Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of factors contributing to virulence in Escherichia coli

Title of Document: REGULATION OF FACTORS CONTRIBUTING TO VIRULENCE IN ESCHERICHIA COLI Arindam Mitra, Doctor of Philosophy, 2008 Directed By: Assistant Professor, Dr. Suman Mukhopadhyay, Department of Veterinary Medicine Extraintestinal pathogenic strains of Escherichia coli cause a wide range of diseases including colibacillosis in chickens and urinary tract infections in humans. Persistent infections in E. coli and other gram-negative species are associated with populationdependent physiological processes such as cell-cell signaling and biofilm formation. Such social behaviors require careful coordination and modulation of gene expression in response to environmental cues. Adaptive response of bacteria in new environment is predominantly achieved through a signaling cascade called twocomponent regulatory systems. The function of the BarA/UvrY two-component regulatory system and its downstream factors in controlling virulence associated processes, specifically regulation of AI-2 based signaling and biofilm formation was investigated. In E. coli, a type of cell-cell signaling termed Quorum Sensing involves release, detection, and response to small molecule called autoinducer (AI-2), synthesis of which is dependent on luxS gene products via methyl cycle. The BarA-UvrY and Csr system displayed dual regulation on luxS expression at the level of transcription and post-transcription. The uptake of AI-2 by the Lsr transporter is also modulated by the signaling cascade suggested a balance between AI-2 synthesis and uptake in the cell. The role of transcriptional regulator uvrY in biofilm formation in Uropathogenic Escherichia coli was also studied. Mutation of uvrY reduced expression of fimA and papA, major fimbrial subunit of Type 1 and Pap pilus respectively. Acidic exopolysaccharide accumulation and the ability to swarm are also being impaired. Finally, uvrY mutants demonstrated poor colonization in kidneys and bladders in an ascending model of UTI. Overall, the effect of uvrY on biofilm formation seems to be multi-factorial and might play a critical role in adaptation and colonization of UPEC. The fine tuning of processes associated with cell-cell communication and biofilm formation at the level of transcription and post-transcription by the BarA/UvrY/CsrA signaling cascade indicated that this system might be crucial for quick adaptation, social behavior, colonization and virulence attributes in Escherichia coli. REGULATION OF FACTORS CONTRIBUTING TO VIRULENCE IN ESCHERICHIA COLI
Ten years after Copenhagen: Reimagining climate change governance in urban areas

In this review, we take stock of the last decade of research on climate change governance in urban areas since the 2009 conference in Copenhagen. Using a systematic evaluation of academic publications in the field, we argue that the current moment of research has been shaped by two recent waves of thought. The first, a wave of urban optimism, which started in 2011 and peaked in 2013, engaged with urban areas as alternative sites for governance in the face of the crumbling international climate regime. The second, a wave of urban pragmatism, which started in 2016, has sought to reimagine urban areas following the integration of the “sub‐national” as a meaningful category in the international climate regime after the 2015 Paris Agreement for Climate Action. Four themes dominate the debate on climate change governance in urban areas: why there is climate action, how climate action is delivered, how it is articulated in relation to internationally reaching networks, and what implications it has to understand environmental or climate justice within urban settings. Calls to understand the impacts of climate change policy have fostered research on climate change politics, issues of power and control, conflicts, and the inherently unjust nature of much climate policy. What is largely missing from the current scholarship is a sober assessment of the mundane aspects of climate change governance on the ground and a concern with what kind of cultural and socio‐economic change is taking place, beyond comparative analyses of the effectiveness of climate policies.
Etude fonctionnelle de Pmp23, une nouvelle enzyme de clivage du peptidoglycane chez Streptococcus pneumoniae

