Miracle-dz/UniFAR-FTUs huggingface dataset:
A single cell based model for cell divisions with spontaneous topology changes

The development of multicellular organisms is accompanied by the formation of tissues of precise shapes, sizes and topologies. Remarkable similarities between tissue topologies, in particular proliferating epithelial topologies, in various species suggest that the mechanisms that govern the formation of tissues are conserved among species. To understand these mechanisms various models have been developed. In this thesis, we present a novel mechanical model for cell divisions and tissue formation. The model accounts for cell mechanics and cell-cell adhesion. In our model, each cell is treated individually, thus the changes in cell’s shape and its local rearrangements occur naturally as a response to the evolving cellular environment and cell-cell interactions. We introduce the processes of cell growth and divisions and numerically simulate tissue proliferation. As tissue grows starting from few cells, we follow the dynamics of the tissue growth and cell packing topologies. The outcomes are compared with experimental observations in Drosophila wing growth. Our model accounts for the exponential decay of the mitotic index and reproduces commonly observed cell packing topologies in proliferating epithelia. Next, we consider two biologically relevant division schemes, namely, division through asymmetric division plane and division by Hertwig’s rule. We study the impact of division planes on tissue growth and show that the division plane may affect cell packing topologies. Development of the tissue is accompanied by cellular rearrangements. We vary the extent of cellular rearrangements and analyse their effects on tissue topology. We find that when cells are allowed to move freely, more organized packing topologies emerge.
Effect of Nickel on Membrane Integrity, Lipid Peroxidation and Fatty Acid Composition in Wheat Seedlings

The influence of 50 and 100 μm Ni on membrane integrity, hydrogen peroxide content, lipid peroxidation as well as total fatty acid composition was studied in shoots and roots of wheat seedlings. In both organs, treatment with Ni led to significant increase in electrolyte leakage reflecting the metal-induced enhancement of membrane permeability. In the shoots, it was accompanied by significant increase in lipid peroxidation. Accumulation of hydrogen peroxide, more pronounced in the shoots, was also found in Ni-treated wheat. Exposure of wheat seedlings to Ni altered the total fatty acid composition, leading to decrease in their unsaturation, which was indicated by reduction in double bond index. In both organs, a significant decrease in linolenic acid (C18 : 3) content was observed. It was accompanied by increased linoleic (C18 : 2) and oleic (C18 : 1) acid contents in shoots and roots, respectively. In the shoots, parallel increase in palmitic acid (C16 : 0) and decrease in palmitoleic acid (C16 : 1) were found at the end of the experiment. Our results suggest that modification of fatty acid profile in Ni-treated wheat seedlings is partly related to lipid peroxidation and increased electrolyte leakage and may reflect damage of cells caused by the metal.
Turkish Early Childhood Education Curriculum from the Perspective of STEM Education: A Document Analysis

The current study aimed to examine Turkish early childhood education curriculum prepared for 36–72 month children relative to science, technology, engineering, and mathematics (STEM) education. To that end, 240 developmental features, 65 objectives, and 230 indicators under developmental fields in the curriculum and 40 sample activities in a teacher activity book were analyzed by adopting content analysis. The data were analyzed in the light of “A Framework for K–12 Science Education: Practices, Crosscutting Concepts, and Core Ideas” developed by the Committee on a Conceptual Framework for New K–12 Science Education Standards within the National Research Council. Analyses revealed that the curriculum and teacher activity book included core ideas and concepts related to STEM education and it had most of the characteristics of STEM education. Finding out the existence of STEM educationrelated aspects of the early childhood education curriculum inspires conducting further studies that will help early childhood educators’, academicians’, and policy makers’ focus on integrating and implementing STEM education practices not only in Turkey but also in countries adopting similar early childhood education curriculums.
THE FIRST RECORD OF ALTERNARIA TRITICINA THE CAUSATIVE AGENT OF ALTERNARIA LEAF BLIGHT IN WHEAT AND BARLEY IN IRAQ

