Miracle-dz/UniFAR-FTUs huggingface dataset:
Caractéristion de nouveaux substrats des sérine - thréonine protéine-kinases de mycobacterium tuberculosis

Le sequencage integral du genome de Mycobacterium tuberculosis a permis de mettre en evidence l’existence de onze Serine/Threonine Proteine-Kinases (STPKs) chez cette bacterie. Bien que la quasi-totalite des STPKs aient ete biochimiquement caracterisees, tres peu de substrats endogenes ont pu etre identifies. Par consequent, le role physiologique de ces couples kinase/substrat reste a elucider. Tout d’abord, les etudes realisees au cours de ce travail ont concerne la caracterisation biochimique de la proteine-kinase PknL, ainsi que l’identification de ses substrats potentiels, et notamment la proteine Rv2175c. En effet, l’analyse de l’environnement genetique du gene pknL de la kinase a revele la presence du gene adjacent rv2175c, pouvant ainsi representer un substrat eventuel de PknL. Les differentes approches mises en oeuvre ont permis d’identifier cinq sites de phosphorylation sur PknL, et de mettre en evidence le caractere essentiel des residus K48, T173 et T175 dans les mecanismes d’autophosphorylation de PknL et de phosphorylation de Rv2175c, confirmant ainsi Rv2175c comme substrat specifique de PknL. Par ailleurs, la caracterisation par RMN de la structure de Rv2175c a permis de determiner la fonction de cette proteine. Rv2175c possede toutes les caracteristiques structurales d’une proteine capable de fixer l’ADN. Des etudes fonctionnelles ont permis de confirmer la capacite de Rv2175c de fixer l'ADN et ont mis en evidence le mecanisme de regulation via phosphorylation regissant son activite de fixation. Ensuite, nous avons mis en evidence la phosphorylation des proteines chaperonnes mycobacteriennes et, plus particulierement, caracterise GroEL1. Nous avons demontre que GroEL1 etait phosphorylee par PknF, et identifie les residus T25 et T54 comme etant les sites de phosphorylation de GroEL1. L’ensemble de cette etude nous a donc permis de caracteriser de nouveaux substrats de phosphorylation chez M. tuberculosis, de mieux apprehender les interactions kinase/substrat et d’impliquer la phosphorylation dans la regulation de l’activite de ces substrats
Does Pecking Order Theory Hold Among Kenyan Firms?

This study examined the pecking order theory of capital structure through annual data of 37 firms listed at the Nairobi Securities Exchange for the period 2011-2016. Estimation results established a positive relationship between changes in debt and investments and a negative relationship between changes in debt and cash flows. Overall, the findings suggest that financial deficits determine net debt issues and hence a strong case for pecking order theory in Kenya in explaining capital structure decisions.
Financial Spillover Effects in Supply Chains: Do Customers and Suppliers Really Benefit?

Studies have shown that leading supply chain companies are associated with significantly higher company financial ratios than competitors. In contrast, little research has focused on the financial performance of the affiliated suppliers and customers of such supply chain leader (SCL) companies. Thus, the central purpose of this paper is to determine, from a financial perspective, whether suppliers and customers benefit or lose by participating in a SCL network (so called “financial spillover effects”). Companies that were ranked in the Gartner Supply Chain Top 25 were selected as SCLs. For each selected firm, the five largest suppliers and customers were identified and compared with a control sample from the same industry. In order to elaborate on existing insights into the (financial) outcome of supply chain relationships, we applied an explorative approach with abductive reasoning, while comparing the secondary data for 224 SCL supplier (56 firms) and 168 SCL customer (42 firms) firm-years with 1940 (485 firms) and 1544 (386 firms) control firm-years, respectively. The following insights are made: First, the superior financial performance of SCLs was confirmed. Second, the financial performance of suppliers and customers showed superior liquidity and activity ratios but inferior profitability ratios. Third, suppliers showed much more significant results than customers.
Spatial Forecasting of Dissolved Oxygen Concentration in the Eastern Black Sea Basin, Turkey

