Academic literature on the topic 'Viral phenomenon'

ABSTRACTAmong the most fundamental questions in viral evolutionary biology are how fast viruses evolve and how evolutionary rates differ among viruses and fluctuate through time. Traditionally, viruses are loosely classed into two groups: slow-evolving DNA viruses and fast-evolving RNA viruses. As viral evolutionary rate estimates become more available, it appears that the rates are negatively correlated with the measurement timescales and that the boundary between the rates of DNA and RNA viruses might not be as clear as previously thought. In this study, we collected 396 viral evolutionary rate estimates across almost all viral genome types and replication strategies, and we examined their rate dynamics. We showed that the time-dependent rate phenomenon exists across multiple levels of viral taxonomy, from the Baltimore classification viral groups to genera. We also showed that, by taking the rate decay dynamics into account, a clear division between the rates of DNA and RNA viruses as well as reverse-transcribing viruses could be recovered. Surprisingly, despite large differences in their biology, our analyses suggested that the rate decay speed is independent of viral types and thus might be useful for better estimation of the evolutionary time scale of any virus. To illustrate this, we used our model to reestimate the evolutionary timescales of extant lentiviruses, which were previously suggested to be very young by standard phylogenetic analyses. Our analyses suggested that these viruses are millions of years old, in agreement with paleovirological evidence, and therefore, for the first time, reconciled molecular analyses of ancient and extant viruses.IMPORTANCEThis work provides direct evidence that viral evolutionary rate estimates decay with their measurement timescales and that the rate decay speeds do not differ significantly among viruses despite the vast differences in their molecular features. After adjustment for the rate decay dynamics, the division between the rates of double-stranded DNA (dsDNA), single-stranded RNA (ssRNA), and ssDNA/reverse-transcribing viruses could be seen more clearly than before. Our results provide a guideline for further improvement of the molecular clock. As a demonstration of this, we used our model to reestimate the timescales of modern lentiviruses, which were previously thought to be very young, and concluded that they are millions of years old. This result matches the estimate from paleovirological analyses, thus bridging the gap between ancient and extant viral evolutionary studies.

Increasing use of the internet by millennials is a phenomenon that needs to be adapted to. The advertising-marketing world is no exception. Responds to the phenomenon has been varying, for example there’s a new category for advertising media besides Above The Line and Below The Line; Through The Line Media. Through The Line occurred to define internet media which has the quality of both above the line and below the line medias. Another form of adaptation to this situation exists in the form of marketing strategies; that is viral marketing. Viral marketing is a strategy that is only relevant in internet media. This paper will try to explain the kind of impact made from this marketing strategy, and its effectiveness on millennial target audiences by using some case studies on the brand, Go-Jek.

On January 9th, 2021, the Laboratory Medicine & Pathobiology Students Union (LMPSU) hosted their annual scientific conference online, focusing on the theme: “COVID-19: A viral phenomena”. The department of Laboratory Medicine & Pathobiology (LMP) at the Temerty Faculty of Medicine, University of Toronto is home to world-class research in the area of pathobiology, from cancer to immunopathology to neuropathology. The conference began with opening remarks from LMPSU executives Karen Mao and Ziqi Liu, followed by Dr. Rita Kandel, the chair of the department of LMP. The topic of COVID-19 research was timely, to say the least! Invited speakers were asked to share their research and knowledge about various aspects of the COVID-19 pandemic from basic virology to treatment options, and epidemiology. The keynote speakers were Dr. Samira Mubareka and Dr. Robert Kozak; notably members of the team that was among the first to isolate the SARS-CoV-2 virus.

Within only a few years after the launch of video sharing platforms, viral videos have become a pervasive Internet phenomenon. Yet, notwithstanding growing scholarly interest, the suitability of the viral metaphor seems not to have been studied so far. In this paper, we therefore investigate the attention dynamics of viral videos from the point of view of mathematical epidemiology. We introduce a novel probabilistic model of the progression of infective diseases and use it to analyze time series of YouTube view counts and Google searches. Our results on a data set of almost 800 videos show that their attention dynamics are indeed well accounted for by our epidemic model. In particular, we find that the vast majority of videos considered in this study show very high infection rates.

Since the 1990s, Internet communications technologies have influenced human activity. Over the last 15 years, a phenomenon called virality—i.e., when content circulates via Internet among an increasingly broad audience at an exponentially rapid rate—has been especially impactful. Only some information achieves virality, so the phenomenon invites reflection. Yet, scholars have failed to adequately address the topic. The literature is especially sparse when it comes to viral artwork. This essay helps fill that gap in the literature by demonstrating the academic significance of viral artwork through comparative analysis of three cases where Internet-based artworks went viral: “Ten Hours of Princess Leia walking in NYC,” “New Beginnings,” and “McKayla is Not Impressed.” The author asserts that viral artwork merits rigorous study because doing so could: first, augment existing research on other topics; second, fortify investigations in philosophy of art; and third, guide the public toward better-informed engagement with viral artwork.

Endogenous viral elements, or viral genomic fossils, have proven extremely valuable in the study of the macroevolution of viruses, providing important, and otherwise unobtainable, insights into the ancient origin of viruses, and how their ancestors might have co-evolved with their hosts in the distant past. This type of investigation falls within the realm of paleovirology—the study of ancient viruses. Investigations of extant viruses and paleovirological analyses, however, often give conflicting results, especially those concerning viral evolutionary rates and timescales. Reconciling these two types of analyses is a necessary step towards a better understanding of the overall long-term evolutionary dynamics of viruses. The main study system of this thesis is foamy viruses (FVs). FVs are characterised by their stable co-speciation history with their hosts, allowing their evolutionary dynamics to be modelled and investigated over various timescales. This unique evolutionary feature makes FVs one of the best subjects for connecting recent and ancient viral evolution. The work here reports the discovery of several endogenous mammalian FVs, and examines how mammalian FVs co-evolve with their hosts. Analyses reveal a co-diversifying history of the two that could be dated back to the basal radiation of eutherians more than 100 million years ago. However, a small number of ancient FV cross-species transmissions could still be found, mostly involving New World monkey FVs. Based on this extended FV-mammal co-speciation pattern, this thesis investigates the long-term evolutionary rate dynamics of FVs, and shows that the rate estimates of FV evolution appear to decrease continuously as the rate measurement timescale increases, following a power-law decay function. The work presented here also shows that this so-called 'time-dependent rate phenomenon' is in fact a pervasive evolutionary feature of all viruses, and surprisingly, the rate estimates of evolution of all viruses seem to decay at the same speed, decreasing by approximately half for every 3-fold increase in the measurement timescale. Based on this power-law rate-decay pattern, we could infer evolutionary timescales of modern-day lentiviruses that are consistent with paleovirological analyses for the first time. Finally, this thesis reports the discovery of basal FV-like endogenous retroviruses (FLERVs) in amphibian and fish genomes. Phylogenetic analyses reveal that the progenitors of ray-finned fish FLERVs co-diversify broadly with their fish hosts, but also suggest that there might have been several ancient viral cross-class transmissions, involving lobe-finned fish, shark, and frog FLERVs. Again, by using the power-law rate-decay model, analyses in this thesis suggest that this major retroviral clade has an ancient Ordovician marine origin, originating together with their jawed vertebrate hosts more than 450 million years ago. This finding implies that the origin of retroviruses as a whole must be in the early Paleozoic Era, if not earlier. The results presented here bridge ancient and recent viral evolution.