Alternaria leaf blight caused by Alternaria triticina can cause high yield losses at the severe infection in wheat and barley. It is first time for this pathogen to be recorded in Iraq. The investigation process of this disease included 25 locations from 12 sites in 5 provinces that plant wheat and barley in the south and middle of Iraq. The results revealed that the fungus was isolated from almost all examined locations with different frequency. Shethaif- Al Garbie and Sheikh Saad showed higher number of isolates with 60 and 40 in wheat fields respectively; while; Shethaif- Al Garbie and Dabuni expressed the highest number of isolates in barley fields with 45 and 33 respectively. The highest isolation frequency in wheat fields was at Sheikh Saad and Ali Alsharqi with 100% followed by Ali Algharbie with 90% and the lowest was at Al- Kut and Al-Huria with 37.5 and 40% respectively. The highest isolation frequency in barley fields was recorded at Dabuni with 82.5% followed by Shethaif- Al Garbie and Babil / Al-Huria with 75% and the lowest was at Al-Basrah/ Shatt al-Arab with 20%. The fungus was isolated from all plant parts (stem, leaf, and spike); however, spikes recorded the highest isolation frequency reaching 100% in some locations .
Redescription of Parapharyngodon micipsae (Seurat 1917) (Nematoda Pharyngodonidae) from the new host Tarentola parvicarinata Joger 1980 (Squamata Gekkonidae).

This study, based on a morphometric approach for identification of the nematode parasite Parapharyngodon micipsae (Seurat 1917), reports the first record of P. micipsae in a West African species of gecko, Tarentola parvicarinata Joger 1980 (Gekkonidae), collected in the Niokolo Koba National Park, Senegal. Specimens of P. micipsae were examined under a light microscope and for the first time with a scanning electron microscope. The main differences between males of P. micipsae and similar African species ( P. margaritiferi Hering-Hagenbeck 2001, P. kenyaensis Bursey & Goldberg 2005, P. meridionalis (Chabaud & Golvan 1962)) are in the shape and length of spicule, number and distribution of caudal papillae, outgrowths morphology, cloaca-tail distance and host. In the case of females, P. micipsae differs significantly from similar species mainly in oesophagus length, anus-tail end distance and egg size. Morphological differences between P. micipsae and P. echinatus (Rudolphi 1819) males in lateral alae, form of distal end of spicule and morphology of outgrowths were confirmed as stable features.
DESIGN, DEVELOPMENT AND TO FORMULATE ANTIMICROBIAL GEL OF TOONA CILIATA ROEM. LEAVES AND FICUS BENGALENSIS LINN. STEM BARK.

The aim of the present study is to investigate the antimicrobial property and to formulate an antimicrobial Gel of Toona ciliata Roem. leaves and Ficus bengalensis Linn. stem bark. The antimicrobial activity was evaluated by using agar cup plate method and minimum inhibitory concentration against four microorganisms was determined. Soxhlet apparatus was used for successive extraction using solvents - petroleum ether, chloroform, methanol and water. And to formulate polyherbal antimicrobial gel carbopol 940 was used as gelling agent. Petroleum ether extract was found to be the most effective of the three extracts. The antimicrobial activity was observed against the gram positive bacteria Staphylococcus aureus, Bacillus subtilis and gram negative bacteria Pseudomonas aeruginosa ; and the fungus Candida albicans . The minimum inhibitory concentration (MIC) of Toona ciliata petroleum ether extract ranged from 40mg/ml-50 mg/ml and that of Ficus bengalensis petroleum ether extract from 10mg/ml-16 mg/ml at which selected organisms showed inhibition. Then using a range of concentrations of carbopol 940 different gel formulations were formulated with petroleum ether extracts of both plants and tested for their antimicrobial potential. Out of these F2 and F6 formulation were combined in different ratios and one with ratio 3:7 was further tested for antimicrobial activity by Agar Cup method. It was found that ratio 3:7 have synergistic effect and possessed considerable antimicrobial activity and may serve as promising antimicrobial gel formulation. From this study, it can be concluded that Toona ciliata Roem. leaves and Ficus bengalensis Linn. stem bark exhibited antimicrobial activities against selected microorganisms. Keywords: Toona ciliata Roem. , Ficus bengalensis Linn. , Antimicrobial activity, In-vitro diffusion study, Agar cup plate method, MIC, Carbopol 940, Hydrogel, Cold method, Topical.
Técnicas de purificación de aislamientos de Phytophthora contaminados por bacterias

