Miracle-dz/UniFAR-FTUs huggingface dataset:
WEED DETECTION IN WHEAT CROP USING UAV for PRECISION AGRICULTURE

Agriculture plays a significant role in overall GDP of any country. So, there are several efforts those are being made to develop and increase the crop yield. In any of crop, weed i.e. (unwanted crops) is the major concern that may leads to poor production of crop. Therefore, an automatic crop monitoring system is required to monitor the weed. This system will help the farmers to monitor the crops, in gradual fashion, once it has been cultivated. Then specific Vegetation Index (VI) would be applied to locate all green portions in the image that would be part of early wheat crop or weed patches. We used Object Based Image Analysis (OBIA) algorithm to detect the weed patches in RGB and Multispectral imagery captured by UAV at 30-60 m altitude is used to acquire the images of wheat fields. Once the weed patches successfully identified from between the crop rows and within the crop rows then connected component-based classification technique is used that successfully classify the detected object either the object is related to weed patches or actual crop. The core objective of this work is to lessen the human involvement and to introduce the latest techniques and computation technology, peculiarly to identify the weed patches within the crop rows as well as between the crop rows in wheat field. Moreover, exploitation of UAV technology is also the core objective that will significantly provide the site specifically herbicides spraying
Media literacy and cigarette smoking in Hungarian adolescents

Objective: To assess smoking media literacy in a sample of Hungarian youth and to determine its association with current smoking and susceptibility to future smoking. Design: Quantitative cross-sectional survey. Setting: Four elementary and four high schools in Mako, Hungary. Method: A survey form was administered in regularly-scheduled classes to 546 eighth- and twelfth-grade students that included the smoking media literacy (SML) scale and items assessing cigarette use. Logistic regression was used to examine the relationship of smoking media literacy with current smoking, and also separately for susceptibility to smoking in the future, as dependent dichotomous variables. Results: Smoking media literacy was lower among the Hungarian adolescents than what has been previously reported in American adolescents. Multivariate logistic regression analysis results showed smoking media literacy to be associated with reduced risk of current smoking status at a similar level to that found in American adolescents. However, unlike previous research in American adolescents, smoking media literacy and susceptibility to future smoking was not associated. Reduced smoking may be most associated with the representation-reality domain of media literacy, which relates recognition of what is portrayed in the media with reality. Conclusion: Based on this study’s findings, prevention and health promotion planners in Hungary should consider media literacy training as a possible addition to smoking prevention efforts in community- and school-based efforts.
The effects of sex on extinction dynamics and evolutionary rescue of Chlamydomonas reinhardtii depend on the rate of environmental change

The continued existence of sex despite many costs it entails still lacks an adequate explanation. Previous experimental studies demonstrated that sex enhances the rate of adaptation in changing environments. To the best of our knowledge, no experimental study that investigated the effects of sex on adaptation has manipulated the rate of environmental change, which is negatively correlated with the probability of population survival. Since the patterns of adaptation (adaptive walk) depend on the rate of environmental change, the overall effects of sex may also be altered by this factor. To investigate the interplay of sex and the rate of environmental deterioration, we carried out a long-term selection experiment with a unicellular alga (Chlamydomonas reinhardtii), by manipulating mode of reproduction (asexual or sexual populations) and the rate of environmental deterioration (an increase of salt concentration). We monitored both the population size and extinction dynamics and estimated the probability of evolutionary rescue. We detected a faster decline of population size in the asexual group relative to both the obligate sexual and facultative sexual group, irrespective of the rate of environmental deterioration. The results revealed significant interaction between mode of reproduction and the rate of environmental deterioration on extinction rate of experimental populations. Obligate sexual reproduction was advantageous under the intermediate rate of environmental deterioration, while facultative sexuality was favoured under the high rate of environmental deterioration. The populations within the obligate sexual group were most likely to adapt to grow in conditions lethal for the ancestral populations, irrespective of the rate of environmental deterioration. To the best of our knowledge, this is the first study which indicates that different modes of sexual reproduction will be beneficial (slower extinction rate) at different rates of environmental deterioration and that obligate sexuality maximizes the probability of adaptation irrespective of the rate of environmental deterioration.
Transcriptome Analyses of Ascovirus Genome Expression in Lepidopteran Larvae and Host Responses

