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In the setting of Noetherian or Dedekind domains, we investigate the properties of very flat and contraadjusted modules. These are the modules from the respective classes in the cotorsion pair (VF, CA) generated by the set of all modules of the form R[s−1 ]. Furthermore, we introduce the concept of locally very flat modules and pursue the analogy of their relation to very flat modules and the relation between projective and flat Mittag-Leffler modules. It is shown that for Noetherian domains, the class of all very flat modules is covering, if and only if the class of all locally very flat modules is precovering, if and only if the spectrum of the ring is finite; for domains of cardinality less than 2ω , this is further equivalent to the class of all contraadjusted modules being enveloping.

Master of Science / Department of Architectural Engineering / Charles L. Burton / An energy analysis was performed on a Midwestern residence to evaluate its performance based on energy use. A model of the actual house was replicated using eQuest and adjusted until its projected utility bills matched the actual yearly bills. This model was used to gauge how potential improvements made to the envelope and HVAC systems lowered the energy use. The results were documented after each improvement the feasible options were considered. The top alternatives were then combined to see how much money could be saved through renovating an existing home or through constructing a new residence. The overall goal of this report was to use the resulting improvement data as a reference for homeowners or home builders who are interested in conserving energy and money through residential improvements.

<p>Bacterial outer membrane vesicles (OMVs) are spherical buds of the outer membrane (OM) containing periplasmic lumenal components. OMVs have been demonstrated to play a critical part in the transmission of virulence factors, immunologically active compounds, and bacterial survival, however vesiculation also appears to be a ubiquitous physiological process for Gram-negative bacteria. Despite their characterized biological roles, especially for pathogens, very little is known about their importance for the originating organism as well as regulation and mechanism of production. Only when we have established their biogenesis can we fully uncover their roles in pathogenesis and bacterial physiology. The overall goal of this research was to characterize bacterial mutants which display altered vesiculation phenotypes using genetic and biochemical techniques, and thereby begin to elucidate the mechanism of vesicle production and regulation. One part of this work elucidated a synthetic genetic growth defect for a strain with reduced OMV production (&#916;nlpA, inner membrane lipoprotein with a minor role in methionine transport) and envelope stress (&#916;degP, dual function periplasmic chaperone/ protease responsible for managing proteinaceous waste). This research showed that the growth defect of &#916;nlpA&#916;degP correlated with reduced OMV production with respect to the hyprevesiculator &#916;degP and the accumulation of protein in the periplasm and DegP substrates in the lumen of OMVs. We further demonstrated that OMVs do not solely act as a stress response pathway to rid the periplasm of otherwise damaging misfolded protein but also of accumulated peptidoglycan (PG) fragments and lipopolysaccharide (LPS), elucidating OMVs as a general stress response pathway critical for bacterial well-being. The second part of this work, focused on the role of PG structure, turnover and covalent crosslinks to the OM in vesiculation. We established a direct link between PG degradation and vesiculation: Mutations in the OM lipoprotein nlpI had been previously established as a very strong hypervesiculation phenotype. In the literature NlpI had been associated with another OM lipoprotein, Spr that was recently identified as a PG hydrolase. The data presented here suggest that NlpI acts as a negative regulator of Spr and that the &#916;nlpI hypervesiculation phenotype is a result of rampantly degraded PG by Spr. Additionally, we found that changes in PG structure and turnover correlate with altered vesiculation levels, as well as non-canonical D-amino acids, which are secreted by numerous bacteria on the onset of stationary phase, being a natural factor to increase OMV production. Furthermore, we discovered an inverse relationship between the concentration of Lpp-mediated, covalent crosslinks and the level of OMV production under conditions of modulated PG metabolism and structure. In contrast, situations that lead to periplasmic accumulation (protein, PG fragments, and LPS) and consequent hypervesiculation the overall OM-PG crosslink concentration appears to be unchanged. Form this work, we conclude that multiple pathways lead to OMV production: Lpp concentration-dependent and bulk driven, Lpp concentration-independent.</p> / Dissertation

In this thesis, the author presents and analyzes two 4-dimensional Constant Envelope Quadrature-Quadrature Phase Shift Keying constellations. Optimal demodulators for the two constellations are presented, and one of them was designed and implemented by the author. In addition, a novel expanded 16-dimensional CEQ2PSK constellation that doubles the number of points without decreasing the distance between points or increasing the peak energy is generated by concatenating the aforementioned constellations with a particular method and restrictions. This original 16-dimensional set of symbols is set-partitioned and used in a multidimensional Trellis-Coded Modulation scheme along with a convolutional encoder of rate 2/3. Effective gain of 2.67 dB over uncoded CEQ2PSK constellation with low complexity is achieved theoretically. A coding gain of 2.4 dB with 8 dB SNR is obtained by using Monte Carlo simulations. The TCM systems and demodulators were tested under an Additive White Gaussian Noise channel by using Matlab's Simulink block diagrams.

