Miracle-dz/UniFAR-FTUs huggingface dataset:
The Comparison of Agricultural Knowledge and Information Systems (Akis) For Adopters and Non-Adopters of Good Agricultural Practices in Bafra District of Samsun, Turkey

The purpose of the study is to compare Agricultural Knowledge and Information Systems (AKIS) for adopters and non-adopters of Good Agricultural Practices (GAPs) in the Bafra district of Samsun, Turkey. The main materials of this study are the data obtained from a survey and interview with adopters and non-adopters of GAPs in Bafra district. The research data were collected from 77 farmers contained both adopters and non-adopters of GAPs. Statistical analysis, such as Chi-square and t-test was used. The study results presented the socio-economic characteristics of farmers. There was a significant difference between adopters and non-adopters of GAPs, according to household size, organizational membership, farm size, livestock and crop production. Meanwhile, the information sources such as a district agricultural manager/personnel, adviser of the farmers’ union association (GAPs) and pesticide/fertilizer dealers were preferred the main sources of agricultural information for adopters of GAPs. However, it recommended that information sources like research institute, university and cooperatives needs to be improved by strengthening their way of information dissemination. In terms of usefulness of AKIS for this study, it seems that this system was insufficient to analyze this study. Even though the functions of this system are essent ial elements, they are insufficient for establishing a network of complex innovation-oriented institutional arrangements. In the future, this study suggests to analyze GAPs it needs to use Agricultural Knowledge and Innovation System (AKIS) approach, because this system have many interaction networks that can facilitate the researchers to reach the innovation easily to the intended farmers.
Nest site selection patterns of a local Egyptian Vulture Neophron percnopterus population in Turkey

We report the size and density of an Egyptian Vulture population in Turkey and provide insight into its nest site selection patterns. The study was carried out at Beypazari (Turkey), holding one of the densest Egyptian Vulture populations (six pairs per 100 km 2 ) in the Western Palearctic. Random Forests analysis revealed that human impact was a potential factor governing the distribution of nest sites, as the pairs clearly preferred to breed away from nearby villages, towns or roads. Utilisation of elevation gradient and aspect was similar to other studied populations, with the probability of nesting increasing at lower altitudes and for south-facing cliffs. Nearest-neighbour distance between nests was about 1.5 km, indicating territorial behaviour when choosing nest sites at the local scale. Our findings provide guidance for nature conservation NGOs and related government bodies for their various actions including designation of Important Bird Areas, regulation of mining practices and preparation of environmental impact assessments.
First description of the nest, egg, and nestling of Multicolored Tanager (Chlorochrysa nitidissima)

ABSTRACT The genus Chlorochrysa, with three species: C. phoenicotis, C. calliparaea, and C. nitidissima, is distributed throughout the Andes from Colombia to northern Bolivia inhabiting mossy cloud forests between 900–2400 m. We describe for the first time the reproductive biology of the C. nitidissima and the use of different nesting sites. This study was conducted at three sites located on the eastern slope of the Western Cordillera in Colombia. The shallow cup nests were built with small thin sticks and dry bamboo leaves, placed inside hanging mossy clumps located on horizontal branches or inside abandoned dome-shaped songbird nests. We report a clutch size of one white, oval egg with brown spots, which measured 21.45 × 15.0 mm and weighted 2.3 g (n = 2). The average nestling period was 23 days, and the nestling growth rate (K) was, on average, 0.29. Finally, these results could be used to implement plans for the conservation of this endemic and critical endangered species.
Soil biota suppress positive plant diversity effects on productivity at high but not low soil fertility