Author(s): Zaghloul, Heba Ahmed Hamed Mohamed | Advisor(s): Federici, Brian A. | Abstract: Ascoviruses, family Ascoviridae, are large, enveloped ds DNA viruses that mainly attack lepidopteran larvae of the family Noctuidae causing a chronic, but fatal disease. Their cytopathology differs from other viruses by destroying the nucleus, some species using a caspase, followed by cleavage of the cell into numerous viral vesicles, where most virions are produced. Cell cleavage resembles apoptosis, but differs markedly because mitochondria are not destroyed but rescued by ascoviruses, providing energy for replication and membrane synthesis for viral vesicles and virion envelopes. Ascovirus transmission is also unique in that virions are vectored to hosts on the ovipositor of parasitic wasps. In my research, I used molecular techniques to determine genomic expression patterns underlying ascovirus cytopathology in larvae for two ascoviruses, the Spodoptera frugiperda ascovirus (SfAV) and Trichoplusia ni ascovirus (TnAV). Specifically, through in vivo transcriptome studies, including RNA-Sequencing, qRT-PCR, manual genome curating and bioinformatic analysis, I determined three temporal classes for SfAV and TnAV genes; early, late, and very late. In SfAV, three proteins that inhibit apoptosis were synthesized early, whereas the caspase was synthesized very late, which correlates with apoptotic-like events resulting in vesicle formation. I identified 15 SfAV bicistronic and tricistronic messages, and similar transcripts in TnAV, indicating multi-cistronic transcripts are common in ascoviruses, and may regulate transcription or translation. Analyses of viral vesicle transcripts from Trichoplusia ni hemolymph revealed much higher viral genome expression than in the fat body, epidermis and tracheal matrix, showing larval blood is important for virus reproduction. Host responses to SfAV infection in Spodoptera frugiperda larvae showed mitochondrial gene expression was similar to controls or upregulated slightly during vesicle formation. Interestingly, few cytoskeleton genes known to encode motor proteins were upregulated despite mitochondrial involvement in vesicle formation. Analysis of antimicrobial peptides genes showed several where highly upregulated, as much as 32-fold, for example, moricin and gloverin, whereas innate immunity genes of the Toll, melanization, and phagocytosis pathways were activated only moderately by infection. Phenoloxidase and Toll negative regulators increased 15-fold and 3-fold, respectively. Therefore, conserving mitochondria while balancing immunity gene inducers and repressors may explain the chronic nature of ascovirus diseases.
Postharvest Treatment of Tribolium confusum Jacquelin du Val Adults with Commercial Biopesticides

Within the context of the harmful side-effects of chemical pest control applications, the present study investigated the insecticidal effect of three commercial biopesticides, the fungal Metab (Beauveria bassiana, Metarhizium anisopliae) and Lecan (Lecanicillium lecanii), as well as raw zeolite, against Tribolium confusum Jacquelin du Val (Coleoptera: Tenebrionidae), also known as the confused flour beetle. To this end, we sprayed Tribolium confusum adults with suspensions of the said biopesticides, at three different dosages (250 ppm, 500 ppm, and 1000 ppm) on Avena sativa L. and Linum usitatissimum L. hull and no hull seeds. The data were analyzed in terms of three- and four-way ANOVA model, and the overall survival was determined while using the Kaplan–Meier method. The mortality of Tribolium confusum adults was recorded and analyzed in correlation with the following parameters: dose, product (seed), days, and treatment as factors. At the end of the experiment, all of the biopesticides were effectively pathogenic, but there was variation in their effectiveness in terms of the T. confusum mortality that they caused, depending on the product (seed). The type of seed can play a role in the pathogenicity or effectiveness of the biopesticides. Additionally, our results showed that the mortality percentage was dependent on the dose and treatment of the commercial biopesticides.
The Effect of Shade Houses on the Insect Pests and Yield of Three Important Plant Crops in Puerto Rico: Pepper, Capsicum annuum (Solanaceae), Watermelon, Citrullus lanatus (Cucurbitaceae), and Cabbage, Brassica oleracea (Brassicaceae)