The aim of this study was to model, as well as monitor and assess the surface water quality in the Eastern Black Sea (EBS) Basin stream, Turkey. The water-quality indicators monitored monthly for the seven streams were water temperature (WT), pH, total dissolved solids (TDS), and electrical conductivity (EC), as well as luminescent dissolved oxygen (LDO) concentration and saturation. Based on an 18-month data monitoring, the surface water quality variation was spatially and temporally evaluated with reference to the Turkish Surface Water Quality Regulation. First, the teaching–learning based optimization (TLBO) algorithm and conventional regression analysis (CRA) were applied to three different regression forms, i.e., exponential, power, and linear functions, to predict LDO concentrations. Then, the multivariate adaptive regression splines (MARS) method was employed and three performance measures, namely, mean absolute error (MAE), root means square error (RMSE), and Nash Sutcliffe coefficient of efficiency (NSCE) were used to evaluate the performances of the MARS, TLBO, and CRA methods. The monitoring results revealed that all streams showed the same trend in that lower WT values in the winter months resulted in higher LDO concentrations, while higher WT values in summer led to lower LDO concentrations. Similarly, autumn, which presented the higher TDS concentrations brought about higher EC values, while spring, which presented the lower TDS concentrations gave rise to lower EC values. It was concluded that the water quality of the streams in the EBS basin was high-quality water in terms of the parameters monitored in situ, of which the LDO concentration varied from 9.13 to 10.12 mg/L in summer and from 12.31 to 13.26 mg/L in winter. When the prediction accuracies of the three models were compared, it was seen that the MARS method provided more successful results than the other methods. The results of the TLBO and the CRA methods were very close to each other. The RMSE, MAE, and NSCE values were 0.2599 mg/L, 0.2125 mg/L, and 0.9645, respectively, for the best MARS model, while these values were 0.4167 mg/L, 0.3068 mg/L, and 0.9086, respectively, for the best TLBO and CRA models. In general, the LDO concentration could be successfully predicted using the MARS method with various input combinations of WT, EC, and pH variables.
Mass spectrometric characterization and fluorophore-assisted light inactivation of human excitatory amino acid transporter 2

Mass spectrometric characterization and fluorophore-assisted light inactivation of human excitatory amino acid transporter 2. Glia-expressing excitatory amino acid transporter 2 (EAAT2) mediates the bulk of glutamate re-uptake in the human central nervous system (CNS) and is associated with a variety of neurological disorders. Our understanding of the structure and mechanism of this integral membrane protein is limited. The goal of this study was to use pharmacological, mass spectrometric (MS) and photochemical approaches to probe EAAT2. For MS characterization, a hexahis epitope was incorporated into the N-terminus of human EAAT2. The recombinant protein was functionally expressed in HEK 293T cells and purified through a single-step nickel column. In-gel and in-solution trypsin digestions were conducted on the isolated protein. Overall, eighty-nine percent sequence coverage of the protein was achieved. An 88-amino acid tryptic peptide covering the proposed substrate binding site was revealed after N-deglycosylation. This study provided an efficient and simple method to purify, digest and characterize integral membrane proteins by MS. In addition, the EAAT2 peptide fingerprint obtained by digestion offered a template for later protein modification studies. In an effort to design photoaffinity labels for hEAAT2, a series of aryl diaminopropionic acids and aryl aspartylamide compounds were synthesized and characterized as potent EAAT inhibitors. Compounds containing 9-fluorenone groups were found to be able to irreversibly inactivate EAATs under UV-A illumination. The mechanism underlying the photo-inactivation was shown to be singlet oxygen mediated protein oxidation. The specificity of the photo-inactivation was illustrated by the protection effects of inhibitors, as well as the proximity between the transporter and ligands. Trypsin digestion and MS analyses revealed a mass change of a peptide from hEAAT2 binding pocket in the photo-inactivated protein. Molecular docking results supported our speculation that a tryptophan residue was oxidized during the photo-inactivation. The identification of possible EAAT2 photo-inactivation site provided additional information for the location of the EAAT2 lipophilic interaction domain. iii ACKNOWLEDGEMENTS First and foremost I would to express my deep and sincere gratitude to my advisor, mentor, and friend, Dr. Richard Bridges. I have been privileged to have Rich guiding me through the ups and downs of my graduate research. The completion of this dissertation would not have been possible without his scientific insight, leadership and endless support. I would like to thank my committee members: Dr. me to use the Mass Spectrometry facility and the UV photolysis equipments. I thank Dr. Bill Laws for guiding my first …
ANALISA 4 ALGORITMA DALAM KLASIFIKASI LIVER MENGGUNAKAN RAPIDMINER