Le peptidoglycane est un composant majeur de la paroi cellulaire bacterienne dont l'integrite est essentielle a la survie cellulaire. La biosynthese du peptidoglycane est un processus regule faisant intervenir des enzymes de synthese, les « Penicillin-Binding Proteins », et des hydrolases qui agissent, selon toute vraisemblance, de facon concertee lors de la croissance et de la division bacterienne. La comparaison des genomes bacteriens a permis d'identifier un nouveau domaine proteique, probablement implique dans le clivage du peptidoglycane, present uniquement chez les bacteries a Gram positif : le domaine PECACE (PEptidoglycan CArbohydrate Cleavage Enzyme). Ce domaine, predit pour avoir un repliement tridimensionnel analogue aux domaines catalytiques de la transglycosylase lytique Slt70 d'Escherichia coli et du lysozyme de type G d'oie, pourrait participer au clivage de la liaison glycosidique β(1-4) entre les residus acide N-acetyl-D-muramique et N-acetyl-D-glucosamine du peptidoglycane. Chez la bacterie pathogene Streptococcus pneumoniae, ce domaine est present dans la region extracellulaire d'une proteine que nous nommons Pmp23 (Pneumococcal Membrane Protein). La forme recombinante de cette proteine membranaire bitopique de 23 kDa degrade in vitro des extraits bacteriens contenant du peptidoglycane. L'inactivation du gene pmp23 chez S. pneumoniae modifie le comportement de la bacterie en culture, accroit sa sensibilite aux antibiotiques de la famille des β-lactamines et perturbe la localisation du site de division. Ces observations indiquent que Pmp23 est une hydrolase intervenant dans le metabolisme du peptidoglycane septal.
Functional analysis of Arabidopsis chromatin modification and remodeling regulators (CHR5 and JMJ15) in gene expression

Chromatin remodeling and histone modification play important roles in the establishment and dynamic regulation of gene expression states. However, little is known regarding to the regulatory mechanism of chromatin modification and remodeling that control gene expression involved in plant development and responses to environmental cues. My thesis work concerns functional analysis of an Arabidopsis Chromodomain/Helicase/DNA-binding 1 (CHD1) type chromatin remodeling gene known as CHR5 and a histone demethylase gene that specifically removes methyl groups from methylated histone H3 lysine 4 (H3K4me), called JMJ15 in regulating chromatin structure or in resetting chromatin modifications that control the expression of plant developmental and stress responsive genes. In the first part of the study we found that CHR5 expression is activated during embryogenesis and remained to be expressed in developing organs/tissues. Analysis of mutants revealed that loss-of-function of the genes led to decreased expression of key embryo maturation genes LEC1, ABI3 and FUS3 in developing seeds and reduced seed storage protein accumulation. Analysis of double mutants revealed an antagonistic function between CHR5 and PKL, a CHD3 gene, in embryo gene promoter activity and seed storage protein accumulation. CHR5 was directly associated with the promoters of ABI3 and FUS3 and chr5 mutations led to increased nucleosome occupancy near the transcriptional start site. The results suggest that CHR5 is involved in nucleosome occupancy to regulate embryo identity genes expression, which is counterbalanced by PKL during embryo development. The second part of this study showed that expression of JMJ15 was restricted to a few tissues during vegetative growth. The jmj15 gain-of-function mutations reduced the length of seedling hypocotyls and inflorescence stems with higher accumulation of lignin in the stem, while the loss-of-function mutants did not show any visible phenotype. The gain-of-function mutants enhanced salt tolerance, whereas the loss-of-function mutants were more sensitive to salt. Transcriptomic analysis revealed a much higher number of genes down-regulated in JMJ15 over-expression plants, which are highly enriched for H3K4me3 and H3K4me2. Among the down-regulated genes, many encode transcription regulators of stress responsive genes. The data suggest that increased JMJ15 levels may regulate the gene expression program that may coordinate plant growth restrains and enhances stress tolerance. Taken together, my thesis work brought a few new elements to the current understanding of chromatin regulators function in plant gene expression.
The Association between Estrogen and Progesterone Receptors Expression with the Stages of Endometrioid-type Ovarian Carcinoma at Sanglah General Hospital, Bali, Indonesia: A Preliminary Study

