Academic literature on the topic 'IDRs'

Une fraction significative des protéomes reste non annotée, laissant inaccessible une partie du répertoire fonctionnel de la vie, incluant des innovations moléculaires ayant une valeur thérapeutique ou environnementale. Le manque d'annotation fonctionnelle est en partie dû aux limites des approches actuelles pour la détection de relations cachées, ou à des caractéristiques spécifiques telles que le désordre. L'objectif de ma thèse a été de développer des approches méthodologiques reposant sur les signatures structurales des domaines repliés, afin de caractériser plus avant les séquences protéiques dont la fonction est inconnue, même en l'absence d'informations évolutives. Tout d'abord, j'ai développé un score permettant d'estimer le potentiel de repliement d'une séquence d'acides aminés, basé sur sa densité en amas hydrophobes, correspondant principalement aux structures secondaires régulières. J'ai décrit le continuum entre l'ordre et le désordre, couvrant différents états allant des conformations étendues aux globules fondus et ai caractérisé des cas d'ordre conditionnel. Ensuite, j'ai combiné ce score avec les prédictions de structure 3D d'AlphaFold2 (AF2) disponibles pour 21 protéomes de référence. Une grande fraction des acides aminés des modèles AF2 associés à un très faible index de confiance est incluse dans des segments non repliables, soutenant la qualité d'AF2 comme prédicteur du désordre. Cependant, dans chaque protéome, de longs segments repliables avec des prédictions AF2 de faible confiance présentent également des caractéristiques de domaines solubles et repliés. Cela suggère un ordre caché (conditionnel ou inconditionnel), qui n'est pas détecté par AF2 en raison du manque d'informations évolutives, ou des motifs de repliement non répertoriés. Enfin, à l'aide de ces outils, j'ai effectué une exploration préliminaire de protéines ou de régions non annotées, identifiées via le développement et l'application d'une nouvelle procédure d'annotation. Bien que ces séquences soient enrichies en désordre, une part importante d'entre elles présente des caractéristiques de type globulaire soluble. Ces séquences constituent de bons candidats pour de futures validations et caractérisations expérimentales. De plus, l'analyse de gènes de novo validés expérimentalement m'a permis de contribuer au débat encore ouvert sur les caractéristiques structurales des protéines codées par ces gènes, qui présentent un enrichissement en désordre et une grande diversité d'états structuraux<br>A significant fraction of the proteomes remains unannotated, leaving inaccessible a part of the functional repertoire of life, including molecular innovations with therapeutic or environmental value. Lack of functional annotation is partly due to the limitations of the current approaches in detecting hidden relationships, or to specific features such as disorder. The aim of my PhD thesis was to develop methodological approaches based on the structural signatures of folded domains, in order to further characterize the protein sequences with unknown function even in absence of evolutionary information. First, I developed a scoring system in order to estimate the foldability potential of an amino acid sequence, based on its density in hydrophobic clusters, which mainly correspond to regular secondary structures. I disentangled the continuum between order and disorder, covering various states from extended conformations (random coils) to molten globules and characterize cases of conditional order. Next, I combined this scoring system with the AlphaFold2 (AF2) 3D structure predictions available for 21 reference proteomes. A large fraction of the amino acids with very low AF2 model confidence are included in non-foldable segments, supporting the quality of AF2 as a predictor of disorder. However, within each proteome, long segments with very low AF2 model confidence also exhibit characteristics of soluble, folded domains. This suggests hidden order (conditional or unconditional), which is undetected by AF2 due to lack of evolutionary information, or unrecorded folding patterns. Finally, using these tools, I made a preliminary exploration of unannotated proteins or regions, identified through the development and application of a new annotation workflow. Even though these sequences are enriched in disorder, an important part of them showcases soluble globular-like characteristics. These would make good candidates for further experimental validation and characterization. Moreover, the analysis of experimentally validated de novo genes allowed me to contribute to the still-open debate on the structural features of proteins encoded by these genes, enriched in disorder and displaying a great diversity of structura

