the disc structure. Yet, the intense research of the past few years, with the exploration of many new avenues, represents a very significant improvement on the state of the discipline. This chapter reviews current understanding of planet-disc interactions, and highlights their role in setting the properties and architecture of observed planetary systems.
Family influence on early career outcomes in seven European countries

This note uses ECHP data to study the extent to which family characteristics affect the early career outcomes (earnings) of children in seven European countries: Germany, France, Italy, Greece, Spain, Portugal and Austria. The overall importance of family influence on earnings is assessed by computing earnings correlations between siblings using the eight waves of European Community Household Panel (ECHP) data on siblings. Portugal is the country with the highest sibling correlation in earnings, followed by Italy, Greece, Spain and France. Germany and Austria prove to have very low sibling correlations in earnings. The correlation increases when the same–gender sibling samples are used in almost all countries. These findings suggest that the earnings correlation of siblings of different genders is lower because of labor-market discrimination against females.
Integrated curation and data mining for disease and phenotype models at the Rat Genome Database

Abstract Rats have been used as research models in biomedical research for over 150 years. These disease models arise from naturally occurring mutations, selective breeding and, more recently, genome manipulation. Through the innovation of genome-editing technologies, genome-modified rats provide precision models of disease by disrupting or complementing targeted genes. To facilitate the use of these data produced from rat disease models, the Rat Genome Database (RGD) organizes rat strains and annotates these strains with disease and qualitative phenotype terms as well as quantitative phenotype measurements. From the curated quantitative data, the expected phenotype profile ranges were established through a meta-analysis pipeline using inbred rat strains in control conditions. The disease and qualitative phenotype annotations are propagated to their associated genes and alleles if applicable. Currently, RGD has curated nearly 1300 rat strains with disease/phenotype annotations and about 11% of them have known allele associations. All of the annotations (disease and phenotype) are integrated and displayed on the strain, gene and allele report pages. Finding disease and phenotype models at RGD can be done by searching for terms in the ontology browser, browsing the disease or phenotype ontology branches or entering keywords in the general search. Use cases are provided to show different targeted searches of rat strains at RGD.
Predicting circRNA–Disease Associations Based on Improved Collaboration Filtering Recommendation System With Multiple Data

With the development of high-throughput techniques, various biological molecules are discovered, which includes the circular RNAs (circRNAs). Circular RNA is a novel endogenous noncoding RNA that plays significant roles in regulating gene expression, moderating the microRNAs transcription as sponges, diagnosing diseases, and so on. Based on the circRNA particular molecular structures that are closed-loop structures with neither 5′-3′ polarities nor polyadenylated tails, circRNAs are more stable and conservative than the normal linear coding or noncoding RNAs, which makes circRNAs a biomarker of various diseases. Although some conventional experiments are used to identify the associations between circRNAs and diseases, almost the techniques and experiments are time-consuming and expensive. In this study, we propose a collaboration filtering recommendation system–based computational method, which handles the “cold start” problem to predict the potential circRNA–disease associations, which is named ICFCDA. All the known circRNA–disease associations data are downloaded from circR2Disease database (http://bioinfo.snnu.edu.cn/CircR2Disease/). Based on these data, multiple data are extracted from different databases to calculate the circRNA similarity networks and the disease similarity networks. The collaboration filtering recommendation system algorithm is first employed to predict circRNA–disease associations. Then, the leave-one-out cross validation mechanism is adopted to measure the performance of our proposed computational method. ICFCDA achieves the areas under the curve of 0.946, which is better than other existing methods. In order to further illustrate the performance of ICFCDA, case studies of some common diseases are made, and the results are confirmed by other databases. The experimental results show that ICFCDA is competent in predicting the circRNA–disease associations.
New insights into the development of cerebellar nuclei neurons in mice