La peste porcina clásica (PPC) es una enfermedad viral altamente contagiosa de cerdos domésticos y salvajes, incluida en la lista de enfermedades de declaración obligatoria a la Organización Mundial de Sanidad Animal. El agente causal, el virus PPC (VPPC), pertenece al género Pestivirus, familia Flaviviridae. A pesar de los grandes esfuerzos dirigidos a controlar y erradicar la PPC, continúa siendo una de las enfermedades más importantes para la sanidad animal y la industria porcina en todo el mundo. La circulación y la importancia intrínseca de cepas de VPPC de baja y moderada virulencia en las regiones endémicas ha sido objeto de discusión en los últimos años. Varios trabajos han demostrado el papel de cepas de baja virulencia en el nacimiento de lechones persistentemente infectados (PI) con el VPPC. No obstante, los mecanismos involucrados en este tipo de infecciones por VPPC no son bien conocidos, y los estudios existentes datan de hace 40 años. Por otro lado, la posible generación de persistencia viral después de la infección postnatal con VPPC era todavía una cuestión a resolver. Esta tesis demuestra la capacidad de cepas de VPPC de baja y moderada virulencia de inducir persistencia vírica de forma postnatal en cerdo doméstico y salvaje. Para ello, cerditos recién nacidos fueron inoculados de forma intranasal con el VPPC. Durante seis semanas, estos lechones permanecieron aparentemente sanos, a pesar de no generar respuesta inmunológica celular ni humoral específica para VPPC. Se demostró viremia permanente y alta carga de virus en todas las muestras de tejido, secreciones y excreciones de los animales persistentemente infectados (PI), hasta el fin del estudio. Además, se demostró la ineficacia de la vacunación de cerdos PI, de seis semanas de edad, los cuales no generaron respuesta de IFN de tipo I ni de tipo II, ni de anticuerpos durante 21 días tras la vacunación con una vacuna viva atenuada de VPPC (la C-strain). La falta de detección del ARN vacunal mediante RT-qPCR específica en sangre, excreciones y tejidos, incluyendo la tonsila, sugirió la ausencia de replicación del virus vacunal en los animales PI y un posible fenómeno de interferencia viral. Finalmente, jabalíes de seis semanas de vida con infección persistente de VPPC (primera infección) fueron inoculados con una cepa de alta virulencia de VPPC (segunda infección o superinfección). Los jabalíes PI no desarrollaron signos clínicos y mostraron alta carga del virus primario, causante de la persistencia, en todas las muestras analizadas. Por el contrario, el virus secundario no fue detectado ni por RT-qPCR ni por secuenciación, demostrando así el fenómeno de exclusión de la superinfección (ESI). La ausencia de una respuesta de IFN de tipo I y II y de anticuerpos respaldó los resultados previos de los estudios de esta tesis. Estos hallazgos demostraron por primera vez la capacidad del VPPC para inducir ESI in vivo, en cerdos con infección persistente. El fenómeno ESI probablemente explicaría la falta de respuesta de los animales con infección persistente después de la vacunación con la vacuna viva atenuada. Considerando la existencia de cepas de virulencia baja a moderada y su capacidad para producir formas de infección persistente, los resultados aquí presentados pueden tener potenciales repercusiones epidemiológicas, especialmente en el contexto endémico. Es importante destacar que los animales persistentemente infectados pasarían desapercibidos bajo control serológico, dada la ausencia de respuesta de anticuerpos específicos. Esta tesis doctoral ha contribuido a la comprensión de la patogénesis producida por el VPPC, que depende no sólo de la virulencia de la cepa sino también de la interacción virus-huésped, y abre nuevas líneas de investigación para comprender los mecanismos subyacentes que conducen a la generación de inmunotolerancia y persistencia del VPPC.<br>Classical swine fever (CSF) is a highly contagious viral disease of domestic and wild pigs, included in the list of diseases notifiable to the World Organisation for Animal Health. The causative agent, CSF virus (CSFV), belongs to the Pestivirus genus, Flaviviridae family. Over the last century, great efforts have been directed towards the control and eradication of CSF, which today remains one of the most important diseases for animal health and in the pig industry worldwide. The circulation and intrinsic importance of low and moderate virulence strains in the endemic regions has been extensively described. Also, it has been shown the role of these type of viral strains in the generation of “the pregnant carrier sow syndrome” and persistent infection of piglets after trans-placental transmission. However, the mechanisms involved in this form of CSFV infections are not well known, and the existing studies date over 40 years ago. By contrast, the possible generation of viral persistence after postnatal infection of pigs is still a question to resolve. Against this background, this thesis has demonstrated the capacity of low and moderate virulence CSFV strains to produce postnatal persistent infection early after birth. To this end, newborn piglets were inoculated intranasally with CSFV. During six weeks, these piglets remained apparently healthy, although they were not able to generate detectable CSFV specific humoral nor cellular immune responses, maintaining high virus load in blood, organs and body secretions and excretions. In addition, it has been demonstrated the ineffectiveness of vaccination of six-week-old PI pigs, which were unable to elicit a detectable innate immune response, in terms of IFN type-I production, as well as acquired immune responses (i.e. IFN type-II and antibodies) following vaccination with a CSFV live attenuated vaccine (C-strain). The RNA of the vaccine could not be detected by a specific RT-qPCR in any of the samples analysed after vaccination, including the tonsil, suggesting a superinfection exclusion (SIE) phenomenon between the persistently infecting virus (primary infection) and the CSFV vaccine strain (secondary infection). Finally, six-week-old wild boars with CSFV persistent infection (first infection) were inoculated with a CSFV strain of high virulence (second infection or superinfection). PI wild boars did not develop clinical signs and showed a high load of the primary virus, causing persistence, in all samples analysed. In contrast, the secondary virus was not detected by either RT-qPCR or sequence analyses, thus demonstrating the phenomenon of superinfection exclusion (SIE). The lack of innate and acquired immune responses supported the previous studies from this thesis. In addition, in vitro assays with the PBMCs isolated ex vivo from persistently infected animals, a well-known target for the CSFV viral replication, further corroborated the CSFV SIE phenomenon. These findings demonstrated for the first time the ability of CSFV to induce SIE in vivo, in swine with persistent infection. The SIE phenomenon would likely explain the unresponsiveness of animals with persistent infection after vaccination with the live attenuated vaccine. Considering the existence of CSFV strains of low and moderate virulence and their ability to produce persistent infection forms, the results showed here may have potential epidemiological repercussions, especially in the endemic context. Importantly, persistently infected animals would remain unnoticed under serological control, given the absence of specific antibody response. This doctoral thesis has contributed to the understanding of the pathogenesis of CSFV infection, which depends not only on the virulence of the strain but also on the virus-host interaction, and opens new lines of research to understand the immunological bases and of viral pathogenesis for the generation of immunotolerance and persistence, hitherto unknown.

This doctoral thesis commences with a meticulous examination on whether financial, social and institutional determinants associate with the migration performance in Europe and accordingly in Greece. Motivated by the intensity, the magnitude and the financial recession, this thesis presents three empirical chapters on the examination of the determinants that affect the phenomenon of migration. Prior to these three empirical studies a chapter introduces and defines all the variables used as well as the theoretical and methodological framework of the thesis. The first empirical chapter demonstrates a comprehensive sample of 15 European countries from 1990 – 2012, which have been divided into 3 groups (Weak-EMU, Strong-EMU and Non-EMU countries) in order to investigate the behaviour of each group during these periods. It follows a quantitative analysis of the economic and social determinants on migration, in order to comprehend their relationship with the phenomenon. The chapter concludes with the discussion of our results with an analytical review of the selected variables upon migration. Results reveal that Portugal, Ireland, Italy, Greece and Spain are countries that are more exposed to the financial crisis, something that consequently affects negatively the behaviour of each employed economic variable. Additionally, results detect that one significant outcome is that the GDP growth rate, inflation and the imports of goods are related to migration, while on the other hand the 10-year government bond yield is not affiliated to the phenomenon. The second empirical chapter covers the financial, social and institutional determinants that motivate Greek nationals to leave their country and emigrate to wealthier destinations during the recent financial crisis. First, it reviews the theoretical explanations for the efficiency of the factors on migration. It then provides a survey on the relevant empirical studies and subsequently an analysis of the variables, which have a significant impact on labour migration. Based on the theories presented, the study develops a model to explain how financial, social and institutional factors are correlated with the economic downturn and lead to adverse financial and social shocks such as massive migration outflows of Greek nationals. More precisely, the second chapter indicates that Greece has been very exposed to the financial crisis, thus had a strong impact on the decision of Greek natives to emigrate. As conditions deteriorate, Greece was in a severe financial situation due to the financial crisis and was dependent on the monetary policy support, something that emerged the country to experience major and drastic changes on its social cohesion. Further, we can identify, that debt to GDP, exports of goods, ln of imports of goods, long term unemployment and population growth are positively related to emigration from Greece, while on the other hand cash surplus, foreign direct investment and bank capital are negatively associated to the phenomenon. Finally, we employed advanced techniques to model the factors that motivate the existing regular immigrants in Greece to abandon the country and return to their own during the economic crisis period (return-migration). The findings reveal details on the imbalances of the economic, social and political framework of Greece that consequently affected negatively the growth rate of the country and created a fragile economy with high rates of unemployment and inflation. Hence, it compares the economic, social and institutional factors, which are related to the literature of return migration. According to the estimated results, the phenomenon of return migration is neither related in a predetermined way with unemployment rates nor poverty levels, but with tax revenue, corruption and government debt. Consequently, this situation had a strong negative impact in the behaviour of each financial, social and institutional determinant, with immediate result to the migrant families who pursue an improved quality of life back to their home country.

Theoretical studies of the molecular mechanisms responsible for the formation and stability of protein complexes have gained importance due to their practical applications in the understanding of the molecular basis of several diseases, in protein engineering and biotechnology. The objective of this project is to critically analyze and refine a coarse-grained force field for protein-protein interactions based on experimental thermodynamic properties and to apply it to cancer-related S100A4 protein system. Our ultimate goal is to generate knowledge for a better understanding of the physical mechanisms responsible for the association of particular proteins in different environments. We studied the role of short and long-range interactions on the complexation of homo-associations. Furthermore, we analyzed the influence of the pH and its correlation with the charge regulation mechanism. We analyzed and refined the adjustable Lennard-Jones parameter for a mesoscopic model based on experimental second virial data for lysozyme, chymotrypsinogen, and ribonuclease A via Monte Carlo simulations. From of that, the S100A3 protein was used to test the new calibrated parameters. Finally, we evaluated the dimerization process of S100A4 proteins, observing the role of physical-chemistry variables involved in the thermodynamical stability of different oligomers.<br>Estudos teóricos dos mecanismos moleculares responsáveis pela formação e estabilidade dos complexos de proteínas vêm ganhando importância devido às suas aplicações práticas no entendimento da base molecular de várias doenças, em engenharia de proteínas e biotecnologia. O objetivo deste projeto é analisar criticamente e aperfeiçoar um campo de força de granulidade grossa para interação proteína-proteína com base em propriedades termodinâmicas experimentais e aplicá-lo ao sistema proteico S100A4 relacionado com o câncer. Nosso objetivo final é gerar conhecimento para uma melhor compreensão dos mecanismos físicos responsáveis pelas associações de proteínas particulares em diferentes ambientes. Estudamos o papel das interações de curto e longo alcance na complexação de homo-associações. Além disso, analisamos a influência do pH e sua correlação com o mecanismo de regulação de cargas. Por meio de simulações Monte Carlo, analisamos e refinamos o parametro ajustável de Lennard-Jones para um modelo mesoscópico, usando dados experimentais do segundo virial para a lisozima, o quimotripsinogênio e a ribonuclease A. A partir disso, a proteína S100A3 foi usada para testar os novos parâmetros calibrados. Finalmente, foi avaliado o processo de dimerização das proteínas S100A4, observando o papel de algumas variáveis físico-químicas envolvidas na estabilidade termondinâmica de diferentes oligómeros.