<p><p>This dissertation investigates the discourse on Internally Displaced Persons (IDPs) in Uganda and how IDPs in urban areas fit in to the discourse on both the theoretical and practical level. The dissertation reveals that although IDPs in urban areas by definition are included in both international and national IDP definitions, urban IDPs are seen as either economic migrants, or as former IDPs who have now reached a durable solution. The consequences of such exclusion from the IDP label are that IDPs outside camps are not considered for assistance or included in the return and resettlement frameworks or information activities.</p><p>The formation of the IDP label in Uganda has been influenced by the government’s approach of control and military presence aimed at keeping people in camps in the north. Consequently, IDPs are perceived entirely as people residing in camps. The humanitarian community has been complicit with the government’s policy of keeping people in camps by limiting assistance to IDPs registered and residing within them. The obvious lack of resources dedicated to protecting IDPs also influences the way the label is shaped. It is challenging to identify IDPs in an urban setting because of lack of registration and information. It is also difficult to determine who are forced migrants, and which of them have reached a durable solution. Consequently, IDPs in Uganda has in practice been redefined to those staying in camps.</p><p>Upon acknowledging how the voices of urban IDPs are marginalized within the dominant discourse, phase two of the fieldwork progressed towards influencing this discourse by revealing the political and bureaucratic agency in the processes of labelling creating greater awareness of the processes that serve to exclude urban IDPs from return and resettlement frameworks. By facilitating the mobilization of an urban IDP interest group I together with the community outreach organization Refugee Law Project worked together with urban IDP communities advocating for their rights.</p></p>

Tese (doutorado) - Universidade Federal de Santa Catarina, Centro de Tecnológico. Programa de Pós-Graduação em Engenharia Elétrica<br>Made available in DSpace on 2012-10-23T08:11:59Z (GMT). No. of bitstreams: 1 242582.pdf: 1822805 bytes, checksum: 609b5a41dd95627d4cfddc5803190cc7 (MD5)<br>A crescente necessidade de compartilhamento de informações entre organizações parceiras ou membros de organizações virtuais envolve um grande desafio de segurança. Um dos aspectos chave neste desafio é a construção de sistemas de detecção de intrusão (IDSs) que possam operar em ambientes heterogêneos de larga escala. Isto é particularmente difícil devido ao fato de que as diferentes redes envolvidas usam IDSs que não foram projetados para trabalhar de forma cooperativa. O tema central desta tese é a proposta de uma nova abordagem de monitoramento de segurança baseada em composições de IDSs. Uma composição de IDSs é a combinação de elementos de detecção de intrusão, que podem ser IDSs completos ou suas partes, distribuídos entre redes diferentes, mas que operam de forma cooperativa, formando um sistema unificado. Nesta Tese, as composições de IDSs são construídas usando uma arquitetura orientada a serviços baseada na tecnologia de Web Services. A interoperabilidade entre os diversos elementos de uma composição é obtida a partir do amplo emprego de esforços de padronização, sobretudo da IETF, W3C e OASIS. As composições dinâmicas são suportadas pelo uso da orquestração de serviços. Para viabilizar as composições de IDSs, é proposta neste documento uma infra-estrutura de serviços, capaz de suportar elementos de IDs baseados em softwares prontos (commercial off-the-shelf # COTS), uma necessidade fundamental para prover a interoperabilidade e facilitar a implementação. Nesta Tese também são descritas as implementações de protótipos da infra-estrutura proposta e analisados os resultados obtidos por meio de experimentos com estes protótipos. The growing need for information sharing among partnering organizations or members of virtual organizations poses a great security challenge. One of the key aspects of this challenge is deploying intrusion detection systems (IDS) that can operate in heterogeneous, largescale environments. This is particularly difficult because the different networks involved generally use IDSs that have not been designed to work in a cooperative fashion. This Thesis presents a model for integrating intrusion detection systems in such environments. The main idea of this Thesis is a new security monitoring approach, based on IDSs compositions. A IDS composition is a combination of intrusion detection elements (which can be complete IDS systems or their components) distributed across different networks so that they operate in a cooperative fashion, in order to provide a unified service. On this Thesis, the IDSs compositions are constructed using a service-oriented architecture (SOA), based on the Web Services technology. The necessary interoperability among the elements of the compositions is achieved through the use of standardized specifications, mainly those developed by IETF, W3C and OASIS. Dynamic compositions are supported through service orchestration. To make possible the IDSs compositions, is proposed on this document a services infrastructure that is capable of supporting commercial off-the-shelf (COTS) IDS elements, a crucial feature for providing interoperability and deployability. On this Thesis are also described prototypes implementations, tests and results.

