Miracle-dz/UniFAR-FTUs huggingface dataset:
Including rewiring in the estimation of the robustness of mutualistic networks

Species are entangled within communities by their interactions in such a manner that their local extinction may unchain coextinction cascades and impact community dynamics and stability. Despite increasing attention, simulation models to estimate the robustness of interaction networks largely neglect the important role of interaction rewiring, that is, the ability of species to switch partners. Here we propose a new method to incorporate the potential of species to replace lost partners into a widely used coextinction model to estimate network robustness. In this model, species are allowed to rewire their interactions after initial loss of partners according to probabilities derived from well‐known mechanisms that determine mutualistic interactions, for example, trait matching, phenological overlap and abundances. To illustrate the use of this method, we analyzed a well‐sampled dataset of mutualistic plant–hummingbird interactions. We found that (a) in general, rewiring increases the estimated robustness, (b) networks are similarly robust to the loss of pollinators or plants, (c) morphological matching and phenological overlap leads to higher robustness, (d) when multiple rewiring mechanisms are combined, however, robustness increases little, and (e) rewiring tends to increase robustness more in scenarios when the loss of generalist species occurs first. Our results suggest that the same mechanisms known to drive plant–hummingbird network structure are relevant in buffering the effects of species loss via rewiring. The method proposed here can be applied to a wide range of interaction networks and is flexible to the inclusion of other variables important in determining interactions for specific systems. It also allows changes on the assumptions regarding the importance of distinct mechanisms, for instance including a hierarchical relationship, which facilitates insights into the relative importance of multiple variables influencing network disassembling. The analytical framework we offer here represents a step towards a more realistic estimation on how species loss may affect the integrity of interaction networks.
Electron Microscopic Identification of Distant Metastatic Cell in Human Prostate Cancer in Tissue section

Mutation in chromatin/DNA/genes of stem cells is a prerequisite for the development of cancer in the benign prostate. Mutation imparts chronic proliferation advantage to invasive and metastatic cancer cells, but not in benign prostate. We hypothesize that identification of metastatic prostatic cancer (PC) cells in tissue sections can lead to an early diagnosis and treatment of patients, hopefully, reducing death due to this disease. We have tested our hypothesis using biopsy and/or radical prostatectomy specimens of untreated and DES (diethylstilbestrol)-treated prostate cancer and transmission electron microscopy. Materials and methods: Tissue samples embedded in Epon were thin sectioned and examined on RCA EMU 3 or 4 transmission electron microscope. Results: We have identified two types of PC stem cells. Invasive stem cell invades the adjacent stroma whereas metastatic cell, a lineage of stem cell, is dedifferentiated columnar/cuboidal cells. Metastatic cell is identified by nuclear plasticity (pleomorphic nucleus), loss of nuclear membranes, loss of boundary between nucleus and cytoplasm and presence of electron dense molecules. Nuclear chromatin/DNA appears as electron dense molecules which readily pass plasma and basement membranes and enter the capillary before adhering to the red cell surface. Electron dense molecules are found in capillary, undoubtedly, reach metastatic site (s). Discussion and conclusion: Chromatin/DNA are small molecules that can readily cross many barriers, unlike an individual cancer cell. We show that invasive a cell is stem cell and metastasis develops from dedifferentiated columnar/cuboidal nuclear electron dense molecules. This is the first study to cells characterize metastatic cell in tissue sections.
FMRP promotes RNA localization to neuronal projections through interactions between its RGG domain and G-quadruplex RNA sequences