P22 lysozyme, encoded by gene 19, is an essential phage protein responsible for hydrolyzing the bacterial cell wall during lytic infection. P22 lysozyme is related to T4 lysozymein its mode of action, substrate specificities, and in its structure. Gene 19 was located on the phage genome, subcloned, and then sequenced. lysozyme was produced in large quantities and purified for biochemical characterization and for crystallograpic studies. Gene 19consists of 146 codons, and encodes a protein with a molecular weight of 16,117. Amber mutations were created in gene 19 by in vitro primer-directed mutagenesis. The mutations were crossed by homologous recombination onto the phage genome. The phages bearing the amber mutations in gene 19 were screened for the ability to grow on six different amber suppressor strains. Amino acid substitutions that resulted in nonfunctional or less functional lysozyme were determined. Of 60 possible amino acid substitutions at 11 different sites in P22 lysozyme, 20 are deleterious. The phage bearing amber mutations in gene 19that failed to grow on given suppressor strains were reverted and second site intragenic revertants were obtained. The mutations were sequenced. A substitution of serine for glutamine at residue 82 is compensated for by changing residue 46 from serine to leucine. This single change enables the phage to form a plaque at 300C but not at 400C. When the triple change asn42->lys; ser46->leu; and ser43->pro is present the lysozyme produced is no longer temperature sensitive. The crystal structure of P22 lysozyme is not yet solved. Assuming that the structures of T4 lysozyme and P22 lysozyme are similar, one can examine the positions of equivalent residues in the T4 lysozyme structure. The spatial arrangement of the residues changed by the secondary site mutations and the original substitution can then be visualized. The mutations discussed above all map far from the original mutation on the T4 three dimensional model. A substitution of leucine for tyrosine at position 22 is compensated for by the double mutation of arg18->ser and ser23->lys. When the equivalent residues are mapped on the T4 three dimensional model the changes map in close proximity to the original mutation.

The binding of HIV-1 Vif to the cellular cytidine deaminase Apobec3G and subsequent prevention of Apobec3G virion incorporation have recently been identified as critical steps for the successful completion of the HIV-1 viral life cycle. This interaction occurs in the cytoplasm where Vif complexes with Apobec3G and directs its degradation via the proteasome pathway or sequesters it away from the assembling virion, thereby preventing viral packaging of Apobec3G. While many recent studies have focused on several aspects of Vif interaction with Apobec3G, the subcellular localization of Vif and Apobec3G during the viral life cycle have not been fully considered. Inhibition of Apobec3G requires direct interaction of Vif with Apobec3G, which can only be achieved when both proteins are present in the same subcellular compartment. In this thesis, a unique approach was utilized to study the impact of Vif subcellular localization on Vif function. The question of whether localization could influence function was brought about during the course of studying a severely attenuated viral isolate from a long-term non-progressor who displayed a remarkable disease course. Initial observations indicated that this highly attenuated virus contained a mutant Vif protein that inhibited growth and replication. Upon further investigation, it was found that the Vif defect was atypical in that the mutant was fully functional in in vitro assays, but that it was aberrantly localized to the nucleus in the cell. This provided the basis for the study of Vif localization and its contribution to Vif function. In addition to the unique Vif mutant that was employed, while determining the localization and replication phenotypes of the differentially localized Vif proteins, a novel pathway for Vif function was defined. Copious publications have recently defined the mechanism for Vif inhibition of Apobec3G. Vif is able to recruit Apobec3G into a complex that is targeted for degradation by the proteasome. However, this directed degradation model did not fully explain the complete neutralization of Apobec3G observed in cell culture. Other recent works have proposed the existence of a second, complementary pathway for Vif function. This pathway is defined here as formation of an aggresome that prevents Apobec3G packaging by binding and sequestering Apobec3G in a perinuclear aggregate. This second mechanism is believed to work in parallel with the already defined directed degradation pathway to promote complete exclusion of Apobec3G from the virion. The data presented here provide insight into two areas of HIV research. First, the work on the naturally occurring Vif mutant isolated from a long-term non-progress or confirms the importance of Vif in in vivo pathogenesis and points to Vif as a potentially useful gene for manipulation in vaccine or therapy design due to its critical contributions to in vivo virus replication. Additionally, the work done to address the subcellular localization of Vif led to the proposal of a second pathway for Vif function. This could have implications in the field of basic Vif research in terms of completely understanding and defining the functions of Vif. Again, a more complete knowledge about Vif can help in the development of novel therapies aimed at disrupting Vif function and abrogating HIV-1 replication.

Since the first cases were reported over thirty years ago, great strides have been made to control disease progression in people living with HIV/AIDS. However, current estimates report that there are about 34 million individuals infected with HIV worldwide. Critical in the ongoing fight against this pandemic is the continuing development of highly active anti-retroviral therapies, ideally those with novel mechanisms of action. Currently, there are no medications approved for use that exploit the HIV-1 MA protein, despite its central role in multiple stages of the virus life cycle. This thesis sought to examine whether a highly conserved glutamate residue at position 99 in the understudied C-terminal helix of MA is required for HIV-1 replication. I characterized a panel of mutant viruses that contain different amino acid substitutions at this position using viral infectivity studies, virus-cell fusion assays, and immunoblotting. In doing so, I found that substitution of this glutamate with either a valine (E99V) or lysine (E99K) residue disrupted Env incorporation into nascent HIV particles, and abrogated their ability to fuse with target-cell membranes. In determining that the strain of HIV could affect the magnitude of E99V-associated defects, I identified a compensatory substitution at MA residue 84 that rescued both E99V- and E99K-associated impairments. I further characterized the MA E99V and E99K mutations by truncating HIV Env and pseudotyping with heterologous envelope proteins in an attempt to overcome the Env incorporation defect. Unexpectedly, I found that facilitating fusion at the plasma membrane was not sufficient to reverse the severe impairments in virus infectivity. Using quantitative PCR, I determined that an early post-entry step is disrupted in these particles that contain the E99V or E99K MA substitutions. However, allowing entry of mutant virus particles into cells through an endosomal route conferred a partial rescue in infectivity. As the characterization of this post-entry defect was limited by established virological methods, I designed a novel technique to analyze post-fusion events in retroviral infection. Thus, I present preliminary data regarding the development of a novel PCR-based assay that monitors trafficking of the viral reverse transcription complex (RTC) in an infected cell. The data presented in this thesis indicate that a single residue in MA, E99, has a previously unsuspected and key role in multiple facets of HIV-1 MA function. The pleiotropic defects that arise from specific substitutions of this amino acid implicate a hydrophobic pocket in MA in Env incorporation and an early post-entry function of the protein. These findings suggest that this understudied region of MA could be an important target in the development of a novel antiretroviral therapy.

Tolerance-based stem cell transplantation using sub-lethal conditioning is being considered for the treatment of human disease, but safety and efficacy remain to be established. In order to study these two issues, we first established that mouse bone marrow recipients treated with sub-lethal irradiation plus transient blockade of the CD40-CD154 costimulatory pathway develop permanent hematopoietic chimerism across allogeneic barriers. Our conditioning regimen of 6 Gy irradiation, a short course of anti-CD154 mAb and 25 million fully allogeneic BALB/c bone marrow cells consistently produced long-term, stable, and multilineage chimerism in C57BL/6 recipients. Furthermore, chimeric mice displayed donor-specific transplantation tolerance, as BALB/c skin allografts were permanently accepted while third-party CBA/JCr skin allografts were promptly rejected. We next determined both the safety and efficacy of this protocol by infecting chimeric mice with lymphocytic choriomeningitis virus (LCMV) either at the time of transplantation or at several time points afterwards. Infection with LCMV at the time of transplantation prevented engraftment of allogeneic, but not syngeneic, bone marrow in similarly treated mice. Surprisingly, infected allograft recipients also failed to clear the virus and died. Post-mortem study revealed hypoplastic bone marrow and spleens. Hypoplasia and death in these mice required the combination of 6 Gy irradiation, LCMV infection on the day of transplantation, and an allogeneic bone marrow transplant but did not require the presence of anti-CDl54 mAb. Allochimeric mice infected with LCMV 15 days after transplantation were able to survive and maintain their bone marrow graft, indicating that the deleterious effects of LCMV infection on host and graft survival are confined to a narrow window of time during the tolerization and transplantation process. The final section of this thesis studied the mechanisms of graft rejection and death in sublethally irradiated recipients of allogeneic bone marrow and infection with LCMV at the time of bone marrow transplantation. Infection of interferon-α/β receptor knockout mice at the time of transplantation prevented the engraftment of allogeneic bone marrow, but the mice survived. Therefore, IFN-αβ is involved in the development of marrow hypoplasia and death, whereas a second mechanism is involved in blocking the development of chimerism in these mice. Through the use of depleting mAb's and knockout mice we demonstrate that three types of recipients survived and became chimeric after being given sublethal irradiation, anti-CD154 mAb, an allogeneic bone marrow transplant and a day 0 LCMV infection: mice depleted of CD8+ T cells, CD8 knockout mice, and TCR-αβ knockout mice. Our data indicate that the mediator of bone marrow allograft destruction in LCMV-infected mice treated with costimulatory blockade is a radioresistant CD8+ NK1.1- TCRαβ+ T cell. We conclude that a non-cytopathic viral infection at the time of transplantation can prevent engraftment of allogeneic bone marrow and result in the death of sub-lethally irradiated mice treated with costimulation blockade. The abrogation of allogeneic bone marrow engraftment is mediated by a population of CD8+ NK1.1- TCRαβ+ T cells and the mediator of hypoplasia and death is viral induction of IFN-αβ.