It has been well reported that the use of multidimensional constellation signals can help to reduce the bit error rate in Additive Gaussian channels by using the hyperspace geometry more efficiently. Similarly, in fading channels, dimensionality provides an inherent signal space diversity (distinct components between two constellations points), so the amplitude degradation of the signal are combated significantly better. Moreover, the set of n-dimensional signals also provides great compatibility with various Trellis Coded modulation schemes: N-dimensional signaling joined with a convolutional encoder uses fewer redundant bits for each 2D signaling interval, and increases intra-subset minimum squared Euclidean distance (MSED) to approach the ultimate capacity limit predicted by Shannon's theory. The multidimensional signals perform better for the same complexity than two-dimensional schemes. The inherent constellation expansion penalty factor paid for using classical mapping structures can be decreased by enlarging the constellation's dimension. In this thesis, a multidimensional signal set construction paradigm that completely avoids the constellation expansion penalty is used in Band-limited channels and in fading channels. As such, theoretical work on performance analysis and computer simulations for Quadrature-Quadrature Phase Shift Keying (Q2PSK), Constant Envelope (CE) Q2PSK, and trellis-coded 16D CEQ2PSK in ideal band-limited channels of various bandwidths is presented along with a novel discussion on visualization techniques for 4D Quadrature-Quadrature Phase Shift Keying (Q2PSK), Saha's Constant Envelope (CE) Q2PSK, and Cartwright's CEQ2PSK in ideal band-limited channels. Furthermore, a metric designed to be used in fading channels, with Hamming Distance (HD) as a primary concern and Euclidean distance (ED) as secondary is also introduced. Simulation results show that the 16D TCM CEQ2PSK system performs well in channels with AWGN and fading, even with the simplest convolutional encoder tested; achievable coding gains using 16-D CEQ2PSK Expanded TCM schemes under various conditions are finally reported.