Many diseases in agricultural crops and forests are caused by Phytophthora around the world. Even though there are advances in the knowledge of this pathogen, it still causes important losses in agriculture. During the isolation of Phytophthora from diseased tissue or soil, it is common to have isolates contaminated with bacteria even when selective culture media with antibiotics are used. Bacterial contamination inhibits mycelial growth of oomycetes since bacteria form reproductive structures faster. Interfering with studies of morphological and genetic characterization of such isolates. Therefore, it is necessary to have a method to purify the mycelium. Utilization of antibiotics presents two major disadvantages, development of bacterial resistance and the high cost of these products. The objective of this research was to evaluate three techniques to purify the mycelium of Phytophthora contaminated with bacteria. The first method consisted in the use of the Van Tiegham cell, the second one was based on acidification (pH 3.5± 0.1) of potato dextrose agar (PDA) media with tartaric acid. The third one called superposition, consisted in placing a cube of contaminated culture media with mycelium and on top of this a cube of clean media. It was feasible to purify Phytophthora mycelium with the three techniques; it was verified using Luria broth. The method that gave the best results was the acidified culture media, with 90% of pure cultures, followed by the cell method with 25%, and the least effective was the superposition method with 15%. The utilization of acidified culture media represents an alternative of low cost to substitute the addition of antibiotics to purify isolates of Phytophthora contaminated with bacteria.
EDCAT 5. A catchment-based study of endocrine disruptionin surface waters: multivariate evaluation of the health of a sentinel fish species exposed to sewage treatment workseffluent. Annexe to EDCAT Final report – CYP1A gene expression results

Summary: The levels of CYP1A expression vary significantly between sites on the Ray, exhibiting a similar pattern in 2007 and 2008, and these trends seem to be linked with sediment contaminant loading, as reported by EDCAT 3/4, rather than waterborne contamination. If the primary route of exposure to organic chemicals for the fish in the Ray is indeed linked to sediment concentrations (e.g. via sediment-dwelling invertebrates) this may explain the complete absence of effect of remediation on CYP1A expression in fish in the Ray. It also suggests that exposure of the resident fish populations to contaminating chemicals may continue for some time after remediation of the STW effluent. Further chemical and fish monitoring effort would establish how long is required for the system to depurate fully. Relatively high levels of CYP1A expression were detected in fish from sites on the Ock during 2008. This is consistent with data obtained from EROD analyses of fish collected on a different occasion during 2008 and is strongly suggestive of a contaminant episode. The source and nature of this contamination remains unknown.
Efficacy of botanical repellents against Aedes aegypti

A laboratory study was conducted to evaluate the efficacy of repellency of Hyptis suaveolens and Ocimum gratissimum against the adults of Aedes aegypti. The methanol extract of H. suaveolens at 0.03, 0.05, 0.075 and 0.1 mg/cm2 offered 50.00, 66.67, 71.43 and 75.00 percent protection against the mosquito bite. The percent protection against the mosquito bite was 33.33, 50.00, 57.14, 60.00 and at 0.03, 0.05, 0.075 and 0.1mg/cm2. Synergistic action was observed when the plant extracts were mixed in equal quantity and the percent protection was extended up to 83.33. Mosquito coil made with the extracts of H. sauveolens and O. gratissimum provided 75.31 and 70.37 percent protection from mosquito bite. Combined use of plant extracts increased the percent protection than with individual plant extracts.
Regulation of sleep and circadian rhythms by metabolic neuropeptides