BACKGROUND: Ovarian cancer is the most common cause of death among gynecologic malignancies. Poor prognosis is mainly due to the high incidence of advanced stage at the time of diagnosis as well as low estrogen receptor (ER) and progesterone receptor (PR) expression. Based on it, further understanding is needed to predict the course of disease. AIM: This study aims to evaluate the expression of ER and PR with the stages of endometrioid-type ovarian carcinoma as the more frequent type carcinoma at Sanglah General Hospital, Bali. METHODS: An analytical cross-sectional study was conducted among 36 samples of endometrioid-type ovarian carcinoma examined at Anatomical Pathology Laboratory, Faculty of Medicine, Udayana University/Sanglah General Hospital, Denpasar. The histopathological diagnosis, grade, and tumor size, as well as determination on hematoxylin-eosin staining were assessed. The expression of ER and PR was examined using immunohistochemical stain. Data were analyzed using the SPSS version 15 software for risk analysis and p < 0.05 was assumed statistically significant. RESULTS: Most of the samples were from 41 to 50 years of age group (41.7%) and the average age was 51.1 ± 9.80 years old. Based on the degree of differentiation, Grade 2 was the most common cases (38.9%). However, the tumor size assessment revealed that T3 was predominant (41.7%). Positive ER and PR expressions were obtained in 18 samples (50.0%) and 14 samples (38.9%), respectively. Fisher’s exact test showed a significant association between ER expression with grade (odds ratio [OR]: 6.25; 95% confidence interval [CI] 1.327–29.432; p = 0.018) and tumor size (OR: 4.375; 95% CI 1.027–18.629; p = 0.043). A similar findings also found in PR expression with grade (OR: 15.60; 95% CI 1.728–140.829; p = 0.004) and tumor size (OR: 6.12; 95% CI 1.394–26.876; p = 0.016). CONCLUSION: ER and PR expressions are significantly associated with grade and tumor size in the endometrioid-type ovarian carcinoma.
Enabling Suspended Sediment Concentration Detection With Passive RFID Tags

Suspended sediment concentration detection is a critical task for many practical applications. Traditional schemes suffer from complex operation, poor real-time performance and high cost. This paper explores the possibility of detecting sediment concentration in water with low-cost passive RFID tags. We propose a simple yet effective signal model, in which the received signal is separated into static and dynamic components. We establish the relationship between measured signal changes and sediment concentration via polynomial fitting in offline step. Therefore, the sediment concentration can be accurately detected with a simple mapping operation in the following online step. We implement a prototype system with COTS RFID devices, and extensive experiments are conducted to validate our design. The experimental results demonstrate that our scheme is able to achieve more than 95% accuracy for sediment concentration detection in water.
Establishment and Evaluation of a 6-Gene Survival Risk Assessment Model Related to Lung Adenocarcinoma Microenvironment

Objective A survival risk assessment model associated with a lung adenocarcinoma (LUAD) microenvironment was established and evaluated to identify effective independent prognostic factors for LUAD. Methods The public data were downloaded from the TCGA database, and ESTIMATE prediction software was used to score immune cells and stromal cells for tumor purity prediction. The samples were divided into the high-score group and the low-score group by the median value of the immune score (or stromal score). The Wilcoxon test was used for differential analysis. GO and KEGG enrichment analysis of differentially expressed genes (DEGs) was performed using “clusterProfiler” of R package. Meanwhile, univariate and multivariate regression analysis was performed on DEGs to construct a multivariate Cox risk regression model with variable gene expression levels as independent prognostic factors affecting a tumor microenvironment (TME) and tumor immunity. Results This study found that LUAD patients with high immune cell (stromal cell) infiltration had better prognosis and were in earlier staging. Functional enrichment analysis revealed that most DEGs were related to the proliferation and activation of immune cells or stromal cells. A survival prediction model composed of 6 TME-related genes (CLEC17A, TAGAP, ABCC8, BCAN, FLT3, and CCR2) was established, and finally, the 6 feature genes closely related to the prognosis of LUAD were proved. The AUC value of the ROC curve in this model was 0.7, indicating that the model was reliable. Conclusion Six genes related to the LUAD microenvironment have a predictive prognostic value in LUAD.
A db-Scan Hybrid Algorithm: An Application to the Multidimensional Knapsack Problem