The sorting of RNA molecules to distinct subcellular locations facilitates the activity of spatially restricted processes through local protein synthesis. This process affects thousands of transcripts yet precisely how these RNAs are trafficked to their destinations remains generally unclear. Here we have analyzed subcellular transcriptomes of FMRP-null mouse neuronal cells to identify transcripts that depend on FMRP for efficient transport to neurites. We found that these FMRP RNA localization targets contain a large enrichment of G-quadruplex sequences, particularly in their 3′ UTRs, suggesting that FMRP recognizes these sequences to promote the localization of transcripts that contain them. Fractionation of neurons derived from human Fragile X Syndrome patients revealed a high degree of conservation in the identity of FMRP localization targets between human and mouse as well as an enrichment of G-quadruplex sequences in human FMRP RNA localization targets. Using high-throughput RNA/protein interaction assays and single-molecule RNA FISH, we identified the RGG domain of FMRP as important for both interaction with G-quadruplex RNA sequences and the neuronal transport of G-quadruplex-containing transcripts. Finally, we used ribosome footprinting to identify translational regulatory targets of FMRP. The translational regulatory targets were not enriched for G-quadruplex sequences and were largely distinct from the RNA localization targets of FMRP, indicating that the two functions can be biochemically separated and are mediated through different target recognition mechanisms. These results establish a molecular mechanism underlying FMRP-mediated neuronal RNA localization and provide a framework for the elucidation of similar mechanisms governed by other RNA-binding proteins.
Nucleosome assembly pathways, Rrm3p and phosphorylation of CAF-I contribute to the maintenance of silent chromatin at the FLO genes in Saccharomyces cerevisiae

NUCLEOSOME ASSEMBLY PATHWAYS, RRM3P AND PHOSPHORYLATION OF CAF-I CONTRIBUTE TO THE MAINTENANCE OF SILENT CHROMATIN AT THE FLO GENES IN SACCHAROMYCES CEREVISIAE Hollie Rowlands Advisor: University of Guelph, 2019 Professor K Yankulov Predominantly, studies of gene repression in S. cerevisiae focus on Sir2p-dependent silencing at the telomeres and the mating type loci. The FLO genes are heavily repressed in laboratory yeasts by a Sir2p-independent mechanism that is not well understood. Chromatin Assembly Factor I (CAF-I) plays a central role in the reassembly of H3/H4 histones during DNA replication. Two kinases, Cyclin Dependent Kinase (CDK) and Dbf4-Dependent Kinase (DDK), are known to phosphorylate the Cac1p subunit of CAF-I, but their role in the regulation of CAF-I activity is not well understood. In this thesis, I analysed the FLO genes, which encode cellsurface proteins and participate in the formation of floccules and biofilm. I report that the mutations in histone chaperones, the helicase RRM3 and Histone Deacetylases cause derepression of the FLO genes and reconstitute flocculation. This is linked to increased histone acetylation at the promoter of FLO1, but not the promoter of FLO11. Additionally the histone deacetylase inhibitor Nicotinamide or growth under starvation conditions enhances flocculation in strains compromised in chromatin maintenance. These effects are linked to variegated expression FLO11 and elevated expression of all FLO genes. Simultaneous mutations of both CDK and DDK target sites of CAF-I lead to growth retardation, significant cell cycle defects, altered cell morphology and increased sensitivity to DNA damage. Two of these mutants also show the reconstitution of flocculation and expression of FLO genes, but do not re-capitulate the transient losses in HML silencing or losses in sub-telomeric silencing observed in cac1Δ mutants. An additional mutant causes defects in silencing at the sub-telomere, but not at HML or the FLO genes. I provide detailed analysis of the repression of FLO genes and propose that a gain in epigenetic silencing is a major contributing factor for the loss of flocculation in laboratory budding yeast strains. I have also shown that the role of Rrm3p in silencing extends beyond interaction with CAF-I at sub-telomeric replication forks. In addition, dysfunctional CAF-I produces severe phenotypes, and locus-specific loss of silencing phenotypes which reveal a possible role of CAF-I in the coordination of DNA replication, chromatin reassembly and cell
Spray-Dried Hierarchical Aggregates of Iron Oxide Nanoparticles and Their Functionalization for Downstream Processing in Biotechnology