i DEDICATION. iii ACKNOWLEDGEMENT . iv TABLE of CONTENTS . vi LIST of TABELS . xii LIST of FIGURES . xiii ABBREVIATIONS . xvi CHAPTER ONE: INTRODUCTION . 1 1.1 Overview of the central nervous system; structure . 2 1.2 Overview of the central nervous system; development . 4 1.3 Structure and function of the cerebellum . 5 1.4 Histology of the cerebellum . 12 1.5 The development of the cerebellum . 14 1.5. 1 Cerebellar primordium and isthmus organizer . 14 1.5. 2 Cerebellar germinal zones . 18 1.5. 2.1 Rhombic lip derived cells . 18 1.5. 2.2 Ventricular zone derived cells . 21 1.6 Neuronal migration in developing cerebellum . 26
Toxicity, developmental and histological effects of monoterpenes on peach fruit fly, Bactrocera zonata (Diptera: Tephritidae)

In the present study, the toxicity of three oxygenated monoterpenes, viz., (R)-carvone, (R)-camphor and (1R, 2S, 5R)-menthol was evaluated against the adults of the peach fruit fly, Bactrocera zonata (Saunders). Effects of these monoterpenes on oviposition, adult longevity and ovarian development have also been studied. The tested compounds revealed strong toxic effect against the adults of B. zonata. Nevertheless, (-)-carvone showed higher insecticidal activity than (1R, 2S, 5R)-menthol and (R)-camphor. Moreover, the tested monoterpenes induced significant reduction in female longevity at 20 and 50 mg/kg compared with control, with (-)-carvone being the most effective monoterpene. In addition, egg deposition was completely inhibited when the adults were treated with (-)carvone at 20 and 50 mg/kg, and (1R, 2S, 5R)-menthol and (R)-camphor at 50 mg/kg. Histological studies indicated that monoterpenes induced delay in the development of ovarioles of females that fed on artificial diet treated with 20 and 50 mg/kg of compounds. Changes, such as empty egg chambers; constricted germarium, vacant spaces between ovarioles and failure of oocyte formation were observed.
KEY METHODOLOGICAL FEATURES OF TUBULIN CYTOSKELETON STUDIES IN NODULES OF LEGUME PLANTS

and TR3 ( ipd3 ). It has also been shown that the preparation of sections of fixed nodules using a microtome with a vibrating blade can signifi- cantly improve the preservation of the structure of the tubulin cytoskeleton as compared to the use of fixed specimens embedded in Steedman’s wax and subsequent sectioning using a rotary microtome. It was found that the age of the nodules is also an important factor in the visualization of the tubulin cytoskeleton. To compare the patterns of tubulin cytoskeleton in different cell types, quantitative analysis is required. We found that the MicroFilament Analyzer (E. Jacques et al., 2013) with addi-tional scripts seemed well suited for checking the frequency of microtubules with a given orientation.
Isolation, Identification and Biological Activities of Endophytic Fungi from Egyptian Medicinal and Aromatic plants

Eight endophytic fungi were isolated from three Egyptian plants (Chenopodium album, Pelargonium graveolens and Malva parviflora). The fungi endophytes were identified by morphological and molecular methods as Fusarium chlamydosporum MG786540, Fusarium oxysporum MG786541, Alternaria alternata MG786542, Alternaria solani MG786543, Fusarium equiseti MG786544, Alternaria alternata MG786545, Stemphylium sp and Phoms sp. The endophytic fungi isolates exhibited antagonistic activities to phytopathogenic fungi by dual culture bioassay. A. alternata (MG786545) caused 32.58% and 44.68% growth inhibition of Fusarium oxysporum and Phytophthora infestance, respectively. F. equiseti (MG786544) caused 34.64% growth inhibition of Alternaria solani. Spore suspension of A. solani (MG786543), A. alternata (MG786545) and Stemphylium sp endophytes were tested for their herbicidal activity and plant growth promotion. A. solani (MG786543) at10 spore/ ml inhibited 33.1% of seed germination and reduced 31.3%, 23.1% of shoot and root growth of Lolium temulentum, respectively. Stemphylium sp at10 spore/ ml had the ability to enhance Triticum aestivum growth by increasing shoot and root lengths, and fresh and dry weights comparing to control.
Research of Polymorfic Locus (430 C/T) of CYP2c9/*2 Gene Distribution Frequencies among Patients with Epilepsy