Thesis advisor: Welkin Johnson / Endogenous Retroviruses (ERVs) are “fossilized” retroviruses of a once exogenous retrovirus located in the genome of extant vertebrates. Retroviral infection results in a provirus integration into the host genome. An infection of a germline cell could lead to the provirus potentially being inherited by the offspring of the infected individual. Once in the genome, the provirus becomes subject to evolutionary processes and can become either lost or fixed in a population, remaining as “fossils” long after the exogenous retrovirus has gone extinct23. Notably, 8% of the human genome consists of ERVs30. Human Endogenous Retrovirus Type K (HERV-K)(HML-2) family is of particular interest. HERV-K integrations are as old as 30-35 million years, endogenizing before the separation of humans and Old World Monkeys. However, there are human specific insertions, some as young as 150,000 – 250,000 years, making them the youngest insertion in the human genome. There are over 90 insertions in the human genome; the bulk is shared by all humans44,47. Transcripts of HERV-K genes are upregulated in multiple cancer and tumor cell lines 14,39,46, as well as in HIV-1 infected patients 7,11,29. Just as there are human specific insertions of ERV-K, there are also Old World Monkey specific insertions44. I have identified an intact endogenous retroviral envelope open reading frame on chromosome 12 of the rhesus macaque genome. This viral envelope-encoding sequence, which I refer to as rhERV-K env, retains all the canonical features of a retroviral Env protein. An alignment between rhERV-K env and a consensus sequence of HERV-K, HERV-Kcon env, shows a 70% amino acid sequence identity. For experimental purposes, reconstructed HERV-K envelopes have been incorporated into virions of Human Immunodeficiency virus (HIV-1)19,26,49, Murine Leukemia Virus (MLV)12, and Vesicular stomatitis Virus (VSV)26,41,49. While these approaches have illuminated some aspects of HERV-K Env-mediated entry, to date a cell-surface receptor has not been identified for any ERV-K Env. This could be due to its low infectivity levels12,26,49, its seemingly broad cell tropism limiting identification of null cell lines26,49, or possibly the HERV-K consensus reconstructions are not an accurate representation of the progenitor HERV-K virus. I am interested in understanding how the ERV-K retrovirus accessed the human germline (some 150,000 – 250,000 years ago). To do this, I focused specifically on the envelope proteins of HERV-K and rhERV-K, with the goal of analyzing the ERV-K entry process. The identification and inclusion of rhERV-K Env in this study is meant to circumvent the possibility that the previously described consensus reconstructions of human HERV-K Env are not representative, and may also provide a means to compare the endogenization process in the human/ape and old-world monkey lineages. I focused on developing two systems for single-cycle infection, one based on Mason-Pfizer Monkey Virus (MPMV) (which has not been done before), and a second based on MLV, which has previously been reported on. MPMV, like HERV-K, is a betaretrovirus, and I reasoned that possibly using a betaretrovirus would overcome some of the low-infectivity issues associated with prior attempts using HIV and MLV. To develop a system for examining function of the ERV-K Env proteins, I addressed 3 issues: 1. Are the HERV-K Env and rhERV-K Env proteins expressed and properly processed? 2. Can they be incorporated into virions of a heterologous virus? 3. Are ERV-K pseudotyped virions infectious? I have answered these questions in the following thesis. / Thesis (MS) — Boston College, 2017. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

L’assemblage et la propagation du Virus de l’Immunodéficience Humaine de type 1 (VIH-1) met en jeu des évènements moléculaires et cellulaires impliquant des interactions entre protéines virales et co-facteurs cellulaires, tels que les régulateurs du trafic vésiculaire des protéines. Le virus doit notamment échapper aux mécanismes de défense de l’hôte afin de se disséminer dans l’organisme. La protéine BST2 « Bone marrow STromal antigen 2 » (Tetherin/CD317/HM1.24) appartient à une famille de médiateurs de l’immunité intrinsèque de l’hôte : les facteurs de restriction. BST2 inhibe la libération des particules virales néo-formées en les séquestrant à la surface des cellules infectées. La protéine virale Vpu permet de lever cette restriction en excluant BST2 des zones de bourgeonnement viral. Les mécanismes exacts par lesquels Vpu contrecarre l’activité anti-virale de BST2 au site de bourgeonnement ne sont pas complètement élucidés, mais résultent d’une altération du trafic intra-cellulaire du facteur de restriction. Une caractérisation précise des fonctions cellulaires de