Plant community productivity commonly increases with increasing plant diversity, which is explained by complementarity among plant species in resource utilization (complementarity effect), or by selection of particularly productive plant species in diverse plant communities (selection effect). Recent studies have also shown that soil biota can drive the positive plant diversity–productivity relationship by suppressing productivity more in low‐ than in high‐diversity plant communities. However, much remains unknown about whether soil fertility plays a role in determining how soil biota affect plant diversity–productivity relationships. We hypothesized that under high soil fertility conditions, negative soil biota effects dominate, which reduces plant monoculture biomass more than that of high‐diversity plant communities. Conversely, under low soil fertility conditions, we hypothesized positive soil biota effects dominate, which facilitates plant resource partitioning and enhances community‐level biomass in high‐diversity plant communities. Hence, we expected positive plant diversity–community productivity relationships under low and high soil fertility conditions but caused by different mechanisms. We tested these hypotheses using woody seedlings and set up plant assemblages with four species richness levels (one, two, four and eight species), and grew them in sterilized and unsterilized (sterilized soil + living soil inoculum) soils at two nutrient levels (low versus high fertility). We found that at high fertility negative soil biota effects dominated and suppressed plant community biomass more in high‐diversity plant communities than in monocultures, resulting in reduced complementarity effects of diverse plant communities and a non‐significant plant species richness–community biomass relationship in unsterilized soil. Whereas at low fertility soil biota had net neutral to positive effects on plant community biomass but the beneficial effects did not increase with increasing plant species richness. Instead, soil biota neutrally affected the positive plant species richness–community biomass relationship, presumably due to non‐specific effects of beneficial soil biota. Synthesis. Soil biota and soil fertility interactively determine plant species richness–community biomass relationships. Moreover, soil biota modulate the complementary resource use among plant species. These findings suggest that environmental context plays an important role in determining whether and how soil biota generate the biodiversity–productivity relationship. Future studies would benefit from revealing the mechanisms underlying the interactive effects of soil biota, soil fertility, and plant diversity on ecosystem functioning.
Genetic diversity and climate adaption in "Arabidopsis lyrata"

Applied fields of research such as the one on global climate change has heightened the interest to understand the adaptive evolution process and limits to adaptive evolution. Progress in the field depends on knowing of the traits under selection and their genetic variation. The goal of my PhD thesis was to generally assess genome-wide single nucleotide polymorphism (SNP) diversity across an entire species geographic distribution and to detect SNPs and genes linked to adaptation to climatic variables and substrate type within the herbaceous plant Arabidopsis lyrata subsp. lyrata (A. lyrata). For this work, DNA of 52 populations covering the whole geographic range of A. lyrata were analyzed by pooling DNA of multiple individuals of each population, sequencing the pools (Pool-seq) and revealing population SNP frequencies. In the first chapter the wet-lab protocol of Pool-seq and the bioinformatics pipeline were tested. In the second chapter the genetic diversity of different genomic regions was analyzed to trace the history of the populations of A. lyrata. In the third chapter, the climatic variables that determine the ecological niche limits of the species distribution were defined. And, in the fourth chapter the SNP frequencies were associated with climatic variables and substrate type to detect the genomic regions involved in adaptation to climate and edaphic conditions, highlighting potentially relevant genes and pathways.
Exosomes and miRNAs in disease pathogenesis and opportunities for molecular targeting

Exosomes/extracellular vesicles (EVs) are cell-derived mixed-populations of vesicles released by almost all cells into the intercellular microenvironment, ending up in the circulation. Exosomes contain proteins, RNAs and lipid molecules reflecting the status of the parental cell at the time of release, making them promising candidates for biomarker discovery. The contents of exosomes are protected by a lipid bilayer, leading to better stability of bio-macromolecules. Recent evidence suggests a novel role for exosomes as conveyors of information among cells and across tissues, through horizontal transfer of proteins, lipids, and nucleic acids. Exosomes have been the subject of numerous research in recent years; however, their roles still have to be identified in the pathogenesis of different diseases. MicroRNAs (miRNAs) are small (18-25 nucleotide long) non-coding RNAs which play pivotal roles in the gene expression process and it is estimated that about one third of the human genome is controlled by miRNAs. miRNA regulatory processes have been found to influence many essential biological pathways, such as cellular development, proliferation, apoptosis, and cellular signaling. A great proportion of miRNAs has been reported to be associated with the exosome function of different biofluids. The aim of this research was to elucidate the role of exosomes/EVs as well as miRNAs in the pathogenesis of different diseases, including alcoholic liver disease, hepatitis C, and cancer. This knowledge may lead to the development of novel molecular diagnostic approaches, as well as innovative drug delivery modalities for small RNA-targeted therapy. My research resulted in a) the establishment of new methods and approaches to the study of exosomes/EVs, as well as comparative literature on the efficacy of several isolation and characterization techniques. b) identification of the role of exosomes and miRNA-122 in the cross talk between hepatocytes and immune cells in alcoholic liver disease c) identification of the role of exosomes in HCV pathogenesis, including the potential of molecular therapies based on miRNA and exosome targeting in vitro and in vivo d) understanding the bio-distribution of exosomes and miRNA in an in vivo murine model and f) exploring the utility of miRNA and exosomes in biofluids in cancer biomarker discovery.
Effect of small mapping population sizes on reliability of quantitative trait locus (QTL) mapping

