Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterizing the Chemoprevention Potential of Amenity Grass Phenolic Extracts In Vitro and the Corresponding Nutraceutical Targets within HepG2 Carcinoma Cells

Adviser: Roch Gaussoin This research has revealed significant chemopreventive potential belonging to the planet's most renewable and abundant plant source: amenity grasses. The characterization results from Chapter 1 demonstrated the potential chemoprevention attributes of supina bluegrass and bermudagrass crude extracts linked to the extensive phenolic acid profiles of these amenity grasses. In contrast to cereals, amenity grass phenolic extracts (AGPE) offer appreciable amounts of unbound/free ferulic acid that would be available for rapid in vivo absorption. The literature has shown ferulic acid to be a highly available and health benefitting phenolic compound. Chapter 1 in vitro studies demonstrated AGPE-induced antiproliferation and apoptotic induction capacities in HepG2 and Caco-2 carcinoma cell lines. The in vitro chemopreventive influences were shown to be dependent upon AGPE species, extract fraction, dose, and cell line. As with most natural systems, a significant gap in knowledge exists as to how such health promoting components modulate metabolism to maintain health. Thus, the objective of Chapter 2 was to monitor the metabolic alterations attributed to supina bluegrass and bermudagrass phenolic treatments in human hepatocellular liver carcinoma cells, HepG2, using Fourier Transform mid infrared (FT-mIR) spectroscopy. The FT-mIR ! metabolomic method was used to assess temporal changes in the biochemical fingerprint of treated and untreated HepG2 cells compared to resveratrol positive control treatments. The results from this study illustrate amenity grass nutraceutical targets within the HepG2 metabolme compared to the documented biochemical influences of resveratrol. As an outcome to this study, the impacts of nutraceutical stimuli on the biochemical fingerprint were further elucidated by analyzing the ability of phenolics to downregulate the oxidative nature of cancer.
Peanut stunt virus-induced gene silencing in white lupin (Lupinus albus)

White lupin ( Lupinus albus L.) plants develop cluster roots and have strong resistance to phosphorus starvation. Although many expressed sequences have been identified to explain the mechanisms used by white lupin to acquire phosphorus, the lack of a stable transformation technique has made it challenging to evaluate the functions of these expressed sequences. Virus-induced gene silencing (VIGS) is an attractive method for assaying gene function in species that are difficult to stably transform. Here, we show that the Peanut stunt virus (PSV) vector effectively induces silencing of endogenous genes in white lupin. It is unknown whether PSV is useful for VIGS; therefore, we first inoculated Nicotiana benthamiana plants with PSV harbouring fragments of the N. benthamiana phytoene desaturase gene ( NbPDS ). Two out of four distinct sequence fragments of NbPDS induced photo-bleaching in N. benthamiana , indicating that PSV can be used to knockdown endogenous gene sequences in a sequence-dependent manner. White lupin plants inoculated with PSV harbouring fragments of the L. albus PDS gene ( LaPDS ) developed photo-bleaching that was associated with a significant reduction in LaPDS mRNA accumulation. PSV spread systemically in leaves, roots, and cluster roots, and small interfering RNA of LaPDS was detected in these organs. This is the first study to demonstrate the use of VIGS by PSV, suggesting that this vector can be applied to supress endogenous gene expression in shoots and roots of white lupin and to clarify the mechanisms of phosphorus starvation resistance.
Tracking metrical structure changes with sparse-NMF

The estimation of rhythmic properties such as tempo, beat positions or metrical structure are central aspects of Music Information Retrieval (MIR) research. Meter inference algorithms are typically designed to track metrical structure in presence of mild deviations of the feature estimates over time in order to account for performance imprecisions, expressive timing or musical effects such as accelerando. Abrupt changes of metrical structure over time are comparatively rarely addressed. In this paper, we present an unsupervised approach to detect metrical structure changes. Formulating the problem as a metrical structure based segmentation retrieval task, we present a variant of sparse NMF and compare it to existing methods. For evaluation, we introduce a new dataset of music recordings containing metric modulations with the corresponding annotations.
Revision of the Spider Mite Family Tetranychidae of Japan (Acari, Prostigmata)

A total of 78 Japanese species belonging to the family Tetranychidae (spider mites) are assigned to two subfamilies, five tribes, 16 genera, and 13 species groups (only in four genera). A guide to identification of the Japanese species is provided, and information is also given about the important literature references, host plants, and distribution of each species. Three new species, Eotetranychus rubricans, Oligonychus gotohi, and Tetranychus parakanzawai are described. Eotetranychus lewisi (McGregor), recently recorded from Japan, is redescribed.
Human retroviruses and AIDS 1996. A compilation and analysis of nucleic acid and amino acid sequences