Hati merupakan salah satu organ penting dalam tubuh manusia yang berfungsi untuk detoksifikasi racun atau penetral racun dari segala sesuatu yang masuk ke dalam tubuh kita, sehingga tubuh menjadi lebih sehat. Hati dapat terserang suatu penyakit yang mampu mengganggu tugasnya, apabila penyakit hati sudah menyerang maka racun akan tersebar ke seluruh tubuh dan membuat tubuh menjadi tidak sehat. Penyakit liver merupakan penyakit hati yang disebabkan oleh virus, alkohol, pola hidup dan lainnya. Menurut data WHO (World Health Organization) menunjukkan hampir 1,2 juta orang per tahun khususnya di Asia Tenggara dan Afrika mengalami kematian akibat terserang penyakit liver. Seseorang sering tidak menyadari atau terlambat mengetahui penyakit liver sehingga ketika diperiksa penyakit liver sudah parah, akan lebih baik apabila dilakukan penanganan lebih awal dengan mengetahui gejala-gejala yang diderita. Data mining mampu membantu diagnosa penyakit liver dengan lebih mudah terutama untuk membantu para dokter dalam menentukan apakah pasien menderita penyakit liver atau tidak, dengan gejala hampir mendekati penyakit liver. Proses diagnosa penyakit liver dilakukan dengan proses klasifikasi dan hasilnya berupa pasien tersebut menderita liver atau tidak. Penelitian ini menggunakan 4 algoritma data mining yaitu Naïve Bayes, K-Nearest Neighbor (KNN), Decision Tree dan Neural Network. Dataset yang digunakan yaitu Indian Liver Patient Dataset (ILPD) dari website UCI Machine Learning Repository. Keempat algoritma tersebut dibandingkan manakah yang lebih baik akurasinya untuk kasus diagnosa penyakit liver. Hasilnya menunjukkan bahwa algoritma Naïve Bayes memiliki akurasi 55,75%, algoritma K-Nearest Neigbor memiliki akurasi 66,36%, algoritma Decision Tree memiliki akurasi 67,04%, dan algoritma Neural Network memiliki akurasi 70,50%. Akurasi tersebut tergolong rendah karena kelas atau label antara pasien penyakit liver dan pasien tidak memiliki liver tidaklah seimbang, kelas pasien penyakit liver lebih banyak dibandingkan pasien tidak memiliki liver, sehingga banyak data yang diklasifikasikan sebagai pasien penyakit liver. Keywords— Data Mining, Decision Tree, Klasifikasi, KNN, Liver, Naïve Bayes, Neural Network
Evaluation of Sampling Methods for the Study of Avian Respiratory Microbiota

SUMMARY. Although poultry microbiome discoveries are increasing due to the potential impact on poultry performance, studies examining the poultry respiratory microbiome are challenging because of the low microbial biomass and uniqueness of the avian respiratory tract, making it difficult to sample enough material for microbial analysis. Invasive sampling techniques requiring euthanasia are currently used to increase microbial mass for the analysis, thus making it impossible to sample individual birds longitudinally. In this study, we compared invasive (nasal wash, upper tracheal wash, lower tracheal wash, and lower respiratory lavage) and noninvasive (tracheal and choanal swabs) respiratory sampling techniques in two independent experiments by using 4-wk-old chickens. We first established the experimental baseline of respiratory microbiota by using invasive techniques to enable reasonable comparisons between sampling methods and between experiments. Although noninvasive sampling (live-bird swabs) resulted in lower 16S ribosomal RNA gene copy numbers compared with invasive sampling, live swabs were able to detect the dominant microbes captured by invasive techniques. Nevertheless, swabs from euthanatized birds were more reflective of the microbiota captured through invasive methods than live swab. Furthermore, from two separate experiments, we also demonstrated that respiratory microbiota sampling is highly reproducible, especially in the trachea and lower respiratory tract. Our study provides new insights and perspectives on decision making when sampling and studying poultry respiratory microbiota.
Antimicrobial activity and chemical characterization of the bark decoction of cumaru stem