Intrusion Detection Systems (IDS) tools are deployed within networks to monitor data that is transmitted to particular destinations such as MySQL,Oracle databases or log files. The data is normally dumped to these destinations without a forensic standard structure. When digital evidence is needed, forensic specialists are required to analyse a very large volume of data. Even though forensic tools can be utilised, most of this process has to be done manually, consuming time and resources. In this research, we aim to address this issue by combining several existing tools to archive the original IDS data into a new container (Digital Evidence Bag) that has a structure based upon standard forensic processes. The aim is to develop a method to improve the current IDS database function in a forensic manner. This database will be optimised for future, forensic, analysis. Since evidence validity is always an issue, a secondary aim of this research is to develop a new monitoring scheme. This is to provide the necessary evidence to prove that an attacker had surveyed the network prior to the attack. To achieve this, we will set up a network that will be monitored by multiple IDSs. Open source tools will be used to carry input validation attacks into the network including SQL injection. We will design a new tool to obtain the original data in order to store it within the proposed DEB. This tool will collect the data from several databases of the different IDSs. We will assume that the IDS will not have been compromised.

This essay focuses on the possibilities and problems that come with having teleportation mixed with horror and fear and not having monsters in fear games. How it is to play a horror game without enemies and just being able as an Interactiondesigner to relay on the psychological feeling within the player, if the feeling is more than enough if the player him self get to fantasies and let their deepest fright feelings take over. Is there no difference if there are monsters/enemies or not. Is fright and fear already there before you encountering the enemies? These questions are answered as the paper also presents a game in the shape of a course that has been paralleled worked with. The world with the complete and finished game have bin done in the Hammer editor which the game HalfLife2 (VU games/Valve Software, 2004) is built on. The finished game is a result of several user tests from the prototype game and user questionnaires. Fear games are mainly built on humans’ psychological feelings, the imaginations and how one feel. Through strong usage and building upon these main factors to create fear I have worked from that perspective and investigated how I by best possible means, should do to create fear to fright players by not using enemies as main frightening objects. Focus has been on the narrative of both visual and auditive narration. I have also given an account of the advantage and disadvantages with working with the tool I have chosen, how it has affected my work and my result. The Result turned out to be even better than I had in mind and a positive attitude towards my game from all the test persons. They thought it was a good example that a horror game is not bound to have monsters in order to fright the player. I got a loot of good feedback, response and ideas of what I could improve and what was already good. Some wanted more light effects on the first part and others less sound in the last part. By listening to the test persons I started to create and shape the final version of the game. Everyone became scared and felt more or less frightened through all four parts of the game. I also got positive feedback on my theory from the test persons, that teleportation mixed with horror and fear is something that they could consider using more in games and that this was a good start in the right direction.