This compendium and the accompanying floppy diskettes are the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses. The scope of the compendium and database is best summarized by the five parts that it comprises: (1) Nuclear Acid Alignments and Sequences; (2) Amino Acid Alignments; (3) Analysis; (4) Related Sequences; and (5) Database Communications. Information within all the parts is updated throughout the year on the Web site, http://hiv-web.lanl. gov. While this publication could take the form of a review or sequence monograph, it is not so conceived. Instead, the literature from which the database is derived has simply been summarized and some elementary computational analyses have been performed upon the data. Interpretation and commentary have been avoided insofar as possible so that the reader can form his or her own judgments concerning the complex information. In addition to the general descriptions of the parts of the compendium, the user should read the individual introductions for each part.
Biogenesis of Y RNA–derived small RNAs

Small non-coding RNAs (sRNAs) constitute a significant portion of the transcriptome in eukaryotes. Many of these sRNAs regulate gene expression. Next-generation sequencing (NGS) has revealed a plethora of previously uncharacterised sRNAs with potential biological function, a number of which originate from longer RNAs. Here, the biogenesis of sRNAs derived from the non-coding Y RNAs (YsRNAs) was characterised as a model for understanding this emerging class of sRNA fragments. Y RNAs are highly conserved, 100 nt long molecules involved in DNA replication which bind to the autoimmune proteins Ro60 and La. YsRNAs are produced in cells undergoing apoptosis. Here, it was demonstrated that YsRNAs are generated from the 5’ and 3’ ends of all four Y RNAs in stressed and unstressed cells. Furthermore, production of these fragments was observed in both cancerous and non-cancerous cells. Although YsRNAs have been proposed to have gene silencing activity, experiments done here found that YsRNAs do not enter the microRNA pathway and are not generated by the gene silencing-related protein Dicer. Furthermore, experiments established that the enzyme which produces fragments from tRNAs, angiogenin, was also not responsible for YsRNA generation. Using mammalian cultured cells along with gene knockout and RNA interference (RNAi) technology, it was determined that RNase L contributed to YsRNA generation. Furthermore, the Y RNA binding protein Ro60 was shown to be essential for YsRNA production through a model of RNase protection. Analysis of deep sequencing data in Ro60 knockout cells revealed that many other sRNAs are also dependent on Ro60. Finally, a ‘high definition’ (HD) protocol to improve NGS detection of sRNAs was tested. The HD protocol was found to be better at detecting sRNAs than current methods. This will facilitate more efficient detection of novel sRNAs in the future.
Lymphokines and the immune response

Perspectives on Cell Mediated Immunity In Vivo. The Cytokine Concept: Historical Perspectives and Current Status of the Cloned Cytokines. T Cell Clones as Sources of Lymphokines. Receptors on T and B Lymphocytes. Intracellular and Extracellular Factors Promoting Lymphocyte Activation and Proliferation. Transmembrane Signaling in B Cell Activation. Lymphoid Growth Factors: Gene Regulation and Biochemical Mechanisms of Action. Interleukin 1 and its Biologically Related Cytokines. Interleukin 2. Cachectin (Tumor Necrosis Factor) and Lymphotoxin as Primary Mediators of Tissue Catabolism, Inflammation, and Shock. Production of Hemopoietic Colony Stimulating Factors. Lymphokines and Tumor Immunity. Lymphokines and Cytokines in Reparative Processes.
Cytochromes P450 : role in the metabolism and toxicity of drugs and other xenobiotics

PART A: Chapter 1: Cytochrome P450 Structure and Function: An Evolutionary Perspective Chapter 2: Generation of reactive intermediates by cytochromes P450 PART B: Chapter 3: The CYP1A subfamily Chapter 4: The CYP1B subfamily Chapter 5: The CYP2A subfamily Chapter 6: The CYP2B subfamily Chapter 7: The CYP2C subfamily Chapter 8: The CYP2D subfamily Chapter 9: The CYP2E subfamily Chapter 10: The CYP2F, CYP2G and CYP2J subfamilies Chapter 11: The CYP3 family Chapter 12: The CYP4 family PART C: Chapter 13: Receptor-mediated regulation of cytochromes P450 Chapter 14: Modulation of cytochrome P450 activity by phytochemicals Chapter 15: Cytochromes P450 in cancer therapeutics
Identification and characterization of low pH-triggered conformational changes in the herpes simplex virus glycoprotein B