BST2, encore mal définies, et des mécanismes moléculaires et cellulaires régulant cette protéine et son activité permettrait de mieux appréhender son rôle au cours de l’infection, ainsi que les mécanismes développés par Vpu pour contrecarrer son activité anti-virale. Dans cette optique, nous avons entrepris un crible protéomique dans le but d’identifier des co-facteurs cellulaires de BST2. Compte tenu de l’importance des machineries de régulation du trafic intra-cellulaire dans la biogenèse virale et les contre-mesures par lesquelles Vpu contrecarre BST2, nous nous sommes essentiellement focalisés sur deux protéines de la famille EHD (Eps15 Homology Domain) : EHD4 et EHD1, deux GTPases impliquées dans la régulation du trafic vésiculaire des protéines au niveau des endosomes précoces et de recyclage respectivement. EHD4 en particulier a précédemment été décrite comme étant un régulateur de la biogenèse de virions VIH-1 infectieux selon des modalités qui restent à définir. Les objectifs de mon projet de thèse ont été (i) d’analyser / valider le rôle d’EHD4 dans la régulation du trafic intra-cellulaire de BST2 en conditions non-infectieuses, (ii) d’évaluer le rôle d’EHD4 dans l’activité anti-virale de BST2 et son antagonisme par la protéine virale Vpu, et finalement (iii) de documenter la contribution des protéines EHD4 et EHD1 dans le de cycle de réplication du VIH-1. Nous avons pu montrer qu’EHD4 interagit avec BST2 et régule son trafic intra-cellulaire au niveau des endosomes précoces. La déplétion d’EHD4 induit une altération majeure du trafic de BST2, caractérisée par une rétention de BST2 au niveau des endosomes précoces, associée à un ralentissement de son adressage vers les compartiments de dégradation lysosomale. Dans un contexte infectieux, EHD4 ne semble pas requise pour la dégradation de BST2 induite par Vpu, ni pour l’antagonisme de son activité anti-virale par la protéine virale. Cependant, nous avons révélé une implication majeure d’EHD4 et d’EHD1 dans le cycle de réplication du VIH-1 : en effet, leur déplétion respective aboutit à un ralentissement drastique de la propagation virale. EHD4 et EHD1 favorisent le déroulement d’une étape précoce de l’infection antérieure à la rétro-transcription du génome virale dans la cellule nouvellement infectée. De plus, EHD4 et EHD1 contribuent à la biogenèse de virus infectieux : leur déplétion respective perturbe le trafic intra-cellulaire des constituants viraux, l’intégrité des zones de bourgeonnement viral et l’incorporation de la glycoprotéine d’enveloppe dans les virions nouvellement produits. Ces altérations se traduisent par une diminution de l’infectivité des virions produits en l’absence des protéines EHD4 et EHD1. / Assembly and egress of Human Immunodeficiency Virus (HIV) involve a highly orchestrated series of interactions between proteins encoded by the virus and cellular cofactors, such as regulators of intra-cellular vesicular trafficking. One key challenge for the virus is to overcome several levels of host defence mechanisms to propagate. The cellular protein BST2 (Bone marrow STromal cell antigen-2), also called Tetherin, was recently identified as a cellular restriction factor that retains viral particles at the surface of infected cells, thereby considerably reducing viral release. The accessory protein Vpu encoded by the HIV-1 counteracts this restriction by reducing BST2 expression at the viral budding sites. This process comes along with a diminished global expression of BST2 in the cells. The mechanisms underlying Vpu-mediated BST2 down-regulation at the viral budding sites are not fully understood. Studies performed in the laboratory, along with others published by international research groups, showed that this activity relies on interference with BST2’s intra-cellular trafficking. A deeper caraterization of BST2’s cellular functions and modes of regulation would allow for a better understanding of its role against HIV-1 infection and the viral countermeasures antagonizing its antiviral activity. To this aim, we performed a protemic screening in order to identify new BST2 cofactors. As HIV-1 hijacks the cellular machineries involved in the regulation of vesicular intra-cellular traffcking to promote virion biogenesis and BST2 antagonism, we focused our investigations on two hits belonging to the EHD family (Eps15 Homology Domain) : EHD4 and EHD1. Both proteins are GTPases that regulate the intra-cellular vesicular trafficking, respectively at early and recycling endosomes. EHD4 has previously been involved in the regulation of the biogenesis of infectious HIV-1 viral particles, the underlying mecanisms remaining unclear to date. The goals of the research project constituting my Ph.D were to (i) analyze / validate the implication of EHD4 in the regulation of BST2’s intra-cellular