Current practices includes the integration of IDMS system and OpenStack for easy, better, balanced provisioning, identity management and user management for different types of users in order to securely access the service on cloud platform. These solutions will provide the basic building block structure which provides the motivation to enterprises to come in, out, around the cloud services. Based the research artifacts, design challenges and some current constraints, we have built these cure IDMS for cloud environment under architecture of “CryptoNET™ Security Providers”. Secure IDMS is designed by considering the SCIM schema and OpenStack cloud platform to offer better user management, secure authentication, enhanced security components, secure communication, controlled attributes and synchronized data in order to provide secure services trousers in cloud environment. Security model is based on type of users identity in OpenStack, based on roles. This enables to control and provide different types of user needs as Software as a Services(SaaS), better web application interaction including better provisioning/deprovisioing, secure identity information storage and better access control “role based-RBAC” as Platform as a Services(PaaS). Secure IDMS, provides more solutions for problems that cover the Identity and Access Management (IAM) rather than Managed Identity Services (MIS). Based on cloud IAM challenges and requirements for financial institutions, our design artifact was also evaluated. We considered central identity management approach based on security policy implementation. This research will brings the reader to understand secure IDMS platform with basic real world implementation and motivates the reader to study more cloud challenges, security enhancements and future guidelines for additional research in this area.

There is a grave concern for the life, liberty and security of individuals who have been forced to leave their homes and have become dispersed within their native countries and throughout the Asian continent. These internally displaced persons and refugees are the subject of this study. Some of the themes that will be discussed include: civil war, human rights violations and the economy, since these are the problems affecting the populations of Afghanistan, Pakistan and Myanmar. These case studies are of particular interest because Afghanistan is where most refugees come from, Myanmar has the longest-running military regime and Pakistan hosts the most refugees in the world. All three case studies are currently in a state of civil war, are breeding grounds for violations of human rights and have corrupt economies. Thus, the goal is to end armed conflict, to put an end to the human rights violations that come with it and to restructure the economies in each of these nation states so that the internally displaced persons and refugees can be repatriated, since displacement has become too much of a burden for Afghanistan, Pakistan and Myanmar's neighboring countries, who have been taking in all of the refugees from said countries. Theoretically, if the issues causing displacement were to be solved, then the countries that host refugees would be able to concentrate on their own populations. This study can potentially address the gap between knowledge, policy formation, and policy implementation to realize the goals of the international community in dealing with the displacement crisis.<br>B.A.<br>Bachelors<br>Sciences<br>Political Science