In this work, the structuring of iron oxide nanoparticles via spray-drying (SD) of aqueous suspensions is investigated, leading to micrometer-sized aggregates with saturation magnetization comparable to that of the individual nanoparticles. Interestingly, the superparamagnetic behavior is retained despite the multicore structure. Modification of the aggregates via the addition of silica nanoparticles to the suspension allows for control of the resulting magnetization by adjusting the iron oxide content. Moreover, the morphology of the produced aggregates is gradually shifted from irregular inflated-like shapes in case of pure iron oxide aggregates to reach spherical structures when bringing the silica content to only 20%. The aggregates with different magnetization can be effectively separated in a simple column with an attached permanent magnet. Functionalization of pure iron oxide aggregates with a previously coupled ligand holding a nitrilotriacetic acid (NTA)-like moiety and subsequent loading with Ni2+ ions leads to the ability to bind 6-histidine (His6)-tagged target proteins via chelation complexes for magnetic separation. The application of the presented system for the purification of recombinant protein A in multiple cycles is shown. The recyclability of the separation system in combination with the high degree of magnetic separation is promising for future applications in the field of preparative in situ protein purification.
ENDOPHYTIC FUNGI COMMUNITIES FROM Centella asiatica OF BENGKULU ACCESSION

Various species of endophytic fungi have been isolated and reported from various types of plants and tissues, but how host or plant tissue determines endophytic community structure has not been explored quantitatively. The aim of this research was to understand community structure of endophytic fungi in various organs of Centella asiatica of Bengkulu accession. The analysis data use to Shannon Wienner diversity index (H’), dominance index, colonization rate, frequency of occurrence and UPGMA analysis with Jaccard Coefficient. Total 61 isolates were obtained and grouped into 19 morfotypes, consist of 15 Asomycetes & 4 Basidiomycetes and 10 Genera. The highest colonization rate was in stolons (16%) and the lowest is in petiols (4%). Endophytic fungi were distributed in all of the organs. Leaves harbored more diverse endophytic fungi (H’= 2,138) than the other organs and classified as medium. Fusarium solani, Fusarium oxysporum dan Phoma multirostrata were the dominant species.This research showed that different type of host-pant organs influenced community structure of endophytic fungi from C. asiatica of Bengkulu accession. This is the first report, on the community strcuture of endophytic fungi from C. asiatica from leaves, petiols, stolons, and roots part of the organ plant. Overall, our results indicated that the isolate can be used to analyzed of it’s potential as bioactive compuond same as the host.
Improving the algorithm of effective air management in ventilation systems of complex topology

Объем добычи руды постоянно увеличивается, и, как следствие, увеличивается потребность рабочих зон в свежем воздухе. Управление воздухораспределением в вентиляционных сетях крупных рудников становится сложной задачей, эффективное решение которой в рамках жестких требований к безопасности ведения горных работ трудновыполнимо без использования средств автоматического управления проветриванием. Сложность задачи разработки эффективного алгоритма управления и его технической реализации приводит к тому, что средства автоматического управления проветриванием подземных рудников в настоящее время практически не используются. Задача алгоритма оптимального управления заключается в нахождении таких углов поворота жалюзийных регуляторов автоматических вентиляционных дверей (АВД) и частоты вращения рабочего колеса главного вентилятора, при которых вентилятор развивал бы минимальную мощность N и при этом не нарушались бы условия соблюдения минимальных расходов. Эффективность алгоритма также во многом определяется его универсальностью, а универсальность алгоритма определяется в первую очередь структурой системы управления, выбором ее составных элементов. В данной работе в качестве структурной единицы системы управления проветриванием выбирается не отдельная АВД, а АВД-связка. На базе введенной в данной работе теории АВД-связок строится универсальный алгоритм управления вентиляцией. Также предлагается уравнение управления частотой оборотов главной вентиляторной установки. Работоспособность построенного алгоритма управления проветриванием демонстрируется на модельной вентиляционной сети рудника БКПРУ-4. Ключевые слова: вентиляция, система оптимального управления проветриванием, рециркуляция, автоматическая дверь, главная вентиляторная установка, расчетная вентиляционная сеть, теория автоматического управления, дифференциальное исчисление, расход электроэнергии, скорость воздуха, газовая обстановка, программно-вычислительный комплекс, депрессия, воздушно-депрессионная съемка, математическая модель.
New Approach for 3D Mesh Retrieval Using Artificial Neural Network and Histogram of Features