The aim of the study was to establish the association of polymorphism (430 C/T) of the CYP2C9/*2 gene with the risk of developing pharmacoresistant epilepsy. The study included patients with pharmacoresistant and controlled forms of epilepsy. There was a tendency to associate the T allele and the heterozygous C/T genotype with the pharmacoresistant form of epilepsy.
The Wolf Cave Gabbro: alkaline olivine basaltic magmatism in Jersey, Channel Islands

An 8m thick coarse-grained olivine dolerite dyke, with well-developed chilled margins, trending NNE-SSW and occupying a steep-sided cove on the north Jersey coast, may show evidence for some flow differentiation. Texturally, the dyke is remarkable for the pronounced poikilitic relationship between the constituent mafic minerals. The textural and chemical relationships between the mineral phases are discussed. Rock and mineral chemistry indicate that magmatism was of alkaline-olivine basaltic type, contrasting markedly with most other hypabyssal basic magmatism in the island. A link with the prominent swarm of N-S basic dykes found on the adjacent North Brittany coast is postulated.
Natural killer cell function in chronic HCV infection

NK cells control viral replication through cytotoxicity and IFNγ production. These functions were assessed in chronic HCV infected patients undergoing treatment. Aboriginals have genetic polymorphisms that may enhance NK cell function suggesting more effective clearance of chronic HCV than Caucasians. NK cell function was similar at baseline between ethnicities. At 3 months of treatment, Caucasian had higher NK killing potential compared to Aboriginal patients. This had no effect on treatment outcomes. NK cell cytotoxicity negatively correlated with viral loads while NK IFNγ production, particularly within the CD56bright subset, positively correlated with viral load suggesting that viral loads control NK cells function through an unknown mechanism. NK cell killing reflect fibrosis, but not liver damage measured by liver enzymes. IFNγ production,by NK cells does not reflect fibrosis nor liver enzymes levels. Lastly, NK cell function does not associate with therapeutic outcomes of chronic HCV infection suggesting that they do not directly play a role in therapeutic clearance of HCV.
Multi-Dimensional Machine Learning Approaches for Fruit Shape Recognition and Phenotyping in Strawberry

Background Shape is a critical element of the visual appeal of strawberry fruit and determined by both genetic and non-genetic factors. Current fruit phenotyping approaches for external characteristics in strawberry rely on the human eye to make categorical assessments. However, fruit shape is multi-dimensional, continuously variable, and not adequately described by a single quantitative variable. Morphometric approaches enable the study of complex forms but are often abstract and difficult to interpret. In this study, we developed a mathematical approach for transforming fruit shape classifications from digital images onto an ordinal scale called the principal progression of k clusters (PPKC). We use these human-recognizable shape categories to select features extracted from multiple morphometric analyses that are best fit for genome-wide and forward genetic analyses. Results We transformed images of strawberry fruit into human-recognizable categories using unsupervised machine learning, discovered four principal shape categories, and inferred progression using PPKC. We extracted 67 quantitative features from digital images of strawberries using a suite of morphometric analyses and multi-variate approaches. These analyses defined informative feature sets that effectively captured quantitative differences between shape classes. Classification accuracy ranged from 68.9 – 99.3% for the newly created, genetically correlated phenotypic variables describing a shape. Conclusions Our results demonstrated that strawberry fruit shapes could be robustly quantified, accurately classified, and empirically ordered using image analyses, machine learning, and PPKC. We generated a dictionary of quantitative traits for studying and predicting shape classes and identifying genetic factors underlying phenotypic variability for fruit shape in strawberry. The methods and approaches we applied in strawberry should apply to other fruits, vegetables, and specialty crops.