Computational frameworks for microRNA functional analysis of inter-kingdom and indirect targeting.

Genes are DNA sequences that encode the information needed to synthesize molecules necessary for the function of the cell. Some genes are called protein-coding genes because they have the code required to manufacture proteins. The expression of a certain gene means its product (protein) is produced. Although some genes are not protein-coding, they regulate the gene expression of other protein-coding genes. Of these, microRNAs (miRNAs) are small RNA molecules that inhibit the expression of other genes by binding to their mRNA transcripts. miRNAs have been shown to be linked to several biological processes like development and diseases like cancer. Recently, researchers have hypothesized that miRNAs are involved in the regulation of the expression of genes from other species. Although tools to predict miRNA target genes are available in the case when miRNAs and target genes belong to the same species, to our knowledge there are no available tools to predict inter-kingdom miRNA target genes (miRNA and target genes belong to two different kingdoms). To address this limitation, we developed an efficient tool to predict potential gut bacterial genes targeted by miRNAs from edible plants. We successfully predicted ginger miRNAs that target two genes from a gut bacterial strain called Lactobacillus rhamnosus GG. To maintain the efficiency of our tool while using a larger number of miRNAs and bacterial strains, we used a hash-table to index the sequences of bacterial genes. To predict the function of a miRNA, we start by compiling the list of direct target genes (ones with binding sites) and then we search for biological process in which these genes are enriched. This approach does not include other genes affected by the miRNA but do not necessarily have a physical binding site (indirect targets). An example of an indirect target is the gene that doesn’t have a binding site and is regulated through other direct targets like transcription factors. To overcome this limitation, we developed miRinGO an interactive web application to include these indirect targets in the functional analysis. Our approach showed better performance compared to the existing approach in predicting biological processes known to be targeted by certain miRNAs

From Gradgrind to Brodie: Two Philosophies, One World!

Despite the big considerable differences between Charles Dickens’ classic and most pedagogical novel Hard Times (1854) and Muriel Spark’s The Prime of Miss Jean Brodie (1961), they have much in common as both feature an unorthodox theory of teaching, which turns out to be thoroughly detrimental to their students’ independent, creative thinking. In their most extreme form, the teaching philosophies of their protagonists, Mr Thomas Gradgrind in Hard Times and the eponymous character of Miss Jean Brodie in The Prime of Miss Jean Brodie, though much different, lead up to one single result: they do obliterate students’ free thinking and critical capacities. It is simply a system that does reduce students to “little vessels…arranged in order, ready to have imperial gallons of facts [or whatever] poured into them until they were full to the brim” (Dickens, 1994, p.2). This article is an explicitly comparative reading of Dickens’ and Spark’s responses to educational philosophies. Whereas Miss Brodie is a nonconformist who goes against the conventional educational methods, Mr Gradgrind relentlessly espouses the traditional education system verbatim by exalting reason and underestimating imagination.

"RITE OF PASSAGE IN DIASPORA: JAMAICA KINCAID'S LUCY AS A POSTCOLONIAL KÜNSTLERROMAN"

Jamaica Kincaid's novel Lucy (1990) is a coming-of-age story, or a Künstlerroman to be more specific in the tradition of James Joyce's A Portrait of the Artist as a Young Man (1917), that simply revolves around a young woman artist, who learns much from the school of life and personal experiences other than from ordinary education at academic institutions. The eponymous protagonist breaks away from such forces as colonial and patriarchal mores, which eventually contributes to her construction of her own hybrid identity and inaugurates her maturity. This struggle is established perfectly well through her apparent resistance to the constraints primarily imposed on her race and gender by both the Eurocentric society, which she has just left behind at home, and the androcentric society she encounters in diaspora. Surprisingly enough, Lucy, who is chastened towards the end of the book, creates her rite of passage towards development and independence through her valiant efforts to overcome such confines at any cost. The aim of the present article is to analyse the young artist's character formation and growth both at home and in diaspora from a postcolonial perspective. This way, it intertwines discussions of transition from innocence to experience along with such elements as androcentrism, colonial and postcolonial rebellion, and questions of identity, hybridity, diaspora and cultural displacement, which are all inextricably linked with the postcolonial discourse

Law and development of technology : the Iranian case.

PhDThis thesis is essentially a study of how intellectual property, transfer of technology and competition rules can be interfaced properly in Iran to facilitate the flow of technology into the country. The law governing the transfer and development of technology is a relatively new and non-traditional discipline. The thesis is intended to make a significant contribution to the limited number of publications available on the subject especially in examining within one volume the principles of three branches of law of great significance to economic development. The focus of this thesis is Iran. Iran is a country with a rich culture and a history that goes back to thousands of years. She has abundant natural resources including oil and a large domestic market and enjoys a strategic position in international trade and politics. Seven decades have passed since Iran attempted to acquire foreign technology to industrialise important sectors of her economy but the country continues to be dependent heavily on foreign technology and her economy remains an oil driven one. Part of the problem is the absence of a strong legal and institutional framework within which secure investments both local and foreign can take place on an enduring basis. The thesis shows that the international community has failed to provide an international legal framework responsive to the special needs of developing countries which are, therefore, constrained to rely on their own domestic institutions to tap into the technology available across the world. Given that international Conventions - such as the Paris Convention and the GATUTRIPS Agreement provided developing countries with space within which they can fashion their national laws and institutions regarding the transfer and promotion of technology, how should Iran reconstruct its local laws to secure indigenous development of its industrial and technological infrastructure? The thesis proposes a package of legal reforms and institutional changes which are intended to encourage the flow of technology into the country by guaranteeing the protection of acquired rights and assuring mutual benefits to both technology suppliers and recipients. The thesis is divided into four sections: Section I provides a historical background to Iran's attempts to industrialise, Section 11 is an analysis of the interfacing between intellectual property laws, competition laws, transfer of technology laws and international law to uncover the legal problems relating to the transfer of technology to the developing countries, Section III examines the existing national legal framework within which the flow of technology takes place in Iran and Section IV devises an optimum legal and institutional regime to maximise the transfer of foreign technology and promotion and development of domestic innovative activities with particular reference to Iran. In this thesis, the proposed Development of Technology Law of Iran lays down rules for patent grants, transfer of technology agreements and protection of competition and, for the first time, will bring the three areas of law under the supervision of a single independent agency of the government whose central purpose will be to develop a technological base in the country and advance industrial progres

