Miracle-dz/UniFAR-FTUs huggingface dataset:
Tomen : A Plant monitoring and smart gardening system using IoT

Abstrac t — This paper automates plant monitoring and smart gardening using Iot in the Raspberry Pi platform. The main purpose of automation is to provide comfort to the people by reducing the manual work and to improve the overall performance of any system without the user interaction. The important parameters for the quality and productivity of plant growth are soil and air temperature, humidity, sunlight, soil moisture and pH. Information to the user about the plant health and growth may be provided to the user by continuously monitoring and recording these garden parameters. It provides a better understanding of how each parameter affects the growth of plants. All the sensors (Temperature, moisture, humidity, LDR, pH) used in this project interface with the Raspberry Pi controller. And this information about the garden can be directly monitored and controlled by the owner of the garden through his or her smart phone using IoT. A camera is provided in this system to monitor the garden through smart device. This smart gardening system will provide convenience and comfort to the user by sensing and controlling the parameters of the garden without their physical presence. Any android supported device can be used to install the smart gardening application. The software’s used are PHP, CSS, HTML, Apache 2, Python, and SQL. The CSS and PHP software’s are used to develop and design a web page. Apache 2 is used as a web server in Linux system. The Python environment provides the space for coding in Raspberry Pi. SQL is used in programming and designed for managing data held in a relational database management system. All data are stored in the database and can be retrieved at any time. This will help the user to understand the relation between the plant growth and the mentioned garden parameters.
Cerebral cortex damage induced by acute oral alcohol intake is associated with oxidative stress in Wistar rats ( Rattus norvegicus )

The prefrontal cortex undergoes functional and structural changes due to binge or chronic alcohol consumption. This study examines alcohol-induced cerebral cortex damage and the association with oxidative stress in an animal model. Twenty-four Wistar rats (12 males and 12 females) weighing 150g to 250g were divided into four groups, A, B, C and D according to their weights. The rats in groups B, C and D were administered with 2mls of 52.5%, 16.5% and 4.3% v/v aqueous alcoholic solution respectively for 21 days. While rats in group A (control group) were given distilled water only, for the same period. The brain of each rat was excised, weighed and fixed in 10% formal saline for histological analysis while others were immersed in ice cold 30% sucrose solution, homogenized and analyzed for superoxide dismutase, malondialdehyde and acetylcholinesterase activity. Results indicate chromatolysis of Nissl bodies, cortical necrosis, and uneven neuronal loss with varying range of vacuolations in the prefrontal cortices of the alcohol treated rats in a dosedependent manner when compared with the control group. Cerebral cortex damage due to acute oral alcohol intake is associated with oxidative stress. Keywords: Brain, cerebral cortex, alcohol, Wistar rats, oxidative stress
2 p core-level binding energies of size-selected free silicon clusters: Chemical shifts and cluster structure

M. Vogel,1 C. Kasigkeit,1,2 K. Hirsch,1,2 A. Langenberg,1,2 J. Rittmann,1,2 V. Zamudio-Bayer,1,2 A. Kulesza,3 R. Mitrić,3 T. Möller,2 B. v. Issendorff,4 and J. T. Lau1,* 1Institut für Methoden und Instrumentierung der Forschung mit Synchrotronstrahlung, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Straße 15, 12489 Berlin, Germany 2Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstraße 36, 10623 Berlin, Germany 3Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany 4Fakultät für Physik, Universität Freiburg, Stefan-Meier-Straße 21, 79104 Freiburg, Germany (Received 23 March 2012; published 25 May 2012)
Mapping the Peaks: Fitness Landscapes of the Fittest and the Flattest