This article proposes a hybrid algorithm that makes use of the db-scan unsupervised learning technique to obtain binary versions of continuous swarm intelligence algorithms. These binary versions are then applied to large instances of the well-known multidimensional knapsack problem. The contribution of the db-scan operator to the binarization process is systematically studied. For this, two random operators are built that serve as a baseline for comparison. Once the contribution is established, the db-scan operator is compared with two other binarization methods that have satisfactorily solved the multidimensional knapsack problem. The first method uses the unsupervised learning technique k-means as a binarization method. The second makes use of transfer functions as a mechanism to generate binary versions. The results show that the hybrid algorithm using db-scan produces more consistent results compared to transfer function (TF) and random operators.
On the use of textile materials in robotics

Robots can be used, among a broad variety of different applications, in the textile industry to fulfill mechanically challenging tasks which common automats are not capable of. On the contrary, textile fabrics can also be integrated in robotics. Textile-based laminates can be applied as actuators; spacer fabrics can prevent robot arms from hurting men or autonomous robots from damaging themselves on difficult terrain; or as flexible sensors in soft and traditional robotics. Here, we give an overview of recent applications of textile materials in robotics and point out possible future utilization of diverse textile materials in this emerging field of research and development with increasing importance for industrial processes as well as services.
Biochar and Other Organic Amendments Improve the Physicochemical Properties of Soil in Highly Degraded Habitat

Land degradation is an endless challenge in the world. Thus, rehabilitation with organic amendments (OAs) is an urgent priority issue. The purpose of this study is to assess the effect of biochar and other OAs application on soil physicochemical properties and growth parameters of cover crops in greenhouse. Biochar, compost and manure were used as OAs. Soil samples were collected from nine random corners of 30 cm depth and composited. In each experiment, five treatments were considered (biochar, compost, manure, mixed and control) at 1:1 ratio of OAs and soil in a pot, with completely randomized design arrangement in triplicate. The field experiment was made on completely randomized block design and each block contained five 41 x 4 m plots assigned at random within the block and separated by 1 m walkways. OAs additions increased soil pH (5.69-8.13), cation exchange capacity (43.78-49.98 cmolc/kg), organic carbon (1.41-2.46%), organic matter (2.43-3.91%), total nitrogen (0.13-0.76%), available P (18.89-28.53 ppm) and (iron, Fe, manganese, Mn, copper, Cu and zinc, Zn) in comparison to non-treated soil. Tripartite treatments had the largest effect on the biomass of cover crops with 3.43 g fivefold of the control (0.7 g) in alfalfa and 4.54 g twofold of the control (2.07 g) in grass pea p ≤ 0.05. Both in field and greenhouse experiments combination of biochar and other OAs showed a better soil fertility increment and plant growth parameters. The study concluded that there is a synergistic effect in OAs on the soil fertility restoration and plant growth performance.
Instrumental Philanthropy, Nonprofit Theory, and Information Costs