The increasing prevalence of metabolic disease in modern society has accelerated our need to understand factors that may be contributing to its development. Both circadian disruption and sleep deprivation are associated with metabolic dysfunction. Thus, for my dissertation I sought to gain insight into this association by studying the genetic and neural basis of interactions between circadian rhythms, sleep and metabolism. The relative simplicity of fly neuroanatomy and physiology, vast array of available genetic tools, and conservation across many organisms, makes Drosophila melanogaster an ideal model to dissect complex interactions between physiological systems. Through our studies we identified a novel role for a molecule that regulates feeding behavior, Neuropeptide F (NPF), in the circadian system. We found that NPF drives circadian gene expression of the detoxification gene sex-specific enzyme 1 in a peripheral metabolic tissue, possibly to coordinate consumption of toxins with their removal. Our results support a role for NPF in synchronizing behavior and metabolism to ensure circadian coherence and promote survival. In addition, we studied the interaction between sleep and metabolism by evaluating whether alterations in sleep cause metabolic dysfunction or are the result of shared molecular pathways. The insect equivalent of norepinephrine, octopamine, promotes wake in flies by signaling through insulin-producing neurons. We determined that although sleep and metabolic neural circuitry intersect, the octopamine signaling pathway regulates sleep and metabolism independently. This dissertation highlights the great power of Drosophila as a model organism to investigate complex interactions between different biological systems. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Amita Sehgal Second Advisor Tom Jongens
Flora of the Northeast: A Manual of the Vascular Flora of New England and Adjacent New York

Designed as both a reference work and a year-round field manual, this volume contains more than 2,400 range maps and 995 line drawings, designed to clarify descriptions used in the keys. For botanists, naturalists, and students interested in an up-to-date treatment of the vascular flora of greater New England, it has proved to be an invaluable resource. The geographic scope of the work extends from the Canadian border south through Long Island and west to the Hudson River. The "General Keys" section contains fourteen keys that include such groups as aquatic plants, vines, and woody plants in winter condition. For both woody and herbaceous families, the keys cover flowering as well as fruiting conditions and rely heavily on the use of vegetative features to extend the utility of the book beyond the reproductive period. The "Descriptive Flora" section includes keys to all of the genera and species, descriptions of the families and genera, and accounts of the individual species. The latter incorporates information on wetland site index, rare status, wildlife food value, food and medicinal value for humans, and poisonous or hallucinogenic properties. This revised edition includes an updating of plant scientific names that changed since the first edition and an alphabetized list of plant families with page numbers on the inside front cover for easy reference. This edition also includes a new CD-ROM with a multiple-entry identification guide, hundreds of accompanying photographic images of genera, an illustrated glossary, and page reference numbers to genus descriptions in the manual. Presenting a wealth of scientifically accurate information in a precise and clear format, this volume serves as a reference work, as a textbook for classes in plant identification, and as a field manual.
Laboratory Consistency in Extraction of Nematodes from Soil and Roots

We found inconsistency in reports of extracted nmatodes between two nematode diagnostic laboratories. Each laboratory analyzed 200 matched soil and 200 matched root samples. Agreement in detection and nondetection for three nematode species in soil was less than 85%, and in roots agreement was greater than 85% for one of the three species. Relationships were not found to support consistency between matched samples in which the same nematode was detected by both laboratories. An explanation, in part, for the inconsistency may lie in the dilution and counting procedure of the extraction process. A first approximation to a model for minimizing counting errors suggests that, when dilution is required for the counting of nematodes, differing dilutions should be used, and that, if a single sample is taken, about 840 nematodes should be present in the sample. However, the same precision can be achieved with about 170 nematodes per sample if four samples are counted and averaged.
Prevalence of four enteropathogens with immunochromatographic rapid test in the feces of diarrheic calves in east and southeast of Turkey.