S Pfab, K. E. , S. J. Dollery and A. V. Nicola. 2010. Low pH-Triggered Conformational Changes in Herpes Simplex Virus Glycoprotein B are Associated With Viral Entry and Membrane Fusion. Medical Science Internship Program, Virginia Commonwealth University, Richmond, Virginia. Dollery, S. J., C. Siekavizza-Robles and A. V. Nicola. 2010. Reversible, Low pHtriggered Changes in the Antigenic and Trimeric Conformation of HSV gB are Associated with Viral Entry and Membrane Fusion. 35 International Herpesvirus Workshop, Salt Lake City, Utah. Dollery, S. J., C. Siekavizza-Robles and A. V. Nicola. 2010. Reversible, Low pHtriggered Changes in the Antigenic and Trimeric Conformation of HSV gB are Associated with Viral Entry and Membrane Fusion. FASEB “Virus Structure and Assembly” meeting, Saxtons River, Vermont.
Mating in the Smut Fungi: From a to b to the Downstream Cascades

Smut fungi induce disease only in their dikaryotic stage, which is generated by mating. Mating is regulated by two loci, which harbor conserved genes. In the a locus these genes specify pheromones and receptors, while in the b locus two transcription factors are encoded. This chapter focuses on the signaling cascades, which coordinate cyclic AMP (cAMP) and mitogen-activated protein kinase (MAPK) signaling in response to pheromone, as well as the transcriptional cascade triggered by the products of the b locus. The first part of this chapter highlights variations in the organization of the mating-type loci in Ustilago maydis, Sporisorium reilianum, and U. hordei, their consequences for mating, and finally evolutionary implication. The chapter reviews the signaling pathway underlying pheromone perception as well as the regulatory cascade triggered by the homeodomain heterodimer. Pheromone perception in smut fungi elicits the formation of conjugation hyphae. The connection between mating and cell cycle in U. maydis may also provide an explanation for the observation that the pheromone-induced formation of conjugation tubes is prf1 independent. One of the driving forces for many of the studies described in this chapter has been the assumption that finding the complete set of targets for the bE/bW heterodimer will explain sexual development and its connection to pathogenesis.
Machine learning approaches to modelling bicoid morphogen in Drosophila melanogaster

Bicoid morphogen is among the earliest triggers of differential spatial pattern of gene expression and subsequent cell fate determination in the embryonic development of Drosophila melanogaster. This maternally deposited morphogen, diffusing along the anterior-posterior axis of the embryo, establishes a concentration gradient which is sensed by target genes. In most computational model based analyses of this process, the translation of the bicoid mRNA is thought to take place at a fixed rate in the anterior pole of the embryo. Is this process of morphogen generation a passive one as assumed in the modelling literature so far, or would available data support an alternate hypothesis that the stability of the mRNA is regulated by active processes? This thesis demonstrates a Bicoid spatio-temporal model in which the stability of the maternal mRNA is regulated by being held constant for a length of time, followed by rapid exponential degradation. With the mRNA regulation, three computational models of spatial morphogen propagation along the anterior-posterior axis are analysed: (a) passive diffusion with a deterministic differential equation, (b) diffusion enhanced by a cytoplasmic flow term and (c) stochastic diffusion modelled by Gillespie simulation. Comparison of the parameter estimation in these models by matching to the publicly available data, FlyEx, suggests strong support for mRNA regulated stability. With a non-parametric Bayesian setting, we have applied Gaussian process regression to infer the mRNA regulation function as a posterior density. With synthetic data obtained from a linear spatio-temporal dynamical system and the experimental measurements (FlyEx), this approach is capable of inferring the driving input. Apart from confirming the validity of a regulated mRNA source, this work also demonstrates the applicability of a powerful non-parametric model of Gaussian processes in a spatio-temporal inference problem. In line with recent experimental works, we have also analysed this model with a spatial gradient of maternal mRNA, rather than being fixed at the anterior pole. Our final work is to analyse the dynamical topology of the gap gene network, which is the major developmental activity, taking place after the establishment and interpretation.
The effect of the sheep dip pesticide diazinon on behavioural and molecular markers in the freshwater shrimp Gammarus pulex