Shade houses are structures commonly used to grow plants while shielding them from unfavorable meteorological conditions. Differences in the insect pests, growth, and yield were determined for pepper, Capsicum annuum Linnaeus (Solanaceae); cabbage, Brassica oleracea L. (Brassicaceae); and watermelon, Citrullus lanatus (Thunberg) Matsumura and Nakai (Cucurbitaceae) grown inside and outside shade houses during 2016 and 2017 at the Agricultural Experiment Station in Juana Díaz, Puerto Rico. Only in peppers were populations of Anthonomus eugenii Cano, 1894 (Coleoptera: Curculionidae) and Helicoverpa zea (Boddie, 1850) (Lepidoptera: Noctuidae) lower within the shade house as compared to plantings in open field (100% and 98%, respectively). In contrast, there were no significant differences in insect pest abundances or in yield between the shade house and open field plants in watermelon, C. lanatus. Cabbage plants did not develop their characteristic “head” in the shade house. Some implications of the observed differences in crop health and growth are discussed.
The complete chloroplast genome of Enhalus acodoides and its phylogenetic analysis

Abstract Complete chloroplast genome of Enhalus acodoides was obtained in this work. Circular mapping revealed that the complete chloroplast sequences of E. acodoides was 176,748 bp in length and had an overall GC content of 38.3%, encoded 132 genes which contained 86 protein-coding genes (PCGs), 38 transfer RNA genes (tRNA) and 8 ribosomal RNA genes (rRNA). The phylogenetic tree shows that E. acodoides had a closer relationship with Thalassia hemprichii in Hydrocharitaceae and its analysis will help better understand the evolution of Alismatales species.
AutoTuner: High fidelity, robust, and rapid parameter selection for metabolomics data processing

Untargeted metabolomics experiments provide a snapshot of cellular metabolism, but remain challenging to interpret due to the computational complexity involved in data processing and analysis. Prior to any interpretation, raw data must be processed to remove noise and to align mass-spectral peaks across samples. This step requires selection of dataset-specific parameters, as erroneous parameters can result in noise inflation. While several algorithms exist to automate parameter selection, each depends on gradient descent optimization functions. In contrast, our new parameter optimization algorithm, AutoTuner, obtains parameter estimates from raw data in a single step as opposed to many iterations. Here, we tested the accuracy and the run time of AutoTuner in comparison to isotopologue parameter optimization (IPO), the most commonly-used parameter selection tool, and compared the resulting parameters’ influence on the quality of feature tables after processing. We performed a Monte Carlo experiment to test the robustness of AutoTuner parameter selection, and found that AutoTuner generated similar parameter estimates from random subsets of samples. We conclude that AutoTuner is a desirable alternative to existing tools, because it is scalable, highly robust, and very fast (∼100-1000X speed improvement from other algorithms going from days to minutes). AutoTuner is freely available as an R package through BioConductor.
Decomposition of Forest Litter and Feces of Armadillidium vulgare (Isopoda: Oniscidea) Produced from the Same Litter Affected by Temperature and Litter Quality