La hepatitis B es un problema de salud mundial, con unos 400 millones de personas infectadas crónicamente. En nuestro medio se calcula una prevalencia del 0.7%, siendo la mayoría de los sujetos HBeAg negativo. En esta fase de la infección, uno de los retos es distinguir entre aquellos sujetos portadores inactivos, que presentarán un buen pronóstico de la enfermedad a largo plazo, y los pacientes con hepatitis crónica HBeAg negativo, que tienen riesgo de desarrollar fibrosis hepática y por tanto precisar tratamiento antiviral. El primer trabajo se centró en pacientes bajo tratamiento antiviral con análogos de nucleós(t)idos de segunda generación (Entecavir y Tenofovir). Las hipótesis del mismo fueron que la eficacia y tasa de efectos adversos en práctica clínica era similar a la de los estudios de registro y la validación del modelo Page-B para predicción del riesgo de carcinoma hepatocelular (CHC). Para dicho fin se analizó la base CIBERHEP que incluye sujetos con infección crónica por el VHB, seleccionándose un total de 609 pacientes caucásicos en tratamiento con Tenofovir o Entecavir. Las tasas de respuesta virológica y bioquímica fueron altas, con pocos efectos adversos y discontinuación de tratamiento, sin observarse deterioro de la función renal. A pesar de la supresión de la replicación viral, se observaron 12 casos de CHC, número inferior a los estimados por la puntuación Page-B. Al igual que en la cohorte original, todos aquellos sujetos que presentaron CHC tenían basalmente una puntuación Page-B ≥10 puntos, confirmándose el valor predictivo negativo del 100% de dicho punto de corte. La hipótesis del segundo de los estudios, fue que los niveles séricos de antígeno de superficie (HBsAg) o antígeno relacionado con el core (HBcrAg) podrían ser útiles para identificar a los verdaderos portadores inactivos del VHB. Para ello se realizó un estudio prospectivo con al 3 determinaciones analíticas en 1 año para caracterizar a los sujetos como portadores inactivos (niveles de alanino transferasa persistentemente normales y ADN VHB≤2.000 UI/mL) o con actividad por el VHB. En primer lugar se observó que los niveles de HBsAg estaban influidos el por genotipo del VHB, dato que dificultó la búsqueda de un único punto de corte con altos índices diagnósticos en todos los genotipos, siendo el HBsAg <3 logUI/mL útil sólo para el genotipo D. Por contra, los niveles de HBcrAg no difirieron entre los diferentes genotipos, siendo la exactitud diagnóstica para la identificación de portadores inactivos mayor que los niveles de HBsAg. La combinación en una única determinación de HBcrAg ≤3 logU/mL más ADN VHB ≤2.000 UI/mL presentó una exactitud diagnóstica >85% en todos los genotipos excepto el H o F (73%).<br>Hepatitis B virus (HBV) infection is a worldwide health problem, with around 400 million people chronically infected. In our setting, the prevalence is 0.7% and the majority of subjects are HBeAg negative. In this stage of the disease, one of the most challenging issues is to discern between the inactive carriers, who have a long-term good prognosis of the disease, and patients with HBeAg negative chronic hepatitis B, who are at risk of fibrosis development and therefore may require antiviral therapy. The first study of this thesis is focus on patients undergoing antiviral therapy with second generation nucleos(t)tides analogs (Entecavir and Tenofovir). The hypotheses were that the effectiveness and rate of side effects in daily clinical practice were similar to the registration studies and the validation of the Page-B score for prediction of hepatocellular carcinoma (HCC) development. From the collaborative database CIBERHEP, 609 caucasian subjects with chronic hepatitis B treated with Tenofovir or Entecavir were selected. The rates of biochemical and virological response were very high, and no worsening on renal function was observed. Despite suppression of viral replication, 12 cases of HCC were reported, a number lower to the estimated by the Page-B score. Similar to the original cohort, in the CIBERHEP all patients who developed HCC presented a baseline Page-B punctuation ≥10 points, supporting the previously described 100% negative predictive value of that cut-off. The hypothesis of the second study was that the serum levels of hepatitis B antigen (HBsAg) o core-related antigen (HBcrAg) could be useful for identification of HBV inactive carriers. To achieve this goal, a prospective work with 3 consecutive blood analyses throughout 1 year was carried out. Subjects were classified as inactive carriers (defined as persistently normal alanine transferase levels and HBV DNA ≤2.000 IU/mL) or subjects with HBV activity. Firstly, it was observed that HBsAg levels varied across the different HBV genotypes. This finding hindered the search of a unique HBsAg cut-off for diagnosing the inactive carrier state among the different HBV genotypes. Previously described HBsAg <3 logIU/mL was only useful of genotype D. However, HBcrAg did no vary among genotypes, and on the whole, the diagnostic accuracy of HBcrAg was higher than HBsAg levels. The combination on a single determination of HBcrAg ≤3 logU/mL plus HBV DNA ≤2.000 IU/mL presented a diagnostic accuracy ≥85% in all genotypes except H or F (73%).

This study explores how Donbass IDPs in Kyiv view the role of the state in relation to ‘durable solutions’ to their displacement. Specifically, it examines the expectations on the state as a provider of rights and entitlements vis-à- vis IDPs. Drawing on semi-structured interviews with Donbas IDPs, experiences of displacement and perceptions of durable solutions and citizen-state relations are exemplified. The data collection and analysis methodologies applied allow for the elicitation of the views and opinions of IDPs, in an attempt to mitigate vertical policy-making. The concepts of citizenship, state and sovereignty are applied to analyze the relationship between IDPs and the state. Further, the IASC framework for durable solutions to internal displacement is used to as a structure to outline the views of the IDPs. The results show a large discrepancy between the expectations of the respondents on the states’ role in durable solutions to displacement, and the experience of this in reality. Furthermore, the results reveal high levels of discontent, resignation and apathy towards the state as a provider of durable solutions, especially in terms of returning to Donbass.