Developing Novel Criteria to Classify ARDS Severity using a Machine Learning Approach

Davant de les dificultats mèdiques per abordar correctament els problemes del ARDS, tal com es reporten en múltiples publicacions especialitzades, en aquesta tesi hem plantejat la hipòtesi que l'ús de tecnologies modernes d'aprenentatge automàtic (ML) podria millorar el nostre coneixement i la nostra capacitat per predir i abordar aquests ARDS. qüestions. Per assolir aquests objectius (i) vam proposar una fórmula nova [PaO2/(FiO2xPEEP) or P/FPE] per a PEEP≥5 i els valors de tall corresponents per abordar la bretxa de definició de Berlín per a la gravetat de l'ARDS mitjançant enfocaments ML. Es van examinar els valors de P/FPE que delimiten els límits de l'ARDS lleu, moderat i greu. Hem aplicat ML per predir la gravetat del ARDS després de l'aparició al llarg del temps comparant els criteris actuals de PaO2/FiO2 de Berlín amb P/FPE en tres escenaris diferents, (ii) vam tenir com a objectiu caracteritzar el millor escenari precoç durant els dos primers dies a la unitat de cures intensives (ICU) per predir la durada de la MV després de l'inici de l'ARDS mitjançant enfocaments de ML, i (iii) vam validar P/FPE com a predictor de la mortalitat de la ICU més enllà de l'estat actual de la tècnica mitjançant llindars de classificació intuïtius basats en ML.Frente a las dificultades médicas para abordar adecuadamente los problemas de ARDS, tal como se reportan en múltiples publicaciones especializadas, en esta tesis planteamos la hipótesis de que el uso de tecnologías modernas de aprendizaje automático (ML) podría mejorar nuestro conocimiento y nuestra capacidad para predecir y abordar estos ARDS. cuestiones. Para lograr estos objetivos (i), propusimos una fórmula novedosa [PaO2/(FiO2xPEEP) or P/FPE] para PEEP≥5 y los valores de corte correspondientes para abordar la brecha de definición de Berlín para la gravedad del ARDS mediante el uso de enfoques ML. Examinamos los valores de P/FPE que delimitan los límites del ARDS leve, moderado y grave. Aplicamos ML para predecir la gravedad del ARDS después del inicio a lo largo del tiempo comparando los criterios actuales de PaO2/FiO2 de Berlín con P/FPE en tres escenarios diferentes, (ii) apuntamos a caracterizar el mejor escenario temprano durante los dos primeros días en la unidad de cuidados intensivos (ICU) para predecir la duración de la MV después del inicio del ARDS utilizando enfoques de ML, y (iii) validamos P/FPE como predictor de mortalidad en la ICU más allá del estado actual del arte utilizando umbrales de clasificación intuitivos basados en ML.In front of the medical difficulties to properly address ARDS issues, as they are reported in multiple specialized publications, in this thesis we hypothesized that the use of modern machine learning (ML) technologies could improve our knowledge and our capacity to predict and address these ARDS issues. In order to achieve these objectives (i) we proposed a novel formula [PaO2/(FiO2xPEEP) or P/FPE] for PEEP≥5 and corresponding cut-off values to address Berlin’s definition gap for ARDS severity by using ML approaches. We examined P/FPE values delimiting the boundaries of mild, moderate, and severe ARDS. We applied ML to predict ARDS severity after onset over time by comparing current Berlin PaO2/FiO2 criteria with P/FPE under three different scenarios, (ii) we aimed at characterizing the best early scenario during the first two days in the intensive care unit (ICU) to predict MV duration after ARDS onset using ML approaches, and (iii) we validated P/FPE as a predictor of ICU mortality beyond the current state of the art using intuitive classification thresholds based on ML

EFFICIENT ROUTING PROTOCOL ALGORITHM FOR WIRELESS SENSOR NETWORKS

Recently, different applications of wireless sensor networks (WSNs) in the industry fields using different data transfer protocols has been developed. As the energy of sensor nodes is limited, prolonging network lifetime in WSNs considered a significant occurrence. To develop network permanence, researchers had considered energy consuming in routing protocols of WSNs by using modified Low Energy Adaptive Clustering Hierarchy. This article presents a developed effective transfer protocols for autonomic WSNs. An efficient routing scheme for wireless sensor network regarded as significant components of electronic devices is proposed. An optimal election probability of a node to be cluster head has being presented. In addition, this article uses a Voronoi diagram, which decomposes the nodes into zone around each node. This diagram used in management architecture for WSNs