To explore the question how litter and macrofauna feces respond to temperature and how respiration differs for litter with a different CN ratio, we compared the decomposition rates of leaf litter (Alnus glutinosa, Salix caprea, and Acer campestre) and isopod (Armadillidium vulgare) feces produced from the same litter in response to three constant (8, 16, and 24 °C) and one fluctuating (first week 8 °C, the other week 24 °C) temperatures in a 50 week laboratory experiment and in a field trial. Microbial respiration of litter with lower CN ratio (alder and willow) was significantly higher than respiration of feces, no significant difference was found for maple litter with higher CN ratio. This was supported by field litter bag experiments where alder and willow litter decomposed faster than feces but the opposite was true for maple litter. Litter respiration was significantly affected by temperature but feces respiration was not. Fluctuating temperature caused either lower or equal respiration as compared to mean constant temperature. The content of phenolics was significantly higher in intact litter in comparison with decomposed litter and feces, either fresh or decomposed. The CN ratio decreased as litter turned to feces in maple and alder litter but increased in willow litter. In conclusion, microbial respiration of both litter and feces were substantially affected by litter quality; the litter was more sensitive to temperature than feces.
Retinoic acid organizes the vagus motor topographic map via spatiotemporal regulation of Hgf/Met signaling

The topographic map, in which the positions of neuron cell bodies correspond with the positions of their synaptic targets, is a major organizational motif in the nervous system. To understand how topographic axon targeting is controlled during development, we examine the mechanism underlying topographic innervation of the pharyngeal arches by the vagus motor nerve in zebrafish. We reveal that Retinoic Acid organizes the topographic map by specifying anterior-posterior identity in post-mitotic vagus motor neurons. We then show that chemoattractant signaling between hepatocyte growth factor (Hgf) and the Met receptor is required for pharyngeal arch innervation by the vagus motor nerve. Finally, we find that Retinoic Acid controls the spatiotemporal dynamics of Hgf/Met signaling to coordinate axon targeting with the developmental progression of the pharyngeal arches and show that experimentally altering the timing of Hgf/Met signaling is sufficient to redirect axon targeting and disrupt the topographic map. These findings establish a new mechanism of topographic map development in which regulation of chemoattractant signaling in both space and time guides axon targeting.
Mate choice, parental care and foraging behaviour of the northern trout gudgeon, Mogurnda mogurnda (Pisces : Eleotridae)

1 CHAPTER 1 GENERAL INTRODUCTION. 3 1.1 Sexual selection.3 1.1.1. An overview.3 1.2 Female choice and male competition. 4 1.3 Direct benefits model. 6 1.4 Indirect benefits of female choice. 6 1.4. 1. Genetic compatability.7 1.4. 2. “Good genes” model. 7 1.4. 3. The Fisher process. 7 1.4. 4. The Lek paradox. 8 1.4. 5. Strength of indirect selection. 9 1.5 Sexual conflict.9 1.6 Male-male dominance.11 1.7 Fish as models for parental care. 12 1.8 Parental care behaviours.13 1.9 Variation in parental care.15 1.10 Costs and benefits of parental care.15 1.11 Honest Signalling.16 1.12 Foraging: maximising energy gain.18 1.13 Aims of this study.20 1.14 Study species.21 References.24 CHAPTER 2 MATE CHOICE IN THE NORTHERN TROUT GUDGEON (MOGURNDA MOGURNDA). 47 2.
Adaptive Security Support for Real-time Transmissions in Ad Hoc Networks ( Extended Abstract )

In networks with highly volatile communication dynamics, it is appealing to employ adaptive applications to improve system performance. In this extended abstract we define the concept of mobile real-time data collector and present an adaptive security framework to ensure data security for real-time communications in ad hoc networks. In particular, we analyze the security requirements for mobile data collectors and develop a throughput adaptive scheme to ensure data privacy. In ad hoc networks, the adaptive scheme can be integrated with differentiated and end-to-end QoS services to provide qualitative security support to real-time transmissions.
Defining the Apicomplexan Amino Acid Transporter (ApiAT) Family