A limitation of quantitative trait loci (QTL) mapping is that accuracy of determining QTL position and effects are largely determined by population size. Despite the importance of this concept, known as the "Beavis effect there has generally been a lack of understanding by molecular geneticists and breeders. One possible explanation for this may be that this concept has been explored by using computer simulations and that these findings may not be clearly understood. In this study, we demonstrated the effect of population size on the accuracy of determining QTL positions and effects in a simple and concise manner. Simulated data was generated for extremely large mapping populations (n = 1000) and smaller mapping populations (n = 94 or n = 190) were obtained by random sampling. Populations were defined to segregate for either three or five QTLs with heritabilities of h 2 = 0.75 or h 2 = 0.50. When small populations were used, errors were detected in determining QTL positions, and in some cases, QTLs were not detected (that is, false negatives) especially when h 2 = 0.50. More importantly, R2 values were overestimated or underestimated. Composite interval mapping was more reliable for detecting QTLs compared to simple interval mapping. These findings have important implications for QTLs which are selected in breeding programs via marker-assisted selection. Key words : Quantitative trait loci (QTL) mapping, Beavis effect, population size, confidence intervals, marker-assisted selection.
A positive valorization way of sludge compost: recycling it to turfgrass instead of partial conventional substrate

ABSTRACT Sludge is known to be a suitable amendment material to substrate used for horticultural products because of its soil-like physical and nutritional characteristics. Replacing a portion of substrate used for turfgrass with sludge has been shown to have positive effects, such as improved biomass productivity, root length and density as well as persistence of vegetation cover. Although the effects of adding sludge compost to turfgrass substrate have been widely investigated, the characteristics of commercial qualitative indicators of the generated turfgrass, substrate and sod products have been reported separately or incompletely. Therefore, this study was conducted to assess the effects of recycling composted sludge to turfgrass on commercial qualitative indicators. The results revealed positive and negative effects of sludge compost on the investigated parameters, with some factors showing positive responses to addition of sludge compost to a threshold, above which negative responses were observed. For example, water-holding porosity, biomass and chlorophyll content increased in response to sludge amendment, but increased salinity and weed density, as well as decreased tensile strength and intactness were also observed. Overall, sludge compost in moderate dose is a suitable material for replacement of partial turfgrass substrate, but excessive dose results in adverse effects.
Direct seeding of 16 Brazilian savanna trees: responses to seed burial, mulching and an invasive grass

Aims: To address whether seed and seedling functional traits have a significant effect on germination rates and seedling survival in direct-seeding restoration efforts. We tested the hypotheses that: (1) seed burial only favours the emergence of round seeds; and (2) straw mulching improves soil moisture and prevents the emergence of the invasive grass Urochloa decumbens, promoting the establishment of native tree seedlings.
EPIDEMIOLOGICAL INVESTIGATION ON DUCK SALMONELLOSIS IN SOME SELECTED AREAS OF BANGLADESH