Background Populations exposed to a high mutation rate harbor abundant deleterious genetic variation, leading to depressed mean fitness. This reduction in mean fitness presents an opportunity for selection to restore adaptation through the evolution of mutational robustness. In extreme cases, selection for mutational robustness can lead to “flat” genotypes (with low fitness but high robustness) out-competing “fit” genotypes with high fitness but low robustness—a phenomenon known as “survival of the flattest”. While this effect was previously explored using the digital evolution system Avida, a complete analysis of the local fitness landscapes of “fit” and “flat” genotypes has been lacking, leading to uncertainty about the genetic basis of the survival of the flattest effect. Results Here, we repeated the survival of the flattest study and analyzed the mutational neighborhoods of fit and flat genotypes. We found that flat genotypes, compared to the fit genotypes, had a reduced likelihood of deleterious mutations as well as an increased likelihood of neutral and, surprisingly, of lethal mutations. This trend holds for mutants one to four substitutions away from the wild-type sequence. We also found that flat genotypes have, on average, no epistasis between mutations, while fit genotypes have, on average, positive epistasis. Conclusions Our results demonstrate that the genetic causes of mutational robustness on complex fitness landscapes are multifaceted. While the traditional idea of the survival of the flattest effect emphasized the evolution of increased neutrality, others have argued for increased mutational sensitivity in response to strong mutational loads. Our results show that both increased neutrality and increased lethality can lead to the evolution of mutational robustness. Furthermore, strong negative epistasis is not required for mutational sensitivity to lead to mutational robustness. Overall, these results suggest that mutational robustness is achieved by minimizing heritable deleterious variation.
To B or not to B: Arsenophonus as a source of B-vitamins in whiteflies

Insect lineages feeding on nutritionally restricted diets such as phloem, xylem, or blood, were able to diversify by acquiring bacterial species that complemented the missing nutrients. These bacteria, considered obligate/primary endosymbionts, share a long evolutionary history with their hosts. In some cases, however, these endosymbionts are not able to fulfill all the nutritional requirements of their host, driving the acquisition of additional symbiotic species. Whiteflies, which feed on phloem, established an obligate relationship with Candidatus Portiera aleyrodidarum, who provides essential amino acids and carotenoids to the host. As many Whiteflies species harbor additional endosymbionts, they could provide their hosts with missing nutrients. To test this hypothesis, genomes of several endosymbionts from the whiteflies Aleurodicus dispersus, A. floccissimus and Trialeurodes vaporariorum were sequenced and analyzed. All three species were found to harbor an endosymbiont from the genus Arsenophonus, and the two former also host Wolbachia. A comparative analysis of the three Arsenophonus genomes revealed that although all of them are capable of synthesizing B-vitamins and cofactors, such as pyridoxal, riboflavin, or folate, their genomes and phylogenetic relationship vary greatly. Arsenophonus of A. floccissimus and T. vaporariorum belong to the same clade and display characteristics of facultative endosymbionts, such as large genomes (3 Mb) with thousands of genes, many pseudogenes, intermediate GC content, and mobile genetic elements (MGEs). In contrast, Arsenophonus of A. dispersus belongs to a different lineage and displays the characteristics of a primary endosymbiont, such as a reduced genome (670 kb) with 400 genes, 32% GC content, and no MGEs. However, the presence of 274 pseudogenes suggests that this symbiotic association is more recent than other reported hemipteran’s primary endosymbionts. Arsenophonus of A. dispersus gene repertoire is completely integrated in the symbiotic consortia, and the biosynthesis of most vitamins occurs in shared pathways with its host. In addition, Wolbachia have also retained the ability to produce riboflavin, FAD, and folate, and may have a nutritional contribution. Taken together, our results show that Arsenophonus have a pivotal place in whiteflies nutrition by their ability to produce B-vitamins, even if they diverge and/or go through a genome reduction process.
ENVIRONMENTAL IMPACT ASSESSMENT (EIA) OF ALTERNATIVE POTATO CROPPING SYSTEMS IN HAMADAN PROVINCE, IRAN