ABSTRACT: The plant, Amburana cearensis A. C. Smith (Fabaceae), commonly called cumaru, is widespread in the Caatinga cearense, a less known ecosystem in Brazil. A. cearensis is rich in several compounds like protocatechuic acid, tannins, coumarin, flavonoids and phenolic heterosides, such as amburosides A and B, that have been isolated. The aim of this study was to determine the antimicrobial potential and draw the chemical profile of the distinct characteristics of A. cearensis stem bark decoction, for its possible potential as a food conservation agent. The chemical compounds were characterized by one- and two-dimensional 1H and 13C NMR analyses and Liquid Chromatography-Mass Spectrometry (LCMS). The compounds of coumarin, amburosides A and B, and glycosylated (Z)-o-coumaric acid. Using the plaque microdilution technique, the antimicrobial action was tested on Escherichia coli, Salmonella Enteritidis, Pseudomonas aeruginosa, Staphylococcus aureus and Listeria monocytogenes. The decoction demonstrated antimicrobial activity on Gram-positive bacteria. This was encouraging because natural antimicrobials are beneficial for food production, as they can inhibit the pathogenic microorganisms and boost the quality of hygiene and cleanliness.
What explains managers’ escalating behaviors in a failing NPD project? The impact of managerial perceptions of opportunities and threats in a stage-gate process

ABSTRACT Drawing on recent advancement in behavioral decision-making theory and the escalation-of-commitment literature, we examine how managers’ perceptions of threats and opportunities in the external environment may shape their decision to escalate investment in a failing new product development (NPD) project. We test our theoretical model with two studies: first, a behavioral decision-making experimental study with a sample of 128 managers; and, second, an interview study with 12 managers. Our results show that managers’ perceptions of environmental opportunities and business threats significantly shape their decision to escalate commitment and that the impact of such managerial perceptions on escalating tendency is contingent on the stage of the innovation process.
Relationships Between People with Cancer and Their Companion Animals: What Helps and Hinders

ABSTRACT This qualitative research project examined the impact of the relationships between persons with cancer and their companion animals. The goal of this study was to explore the helpful and unhelpful aspects of having a companion animal for people with cancer dealing with the emotional challenges accompanying diagnosis and treatment. The Enhanced Critical Incident Technique method was used to gather information on, and analyze and interpret the interviews of, 13 British Columbian women with cancer about their relationships with their companion animals. The face-to-face interviews yielded rich descriptions of these relationships and the ways in which companion animals contributed to or detracted from the participants’ sense of wellbeing during their illness. The analysis of relational impacts resulted in 13 categories, in rank order by participation rate: Companionship & Presence; Emotional & Social Support; Purpose & Role; How Companion Animals are Different from People; Health and Pain Management; Companion Animal Intuition & Adaptability; Being Positive & in the Moment; Companion Animal as Protector & Caregiver; Touch; Unconditional Love & Devotion; Existential & Spiritual Factors; Family Members & Family Finances; and Caretaking of Sick or Dying Companion Animal. The findings are congruent with current human– animal bond literature, confirming the significant and primarily positive impact of the psychosocial support experienced by human beings from their companion animals. It is recommended that, for practice and research, the areas of counselling, psychosocial oncology, and psychological theory include and explore the impact of companion animals in their clinical work and understanding of the experiences and needs of people with cancer and other conditions.
Detection of genetic diversity using microsattelites in rice (Oryza sativa L.).

The objective of this research was to detect useful microsatellite markers for studying genetic diversity among eight rice varieties to reveal the genetic relationships among these varieties and to evaluate the potential of this technique for fingerprinting and clustering of rice genotypes. The 14 rice microsatellites markers used in this study produced a total of 112 alleles from the eight genotypes analyzed. The sizes of the alleles observed with automated fluorescent detection ranged from 65 bp to 336 bp. The PIC values reflection of alleles diversity and frequency among the varieties, were high for all microsatellites with average 0.782 and ranged from a low of 0.438 for RM50 to a high of 0.891 for RM206 and RM241. In addition, a cluster analysis was conducted to grouping the varieties and to construct a dendogram. The dendogram indicated that the classification of the varieties was in agreement with their parentage. This result proved that fluorescently labeled microsatellite markers were a good tool for testing genetic diversity. Finally, in this study the automated fluorescence detection was used to improve the efficiency of microsatellite analysis to a level comparable to that of multi-locus fingerprinting techniques. Therefore, this analysis can be expected to greatly increase the efficiency of genetic diversity assessment, variety fingerprinting and identification, the genetic physical mapping of genes and quantitative trait loci and marker-assisted selection during plant breeding.
A Triple‐Stack Column Procedure for Rapid Separation of Cu and Zn from Geological Samples