Received: Revised: Accepted: August 29, 2012 November 17, 2012 May 18, 2013 In this study, fecal specimens taken from 192 diarrheic and 14 healthy calves (2-40 days old) were examined for the presence of bacterial and parasitic agents. Fecal samples from diarrheic calves with the four immunochromatographic rapid tests were 92.7% positive for four enteropathogens. The individual prevalence was 25, 21.8, 9.4 and 2.1% for Rotavirus, Cryptosporidium parvum, E. coli K99 and Coronavirus, respectively. Concomitant infections caused by two agents were 15.6% for Rotavirus+Cryptosporidium, 1.0% for Rotavirus+Coronavirus, 5.2 % for Cryptosporidium+E. coli K99, and 7.3% for Rotavirus+E. coli K99. Besides concomitant infections caused by three agents were 3.1% for Cryptosporidium +Rotavirus+E.coli K99 and 1.0%, Cryptosporidium+Rotavirus+Coronavirus. In addition one calf (1.0%) was infected by combination of four agents as Cryptosporidium, Rotavirus, Coronavirus, and E. coli K99. The calculated individual prevalence was 56.9% for Rotavirus, 47.8% for C. parvum, 26.0% for E. coli K99 and 5.2% for Coronavirus. However, 88 samples were positive in smear detection for Cryptosporidium while 92 were positive in rapid test. As a result of this study it can be concluded that multiple etiologies of diarrhea can be seen and this can help in the development of a specific treatment and preventative measures for practitioners in east and southeast of Turkey. ©2013 PVJ. All rights reserved
Characterization of HIV-1 host interactions by advanced fluorescence microscopy

HIV-1 is responsible for the current AIDS epidemic that caused 30 million dead so far. Albeit an overall stabilization of incidence rates and declining new infections, AIDS represents a major health and economic problem to some developing countries. HIV-1 infection mainly occurs through unprotected sexual intercourse and subsequent mucosal transmission. In mucosal tissue dendritic cells (DC) can capture HIV-1 through cell surface receptors (e.g. the C-type lectin DC-SIGN), degrade virions and present viral antigens to T-cells. Remaining intact virions are transferred to CD4+ T-cells at cell-to-cell contacts, called infectious synapses. Both DC-SIGN signaling and actin-containing cellular protrusions are implicated in HIV-1 cell-to-cell transfer, but their definitive role in highly relevant immature DC T-cell transfer remains unclear. HIV-1 replication in CD4+ T-cells and macrophages leads to general immune activation, T-cell depletion and final failure of the immune system. In contrast, most SIV infections in their natural hosts are nonpathogenic. Primate lentiviruses use their Nef proteins to manipulate the communication of T cells with antigen-presenting cells (APC) through cell-contacts named immunological synapses. The interaction of individual HIV-1 virions with cellular proteins during entry and assembly occurs at scales below the diffraction limit of light that is ~200nm. Novel super-resolution microscopy techniques achieve nanometer resolution of fluorescently labeled molecules in intact cells. The cellular factor tetherin directly interacts with budding HIV-1 virions and inhibits their release. The restriction mechanism at the molecular scale remains largely unclear. Establishment of quantitative multicolor super-resolution microscopy enabled the visualization of HIV-1 virions, assembly sites and the cellular organization and restriction mechanism of tetherin. New quantitative tools were established to determine sizes of tetherin clusters, number of tetherin molecules and to test models for tetherin recruitment to HIV-1 budding sites. Live-cell fluorescence and electron microscopy together with genetic and pharmacological approaches were used to show that HIV-1 activates Cdc42 via DC-SIGN signalling to induces membrane extensions in immature dendritic that play important roles in cells to cell-to-cell transfer. The effect of primate Nef proteins on immunological synapses between infected primary T-cells and APCs was characterized by immunofluorescence and high resolution confocal laser scanning microscopy. The inability to disrupt the immunological synapse between infected human T cells and APCs distinguishes HIV-1 from most other primate lentiviruses and could explain important differences in lentiviral pathogenesis. In this thesis, super-resolution and confocal fluorescence microscopy allowed a detailed characterization of HIV-1 tetherin interaction, infectious and immunological synapses that play important roles in HIV-1 transmission and pathogenesis.