HIV-1 protease is a very important drug target for AIDS therapy. Nine protease inhibitors have been proved by FDA and used in AIDS treatment. Due to the high replication rate and the lack of fidelity of the HIV-1 reverse transcriptase, HIV-1 virus developed various drug-resistant variants. Although experimental methods such as crystallography and isothermal titration calorimetry provide structural and thermodynamic data on drug-resistant variants, they are unable to discern the mechanism by which the mutations confer resistance to inhibitors. Understanding the drug-resistance mechanism is crucial for developing new inhibitors more tolerant to the drug-resistant mutations. Computational methods such as free energy calculations and molecular dynamic simulations can provide insights to the drug resistance mechanism at an atomic level. In this thesis, I have focused on the elucidation of the energetic and dynamics of key drug-resistant variants of HIV-1 protease. Two multi-drug resistant variants, in comparison with wild-type HIV-1 protease were used for the comparisons: Flap+ (L10I, G48V, I54V, and V82A) which contains a combination of flap and active site mutations and ACT (V82T, I84V) that only contains active site mutations. In Chapter II, I applied free energy simulations and decomposition methods to study the differential mechanism of resistance to the two variants, Flap+ and ACT, to the recently FDA-approved protease inhibitor darunavir (DRV). In this study, the absolute and relative binding free energies of DRV with wild-type protease and the two protease variants were calculated with MM-PB/GBSA and thermodynamic integration methods, respectively. And the predicted results are in good agreement with the ITC experimental results. Free energy decomposition elucidates the mutations alter not only its own interaction with DRV but also other residues by changing the geometry of binding pocket. And the VdW interactions between the bis-THF group of DRV is predominant even in the drug-resistant variants. At the end of this chapter, I offer suggestions on developing new inhibitors that are based on DRV but might be less susceptible to drug-resistant mutations. In Chapter III, 20-ns MD simulations of the apo wildtype protease and the apo drug-resistant protease variant Flap+ are analyzed and compared. In these studies, these mutations have been found to decrease the protease flexibility in the apo form but increase the mobility when the protease is binding with inhibitor. In Chapter IV, more details of the free energy simulation and decomposition are discussed. NMR relaxation experiments were set up as a control for the MD simulation study of the dynamics of the Flap+ variant. The difficulty of finishing the NMR experiment is discussed and the solution and some preliminary results are shown. In summary, the scope of this thesis was to use computational methods to study drug-resistant protease variants’ thermodynamic and dynamic properties to illuminate the mechanism of protease drug resistance. This knowledge will contribute to rational design of new protease inhibitors which bind more tightly to the protease and hinder the development of drug-resistant mutations.