Recently 3D models become more popular in diverse fields such as medicine biology and engineering; this expansion created the need of a robust descriptor system that will allow a fast and compact classification, comparison and retrieval of 3D models. A diversity of methods and approaches have been proposed to solve this problem, but recently researchers got interested in the use of the potential and the effectiveness of machine learning methods to create a powerful retrieval system. In this paper, we present a new method to extract a descriptor or signature representing the 3D model. The proposed method consists of using an artificial neural network (ANN) trained with a histogram of features extracted directly from the 3D object; this last point helps to train the ANN fast and with consistent data. Once trained we concatenate the result of the hidden layers to be used as a descriptor in the retrieval system. The achieved experimental demonstrate the power and the effectiveness of our method which outperform some well-known methods in the literature.
Analysis of Non-Coherent Detectors for Opportunistic Spectrum Access in Broadband Wireless Networks

The exponential growth in the number of wireless broadband service users demands an enormous increase in the available communication bandwidth, which inherently translates into an increased demand for the radio frequency spectrum. Opportunistically accessing the unused portions of the spectrum requires sensing the availability of unused bands. In this thesis, non-coherent detectors such as the energy detector and its more generalized version, the p-norm detector, which offer low-cost low-complexity spectrum sensing are considered and comprehensive techniques for performance analyses are developed. To this end, a new approximate representation for the wireless fading channels is proposed and applied to facilitate accurate, asymptotic performance analysis for the energy detector across a variety of operating conditions including fading, antenna/cooperative diversity and interference. To address the analytical difficulty involved in spectrum sensing using the p-norm detector, several accurate analytical expressions are developed and utilized to comprehensively characterize the spectrum sensing performance in generalized fading channels and in fading channels with antenna diversity. To promote tractable spectrum sensing performance analysis for arbitrary sample sizes, five accurate approximations are introduced and investigated. In another comprehensive system setup, spectrum sensing performance of the p-norm detector under the cumulative effects of path-loss, fading, and a large number of randomly deployed interfering nodes is characterized by developing a comprehensive semi-analytical technique and extended to cooperative spectrum sensing.
Effects of Temperature and Thyroid Hormone on Oxidative and Lipid Metabolism in Juvenile Lake Whitefish (Coregonus Clupeaformis)

ii ACKNOWLEDGMENTS . iv TABLE OF CONTENTS . v LIST OF FIGURES . viii LIST OF TABLES . xi LIST OF ABBREVIATIONS AND SYMBOLS . xiii 1. GENERAL INTRODUCTION . 1 1.1. Physiological consequences of a changing thermal environment . 1 1.1.1. Thermal plasticity and its predicted scope of impact in teleosts . 1 1.1.2. Thermal plasticity and energy metabolism . 4 1.1.2.1. Oxidative metabolism and thermal acclimation . 5 1.1.2.2. Lipid metabolism and thermal acclimation . 7 1.1.3. Cellular mechanisms of thermal plasticity . 10 1.2. Thyroid hormones and energy metabolism . 12 1.2.1. Thyroid hormones . 12 1.2.2. Relationship between thyroid hormones and metabolic pathways . 14 1.2.2.1. Relationship of thyroid hormones with oxidative pathways . 14 1.2.2.2. Relationship of thyroid hormones with lipid pathways . 15 1.2. 3. Cellular mechanisms of thyroid hormone action . 16 1.3. Integration and opportunities for study . 18 1.3. 1. Predicted relationships between temperature and thyroid hormones in teleosts . 18 1.3. 2. Thesis objectives . 20 2. CHAPTER ONE: Effects of temperature and thyroid hormone on oxidative metabolism in juvenile lake whitefish . 22 2.
Hip Arthroscopy Made Simple, Easy, and Elegant. A Novel Variant of the Outside-In Technique

Hip Arthroscopy (HA) is considered to be a demanding surgery with a steep and slow learning curve. Adequate HA instrumentation is required to perform a reproducible surgery. The technique most commonly used to access the hip is through the central compartment or from the “Inside-Out” with continuous distraction and specialized access equipment. Newer techniques start from the peripheral compartment called “Outside-In” techniques, these techniques have a safer access with a more controlled environment avoiding iatrogenic scuffing of the acetabulum, labrum or femoral head. The purpose of this surgical and novel variant technique from the “Outside-In” which we call simple, easy, and elegant is an excellent choice and can be part of the armament for young surgeons who are initiating in hip arthroscopy and preservation, our technique has been very reproducible and reliable with good to excellent results with very few complications.
First Complete Genome Sequence of the Novel Lineage G-IX (BD-18) of FMDV Serotype Asia1