We present a new procedure for the separation and purification of Cu and Zn from geological samples. Our procedure employed a single pass, triple‐stack column set‐up. The first column, filled with TRU resin (TrisKem International), quantitatively removed Fe and Ti from sample matrices. A second column, filled with pre‐filter resin (TrisKem International), removed organic compounds. Finally, a third column, filled with anion exchange resin (AG1‐X8, 200–400 mesh, Bio‐Rad), was used to separate Cu and Zn from the remaining matrix. Our procedure required about 50% less acid volume than previously reported methods for Cu and Zn separation, thereby minimising analytical blanks and column running times. Copper and Zn stable isotope ratios were determined by a Thermo Neptune Plus MC‐ICP‐MS using Zn and Cu external normalisation, respectively, in addition to sample‐standard bracketing to correct for instrumental mass bias. We explore the inter‐calibration of Cu and Zn isotope fractionation coefficients during analysis by measuring mixed Cu–Zn solutions with enhanced mass bias variation generated by varying sample gas flow rates. Our results demonstrate that this procedure is useful when variation in instrumental mass bias throughout analytical sequences is insufficient to inter‐calibrate Cu and Zn fractionation coefficients.
The Effects of Light Intensity on the Flowering Phenology and Inter-Population Differences of the Androdioecious Plant Species, Mercurialis annua

Mercurialis annua is an androdioecious plant species, meaning populations may contain both male and cosexual individuals. It is able to modify resource allocation to male and female function in varying conditions, such as light and competition regimes. One component of resource allocation may involve changes in the relative timing of production of male and female flowers. A controlled greenhouse experiment was performed to test for the effects of shading on the production of male and female flowers in four populations. Evidence suggested that plants grown in shade would be relatively less female than those grown in the sun. Although the average number of day to the production of male versus female flowers did not show a response to shading, the number of plants producing male versus female flowers during early development differed between light treatments. The shade treatment induced a reduction in number of plants producing female flowers, as predicted by my hypothesis. The populations differed in their specific responses to shading, suggesting that populations have adapted individually to local selective pressures. Degree Type Open Access Senior Honors Thesis
Occurrence of different development time patterns induced by photoperiod in Anagrus atomus (Hymenoptera: Mymaridae), an egg parasitoid of Empoasca vitis (Homoptera: Cicadellidae)

The wasp Anagrus atomus L. parasitizes eggs of the cicadellid Empoasca vitis (Göthe) on grapevines during the vegetative season. In vineyards, abundant parasitoid emergence occurs in the autumn as a result of a developmental delay in part of the A. atomus population. In this context, physiological times required by the parasitoid to develop in E. vitis eggs are recorded during the summer. In early summer, all individuals develop fully, with physiological times in agreement with those reported in the literature. From early August onwards, an increasing proportion of parasitoids show a delay in development involving pre‐imaginal stages. Under transmission microscopy, larvae of A. atomus inside the eggs of E. vitis can be clearly differentiated as ‘light’ and ‘dark’ types, which are associated with normal and delayed development, respectively. The decreasing photoperiod as autumn approaches appears to promote the retardation of growth. This phenomenon can be considered a typical case of risk spreading because, when the availability of E. vitis eggs in vineyards is high (i.e. in early summer), A. atomus shows (i) only a normal developmental pattern that allows a faster population increase, whereas (ii) when E. vitis egg availability begins to be scarce (i.e. from mid summer), an increasing proportion of individuals having delayed development provides better fitness because it allows the parasitoid to synchronize its life history with leafhopper species that lay overwintering eggs on plants other than grapevines.