The study was performed with a view to collect epidemiological data to proper control of Duck Salmonellosis in Bangladesh. A total of 12 small to medium sized duck farms and 28 individual households were visited for data collection. On the basis of history and clinical signs and as per the information provided by the farmers the prevalence rate of Duck Salmonellosis was recorded as 38.1% and the P value was calculated as 0.003 (p<0.01) which was noted as highly significant. Based on tentative occurrences of Duck Salmonellosis as per information taken from the structured questionnaire a total of 120 fecal samples were collected from apparently healthy and diseased ducks on the basis of age, sex, season, location and health status. The isolated bacteria were identified by studying cultural properties on different selective media, biochemical tests, and finally by PCR. The test results of cultural and biochemical exhibited the typical characteristics of bacteria. On the basis of their cultural and biochemical characteristics it was found that among 120 fecal samples 32 (26.67%) were found to be positive for Salmonella and the P value was recorded as 0.0019 (p<0.01) which was also considered as highly significant. In motility test Duck Salmonella were identified as motile and all tested Duck Salmonella showed indole and VP test negative with MR test positive. In PCR reaction, the organism was further confirmed as Salmonella species using the SAL-G primer. Results of antibiotic susceptibility test shows that the selected isolated Salmonella were highly sensitive to ciprofloxacin and azithromycin, intermediate sensitive to tobramycin and gentamicin and resistant to Oxacillin.
Response of some beneficial insect species to colored sticky traps in citrus

Colored sticky traps have been commonly used for the sampling of detrimental insect species worldwide. However, there is no information about the catches of non-target insects such as predaceous and pollinating insects by colored traps. In this study, trials with colored sticky traps (white, yellow, blue and green) in mandarin cv Okitsu (Satsuma) trees were carried out during 2011 and 2012 in Adana Province, Turkey. Colored plates were hung, at about 1.7 m above ground level, from the exterior canopy of the selected trees and were positioned to the four cardinal directions. A total of 15 beneficial insect species were captured on various colored plates. Yellow and green traps were more attractive to the coccinellid, Oenopia conglobata (L., 1758), than the other colored traps. Significantly more of the predaceous hoverfly, Episyrphus balteatus (De Geer, 1776) and the honey bee, Apis mellifera L. , 1758 were obtained on white traps. Green and blue traps were the least attractive to A. mellifera . The yellow, blue and green traps hung on the west side of the trees captured significantly more beneficial insects, but white traps hung on the south sides of outer branches trapped considerable numbers of E. balteatus and O. conglobata . White and yellow sticky traps may provide more ecological data for beneficial insects.
An Analysis of Forest Management Non-Conformities to FSC Standards in Different European Countries

The purpose of this study was to assess the most frequent non-conformities identified in different European countries in the processes of forest management certification according to FSC standards. A total of 31 active certificates from five countries (Bosnia and Herzegovina, Estonia, Romania, Slovenia and the United Kingdom) were analysed, including all active certificates (as of 1st of June 2014) from three countries along with a sample of 13 FSC certificates issued in the UK and one certificate covering 95% of the certified forest area in Slovenia. 253 non-conformities in relation to FSC standard requirements were identified as formulated by the audit teams and the most frequently identified non-conformities in the certification process were those related to Principle 6 - Environmental impact (34%), Principle 4 - Community relations and workerâ€™s rights (17%) and Principle 8 - Monitoring and Assessment (13%). A slight positive correlation was noticed between the FSC certified area and the total number of non-conformities, with a closer link in the case of Principle 9 - Maintenance of high conservation value forests, and Principle 4. The non-conformities related to Principles 4, 6 and 9 appeared to be significantly influenced in occurrence by country development; less often in the UK compared with the other four countries.
Control of some sugar beet pathogens using β-alaninein vitro and in vivo