Potato is a staple food crop and a most important agricultural commodity in Hamadan Province, Iran. However, the province is facing such problems as water scarcity, nitrate pollution, and plant disease epidemics. This study explored the environmental impact assessment of potato cropping systems in Hamadan Province, Iran. To this purpose, 8 agri-environmental indicators were used for the EIAs of 4 potato cropping systems. These indicators included environmental potential risk indicator for pesticides, water use efficiency, nitrogen leaching, CO2 emission, energy use, biodiversity, golden potato cyst nematode, and land use. The 4 systems included traditional potato system, quasi-industrial potato system, industrial potato system, and government-promoted potato system and 5 groups of features were used to describe the mentioned systems: (1) irrigation methods; (2) seed placement; (3) machinery use; (4) agrochemical use; and (5) crops rotation. The results revealed that the traditional potato system had the lowest negative impact on the environment. Of the potato production systems studied, the government-promoted potato system, quasi-industrial potato system, and industrial potato system had successively fewer negative effects on the environment. Finally, some strategies are recommended for designing a new benchmark encompassing environmental thresholds using agri-environmental indicator scores and their relationships.
OTU Clustering: A window to analyse uncultured microbial world

– Clustering is the technique used to deal with higher amounts of data by partitioning the data into some groups based on some attributes. Clustering technique has many applications in different fields of science and technology. It is an important tool in genomics and metagenomics which performs taxonomic profiling of the microbial world by grouping 16S RDNA amplicon reads into clusters called as Operational Taxonomic Units (OTUs). With the help of Next Generation Sequencing (NGS) tools and clustering it has become easy for scientists to find the microbial diversities in different environments without culturing the microbes. Assignment of 16s rDNA sequences to the clusters called as OTUs is the main task in metagenomics algorithms and is also the main bottleneck for analysing microbial communities. Taxonomic profiling of 16S rDNA is an important step in Metagenomic pipeline analysis. There are several OTU clustering algorithms which clusters the amplicon reads of 16S rDNA into OTUs, each algorithm use a specific type of clustering technique to cluster the sequence reads. Some of the mostly used algorithms are Uclust, swarm, SUMACLUST, SortMeRNA, USEARCH. In this paper, we first give a brief overview of major clustering techniques and their types. Furthermore, we provide a comprehensive overview of OTU clustering algorithms
Laetiporus sulphureus – CHEMICAL COMPOSITION AND MEDICINAL VALUE

The higher fungi are a rich source of chemical compounds with multi-directional therapeutic and pro-health effects. This review summarizes the results of the most important chemical and biological studies of the fruiting bodies and the mycelial cultures of Laetiporus sulphureus . Numerous studies have demonstrated the antimicrobial, anticancer, cytotoxic, hypoglycemic anti-inflammatory and antioxidant activity of the extracts. Currently, only a few wood-decay fungi have practical use in medicine. Therefore it seems important to continue research on the effectiveness and safety of extracts and compounds of natural origin, including fungi, whose potential is not still used.
Vitellogenin in inflammation and immunity in social insects

Social insects, such as the honey bee and ants, form vast colonies that are only rivalled by human settlements. Living in dense, often stationary groups is prone to increase disease transmission. Yet, social insect queens and certain worker types can lead lengthy lives compared to the life span of most solitary insects. Social insects appear to have modified insulin/insulin like signaling pathway that regulates insect life history. This modification results in extremely elevated levels of the multifunctional lipoprotein vitellogenin in the individuals with longer life span. Vitellogenin is an egg-yolk precursor, but it also regulates caste-related behaviors in social insects, has shielding effects in inflammation and infection, and it is a mediator of transgenerational immunity. Here, we compile what is known about the life span and immune actions of vitellogenin and the evolution of this protein in the honey bee and ants. Recently we identified proteins homologous to vitellogenin in several Hymenopteran species, and showed that at least one of these vitellogenin-like proteins can have a protective role similar to vitellogenin in the honey bee. The newly identified vitellogenin homologs hint that the regulation of social insect life span can be more complex than thought before.
A study of Some Hormones and Antioxidant Systems Disturbances in Older Men