Foot-and-Mouth Disease (FMD) has been a major threat to livestock worldwide, and is caused by FMD Virus (FMDV) existing as seven serotypes (A, O, C, Asia1 and SAT 1-3), each having variability into topotypes, genetic lineages, sublineages, and strains. Three serotypes are circulating in Indian subcontinent with the widespread distribution of serotype O, whereas serotype A and Asia1 are restricted to certain geographical regions. During 2017-2018, the Sindh-08 lineages of Asia1 serotype was reported from Pakistan, however, in 2018, a novel circulatory foot-and-mouth disease virus serotype Asia1 BD-18 (G-IX) lineage containing a unique mutation has emerged in Bangladesh. The first complete genome of the Asia1/ASIA/G-IX novel lineage strain, isolated from Bangladesh, is reported here. Amino acid substitutions at critical antigenic sites of capsid were identified compared to genome of existing vaccine strain (IND/63/72), and contemporary FMDV serotype A isolate of Bangladesh.
A 5-GHz frequency-doubling quadrature modulator with a ring-type local oscillator

A 5 GHz direct-conversion quadrature modulator has been developed using a frequency-doubling circuit technique to integrate a local oscillator on a single silicon chip. A three-level mixer, newly designed with symmetrical topology for two local oscillator inputs, is used to apply the frequency-doubling technique, so low image component levels of the modulated signals are achieved. The modulator is implemented on a single chip using Si bipolar process technology with a cutoff frequency of 40 GHz. The image ratio is less than -34 dBc at a 5 GHz carrier frequency.
Docking Simulation of Chemerin-9 and ChemR23 Receptor

Chemerin-9 is a nonapeptide that corresponds to the YFPGQFAFS sequence on the C-terminus of Chemerin protein. Recent clinical and animal studies using mice, it has been recently reported that Chemerin-9 binds to the ChemR23 receptor and can suppress the inflammation-related diseases such as arteriosclerosis. In this study, molecular dynamics simulations were performed with the Chemerin-9 peptide to identify structures with high and low free energy. Docking simulations of these structures of Chemerin-9 and ChemR23 receptor were performed, and the docking model with the lowest free energy and binding energy of Chemerin was identified. For this model, the binding sites and binding forces were evaluated. Based on these findings, we aim to provide insights into the development of new drugs that suppress arteriosclerosis.
Phytoplankton, Trophic State and Ecological Potential in reservoirs in the State of São Paulo, Brazil

This study evaluated the ecological potential of reservoirs in the Brazilian state of São Paulo, having phytoplankton as a biological quality element. Integrated water column sampling was carried out in the dam, and in the intermediate and fluvial zones of the Igaratá, Atibainha, Paiva Castro, Rio Grande, Itupararanga, Broa, Barra Bonita, Guarapiranga and Salto Grande reservoirs in July 2015. Physico-chemical and biological parameters were analyzed in all environments. The phytoplankton was analyzed under an inverted microscope, and measurements of density, diversity, equitability and dominance were determined. The data was ordered using PCA and CCA analysis. The ecological potential of the reservoirs was determined through the evenness index. The electrical conductivity, nitrate, nitrite and orthophosphate were higher in the more eutrophic reservoirs: Salto Grande, Barra Bonita, Guarapiranga and Rio Grande. A trophic gradient was observed among the sampling points, suggesting a conservation spectrum. There was dominance of cyanobacteria in the eutrophic reservoirs associated with low diversity and high dominance. The total density was correlated with TP, TN, and pH. A divergent relationship between the trophic state index and the evenness index was observed. The Atibainha, Itupararanga, Broa, Barra Bonita and Salto Grande reservoirs were classified as water bodies of very poor ecological quality (Bad). The evenness index seems to be a good alternative to the biomonitoring of the studied reservoirs.