Beta (β) -alanine is a naturally occurring non-proteingenic amino acid. β-alanine suppressed the growth activities of sugar beet pathogens Rhizoctonia solani Kuhn (AG2-2), Sclerotium rolfsii Sacc. and Fusarium solani (Mart) Sacc.when applied to the growth medium at different concentrations (12.5-100 Âµg/ ml). When applied to soil, β-alanine suppressed fungal infection of two sugar beet cultivars Raspoly and TOP. In absence of β-alanine, R. solani was the most virulent against cvs. Raspoy and TOP. Virulence was directly correlated with the activities of cell wall-degrading enzymes produced by these pathogens in vivo. Reduced virulence of R. solani, S. rolfsii and F. solani under β-alanine stress was due to decreased inoculum potential of the pathogens as result of the reduction of the cell wall-degrading enzymes. Growth parameters including emergence, plant length and dry weight of sugar beet were significantly increased at all investigated β-alanine concentrations . The infection rate was significantly decreased with increasing β-alanine stress, whereas the total sugar reducing values (TRV) was significantly increased in the tested sugar beet cultivars. The results indicated the possibility of the tested amino acid for protection of sugar beet plant cultivars against fungal infection.
Synthesis of allitol from D-psicose using ribitol dehydrogenase and formate dehydrogenase

Purpose: To synthesize allitol from D-psicose by a combination of novel ribitol dehydrogenase (RDH) and formate dehydrogenase (FDH) under optimised production conditions. Methods: RDH and FDH genes were cloned and introduced into pET-22b(+) vectors for expression in Escherichia coli to produce the corresponding enzymes. The effects of temperature, pH, shaking velocity (75, 100, 125, and 150 rpm), and shaking type (horizontal and vortex) were optimised to maximise the production yield of allitol. The final product was purified and subjected to nuclear magnetic resonance (NMR) spectroscopy, infrared (IR) spectrometry, and liquid chromatography-mass spectrometry (LC-MS) to confirm its structure. Results: The optimal pH and temperature for the reaction were 7.5 and 40 °C, respectively. The results revealed that allitol yield significantly increased with increase in reaction shaking velocity and reached a maximum yield of 95.60 ± 0.54 % at 150 rpm shaking velocity after 6 h of reaction. When the reaction was run under horizontal shaking, allitol yield increased from 100.00 ± 6.05 (without shaking) to 124.20 ± 9.70 %. Twenty milligrams of D-psicose were successfully reduced to allitol under optimum conditions with a high production yield of 16.7 ± 0.62 mg after 6 h. No by-products were formed during or after the reaction. The produced allitol had a purity of 95 %, and its structure was confirmed by HPLC, IR, LCMS, and NMR spectral analyses. Conclusion: Using D-psicose as a substrate, allitol with 95 % purity was successfully produced by the combination of novel RDH and FDH. Keywords: Allitol, Ribitol dehydrogenase, Formate dehydrogenase, D-Psicose, Providencia alcalifaciens
Modeling the Mammalian Ovary: A Cell-based Computational Model of Early Ovarian Development in Mice and Preliminary Data for A Model of Folliculogenesis in Rhesus Monkeys.

Proper development and function of the ovary is vital for female mammalian reproduction. Development of the ovary plays an important role in the formation of the ovarian follicle reserve, which governs the female reproductive lifespan. One of the main functions in the developed ovary is the maturation of ovarian follicles, a process known as folliculogenesis. Exposure to reproductive toxicants and reproductive diseases can cause adverse reproductive outcomes, possibly leading to infertility. Computational modeling is a cost-effective, efficient, and humane method for studying the effects of disease and toxicant exposure to ovarian development and function. Understanding normal development and function of the ovary can aid in the study of the effects from disease and toxicant exposure. Computational models of normal ovarian development and function can be utilized as a baseline for modeling toxicity and disease, to make predictions and hypotheses about ovarian physiology, and as a learning resource. Despite its importance in reproduction, a model for mammalian early ovarian development does not exist. Likewise, a model of the preantral stages of folliculogenesis does not exist. The purpose of this thesis was to construct a model of early ovarian development, spanning the origin primordial germ cells to formation of primordial follicles, in mice and to gather data to be used for the development of a model of the preantral stages of folliculogenesis, the generation of secondary follicles from primordial follicles, in rhesus macaque. Early ovarian development was chosen to be modeled in mice due to the abundance of data in the literature compared to other mammalian species. Data gathering for a model of the preantral stages of folliculogenesis was undertaken in rhesus macaques due to the fidelity