The purpose of this research was to determine the effects of the organophosphorothioate pesticide diazinon, its metabolite diazinon oxon and diazinon in a commercial formulation on the freshwater amphipod Gammarus pulex. It was found that diazinon in the commercial formulation was significantly more toxic to G. pulex than diazinon oxon, which in turn was significantly more toxic than diazinon.
The effect of ionic liquids with the tetrafluoroborate anion on terrestrial plants

Ionic liquids have attracted considerable interest as excellent alternatives to organic solvents to be used in homogeneous and biphasic processes. Ionic liquids are non-volatile, non-flammable and their “green” character has usually been justified with their negligible vapour pressure. However, the mar-keting of any chemical substance requires the determination of their impact on all elements of nature. Determination of the potential ecotoxicity of new chemical compounds is associated with conducting research on the effects of those compounds on the growth and development of selected organism. The phytotoxic properties of chiral ionic salts with the alkylimidazolium cation and the tetrafluoroborate anion were assessed for selected weeds popular in Poland: gallant soldier ( Galinsoga parviflora Cav.), white goosefoot ( Chenopodium album L.) and common sorrel ( Rumex acetosa L.). It was found that 3-alkyl-1-[(1 R ,2 S ,5 R )-(–)-menthoxymethyl]imidazolium tetrafluoroborates – ([C 8 -Im-Men][BF 4 ]) and ([C 9 -Im-Men][BF 4 ]) were low toxic to plants. A higher toxicity to terrestrial plants was characterized by ([C 11 -Im-Men][BF 4 ]). The toxicity effect of compounds depended non only on the length of the alkyl chain in the function group but also on the concentration of the used compound and the type of plant which was sprayed with the tested compound.
Deep convective events influence ozone variability in southeast South America

Human activities have led to changes in the atmospheric concentrations of several greenhouse gases, including tropospheric and stratospheric ozone and ozone depleting substances (ODS). Changes to the concentrations of these gases alter the radiative balance of the Earth’s atmosphere by changing the balance between incoming solar radiation and outgoing infrared radiation (IPCC/TEAP Special Report). While tropospheric ozone is directly related to anthropogenic activities, the key to stratospheric ozone is stratospheric water vapor which affects ozone, surface climate, and stratospheric temperatures (Shindell, 2001). In South America, deep convective storms in subtropical South America are some of the most intense in the world (Rasmussen et al, 2013.), where overshooting convective processes detrain tropospheric greenhouse gasses and reduce ozone concentrations.
Impact de l'extinction génique de la sialoprotéine osseuse (BSP) sur la différenciation des ostéoblastes et l'ostéogenèse in vitro : développement et validation d'un bioréacteur pour la culture ostéoblastique en trois dimensions

La culture cellulaire traditionnelle en deux dimensions (2D) ne peut pas reproduire les proprietes des tissus observees dans des organes en trois dimensions (3D). Ces tissus, en particulier les tissus de soutien comme l'os, sont soumis a des contraintes mecaniques, facteurs majeurs de regulation des interactions cellulaires et cellules/matrices. Il y a donc un interet croissant pour les modeles 3D, afin de mieux comprendre les differents aspects du fonctionnement cellulaire et du remodelage osseux, dans des systemes de moindre complexite que les modeles in vivo. Nous nous sommes interesses ici aux cellules osteoblastiques et a une de leur proteine matricielle, la sialoproteine osseuse (BSP). La BSP appartient a la famille des "small integrin-binding ligand N-linked glycoproteins" (SIBLING), impliquees dans le developpement, le remodelage et la mineralisation de l’os, et repondant rapidement a la contrainte mecanique. Notre objectif etait d’analyser l’impact de cette proteine sur la differenciation osteoblastique et l’osteogenese in vitro a partir de cellules de calvaria de souris presentant une extinction genique de la BSP (BSP-/-) cultivees en 2D et en 3D. Nous avons montre que les cellules BSP-/- presentaient un defaut de formation osseuse et de mineralisation qui est dependant de la densite cellulaire. Puis nous avons developpe et valide un bioreacteur perfuse et stimulable mecaniquement via le systeme ZetOsTM. Les premiers resultats obtenus avec cet outil controle montrent que l’environnement 3D ameliore la differenciation des cellules BSP-/-. Ces travaux restent a developper, notamment pour analyser l’effet des contraintes mecaniques sur ces cellules
Penerapan Metode Sample Bootstrapping untuk Meningkatkan Performa kNearest Neighbor pada Dataset Berdimensi Tinggi

Dalam klasifikasi semakin banyak atribut yang relevan yang dipakai akan mempengaruhi hasil akurasi dari algoritma tersebut. Seleksi fitur merupakan salah satu tahapan pre processing klasifikasi dengan cara menghilangkan fitur yang tidak relevan dalam data. Proses ini juga dapat mengurangi dimensi data serta meningkatkan akurasi klasifikasi. Algoritma kNearest Neighbor (kNN) merupakan metode untuk melakukan klasifikasi terhadap objek baru berdasarkan k tetangga terdekatnya. Algoritma kNN memiliki kelebihan karena sederhana, efektif dan telah banyak digunakan pada banyak masalah klasifikasi. Pada penelitian ini penggunaan metode Sample Bootstrapping diusulkan untuk meningkatkan akurasi yang optimal pada algoritma kNN. Metode Sample Bootstrapping digunakan untuk mengurangi jumlah data training yang akan diproses. Dalam penelitian ini menggunakan dataset yang memiliki dataset dengan dimensi yang tinggi. Dari hasil penelitian, penggunaan Sample Bootstrapping dengan algoritma pada dataset credit approval akurasinya meningkat 5.4% (96.87%-91.52%) dibandingkan algoritma kNN standar. Dari hasil penelitian yang dilakukan, dapat disimpulkan bahwa penggunaan Sample Bootstrapping dengan algoritma kNN menghasilkan akurasi yang lebih baik daripada algoritma kNN standar.
Characterization of Pea (Pisum Sativum L.) genes implicated in arbuscular mycorrhiza formation and function

The arbuscular mycorrhizal (AM) association results from a successful interaction between the genomes of the two symbiotic partners. In this context, the aim of my research was to better characterize the role of the late stage symbiosis-related pea genes PsSym36, PsSym33 and PsSym40 in the functional AM (i) by investigating the effect of mutations in the three genes on fungal and plant gene responses and (ii) by creating conditions for the localization of two of the genes, PsSym36 and PsSym40, on the pea genetic map for future map-based cloning. The expression of a subset of ten fungal and eight plant genes,previously reported to be activated during mycorrhiza development, was compared in Glomus intraradices-inoculated roots of wild type and Pssym36, Pssym33 and Pssym40 mutant pea plants. Most of the fungal genes were down-regulated in roots of the Pssym36 mutant where arbuscule formation is defective, and several were upregulated with more rapid fungal development in roots of the Pssym40 mutant. Microdissection of mycorrhizal PsSym40 roots corroborated preferential expression of the three G. intraradices genes SOD, DESAT and PEPISOM in arbuscule-containing cells. Inactivation of PsSym36 also resulted in down regulation of plant genes whilst mutation of the PsSym33 and PsSym40 genes affected plant gene responses in a more time-dependent way. Results thus indicate an implication of the investigated pea SYM genes in the modulation of plant and fungal molecular interactions linked to signaling, nutrient exchange or stress response regulation during AM symbiosis formation and functioning. Conditions for localization of the PsSym36 and PsSym40 genes on the pea genetic map were developed for their future map-based cloning. Based on the molecular markers obtained, it was possible to conclude that localization of the PsSym40 gene most likely resides outside the linkage groups I, II, III or V of the genetic map of pea.
Protease nexin 1: A novel inducer of prostate tumor cell apoptosis

Protease nexin 1 (PN1), a member of serine protease inhibitors (SERPINs) family, is known for its ability to bind and inhibit a wide range of proteases. Recently, we have found that PN1 is able to induce prostate cancer cell undergoing apoptosis through a distinct mechanism of engaging uPA-uPAR complexes and the regulation of two independent downstream signaling cascades, leading to the repression of X-linked inhibitor of apoptosis protein (XIAP). In this process, PN1 expression reduces the expression of NF-κB signalling component p65 and thereby lessens xiap transcription. Alternately, PN1 activity can prevent the stability of XIAP by reducing XIAP phosphorylation at serine 87 via a blockade of AKT signaling. A combination of exogenous PN1 and TRAIL leads to a substantial growth lag in prostate cancer xenografts, indicating the potential of PN1 as a promising target for improving prostate cancer therapy. Furthermore, human prostate tissue arrays show inverse levels of PN1 and XIAP in tumor and normal prostate. Hence, the PN1-uPA regulatory axis may serve as an inducer of tumor cell apoptosis by modulating survival pathways, and therefore delay the tumor growth of prostate cancer.