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2016-08-26T15:37:10Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Tese NormandoJQViana_Biblioteca Central_UFPE (0).pdf certa.pdf: 2847669 bytes, checksum: 035b1ec1bda1217eaae08822bf17ca9e (MD5)<br>Made available in DSpace on 2016-08-26T15:37:10Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Tese NormandoJQViana_Biblioteca Central_UFPE (0).pdf certa.pdf: 2847669 bytes, checksum: 035b1ec1bda1217eaae08822bf17ca9e (MD5) Previous issue date: 2016-02-29<br>CNPq<br>Vem de longa data o interesse da ciência psicológica pela busca do autoconhecimento (James, 1890/1983). Neste contexto, os estudos oriundos do campo da autoconsciência, em especial com o advento da Teoria OSA (Duval & Wicklund, 1972), uma das primeiras teorias a considerar as discrepâncias entre o self e os padrões (Duval & Silva, 2001), têm reunido esforços no intuito de superar tamanha lacuna. Neste contexto, entusiasmado pela compreensão do self, em especial em sua vertente simbólica, bem como no instanciamento dos processos autoavaliativos por este operados, tramados à identificação da natureza dos padrões de atratividade e a forma como estes têm sido fenomenologicamente consciencizados no fluxo da experiência interna dos sujeitos, o presente estudo de tese objetiva identificar o que são os padrões de autoatratividade, qual sua dinâmica representacional no seio da experiência interna e o enlaçamento no processo autoavaliativo dos processos de atratividade autopercebida, autofocalização (autoconsciência situacional e disposicional), autoestima, bem estar (satisfação com a vida e felicidade), humor depressivo e religiosidade. Para o estudo em questão, foi recrutada uma amostra mista composta por 657 participantes (563 brasileiros e 94 portugueses), adolescentes, jovens, adultos e idosos, de ambos os sexos e orientações sexuais homossexual e heterossexual, residentes na Região Metropolitana do Recife e na cidade de Lisboa, Portugal. Os procedimentos relativos à coleta ocorreram em três etapas: a primeira com objetivo de levantar emicamente, por intermédio de procedimentos multimétodos, o campo semântico de autoatratividade (Estudo 1 – Qualitativo); a segunda, com base nos achados da etapa anterior, corresponde ao processo de elaboração e validação da Escala de Autoatratividade - EAA junto à pesquisa desta com o conjunto de instrumentos utilizados (Escala de Apreciação Corporal (EAC); Escala de Autoconsciência Situacional (EAS); Escala de Autoconsciência Disposicional (EAD); Escala de Autoestima de Rosenberg; Escala de Satisfação com a Vida; Escala de Felicidade Subjetiva; Escala CES-D (Rastreamento de depressão); Escala de Religiosidade Global (ERG) e Escala de religiosidade de item único, bem como o roteiro de entrevista Fenomenológico-Cognitiva dos Estados Autoconscientes – EFEA), a fim de permitir a identificação da multidimensionalidade da maquinaria psíquica atrelada ao construto atratividade dentre a amostra recrutada (Estudo 2 – Ex-post-facto) e a terceira etapa refere-se ao aprofundamento dos achados da etapa que a antecede, por intermédio da apresentação do gradiente fenomenal dos padrões de atratividade com base na identificação dos modos como estes são representados no fluxo da experiência dos participantes durante estado autoconsciente relacionado a autoatratividade (Estudo 3 – Fenomenal). A hipótese geral que dá sustentação ao estudo em questão considera que quanto mais autoconscientes e de modo reflexivo as pessoas são maior seria a capacidade que estas têm de minorar as influências que os padrões de atratividade exercem sobre os processos autoavaliativos, ocasionando prejuízos ao funcionamento psicológico saudável, além de que, os padrões, caso emerjam à consciência, no seio da experiência interna, se realizarão cognitivamente em elementos variados de natureza representacional, em especial na forma da fala interna e visualização interna. De modo específico, dentre o conjunto de hipóteses que dá sustenção ao referido estudo, destaca-se aquela que chama atenção ao papel moderador da religiosidade no possível impacto deletério que os padrões de atratividade ocasionam à vida das pessoas, haja vista, a importância e centralidade de tal dimensão para subjetividade humana. O modelo de análise de dados adotado no presente estudo de tese prezou, no tocante ao material quantitativo, pela investigação da dimensionalidade das escalas por via da metodologia das facetas (Guttman, 1968), com base nas Análises Multidimensionais não-métricas do tipo SSA (Similarity Structure Analysis, ver Guttman, 1968; Roazzi, 1995). Por sua vez, o material qualitativo foi submetido à análise de conteúdo (Estudo 1, Bardin, 1970) e a metodologia fenomenológica padrão (Estudo 2, Cott & Rock, 2008). Os principais achados do presente estudo de tese apontam que os padrões de autoatratividade e sua fenomenologia são representados cognitivamente na consciência por intermédio dos elementos da fala interna e das visualizações internas, associadas aos elementos do sentimento, bem como a consciência sensória. Não se encontrou, todavia, ocorrência de pensamento não simbolizado na análise fenomenal operada. A estrutura de tal padrão se organiza a partir de duas dimensões, uma física e outra não física, representadas pelos fatores: sensualidade, moralidade, apresentação pessoal, afetividade, inteligência, bom humor e asseio. Tais fatores quando correlacionados entre si, e junto as demais medidas utilizadas, apontam a presença de correlações estatisticamente significantes, em especial, no tocante às variáveis: Orientação sexual, no âmbito geral, os heterossexuais encontram-se mais próximos de um campo de afeto positivo, e os homossexuais nas cercanias do afeto negativo; Idade, os mais jovens, também situados num campo do afeto negativo, passando por um campo intermediário, onde há a presença de jovens adultos, findando com os participantes com idades entre 36 e 76 anos, cravados num campo de afeto positivo; Religiosidade, igualmente caracterizada por uma disposição polar, nas cercanias desta variável, os que se dizem religiosos, os heterossexuais e os adultos e idosos, e distanciando-se da religiosidade, localizados em plano antagônico, os que relatam não professar nenhuma fé, os adolescentes de 14 a 20 anos e os jovens homossexuais; e Nacionalidade, os portugueses mais próximos de um padrão de atratividade com base em princípios morais e os brasileiros simpáticos às variáveis sociodemográficas de natureza religiosa, inferindo que estas exercem influência sobre o instanciamento dos processos autofocalizadores, correlações estas cujos significados são corroborados pelos achados oriundos do estudo fenomenal. Tal estudo representa um esforço em dar visibilidade a uma temática pouco investigada na ciência psicológica, a natureza dos padrões de correção e o impacto destes nos processos autofocalizadores, em diálogo com uma perspectiva de mente dual, que contempla aspectos psicológicos e fenomenais da subjetividade e cognição humanas, a fim de contribuir com uma compreensão mais profunda sobre os aspectos cognitivos cruciais relacionados ao instanciamento de modos mais adaptados e, consequentemente, menos comprometedores da existência significativa e feliz.<br>The interest of the psychological science in the search for self-knowledge has come a long way (James, 1890/1983). In this context, studies from the self-awareness field, especially with the advent of the OSA Theory (Duval & Wicklund, 1972), one of the first to consider the discrepancies between the self and the patterns (Duval & Silva, 2001), have gathered efforts in order to overcome such gap. Within this framework, keen on understanding the self, especially in its symbolic aspect as well as in the instantiation of the self-assessment processes it operates, hatched in the identification of the nature of attractiveness patterns and how they have phenomenologically been made aware in the flow of the subjects‟ inner experience, this study aims to identify self-attractiveness patterns, their representational dynamics within the inner experience and the intertwining of the self-perceived attractiveness processes, of self-focusing (situational and dispositional self-awareness), self-esteem and well-being (life satisfaction and happiness), depressive mood and religiosity in the self-assessment process. For this study, a mixed sample of 657 participants (563 Brazilian and 94 Portuguese) was recruited, among whom were teenagers, adults and elderly people of both sexes, as well as homo and heterosexual orientations, living in the metropolitan area of Recife and in Lisbon, Portugal. The collecting-related procedures were carried out in three steps: the first one, to emically raise, through multimethod procedures, the semantic field of self-attractiveness (Study 1 - Qualitative); the second, based on the findings from the previous step, corresponds to the process of development and validation of the Self-attractiveness Scale – SAS, along with its survey with the set of instruments used (Body Assessment Scale - BAS); Situational Self-Awareness Scale (SSAE); Dispositional Self-Awareness Scale (DSAS); Rosenberg Self-Esteem Scale; Life Satisfaction Scale; Subjective Happiness Scale; CES-D Scale (Depression Tracking); Global Religiosity Scale (GRS) and Single-item Religiosity Scale, as well as the Self-Aware States Phenomenological-Cognitive interview script – SASPG), to enable the identification of the multidimensionality of the psychic machinery linked to the attractiveness construct within the recruited sample (Study 2 - Ex-post-facto). The third stage refers to deepening the findings of the previous one through the presentation of the phenomenal gradient of attractiveness patterns based on the identification of the ways they are represented in the flow of the participants‟ experience during the self-aware state related to self-attractiveness (Study 3 - Phenomenal). The general hypothesis that supports the present study considers that the more self-aware and reflective people are, the greater the capacity they have to reduce the influence attractiveness patterns have on self-assessment processes, which bring harm to healthy psychological functioning. Moreover, those patterns, should they emerge to awareness within the inner experience, will cognitively take place in a range of elements of representational nature, especially in the form of inner speech and inner visualization. In particular, among the set of assumptions that support this study, there is one that draws attention to the moderating role of religiosity in the possible deleterious impact attractiveness patterns cause to people's lives, given the importance and centrality of such dimension to human subjectivity. With regard to the quantitative material, the data analysis model adopted in this thesis study valued the investigation of the scale dimensionality by means of the facet methodology (Guttman, 1968), based on the non-metric SSA (Similarity Structure Analysis, see Guttman, 1968; Roazzi, 1995) type Multidimensional Analysis. In turn, the qualitative material was submitted to content analysis (Study 1, Bardin, 1970) and to the pattern phenomenological methodology (Study 2, Cott & Rock, 2008). The main findings of the present study indicate the self-attractiveness patterns and their phenomenology to be represented cognitively in the awareness by means of the inner speech and inner visualization elements, associated with both feelings and sensory awareness. There was no occurrence of non-symbolized thought in the carried out phenomenal analysis, though. The structure of such a pattern is set considering two dimensions, physical and non-physical, represented by the following factors: sensuality, morality, personal presentation, affection, intelligence, good humor and neatness. Such factors, when correlated and with the use of other measures, suggest the presence of statistically significant correlations, especially regarding the variables: Sexual orientation, in general, heterosexuals are closer to a positive affection ground, while homosexuals, around negative affection; Age, the youngest also being in a negative affection ground, passing to a middle ground where young adults are present, ending with between 36 and 76 year-old participants, nailed to a positive affection ground; Religiosity, also characterized by a polar layout around this variable, those who claim to be religious, the heterosexual, the adults and the elderly, as opposed to those distant from religiosity, located in an antagonistic plan, who report not to profess any faith, 14 to 20 year-old adolescents and young homosexuals; and Nationality, with the Portuguese closer to an attractiveness pattern based on moral principles, whilst the Brazilians sympathize with the sociodemographic variables of a religious nature, inferring that they influence the instancing of self-focusing processes, correlations whose meanings are corroborated by findings of the phenomenal study. This study represents an effort to give visibility to a little investigated topic in the psychological science, the nature of correction patterns and their impact on the self-focusing processes, dialoguing with a dual mind perspective, which includes psychological and phenomenal aspects of human subjectivity and cognition in order to contribute to a deeper understanding of the crucial cognitive aspects related to the instancing of more adapted and consequently less compromising forms of a meaningful and happy existence.

Abstract Since the discovery of RNA interference in 1998 as a potent molecular tool for the selective downregulation of gene expression in almost all eukaryotes, increasing research is being performed in order to discover applications that are useful for the pharmaceutical and chemical industry. The ease of use of double-stranded RNA for targeted in vivo gene silencing in animal cells and tissues gave birth to a massive interest from industry in order to discover biotechnological applications for human health and plant protection. For insects, RNAi became the 'Holy Grail' of pesticide manufacturing, because this technology is a promising species-specific environmentally friendly approach to killing natural enemies of cultured plants and farmed animals. The general idea to use RNAi as a pest-control agent originated with the realization that dsRNAs that target developmentally or physiologically important insect genes can cause lethal phenotypes as a result of the specific gene downregulation. Most importantly to achieve this, dsRNA is not required to be constitutively expressed via a transgene in the targeted insect but it can be administrated orally after direct spraying on the infested plants. Similarly, dsRNAs can be administered to pests after constitutive expression as a hairpin in plants or bacteria via stable transgenesis. Ideally, this technology could have already been applied in integrated pest management (IPM) if improvements were not essential in order to achieve higher insecticidal effects. There are many limitations that decrease RNAi efficiency in insects, which arise from the biochemical nature of the insect gut as well as from deficiencies in the RNAi core machinery, a common phenomenon mostly observed in lepidopteran species. To overcome these obstacles, new technologies should be assessed to ascertain that the dsRNA will be transferred intact, stable and in high amounts to the targeted insect cells. In this chapter we will review a wide range of recent discoveries that address the delivery issues of dsRNAs in insect cells, with a focus on the most prominent and efficient technologies. We will also review the upcoming and novel use of viral molecular components for the successful and efficient delivery of dsRNA to the insect cell.

Abstract Since the discovery of RNA interference in 1998 as a potent molecular tool for the selective downregulation of gene expression in almost all eukaryotes, increasing research is being performed in order to discover applications that are useful for the pharmaceutical and chemical industry. The ease of use of double-stranded RNA for targeted in vivo gene silencing in animal cells and tissues gave birth to a massive interest from industry in order to discover biotechnological applications for human health and plant protection. For insects, RNAi became the 'Holy Grail' of pesticide manufacturing, because this technology is a promising species-specific environmentally friendly approach to killing natural enemies of cultured plants and farmed animals. The general idea to use RNAi as a pest-control agent originated with the realization that dsRNAs that target developmentally or physiologically important insect genes can cause lethal phenotypes as a result of the specific gene downregulation. Most importantly to achieve this, dsRNA is not required to be constitutively expressed via a transgene in the targeted insect but it can be administrated orally after direct spraying on the infested plants. Similarly, dsRNAs can be administered to pests after constitutive expression as a hairpin in plants or bacteria via stable transgenesis. Ideally, this technology could have already been applied in integrated pest management (IPM) if improvements were not essential in order to achieve higher insecticidal effects. There are many limitations that decrease RNAi efficiency in insects, which arise from the biochemical nature of the insect gut as well as from deficiencies in the RNAi core machinery, a common phenomenon mostly observed in lepidopteran species. To overcome these obstacles, new technologies should be assessed to ascertain that the dsRNA will be transferred intact, stable and in high amounts to the targeted insect cells. In this chapter we will review a wide range of recent discoveries that address the delivery issues of dsRNAs in insect cells, with a focus on the most prominent and efficient technologies. We will also review the upcoming and novel use of viral molecular components for the successful and efficient delivery of dsRNA to the insect cell.

the article is devoted to the consideration of corruption, which is an element of the shadow economy, as an economic and socio-legal phenomenon that infringes on the vital interests of the individual, society and the state, and poses a threat to national security in General, and to economic security in particular

AbstractHope is a phenomenon many nurses and patients are concerned about. One of the reasons for this interest may be that many patients today live with chronic illnesses, and hope is something positive and focuses on the future and opportunities. Hope is a way of feeling, thinking, and influencing one’s behavior. The way we view our health and health-related challenges are assumed to impact on hope. Hope is forward-looking, realistic, and multidimensional. It is a resource for health and health-promoting processes and can be considered a salutogenic resource and construct. This chapter highlights what hope means during illness, what research has so far been concerned with, how hope can be assessed, and how nurses can strengthen hope in patients.

AbstractThis chapter investigates the hybrid relationships between metabolism, broadly and a-historically understood as the set of processes through which alien matter is made homogeneous to that of the organism, and forms of vitalism from the eighteenth century on. While metabolic processes have long been modeled in a reductionist fashion as a straightforward function of repair and expansion of a given structure (either chemically, or mechanistically), a challenging vitalist view has characterized metabolism as a creative, organizing, vital faculty. I suggest that this tension was overcome in Claude Bernard’s works on “indirect nutrition”, in which nutrition, rightly conceived as a general vital phenomenon common to plants and animals, was both characterized as an instance of the general physico-chemical determinism of all phenomena and as the sign and condition of the “freedom and independence” of the organism with respect to the environment. I propose that Bernard’s theory of indirect nutrition was central in the elaboration of his general physiology and has, at the same time, underpinned a self-centered view of biological identity in which the organism creates itself continuously at the detriment of its external milieu. I further argue that this conception of biological individuality as metabolically constructed has since, and paradoxically, supported a view in which the organism appears as an autonomous and self-creating entity. I then contrast this classical view of the metabolic autonomy of the organism with the challenges raised by microbiome studies and suggest that these emerging fields contribute to sketch an ecological conception of the organism and its metabolism through the reconceptualization of its relationship with the environment. The recent focus on a “microbiota – host metabolism” axis contributes to shift the focus away from the classical concept of organism, somehow externalizing vitalism out of the autonomous individual in favor of an ecological, collaborative, and interactionist view of the living.

AbstractThe paper investigates the phenomenon of vitalism through the lens of vital normativity as expounded by Maurice Merleau-Ponty and Georges Canguilhem. I argue that the two authors independently developed complementary critiques of the mechanical-behaviourist conception of life sciences, which culminated in a surprisingly similar notion of life construed as a normative (polarized) activity, i.e., an activity that is not indifferent to its own conditions of possibility. Such an alternative conception of life has far-reaching consequences for the epistemology of life sciences, for it requires it to reconsider not only its object of inquiry - the nature of (the relationship between) an organism and its environment -, but also, since scientists themselves are living beings, the nature of its epistemic practices. What I call the truth of (a specific variety of) vitalism is thus reflected not only in how life is cognized, but also in how life cognizes (itself). This last point is of particular philosophical importance, as it paves the way towards a more dynamic conception of reflection (tentatively called ouroboric thought), which takes seriously that we, as cognizers of life, at the same time live the lives of cognizers.

Misinformation spread by individuals sharing fake news can cause problems in social, economic and democratic systems. The World Economic Forum considers the viral spread of misinformation online to be one of the main threats to our society. While the reasons why people spread misinformation likely haven't changed in the last millennia, the rise of Internet powered social networks has allowed news to spread rapidly among millions of users, and gave rise to new phenomena such as echo chambers. The question we ask in this paper is whether we can model the dissemination of fake news and the emerging phenomena using relatively simple rules in an agent-based model. We present the current state of research in the field of fake news, the agent-based modelling methodology, and the current state of our model development.

The article considers a case from expert practice, the example of which shows the difficulties that a forensic medical expert may face when establishing the etiopathogenesis of sepsis. Attention is drawn to the bacterial or fungal etiology of sepsis and the doubtfulness of the viral etiology. There is a relatively frequent occurrence of cryptogenic sepsis, when the primary infectious focus is not detected. Possible causes of this phenomenon are considered.

The article, from the standpoint of the «memetic» and «network» paradigms, examines the factors, mechanisms and socio-ecological consequences of information and communication influences. The phenomenon and mechanisms of information infection, the role of meme-viral influences in the processes of socio-cultural evolution are analyzed. The prospects for the development of effective research and socio-performative methods and technologies based on the joint use of the principle of viral information and communication influences and the «network» approach are studied. The ways of determining the intensity of «information infection» of the social space and the degree of «cognitive damage» of the population are discussed. It is shown that important socio-ecological problems of an information civilization are: the problem of uncontrollable side effects of information and communication influences and a tendency to the loss of human-centeredness (dehumanization) of network forms of social organization and control over them by a person.

CFD analysis of flow through high pressure packaging seal passage of a typical land based gas turbine was performed which contained a rotating bolted joint region. Analysis reveals that the annular space between the nut and the counterbore surface acts as a fluid pump, sucking and pumping out fluid with significant temperature rise as high as 40 F. Factorial DoEs were carried out to filter out vital few parameters among geometric, flow and operational parameters that impacts counterbore flow. A detailed space filling DoE with more than 100 CFD models were developed and studied to estimate the influence of parameters impacting counterbore mass flow. A mathematical model (transfer function) developed using PEZ was created to calculate counterbore mass flow as a function of vital few geometric and flow variables. Finally, 2D Axi symmetric thermal analysis with counterbore mass flow modelling better matched the field temperature compared to that of one without counterbore model.

In the last years an increase in the importance of the role of ethical issues in the world has been observed. Research is a process of collecting and analyzing information to increase the understanding of a phenomenon under study. Due to the complexity of such phenomena, nowadays mostly of the times such research work is performed in a group or community, under public grants accomplishing a collaborative research consortium. Consequently to the nature of such collaborations, ethical conduct is vital to the maintenance of such research communities. This paper provides some information about ethical issues clarifying its importance and challenges in collaborative manufacturing research development and exploitation.

Solid state nanopore is a potential candidate for separation of nanoparticles or biomolecules such as proteins, DNA, and RNA. However, efficient separation of particles through nanopores is a challenging task as a number of factors such as externally applied voltage, size and charge density of particle, size and charge density of membrane pore, and the concentration of bulk electrolyte influence the translocation behavior of nanoparticles through pores. This paper uses a mathematical model based on Poisson–Nernst–Plank equations along with Navier-Stokes equations to systematically study these factors. Membrane pore surface charge is found to be a vital parameter in this seperation process. Numerical results reveal that efficient separation of high density lipoprotein (HDL) from low density lipoprotein (LDL) in a 0.2 M KCL solution (resembling blood buffer) through a 150 nm pore is possible if the pore surface charge density is around −4.0 mC/m2.

Brain drain is the phenomenon in which experts on a field abandon their origin country to practice their profession in a different country. It forms part of the migration patterns around the world. However brain drain can have damaging effects on the source of origin when it happens at large scale. This has been problem in several countries of latinamerica, particularly at the postgraduate level. The correct characterization of this phenomena is vital to outline polices that keep or attract the talent needed in these countries. In this research, we propose a methodology to identify evidence of drain brain through results of web search engines which commonly contains links to career information pages given a seed name, however it could be very time consuming explore and analyze all resulting pages. For this reason, in this research we propose to exploit a Reinforcement Learning setting to learn to navigate and extract significant information from the snippet results. In this work we outline the main architecture based on the Dopamine RL framework.