trafficking in a non-infectious context, (ii) decipher the role of EHD4 in the regulation of BST2’s antiviral activity and its Vpu-mediated antagonism, and (iii) assess the invovlment of EHD4 and EHD1 in the replication cycle of HIV-1. We showed here that EHD4 interacts with BST2 and regulates its intra-cellular trafficking at early endosomes in a non-infectious context. EHD4 depletion induces a major alteration of BST2 trafficking, as internalized BST2 seem to be retained at an early endosomal level and unefficiently targeted towards the lysosomal degradation pathway. In the context of HIV-1 infection, EHD4 does not seem to be required in the Vpu-mediated BST2 degradation, nor in the antagonism of BST2’s antiviral activity. Nevertheless, we unveiled a major involvment of both EHD4 and EHD1 in the HIV-1 replication cycle : their respective depletion leads to a severe impairment of viral propagation. EHD4 and EHD1 seem to facilitate an early step of the viral cycle prior to reverse transcription. Moreover, EHD4 and EHD1 participate in the biogenesis of infectious virions : their respective depletion alters the intra-cellular trafficking of viral components, the viral budding sites organization and the incorporation of the viral envelope glycoprotein into nascent particles. Thoses phenotypes combined result in a drastic decrease of the infectivity of virions produced in the absence of either EHD4 or EHD1.

O permanente contato das vedações externas dos edifícios com os materiais integrantes das vedações externas dos edifícios (fachadas e telhados) com os agentes de degradação provocam o surgimento de manchas, que normalmente estão associadas à deposição de poluentes e a proliferação de microorganismos. Para inibir o surgimento dessas manchas existem, atualmente, diversos métodos disponíveis, sendo que nenhum tem se mostrado efetivo. Esta tese de doutorado, com base em um extenso programa laboratorial - com o uso de métodos como MEV, FTIR, ângulo de contato, crescimento acelerado de microrganismos, atividade fotocatalítica, entre outros-, criou um novo método, destinado aos materiais de construção silicosos e porosos, que se baseia na modificação de suas propriedades superficiais, por meio da sobreposição de uma camada hidrofóbica por uma hidrofílica. Para se obter essa disposição superficial, utilizou-se um hidrofugante à de octil-silicone, que apresenta elevada repelência à água e maior durabilidade, e um semicondutor à base de dióxido de titânio, que apresenta atividade fotocatalítica quando incidido por radiação ultravioleta. Como resultado, o método proposto (denominado na tese por WR+TiO2-sequencial) apresenta, comprovadamente, os seguintes benefícios: (i) redução de manchas causadas pela adesão de partículas com características apolares, similares às partículas de poluição dos grandes centros urbanos; (ii) limpeza espontânea de certos tipos de manchas, decorrentes dos processos fotocatalíticos que promovem a oxidação/redução de matéria orgânica; (iii) inibição do crescimento de microrganismo em escala laboratorial; (iv) redução da absorção total de água e, principalmente, da cinética do ganho de massa. Por isso, edificações cujas vedações externas venham a ser tratadas com o método aqui proposto são, potencialmente, células ativas para a sustentabilidade do ambiente construído, pois: reduzem o consumo de energia, reduz os custos de manutenção e contribuem para despoluição da atmosfera urbana. / Building roofs and façades usually show blackening surfaces after few years in large cities. On porous and silicious materials those soiling is caused by particles pollution depositions and mould growth, and the available methods available to prevent this phenomenum do not have a good performance along its service life. This thesis, based on an intensive laboratory research with many test technics as SEM, FTIR, contact angle, accelerated mould growth, and photocatalytical activity, create a new method to prevent soiling on porous and silicous building materials. This method modify the materials surface properties, making the outer surface layers with nano-actived titanium dioxide particles, which has photocatalitycal activity under UV radiation, and below it a hydrophobic layer, composed by octyl-silicones. The main results in laboratory scale experiments obtained by this new method (so-called in this thesis by WR+TiO2-sequencial) are: (i) stainings reductions caused by apolar agent, (ii) self-cleaning properties for some stain and after UV radiation exposition, (iii) mould growth resistance, and (iv) water absorption reduction. As a consequences, building envelopes trated with the new method is supposed to contribute to built and environment sustantability, because: can reduce the energy consumption, reduce de maintenance costs e has a de-pollution properties.