Ageing is a physiological phenomenon that manifested itself with disturbances of many homeostatic regulating mechanisms of the body . The present study was conducted and employed to investigate two major systems( hormones and antioxidant systems) that can be implicated in progress of aging . The total number of subjects included in the present study was fifty (50) healthy men and classified according to their ages into two groups, the first group included 25 younger men (control group) and their ages ranged between 21 to 30 years old whereas the second group included 25 older men and their ages were between 61 to 70 years old. Data obtained from this study indicated a significant decrease(p<0.05) in the levels of thyroid stimulating hormone (TSH) which is associated with marked elevation (p<0.05) of triiodothyronine(T3) and tetraiodothyronine(T4) of older men when compared with younger men. In regard to levels of cortisol and testosterone hormones were significantly decreased (p<0.05) in aged men when matched with their counterparts of younger men. Concerning concentrations of malondehyde (MDA) ,a final product of lipid peroxidation, confirmed a remarkable elevation (p<0.05) in older men compared to younger men and these results were associated with significant lowering (p<0.05) in the activities of antioxidant components including glutathione peroxidase (GPX), reduced glutathione (GSH) and catalase . In addition , there are no significant correlations(p>0.05) occurring among hormones( testosterone , T3) and glutathione peroxidase and of malondehyde . From these results ,one can be concluded that with ageing there are many disturbances and fluctuations of hypothalamic-adrenal and thyroid axis that accompanied with drop of essential antioxidant components that may be lead to suppress of defense against free radicals and the present study concluded that the changes occurring in studied hormones have not relations and effects on the antioxidant systems.
Design and Implementation of an Efficient Cluster based Feature Selection System for Medical Decease Prediction using SVM Classification

The classification of medical data has become an increasingly challenging problem, due to recent advances in medical mining technology. The Clinical organizations have collected large quantities of information about patients and deceases. However in a large dataset not all features contribute to represent the disease prediction, therefore reducing and selecting a number of sufficient features may improve accuracy of the classification. The objective of this Paper is to improve the classification accuracy of the SVM based on the output from RFE feature selection method that use Clustering approach to find the optimal set of features. This approach was applied on the Two UCI datasets namely, Wisconsin Breast cancer and Pima Diabetes in python Language. Experimental results showed that using the cluster based feature selection method with SVM algorithm achieved higher classification accuracy than without feature selection SVM classifier. In our result show that features selection improve significantly the classifier performance.
Slow and unsteady: growth of the Australian eastern long-necked turtle near the southern end of its natural range

Abstract. Knowledge of growth rates and maturation times of freshwater turtles is important in assessing population viability. I analysed growth of Australian eastern long-necked turtles (Chelodina longicollis) from individual capture–recapture records spanning periods of up to 17 years for a population in Gippsland, Victoria, close to the high-latitude end of the species’ natural range. Juvenile growth was rapid and similar among individuals but adult growth was usually slow, highly variable among individuals and erratic within individuals over time. In addition, asymptotic body lengths were disparate among individuals for both males and females. Von Bertalanffy growth models fitted separately to males plus unsexed juveniles and females plus unsexed juveniles performed better than logistic models but tended to underestimate growth rates for very small and very large turtles and overestimate growth for medium-sized individuals. Sexual maturity was estimated to be achieved at 10 years in males and 16 years in females, which is late compared with most estimates for other populations of C. longicollis and for other turtle species in south-eastern Australia. The high variability of individual growth in this population makes age estimation from body size unreliable beyond the first few years of life.
LUMINESCENCE OF THE BLACK SEA MICROSCOPIC FUNGI CULTURES

We studied for the first time luminescence characteristics of the some micromycetes, isolated from the bottom sediments of the Black sea from the 27 m depth. Luminescence parameters were registered at laboratory complex “Svet” using mechanical and chemical stimulations. Fungi cultures of genera Acremonium, Aspergillus, Penicillium were isolated on ChDA medium which served as control. Culture of Penicillium commune gave no light emission with any kind of stimulation. Culture of Acremonium sp. has shown luminescence in the blue – green field of spectrum. Using chemical stimulation by fresh water we registered signals with luminescence energy (to 3.24 ± 0.11)·108 quantum·cm2 and duration up to 4.42 s, which 3 times exceeded analogous magnitudes in a group, stimulated by sea water (p < 0.05). Under chemical stimulation by ethyl alcohol fungi culture luminescence was not observed. Culture of Aspergillus fumigatus possessed the most expressed properties of luminescence. Stimulation by fresh water culture emission with energy of (3.35 ± 0.11)·108 quantum·cm2 and duration up to 4.96 s. Action of ethyl alcohol to culture also stimulated signals, but intensity of light emission was 3–4 times lower than under mechanical stimulation. For sure the given studies will permit not only to evaluate contribution of marine fungi into general bioluminescence of the sea, but as well to determine places of accumulation of opportunistic species in the sea.
Humane Slaughter of Carp – A Comparison between Three Stunning Procedures

Fish welfare at slaughter is an area of considerable scientific and commercial importance during the last decade. The aim of this study was to evaluate the effect of three stunning procedures on stress and meat quality of common carp. The experimental fish were separated in three groups and stunned by percussion (Group PS), electricity (Group ES) or asphyxia (Group AS), followed by decapitation. Blood cortisol and glucose concentrations were measured as stress indicators, whereas drip loss was used as meat quality parameter. The lowest glucose concentration (3.86±1.26 mmol/L) and drip loss (2.02±0.42%) were observed in Group PS. On the contrary, Group AS showed the highest results (11.34±3.07 mmol/L and 3.22±0.75% for blood glucose and drip loss, respectively), whereas the electrically stunned carp took an intermediate position (6.05±1.29 mmol/L and 2.29±0.43%). We conclude that percussive stunning leads to considerable reduction of stress at slaughter and better meat quality (lower drip loss), whereas asphyxia is unacceptable method due to the strong stress reaction and increased drip loss. Electrical stunning can be an effective method for stunning carp, but requires improvements of the electrical device to eliminate the repeated current application.
New and Bioactive Compounds from Penicillium concentricum, an Endophytic Fungus of the Liverwort Trichocolea tomentella

ii Acknowledgments. v Vita . vii Fields of Study . viii List of Tables . xvii List of Figures . xix List of Schemes . xxviii List of Abbreviations . xxix CHAPTER 1: OVERVIEW OF BIOACTIVE NATURAL PRODUCTS AND POTENTIAL PENICILLIUM-DERIVED CLINICAL AGENTS . 1 1. Drug discovery from natural products . 1 1.1. Drugs and lead compounds from plant sources . 2 1.1.1. Podophyllotoxin . 2 1.1.2. Vinca alkaloids. 3 1.1.3. Paclitaxel and docetaxel . 3 1.1. 4. Camptothecin, topotecan and irinotecan . 3 1.2. Drugs and lead compounds from marine sources . 4 1.2. 1. Cytarabine (Ara-C) and vidarabine (Ara-A) . 5 1.2. 2. Ziconotide . 5 1.2. 3. Bryostatin-1. 5 1.2. 4. Trabectedin . 6 1.2. 5. Eribulin mesylate . 6 1.3. Drugs and lead compounds from microorganisms . 7 1.3. 1. Epothilones . 8 1.3. 2. Cephalosporins . 8 1.3. 3. Acarbose . 8 1.3. 4. Anthracylines . 9 1.3. 5. Cyclosporines . 9 1.3. 6. Pneumocandins . 9
Interactions between Trichoderma harzianum and defoliating Verticillium dahliae in resistant and susceptible wild olive clones

I. Carrero-Carr on, M. B. Rubio, J. Ni~ no-S anchez, J. A. Navas-Cort es, R. M. Jim enez-D ıaz, E. Monte and R. Hermosa* Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, R ıo Duero 12, Campus de Villamayor, 37185 Salamanca; Departamento de Agronom ıa, College of Agriculture and Forestry (ETSIAM), Universidad de C ordoba, Alameda del Obispo s/n, 14080 C ordoba; and Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Cient ıficas (CSIC), Avda. Men endez Pidal s/n, 14080 C ordoba, Spain