Understanding how RNA viruses cause disease symptoms in their hosts is expected to provide information that can be exploited to enhance modern agriculture. The helper component-proteinase (HC-Pro) protein of potyviruses has been implicated in symptom development. Previously, we demonstrated that symptom expression is associated with binding of duplex small-interfering-RNA (duplex-siRNA) to a highly conserved FRNK amino acid motif in the HC-Pro of Zucchini yellow mosaic virus (ZYMV). This binding activity also alters host microRNA (miRNA) profiles. In Turnip mosaic virus (TuMV), which infects the model plant Arabidopsis, mutation of the FRNK motif to FINK was lethal providing further indication of the importance of this motif to HC-Pro function. In this continuation project, our goal was to further investigate how ZYMV and TuMV cause the mis-expression of genes in cucurbits and Arabidopsis, respectively, and to correlate altered gene expression with disease symptoms. Objective 1 was to examine the roles of aromatic and positively charged residues F164RNH and K215RLF adjacent to FR180NK in small RNA binding. Objective 2 was to determine the target genes of the miRNAs which change during HC-Pro expression in infected tissues and transgenic cucumber. Objective 3 was to characterize RNA silencing mechanisms underlying differential expression of host genes. Objective 4 was to analyze the function of miRNA target genes and differentially expressed genes in potyvirus-infected tissues. We found that the charged K/R amino acid residues in the FKNH and KRLF motifs are essential for virus viability. Replacement of K to I in FKNH disrupted duplex-siRNA binding and virus infectivity, while in KRLF mutants duplex-siRNA binding was maintained and virus infectivity was limited: symptomless following a recovery phenomenon. These findings expanded the duplex-siRNA binding activity of HC-Pro to include the adjacent FRNK and FRNH sites. ZYMV causes many squash miRNAs to hyper-accumulate such as miR166, miR390, mir168, and many others. Screening of mir target genes showed that only INCURVATA-4 and PHAVOLUTA were significantly upregulated following ZYMVFRNK infection. Supporting this finding, we found similar developmental symptoms in transgenic Arabidopsis overexpressing P1-HC-Pro of a range of potyviruses to those observed in miR166 mutants. We characterized increased transcription of AGO1 in response to infection with both ZYMV strains. Differences in viral siRNA profiles and accumulation between mild and severe virus infections were characterized by Illumina sequencing, probably due to the differences in HC-Pro binding activity. We determined that the TuMV FINK mutant could accumulate and cause symptoms in dcl2 dcl4 or dcl2 dcl3 dcl4 mutants similar to TuMV FRNK in wild type Arabidopsis plants. These dcl mutant plants are defective in antiviral defenses, and the results show that factors other than HC-ProFRNK motif can induce symptoms in virus-infected plants. As a result of this work, we have a better understanding of the FRNK and FKNH amino acid motifs of HC-Pro and their contributions to the duplex-siRNA binding functions. We have identified plant genes that potentially contribute to infectivity and symptoms of virus infected plants when they are mis-expressed during potyviral infections. The results establish that there are multiple underlying molecular mechanisms that lead viral pathogenicity, some dependent on HC-Pro. The potential benefits include the development of novel strategies for controlling diseases caused by viruses, methods to ensure stable expression of transgenes in genetically improved crops, and improved potyvirus vectors for expression of proteins or peptides in plants.

Objectives: (1) Evaluate Immunocompetence-OTL-containing Chromosomal Regions (ICRs), marked by microsatellites or candidate genes, for magnitude of direct effect and for contribution to relationships among multiple immunocompetence, disease-resistance, and growth traits, in order to estimate epistatic and pleiotropic effects and to predict the potential breeding applications of such markers. (2) Evaluate the interaction of the ICRs with genetic backgrounds from multiple sources and of multiple levels of genetic variation, in order to predict the general applicability of molecular genetic markers across widely varied populations. Background: Diseases cause substantial economic losses to animal producers. Emerging pathogens, vaccine failures and intense management systems increase the impact of diseases on animal production. Moreover, zoonotic pathogens are a threat to human food safety when microbiological contamination of animal products occurs. Consumers are increasingly concerned about drug residues and antibiotic- resistant pathogens derived from animal products. The project used contemporary scientific technologies to investigate the genetics of chicken resistance to infectious disease. Genetic enhancement of the innate resistance of chicken populations provides a sustainable and ecologically sound approach to reduce microbial loads in agricultural populations. In turn, animals will be produced more efficiently with less need for drug treatment and will pose less of a potential food-safety hazard. Major achievements, conclusions and implications:. The PI and co-PIs had developed a refined research plan, aiming at the original but more focused objectives, that could be well-accomplished with the reduced awarded support. The successful conduct of that research over the past four years has yielded substantial new information about the genes and genetic markers that are associated with response to two important poultry pathogens, Salmonella enteritidis (SE) and Escherichia coli (EC), about variation of immunocompetence genes in poultry, about relationships of traits of immune response and production, and about interaction of genes with environment and with other genes and genetic background. The current BARD work has generated a base of knowledge and expertise regarding the genetic variation underlying the traits of immunocompetence and disease resistance. In addition, unique genetic resource populations of chickens have been established in the course of the current project, and they are essential for continued projects. The US laboratory has made considerable progress in studies of the genetics of resistance to SE. Microsatellite-marked chromosomal regions and several specific genes were linked to SE vaccine response or bacterial burden and the important phenomenon of gene interaction was identified in this system. In total, these studies demonstrate the role of genetics in SE response, the utility of the existing resource population, and the expertise of the research group in conducting such experiments. The Israeli laboratories had showed that the lines developed by selection for high or low level of antibody (Ab) response to EC differ similarly in Ab response to several other viral and bacterial pathogens, indicating the existence of a genetic control of general capacity of Ab response in young broilers. It was also found that the 10w-Ab line has developed, possibly via compensatory "natural" selection, higher cellular immune response. At the DNA levels, markers supposedly linked to immune response were identified, as well as SNP in the MHC, a candidate gene responsible for genetic differences in immunocompetence of chickens.

- Original objectives and revision: The feasibility study performed in the last year was aimed at determining the symbiotic profiles of eight selected Culicoidesspecies in Israel and the USA by: Comparing bacterial communities among geographic populations of primary bluetongue virus (BTV) vectors. Comparing bacterial communities between adults of field-collected, mammal-feeding BTV vectors and non-vectors. Comparing bacterial communities within and between mammal feeders and bird feeders, with special attention to species with unique immature habitats. We made an effort to collect the eight species during the beginning of the project, however, due to the short available collection season, and the significant changes in habitats available for Israeli Culicoides, we initially determined the symbiotic profile of five species: two BTV vectors (C. sonorensis, C. imicola), one mammal feeders with unknown vectoring ability (C. schultzei), one bird feeder (C. crepuscularis), and one unique habitat species (C. cacticola). In addition, upon preliminary symbiont identification we focused our effort on relevant specific symbionts. Background: Biting midges (Culicoides, Diptera: Ceratopogonidae) are vectors of many major viral diseases affecting farm animals, including BT, which is listed among the most damaging by the World Organization for Animal Health (OIE) and has recently emerged in completely unexpected areas (Northern Europe). One of the strategies to reduce the vectorial capacity of insect vectors is by manipulating their specific symbionts either to affect the vector species or to influence performance of the disease agent within it. Despite significant efforts to elucidate the vectorial capacity of certain Culicoidesspecies, and the critical basis of variability in infection, almost no attention has been given to symbiotic interactions between the vector and its bacterial tenants. It is now established that bacterial symbionts have major influences on their host biology, and may interact with disease agents vectored by their hosts. - Major conclusions, solutions, achievements: During the feasibility project we have found two major bacterial symbionts in Israeli and American Culicoides. In Israel we discovered that C. imicola, a known vector of BT, and C. schultzeigp. a suspected vector of BT, carry the symbiotic bacterium Cardinium, a reproductive manipulator symbiont. In C. imicolathe infection rate was close to 50%, and in C. schultzeiit was lower, and restricted to one of two species within Schultzeigroup. In 3 American species (C. sonorensis, C. crepuscularis, C. cacticola) we found the bacterium Burkholderiasp. In all species tested we have also found other bacterial species in diverse quantities and frequencies. - Implications, both scientific and agricultural: Finding specific symbionts in Culicoidesvector species is the first step in developing symbiont based control (SBC) strategies. Both identified symbionts are known from other insects, and Cardiniumis also known as a reproductive manipulator that can cause cytoplasmic incompatibility, an important phenomenon that can be used for spreading desired traits in infected populations. The role of the symbionts in Culicoideshost can be target for manipulation to reduce the vectorial capacity of the host by either changing its fitness so that it is unable to serve as a vector, or by directly changing the symbiont in a way that will affect the performance of the disease agent in its vector. Since Burkholderiaperhaps can be cultured independently of the host, it is a promising candidate for the later option. Thus, we have now opened the door for studying the specific interactions between symbionts and vector species.

The plant virus family Polyviridae is the largest and most destructive of all plant viruses. Despite the continuous effort to develop resistant plant varieties, there is a desperate need for novel approaches conferring wide-range potyvirus resistance. Based on experiments with the tobacco etch potyvirus (TEV)-derived gene expression vector, we suggested approach for screening of the candidate resistance genes. This approach relies on insertion of the genes into a virus vector and evaluation of the phenotypes of the resulting recombinant viruses. The genes which suppress infection by the recombinant virus are selected as candidates for engineering transgenic resistance. Our analysis of the TEV variants expressing proteins of the beet yellows closterovirus (BYV) revealed that one of those, the leader proteinase (L-Pro), strongly and specifically interfered with the hybrid TEV infection. Since closterovirus L-Pro is evolutionary related to potyviral helper component-proteinase (HC-Pro), we suggested that the L-Pro interfered with HC-Pro function via a trans-dominant inhibitory effect. Based on these findings, we proposed to test two major hypotheses. First, we suggested that L-Pro-mediated suppression of potyvirus infection is a general phenomenon effective against a range of potyviruses. The second hypothesis stated that the suppression effect can be reproduced in transgenic plants expressing L-Pro, and can be utilized for generation of resistance to potyviruses. In accord with these hypotheses, we developed two original objectives of our proposal: A) to determine the range of the closterovirus-derived suppression of potyviral infection, and B) to try and utilize the L-Pro-mediated suppression for the development of transgenic resistance to potyviruses. In the first phase of the project, we have developed all major tools and technologies required for successful completion of the proposed research. These included TEV and ZYMV vectors engineered to express several closteroviral L-Pro variants, and generation of the large collection of transgenic plants. To our satisfaction, characterization of the infection phenotypes exhibited by chimeric TEV and ZYMV variants confirmed our first hypothesis. For instance, similar to TEV-L- Pro(BYV) chimera, ZYMV-L-Pro(LIYV) chimera was debilitated in its systemic spread. In contrast, ZYMV-GUS chimera (positive control) was competent in establishing vigorous systemic infection. These and other results with chimeric viruses indicated that several closteroviral proteinases inhibit long-distance movement of the potyviruses upon co-expression in infected plants. In order to complete the second objective, we have generated ~90 tobacco lines transformed with closteroviral L-Pro variants, as well as ~100 lines transformed with BYV Hsp70-homolog (Hsp70h; a negative control). The presence and expression of the trans gene in each line was initially confirmed using RT-PCR and RNA preparations isolated from plants. However, since detection of the trans gene-specific RNA can not guarantee production of the corresponding protein, we have also generated L-Pro- and Hsp70h-specific antisera using corresponding synthetic peptides. These antisera allowed us to confirm that the transgenic plant lines produced detectable, although highly variable levels of the closterovirus antigens. In a final phase of the project, we tested susceptibility of the transgenic lines to TEV infection. To this end, we determined that the minimal dilution of the TEV inoculum that is still capable of infecting 100% of nontransgenic plants was 1:20, and used 10 plants per line (in total, ~2,000 plants). Unfortunately, none of the lines exhibited statistically significant reduction in susceptibility. Although discouraging, this outcome prompted us to expand our experimental plan and conduct additional experiments. Our aim was to test if closteroviral proteinases are capable of functioning in trans. We have developed agroinfection protocol for BYV, and tested if co- expression of the L-Pro is capable of rescuing corresponding null-mutant. The clear-cut, negative results of these experiments demonstrated that L-Pro acts only in cis, thus explaining the lack of resistance in our transgenic plants. We have also characterized a collection of the L-Pro alanine- scanning mutants and found direct genetic evidence of the requirement for L-Pro in virus systemic spread. To conclude, our research supported by BARD confirmed one but not another of our original hypotheses. Moreover, it provided an important insight into functional specialization of the viral proteinases and generated set of tools and data with which we will be able to address the molecular mechanisms by which these proteins provide a variety of critical functions during virus life cycle.

Gas exchange processes in two-stroke internal combustion engines, commonly referred to as scavenging, are responsible for removing the exhaust gases in the combustion chamber and preparing the combustible fuel-oxidizer mixture that undergoes combustion and converts the chemical energy of the fuel into mechanical work. Scavenging is a complicated phenomenon because of the simultaneous introduction of fresh gases into the engine cylinder through the intake ports, and the expulsion of combustion products from the previous cycles through the exhaust ports. A non-negligible fraction of the gaseous mixture that is trapped in the cylinder at the conclusion of scavenging is composed of residual gases from the previous cycle. This can cause significant changes to the combustion characteristics of the mixture by changing its composition and temperature, i.e. its thermodynamic state. Thus, it is vital to have accurate knowledge of the thermodynamic state of the post-scavenging mixture to be able to reliably predict and control engine performance, efficiency and emissions. Two tools for estimating the trapped mixture state - a simple scavenging model and empirical correlations - were developed in this study. Unfortunately, it is not practical to directly measure the trapped residual fraction for engines operating in the field. To overcome this handicap, simple scavenging models or correlations, which estimate this fraction based on some economically measurable engine parameters, can be developed. This report summarizes the results of event-II of a multi-event project that aims to develop such mathematical formulations for stationary two-stroke natural gas engines using data from more advanced models and experimentation. In this event, results from a GT-Power based model for an Ajax E-565 single-cylinder engine are used to develop a three-event single zone scavenging model and empirical correlations. Both of these mathematical devices produce accurate estimates of the trapped mixture state. The estimates are compared to GT-Power results. In the next event of the project, these results will be validated using experimental data. Various steps followed in the development of the model have been discussed in this report, and at the end some results and recommendations for the next event of the project have been presented.

Global migration has been increasing since the 1990s. People are forced to leave their homes in search of safety, a better livelihood, or for more economic opportunities. Environmental drivers of migration, such as land degradation, water pollution, or changing climate, are acting as stronger phenomena with time. As millions of people are exposed to multiple water crises, daily needs related to water quality, lack of provisioning, excess or shortage of water become vital for survival as well for livelihood support. In turn, the crisis can transform into conflict and act as a trigger for migration, both voluntary and forced, depending on the conditions. Current interventions related to migration, including funding to manage migration remain focused on response mechanisms, whereas an understanding of drivers or so-called ‘push factors’ of migration is limited. Accurate and well-documented evidence, as well as quantitative information on these phenomena, are either missing or under-reflected in the literature and policy discourse. The report aims to start unpacking relationships between water and migration. The data used in this Report are collected from available public sources and reviewed in the context of water and climate. A three-dimensional (3D) framework is outlined for water-related migration assessment. The framework may be useful to aggerate water-related causes and consequences of migration and interpret them in various socioecological, socioeconomic, and sociopolitical settings. A case study approach is adopted to illustrate the various applications of the framework to dynamics of migration in various geographic and hydrological scenarios. The case studies reflect on well-known examples of environmental and water degradation, but with a focus on displacement /migration and socioeconomic challenges that apply. The relevance of proxy measures such as the Global Conflict Risk Index, which helps quantify water and migration interconnections, is discussed in relation to geographic, political, environmental, and economic parameters. The narratives presented in the Report also point to the existing governance mechanisms on migration, stating that they are fragmented. The report examines global agreements, institutions, and policies on migration to provide an aggerated outlook as to how international and inter-agency cooperation agreements and policies either reflected or are missing on water and climate crises as direct or indirect triggers to migration. Concerning this, the new directives related to migration governance, i.e., the New York Declaration and the Global Compact for Migration, are discussed. The Report recommends an enhanced focus on migration as an adaptation strategy to maximize the interconnectedness with the Sustainable Development Goals (SDGs). It calls for the migration discourse to look beyond from a preventative and problematic approach to a perspective emphasizing migration as a contributor towards achieving sustainable development, particularly SDGs 5, 6, 13, and 16 that aim strengthening capacities related to water, gender, climate, and institutions. Overall, the synthesis offers a global overview of water and migration for researchers and professionals engaged in migration-related work. For international agencies and government organizations and policymakers dealing with the assessment of and response to migration, the report aims to support the work on migration assessment and the implementation of the SDGs. The Report may serve as a public good towards understanding the drivers, impacts, and challenges of migration, for designing long-term solutions and for advancing migration management capabilities through improved knowledge and a pitch for consensus-building.

The article investigates the immortality of books, collections, including those, translated into foreign languages, composed of the publications of publications of worldview journalism. It deals with top analytics on simulated training of journalists, the study of events and phenomena at the macro level, which enables the qualitative forecast of world development trends in the appropriate contexts for a long time. Key words: top, analytics, book, worldview journalism, culture, arguments, forecast.The article is characterized intellectual-spiritual, moral-aesthetic and information-educational values of of scientific and journalistic works of Professor Mykola Hryhorchuk “Where are you going, Ukraine?” and “Freedom at the Barricades”. Mykola Ivanovych’s creative informational and educational communication are reviews, reviews, reviews and current works of writers, poets, publicists. Such as Maria Matios, Vira Vovk, Roman Ivanychuk, Dmytro Pavlychko, Yuriy Shcherban, Bohdan Korsak, Hryhoriy Huseynov, Vasyl Ruban, Yaroslav Melnyk, Sofia Andrukhovych. His journalistic reflections are about memorable events of the recent past for Ukrainians and historical figures are connected with them. It is emphasized that in his books Mykola Hryhorchuk convincingly illuminates the way to develop a stable Ukrainian immunity, national identity, development and strengthening of the conciliar independent state in the fight against the eternal Moscow enemy. Among the defining ideological and political realization of the National Idea of Ukrainian statehood, which are mentioned in the scientific and journalistic works of M. Hryhorchuk, the fundamental ones – linguistic and religious – are singled out. Israel and Poland are a clear example for Ukrainians. In these states, language and religion were absolutized and it is thanks to this understanding of the essence of state-building and national identity that it is contrary to many difficulties achieve the desired life-affirming goal. The author emphasizes that any information in the broadest and narrow sense can be perceived without testing for compliance with the moral and spiritual mission of man, the fundamental values of the Ukrainian ethnic group, putting moral and spiritual values in the basis of state building. The outstanding Ukrainian philosopher Hryhoriy Skovoroda emphasized: “Faith is the light that sees in the darkness…” Books by physicist Mykola Hryhorchuk “Where are you going, Ukraine?” and “Freedom at the Barricades” are illuminated by faith in the Victory over the bloody centuries-old Moscow darkness.