A dengue é um dos principais problemas de saúde publica do mundo, especialmente nas regiões tropicais e subtropicais. Apesar da magnitude do problema, ainda existem limitações relacionadas ao diagnóstico, devido à presença de resultados falsos negativos, muitas vezes apresentados nos laudos laboratoriais. Estudos com a proteína do envelope são extremamente importantes para o desenvolvimento de novas vacinas e testes de diagnóstico. Os métodos sorológicos são importantes para o diagnóstico das infecções por dengue, entre eles, o imunoensaio enzimático para detecção de IgM contra o vírus da dengue. Neste estudo, 82 amostras de soro de pacientes com suspeita de dengue foram classificadas como positivas ou negativas utilizando o kit comercial Panbio ELISA de Captura Dengue IgM. O desempenho do ensaio do kit comercial foi comparado com os novos ensaios ELISA indireto usando três peptídeos sintéticos derivados da proteína E como substrato. De um total de 82 amostras de soro, (52,4%) foram positivas pelo kit comercial Panbio Dengue IgM ELISA de Captura, 18 (21,9%) apresentaram reatividade contra Pep1, 40 (48,7%) contra o Pep2 e 66 (80,4%) contra Pep3. Entre as amostras de soro classificadas como positivas pelo kit comercial (42), 11 (26%), também foram classificadas como positivas usando o peptídeo Pep1. Vinte e duas (52,3%), utilizando o Pep2 e 40 (95,23%) utilizando Pep3. Entre as amostras classificadas como negativas por meio do kit comercial (40), 28 (70%) foram classificadas como negativas usando como substrato o Pep1, vinte 20 (50%) utilizando como substrato o Pep2 e 13 (32,5%), utilizando como substrato Pep3. Os resultados demonstram que os peptídeos sintéticos podem ter potencial biotecnológico para o desenvolvimento de novas vacinas, tratamentos e testes de diagnósticos. / Dengue is a major public health problem worldwide, especially in the tropical and subtropical regions of the world. Despite the magnitude of the problem, there are still limitations related to the diagnosis, due to the presence of false negative results often presented in the laboratory reports. Studies using the envelope protein are extremely important for the development of new vaccines and new diagnostic tests. Serological methods are important for the diagnosis of dengue infections, and among them, the enzyme linked immunoassay that detects IgM against Dengue virus is very employed. In this study, a panel of 82 serum samples from dengue suspected patients was classified as positive and negative using the commercial ELISA kit Panbio Capture Dengue IgM. Assay performance of the commercial kit was compared with the new indirect ELISA assays using synthetic peptides derived from E protein (Pep1, Pep2 and Pep3) as substrate. Of a total of 82 serum samples, (52.4%) were positive by the commercial ELISA kit Panbio Capture Dengue IgM, 18 (21,95%) showed reactivity against Pep1; 40 (48,78%) against Pep2 and 66 (80,48%) against Pep3. Among the serum samples classified as positive by the commercial kit (42), 11 (26%) are also classified by positive using Pep1 as substrate, 22 (52,3%) using Pep2 as substrate and 40 (95,23%) using Pep3 as substrate. Among the samples classified as negative by the commercial kit (40), 28 (70%) were also classified as negative using Pep1 as substrate, 20 (50%) using Pep2 as substrate and 13 (32.5%) using Pep3 as substrate. The results showed that the synthetic peptides can have biotechnological potential for the development of new vaccines and treatments and diagnostic tests. / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES