Evolution of Bordetella pertussis post vaccination

Evolution of Bordetella pertussis post vaccination Whooping cough or pertussis is caused by the gram-negative bacterium Bordetella pertussis. It is a highly contiguous disease in the human respiratory tract. Characteristic of pertussis is a paroxysmal cough with whooping sound during gasps of breath after coughing episodes. It is potentially fatal to unvaccinated infants. The best approach to fight pertussis is to vaccinate. Vaccinations against pertussis have been available from the 1940s. Traditionally vaccines were whole-cell pertussis (wP) preparations as part of the combined diphtheria-tetanus-pertussis (DTP) vaccines. More recently acellular pertussis (aP) vaccines have replaced the wP vaccines in many countries. The aP vaccines are less reactogenic and can also be administered to school children and adults. There are several publications reporting variation in the i>B. pertussis virulence factors that are also aP vaccine antigens. This has occurred in the genes coding for pertussis toxin and pertactin about 15 to 30 years after the introduction of pertussis vaccines to immunisation programs. Resurgence of pertussis has also been reported in many countries with high vaccination coverage. In this study the evolution of B. pertussis was investigated in Finland, the United Kingdom, Poland, Serbia, China, Senegal and Kenya. These represent countries with a long history of high vaccination coverage with stable vaccines or changes in the vaccine formulation; countries which established high vaccination coverage late; and countries where vaccinations against pertussis were started late. With bacterial cytotoxicity and cytokine measurements, comparative genomic hybridisation, pulsed-field gel electrophoresis (PFGE), genotyping and serotyping it was found that changes in the vaccine composition can postpone the emergence of antigenic variants. It seems that the change in PFGE profiles and the loss of genetic material in the genome of B. pertussis are similar in most countries and the vaccine-induced immunity is selecting non-vaccine type strains. However, the differences in the formulation of the vaccines, the vaccination programs and in the coverage of pertussis vaccination have affected the speed and timing of these changes.

Defensive responses to threat scenarios in Brazilians reproduce the pattern of Hawaiian Americans and non-human mammals

A former study with scenarios conducted in Hawaii has suggested that humans share with non-human mammals the same basic defensive strategies - risk assessment, freezing, defensive threat, defensive attack, and flight. The selection of the most adaptive strategy is strongly influenced by features of the threat stimulus - magnitude, escapability, distance, ambiguity, and availability of a hiding place. Aiming at verifying if these strategies would be consistent in a different culture, 12 defensive scenarios were translated into Portuguese and adapted to the Brazilian culture. The sample consisted of male and female undergraduate students divided into two groups: 76 students, who evaluated the five dimensions of each scenario and 248 medical students, who chose the most likely response for each scenario. In agreement with the findings from studies of non-human mammal species, the scenarios were able to elicit different defensive behavioral responses, depending on features of the threat. "Flight" was chosen as the most likely response in scenarios evaluated as an unambiguous and intense threat, but with an available route of escape, whereas "attack" was chosen in an unambiguous, intense and close dangerous situation without an escape route. Less urgent behaviors, such as "check out", were chosen in scenarios evaluated as less intense, more distant and more ambiguous. Moreover, the results from the Brazilian sample were similar to the results obtained in the original study with Hawaiian students. These data suggest that a basic repertoire of defensive strategies is conserved along the mammalian evolution because they share similar functional benefits in maintaining fitness.

Distribution of the human leukocyte antigen class II alleles in Brazilian patients with chronic hepatitis C virus infection

Hepatitis C virus (HCV) infection is a global medical problem. The current standard of treatment consists of the combination of peginterferon plus ribavirin. This regimen eradicates HCV in 55% of cases. The immune response to HCV is an important determinant of disease evolution and can be influenced by various host factors. HLA class II may play an important role in immune response against HCV. The objective of the present study was to determine the distribution of HLA class II (DRB1 and DQB1) alleles, their association with chronic HCV infection and their response to interferon therapy. One hundred and two unrelated white Brazilian patients with chronic HCV infection, 52 responders (45 males and 7 females) and 50 non-responders (43 males and 7 females) to antiviral treatment, were included in the study. Healthy Brazilian bone marrow donors of Caucasian origin from the same geographic area constituted the control group (HLA-DRB1, N = 99 and HLA-DQB1, N = 222 individuals). HLA class II genotyping was performed using a low-resolution DRB1, DQB1 sequence-specific primer amplification. There were higher frequencies of HLA-DRB1*13 (26.5 vs 14.1%) and HLA-DQB1*02 (52.9 vs 38.7%) in patients compared with controls; however, these were not significantly different after P correction (Pc = 0.39 and Pc = 0.082, respectively). There was no significant difference between the phenotypic frequencies of HLA-DRB1 (17.3 vs 14.0%) and HLA-DQB1 alleles in responder and non-responder HCV patients. The HLA-DRB1*07 allele was significantly more common in HCV patients (33.3 vs 12.1%) than in controls (Pc = 0.0039), suggesting that the HLA-DRB1*07 allele is associated with chronic HCV infection.

In vivo fluctuation of Tax, Foxp3, CTLA-4, and GITR mRNA expression in CD4+CD25+ T cells of patients with human T-lymphotropic virus type 1-associated myelopathy

HTLV-1 Tax expression exerts an inhibitory effect on the Foxp3 transcription factor in CD4+CD25+ T-regulatory cells (Treg). For a better understanding of the role of Tax mRNA in the gene expression of cellular markers we measured Tax, Foxp3, CTLA-4, GITR, TGF-β, and IL-10 mRNA in Treg cells of 50 patients with human T-lymphotropic virus type 1 (HTLV-1)-associated myelopathy/tropical spastic paraparesis (HAM/TSP; 27 women and 23 men; mean age: 56.7 years). The control group consisted of 23 non-infected subjects (12 women and 11 men) with a mean age of 51.3 years. Real-time PCR was used to measure mRNA of Tax proteins and several cellular markers of Treg function. Determinations revealed a high level of Tax mRNA in HAM/TSP (124.35 copies/100 CD4+CD25+ T cells). Foxp3, GITR, and CTLA-4 mRNA levels were lower in HAM/TSP patients (mean ± SD, 22.07 ± 0.78, 9.63 ± 0.36, and 4.54 ± 0.39, respectively) than in non-infected controls (47.15 ± 12.94, 22.14 ± 1.91, and 21.07 ± 2.31). Both groups had similar levels of TGF-β and IL-10. An inverse relationship was found between Tax levels and Foxp3, CTLA-4, and GITR levels. Conversely, there was a direct correlation between levels of Foxp3, GITR, and CTLA-4. Disease severity and evolution time did not correlate with Tax or Foxp3 levels. The present results suggest that Tax and Foxp3 mRNA vary with the same degree of disease severity in HAM/TSP patients. Tax fluctuations may affect CTLA-4 and GITR expression via the Foxp3 pathway, causing virus-induced dysfunction of CD4+CD25+ T cells in HAM/TSP patients.

Detection, Identification and Molecular Variation of Human Enteroviruses

Picornaviruses are the most common human viruses and the identification of the picornaviruses is nowadays based on molecular techniques, for example, reverse transcriptase polymerase chain reaction (RT-PCR). One aim of this thesis was to improve the identification of picornaviruses, especially rhino- and enteroviruses, with a real-time assay format and, also, to improve the differentiation of the viruses with genus-specific locked nucleic acid (LNA) probes. Another aim was to identify and study the causative agent of the enterovirus epidemics that appeared in Finland during seasons 2008-2010. In this thesis, the first version of picornavirus qRT-PCR with a melting curve analysis was used in a study of rhinovirus transmission within families with a rhinovirus positive index child where rhinovirus infection was monitored in all family members. In conclusion, rhinoviruses spread effectively within families causing mostly symptomatic infections in children and asymptomatic infections in adults. To improve the differentiation between rhino- and enterovirus the picornavirus qRT-PCR was modified with LNA-incorporated probes. The LNA probes were validated with picornavirus prototypes and different clinical specimen types. The LNA probe-based picornavirus qRT-PCR was able to differentiate all rhino- and enteroviruses correctly, which makes it suitable for diagnostic use. Moreover, in this thesis enterovirus outbreaks were studied with a well-observed method to create a strain-specific qRT-PCR from the typing region VP1 protein. In a hand-foot-and-mouth-disease (HFMD) outbreak in 2008, the causative agent was identified as CV-A6 and when the molecular evolution of the new HFMD CV-A6 strain was studied it was found that CV-A6 was the emerging agent for HFMD and onychomadesis. Furthermore, unusual E-30 meningitis epidemics that apeared during seasons 2009 and 2010 were studied with strain-specific qRT-PCR. The E-30 affected mostly adolescents and was probably spread in sports teams.

Automatic evolution of conceptual building architectures

This thesis describes research in which genetic programming is used to automatically evolve shape grammars that construct three dimensional models of possible external building architectures. A completely automated fitness function is used, which evaluates the three dimensional building models according to different geometric properties such as surface normals, height, building footprint, and more. In order to evaluate the buildings on the different criteria, a multi-objective fitness function is used. The results obtained from the automated system were successful in satisfying the multiple objective criteria as well as creating interesting and unique designs that a human-aided system might not discover. In this study of evolutionary design, the architectures created are not meant to be fully functional and structurally sound blueprints for constructing a building, but are meant to be inspirational ideas for possible architectural designs. The evolved models are applicable for today's architectural industries as well as in the video game and movie industries. Many new avenues for future work have also been discovered and highlighted.

Explaining the evolution of educational attainment in the U.S.

We study the evolution of educational attainment of the 1932–1972 cohorts using a calibrated model of investment in human capital with heterogeneous learning ability. The inter-cohort variation in schooling is driven by changes in skill prices, tuition, and education quality over time, and average learning ability across cohorts. A version of the model with static expectations is successful in accounting for the main patterns in the data. Rising skill prices for college explain the rapid increase in college graduation till the 1948 cohort. The measured decline in average learning ability contributes to explain the stagnation in college graduation between the 1948 and 1972 cohorts.

Human Rights Violations in Police Custody

Human rights are the basic rights of every individual against the state or any other public authority as a member of the human family irrespective of any other consideration. Thus every individual of the society has the inherent right to be treated with dignity in all situations including arrest and keeping in custody by the police. Rights of an individual in police custody are protected basically by the Indian Constitution and by various other laws like Code of Criminal Procedure, Evidence Act, Indian Penal Code and Protection of Human Rights Act. The term `custody' is defined neither in procedural nor in substantive laws. The word custody means protective care. The expression `police custody' as used in sec. 27 of Evidence Act does not necessarily mean formal arrest. In India with special reference to Kerala and evolution and development of the concept of human rights and various kinds of human rights violations in police custody in different stages of history. Human rights activists and various voluntary organisations reveals that there are so many factors contributing towards the causes of violations of human rights by police. Sociological causes like ambivalent outlook of the society with respect to the use of third degree methods by the police, economic causes like meager salary and inadequate living conditions, rampant corruption in police service, unnecessary political interference in the crime investigation, work load of police personnel without any time limit and periodic holidays, unnecessary pressure from superior police officers and the general public for speedy detection causing great mental strain to the investigating officers, defective system of recruitment and training, imperfect system of investigation and lack of public co-operation are some of the factors identified in the field survey towards the causes of violations of human rights in police custody.

International Human Rights Movements and Protection of Women's Rights

This thesis is an attempt to explore the problems faced by Indian Women and to examine the ways in which the human rights of women could be better protected in the light of international movements with special reference to national legislation and judicial decisions.The evolution of human rights from early period to Universal Declaration of Human Rights, 1948 is traced in the first chapter. The second chapter deals with the evolution of human rights in India. The evolution of fundamental rights and directive principles and the role played by the Indian Judiciary in enforcing the human rights enumerated in various international instruments dealing with human rights are also dealt with in this chapter. The rights guaranteed to women under the various international documents have been dealt with in the third chapter.It is noticed that the international documents have had their impact in India leading to creation of machinery for protection of human rights. Organised violations of women's rights such as prostitution, devadasi system, domestic violence, sexual harassment at workplaces, the evil of dowry, female infanticide etc. have been analysed in the light of existing laws and decisional jurisprudence in the fourth chapter. The fifth chapter analyses the decisions and consensus that emerged from the world conferences on women and their impact on the Indian Society and Judiciary. The constitutional provisions and legislative provisions protecting the rights of women have been critically examined in the sixth chapter. Chapter seven deals with various mechanisms evolved to protect the human rights of women. The eighth chapter contains conclusions and suggestions.

Semantic web mining and the representation, analysis, and evolution of web space

Semantic Web Mining aims at combining the two fast-developing research areas Semantic Web and Web Mining. This survey analyzes the convergence of trends from both areas: Growing numbers of researchers work on improving the results of Web Mining by exploiting semantic structures in the Web, and they use Web Mining techniques for building the Semantic Web. Last but not least, these techniques can be used for mining the Semantic Web itself. The second aim of this paper is to use these concepts to circumscribe what Web space is, what it represents and how it can be represented and analyzed. This is used to sketch the role that Semantic Web Mining and the software agents and human agents involved in it can play in the evolution of Web space.