Abstract Instrumental philanthropy has gained attention and popularity in recent decades as an approach to maximizing the impact of giving. This article evaluates the suitability of the nonprofit institutional form, specifically the US public charity, as a vehicle for instrumental philanthropy. The analysis identifies an incongruity between the informational requirements of instrumental philanthropy and the form and theory of the nonprofit. An alternative theory of licensure is proposed to illustrate the difficulty of the information problem. Analysis suggests that the viability of instrumental philanthropy hinges upon information costs. Several public policy options are considered as means of better supporting instrumental philanthropy, presuming that allocative efficiency in the production of public benefits is a desirable public policy objective.
Métabolisme du bisphénol A, de la vinchlozoline et de la génistéine dans les systèmes biologiques utilisés pour étudier les perturbateurs endocriniens : conséquences en terme de toxicité

Vu le role du metabolisme dans la bioactivation ou la detoxication des xenobiotiques, il est indispensable de connaitre les capacites de biotransformation de lignees cellulaires MCF7, HepG2 et HC11 utilisees dans l’etude des perturbateurs endocriniens. Elles ont ete etudiees vis-a-vis de la genisteine et du bisphenol A (estrogeniques), et de la vinchlozoline (antiandrogenique), et comparees a celles des tranches de foie de rat. Les resultats font apparaitre au plan qualitatif une bonne expression des enzymes de conjugaison mais un niveau tres faible d’activite de phase I pour MCF7 et HepG2. HC11 semble depourvue de toute capacite metabolique. Au plan quantitatif les vitesses de biotransformation des substrats s'etablissent de la maniere suivante : tranches de foie > HepG2 > MCF7 > HC11. Ces differences metaboliques peuvent expliquer pour partie les ecarts observes en matiere de reponse de ces lignees aux composes agonistes ou antagonistes des recepteurs aux androgenes ou aux estrogenes. ABSTRACT : Since metabolism is responsible of xenobiotics bioactivation or detoxication, we have to know the metabolic capabilities of MCF7, HepG2 and HC11 cell lines used to test endocrine disruptors. We studied it toward genistein and bisphenol A (estrogenic) and vinclozolin (antiandrogenic). We compared these metabolic capabilites to those of precision cut rat liver slices. Qualitatively, our results indicate a good expression of phase II enzymes in MCF7 and HepG2 cells, whereas activity of phase I was very low. No metabolism occurred in HC11 cells. Quantitatively, biotransformation rates can be ranked as follows: rat liver slices > HepG2 > MCF7 > HC11. These results can explain partly the differences in the responsiveness of the cell lines observed with agonistic and antigonistic compounds toward androgen and estrogen receptors.
Oct-4: More than a Pluripotent Marker?

Received: 23/Sep/2008, Accepted: 23/Nov/2008 Oct-4/ Pou5f1/ Oct-3, a POU domain family protein acts as a crucial transcription factor during embryonic development. It helps in maintenance of self renewal as well as pluripotential state of embryonic stem (ES) cells. Its expression starts right from 2 cell stage especially prior to 8 cell stage till the blastocyst stage where it is strongly expressed in inner cell mass (ICM). Thereafter, it is located predominantly in primordial germ cells (PGCs) till the birth. It targets particularly those genes which bear an octameric motif ATGCAAAT in promoter or enhancer region. Most of the target genes of Oct-4 are expressed in undifferentiated ES cells and knockdown of Oct-4 results in ES cell differentiation as a result of down regulation of targets of Oct-4 which are expressed in ES cells. Since, Oct-4 is crucial for embryo survival its expression needs tight regulation. Oct-4 is carefully regulated epigenetically as well as by several other factors. DNA methylation and histone modification play an important role in expression of Oct-4 while proximal promoter, enhancer and distal enhancer are the crucial regulatory elements present on Oct-4 upstream region. There is increasing evidence that Oct-4 is expressed in adult stem cells and these stem cells can get converted to cancer stem cells. Since, it is expressed in germ cells, immunohistochemical localization of Oct-4 and thereby its role as a marker for germ cell tumor detection is increasing. Thus, role of Oct-4 is not only restricted as a marker for undifferentiated cells; it is also proving to be crucial factor which targets several genes involved in ES cell survival as well as help in establishing germ cell origin of metastatic tumors.