The Apicomplexan phylum is a large group of unicellular eukaryotic parasites. These parasites cause some notorious diseases of humankind, including malaria and toxoplasmosis. Apicomplexan parasites can also infect animal species, causing significant animal suffering and economic loss in the livestock industry. The advent of drug resistance and the poor side-effect profiles of some medications provides impetus for the development of new anti-parasitic drugs. Uncovering key aspects of parasite biology may aid in identifying and characterising novel inhibitors of parasite growth. Disruption of nutrient acquisition is one avenue to halt parasite replication and thereby cure infections. Parasites, by definition, rely on their hosts for a source of nutrients. Most nutrients do not diffuse freely across cellular membranes and their acquisition relies on cell-derived processes. One means by which parasites can acquire nutrients is via transporter proteins. Transporters are integral membrane proteins that mediate the movement of solutes across biological membranes. Apart from nutrient acquisition, transporters are also a means by which cells remove waste products and toxins, and control their ionic composition. Despite their importance, the transporters that allow apicomplexan parasites to perform these cell functions are currently not well characterised. Here, I define a family of amino acid transporters that are ubiquitous in apicomplexan parasites, which I name Apicomplexan Amino acid Transporters (ApiATs). I show that 10 of the 16 ApiATs in Toxoplasma gondii are expressed in the disease-causing tachyzoite stage, and 8 of them localise to the parasite plasma membrane. I demonstrate that four ApiAT proteins are important for growth of the tachyzoite stage of the parasite. In T. gondii, the amino acid glutamine is of particular interest because, apart from its role in protein synthesis, it is also used as an energy source. Prior to this work the uptake mechanism for glutamine in T. gondii was unknown. I investigated the substrate specificities of one ApiAT protein, TgApiAT2, demonstrating that it functions as a neutral amino acid transporter and is the major glutamine transporter of the parasite.
Modelling of the Abundance of Malaria Mosquitoes Using Poisson Mixed Model

Anopheles funestus and Anopheles gambiae are malaria vector mosquitoes. Knowing their resting behavior is important for implementing control methods. The aim of this study was to investigate the resting behaviour of the two malaria mosquitoes. The study was conducted in Kilombero River Valley and mosquitoes were collected using indoor and outdoor traps from 2012-2015. Poisson mixed models were used to quantify the impact of environment variables on resting behaviour. A log ratio rate between the type of trap and its interaction with environmental variables was used to determine if there was a change over time in the resting behaviour. A total of 4696 mosquitoes were resting indoors of which 57% were A. funestus and 43% were A. gambiae. Similarly, a total of 12,028 mosquitoes were resting outdoor of which 13% were A. funestus and 87% were A. gambiae. Temperature was significant and affected the resting behaviour of A. funestus. Humidity, saturation deficit and temperature were significant variables influencing the resting behaviour of A. gambiae. A. funestus was resting indoor while A. gambiae was resting outdoor over time generally. The findings of this study on the effects of environmental variables and the variations in the resting behaviour of A. gambiae and A. funestus could be used as a guide to implementing appropriate intervention measures such as indoor residential spraying (IRS), insecticide treated nets (ITNs) and mosquito repellents.
Decommissioning impacts on biotic assemblages associated with shell mounds beneath southern California offshore oil and gas platforms

The decommissioning of southern California offshore oil and gas platforms will create major economic, engineering, and environmental challenges in the next decade. Platform jackets, conductors, and shell mounds often host a diverse and productive marine community, and among the myriad considerations associated with decommissioning planning, platform operators and federal and state regulatory agencies will consider the ecological value of existing underwater structures as artificial reefs. In the event of partial removal of platform structure, fish assemblages on decommissioned platforms may remain unchanged in areas where structure is left intact. However, on the seafloor beneath the platforms, a mound of debris often called the shell mound will likely change over time if the supply of falling mussels and other organisms from the productive surface part of the structure is removed. In this study, we review shell mound research relevant to decommissioning, including mound formation, contaminant loads, associated biological communities, and transitions following the removal of platform structures at four sites. To address the gap in knowledge of shell mound fish community structure, we used manned submersible and remotely operated vehicle surveys from 1997 to 2013 to estimate the biomass, density, species composition and similarity between shell mounds at 22 southern California platforms. We found a wide range of variability in fish density and shell mound areal extent. Species composition also varied among sites, with three significant community clusters primarily distinguished by species depth preferences. These results will help inform a comprehensive net environmental benefit analysis of southern California offshore platform decommissioning alternatives.