Institutions, Behavior and Evolution

The three articles constituting this thesis are for reasons of content or method related to the following three fields in economics: Behavioral Economics, Evolutionary Game Theory and Formal Institutional Economics. A core element of these fields is the concept of individual preferences. Preferences are of central importance for the conceptional framework to analyze human behavior. They form the foundation for the theory of rational choice which is defined by the determination of the choice set and the selection of the most preferred alternative according to some consistency requirements. The theory of rational choice is based on a very simplified description of the problem of choice (object function and constraints). However, that choices depend on many more factors is for instance propagated by psychological theories and is supported by many empirical and experimental studies. This thesis adds to a better understanding of individual behavior to the extent that the evolution of certain characteristics of preferences and their consequences on human behavior forms the overarching theme of the dissertation. The long-term effect of evolutionary forces on a particular characteristic of importance in the theoretical, empirical and experimental economic literature, the concept of inequality aversion, is subject of the article “The evolution of inequality aversion in a simplified game of life” (Chapter 4). The contribution of the article is the overcoming of a restriction of former approaches to analyze the evolution of preferences in very simple environments. By classifying human interaction into three central economic games, the article provides a first step towards a simplified and sufficiently complete description of the interaction environment. Within such an environment the article characterizes the evolutionary stable preference distribution. One result shows, that the interaction of the aforementioned three classes can stabilize a preference of inequality aversion in the subpopulation which is favored in the problem of redistribution. The two remaining articles are concerned with social norms, which dissemination is determined by medium-run forces of cultural evolution. The article “The impact of market innovations on the evolution of social norms: the sustainability case.“ (Chapter 2) studies the interrelation between product innovations which are relevant from a sustainability perspective and an according social norm in consumption. This relation is based on a conformity bias in consumption and the attempt to avoid cognitive dissonances resulting from non-compliant consumption. Among others, it is shown that a conformity bias on the consumption side can lead to multiple equilibria on the side of norm adoption. The article “Evolution of cooperation in social dilemmas: signaling internalized norms.” (Chapter 3) studies the emergence of cooperation in social dilemmas based on the signaling of social norms. The article provides a potential explanation of cooperative behavior, which does not rely on the assumption of structured populations or on the unmotivated ability of social norms to restrict individual actions or strategy spaces. A comprehensive result of the single articles is the explanation of the phenomenon of partial norm adaption or dissemination of preferences. The plurality of the applied approaches with respect to the proximity to the rational choice approach and regarding the underlying evolutionary mechanics is a particular strength of the thesis. It shows the equality of these approaches in their potential to explain the phenomenon of cooperation in environments that provide material incentives for defective behavior. This also points to the need of a unified framework considering the biological and cultural coevolution of preference patterns.

Self-organized sociopolitical interactions as the best way to achieve organized patterns in human social systems: going beyond the top-down control of classical political regimes

La monografía presenta la auto-organización sociopolítica como la mejor manera de lograr patrones organizados en los sistemas sociales humanos, dada su naturaleza compleja y la imposibilidad de las tareas computacionales de los regímenes políticos clásico, debido a que operan con control jerárquico, el cual ha demostrado no ser óptimo en la producción de orden en los sistemas sociales humanos. En la monografía se extrapola la teoría de la auto-organización en los sistemas biológicos a las dinámicas sociopolíticas humanas, buscando maneras óptimas de organizarlas, y se afirma que redes complejas anárquicas son la estructura emergente de la auto-organización sociopolítica.

Human development in an evolutionary perspective

This article presents an evolutionary perspective to the study of human development. Some general assumptions for the study of development are discussed and the principal building blocks of evolutionary psychology are presented. One of them is that there is a universal human nature (which is modulate also by particular conditions of each context) and the cognitive architecture of human beings is the resulted of interactions between genes and environment. Based on those, and other assumptions, directions for the study of child development in an evolutionary stance are discussed, along with the considerations of context and development. Thus, it is assumed there is a relationship between phylogenies and ontogenetic development (the ontogenesis needs to be understood also as a product of evolution), considering the inseparability of biological, socio-cultural, cognitive emotional aspects that constitute this development. It has been concluded that the evolutionary developmental psychology has scientific relevance because it broadens our vision on human development.

Vegetation development and human occupation in the Damascus region of southwestern Syria from the Late Pleistocene to Holocene

Rockshelter Baaz in the Damascus region of Syria provided a variety of botanical remains from the Late Pleistocene and Early Holocene period. These remains provide new information about the vegetation evolution in this region. The earliest occupational levels correspond with a moisture peak during the Late Pleistocene, between ca. 34-32 kyr b.p., when pine expanded. The next occupations took place during extreme arid conditions, ca. 23-21 kyr b.p., and probably during the Last Glacial Maximum when a steppe vegetation was established. The occupation level of the Younger Dryas, represented by Natufian remains, suggests that the area had been covered by almond-pistachio steppe, similar to later periods of the Early Holocene, and was probably located just outside the range of dense wild cereal stands. There is no drastic impact of the Younger Dryas visible on the vegetation in the botanical remains. The lack of fruits and seeds at Baaz indicates that the site was more likely to have been a temporary hunting post rather than a plant processing site for much of its history. It is ideally suited to this purpose because of its location over the Jaba'deen Pass and the associated springs. However, archaeological remains from the Natufian period, suggest that the site was more permanently occupied during this time.