Evolutionary biology and anthropology suggest biome reconstitution as a necessary approach toward dealing with immune disorders

Industrialized society currently faces a wide range of non-infectious, immune-related pandemics. These pandemics include a variety of autoimmune, inflammatory and allergic diseases that are often associated with common environmental triggers and with genetic predisposition, but that do not occur in developing societies. In this review, we briefly present the idea that these pandemics are due to a limited number of evolutionary mismatches, the most damaging being ‘biome depletion’. This particular mismatch involves the loss of species from the ecosystem of the human body, the human biome, many of which have traditionally been classified as parasites, although some may actually be commensal or even mutualistic. This view, evolved from the ‘hygiene hypothesis’, encompasses a broad ecological and evolutionary perspective that considers host-symbiont relations as plastic, changing through ecological space and evolutionary time. Fortunately, this perspective provides a blueprint, termed 'biome reconstitution', for disease treatment and especially for disease prevention. Biome reconstitution includes the controlled and population-wide reintroduction (i.e. domestication) of selected species that have been all but eradicated from the human biome in industrialized society and holds great promise for the elimination of pandemics of allergic, inflammatory and autoimmune diseases

Thermal activation of superconducting Josephson junctions

Thesis (S.B.)--Massachusetts Institute of Technology, Dept. of Physics, 2007.Includes bibliographical references (p. 73-75).Superconducting quantum circuits (SQCs) are being explored as model systems for scalable quantum computing architectures. Josephson junctions are extensively used in superconducting quantum interference devices (SQUIDs) and in persistent-current qubit systems. Noise excitations, however, have a critical influence on their dynamics. Thus, the primary focus of this research was to investigate the effects of thermal activation on the superconducting properties of Josephson junctions. Specifically, thermal noise tends to result in a range of switching currents, values less than the critical current at which a junction switches from the superconducting to the normal state. First, a general review of superconductivity concepts is given, including a treatment of the Josephson phenomena. Next, I describe some of my work on characterizing the current-voltage traces of Josephson junctions tested at 4 K with a Multi-Chip Probe (MCP). Then, I describe thermal activation theory and examine the equations useful for modeling switching current distributions. The Josephson junctions of a SQUID with a ramped bias current were tested for numerous temperatures T =/< 4.5 K (and with various magnetic flux frustrations). Fit parameters of critical current, capacitance, resistance, and temperature were determined from modeling the escape rates and switching current probability distributions. The thermal activation model succeeded in fitting the results to good agreement, where parameters C = 2.000 ± 0.002 pF and T = 1.86 ± 0.06 K were obtained for 1.8 K data. For significantly lower temperatures, the model tends to predict higher than expected temperatures; further analysis would need to include the quantum mechanical tunneling model better in the fitting scheme.by Aditya P. Devalapalli.S.B

Changing expression of vertebrate immunity genes in an anthropogenic environment: a controlled experiment

Background: The effect of anthropogenic environments on the function of the vertebrate immune system is a problem of general importance. For example, it relates to the increasing rates of immunologically-based disease in modern human populations and to the desirability of identifying optimal immune function in domesticated animals. Despite this importance, our present understanding is compromised by a deficit of experimental studies that make adequately matched comparisons between wild and captive vertebrates. Results: We transferred post-larval fishes (three-spined sticklebacks), collected in the wild, to an anthropogenic (captive) environment. We then monitored, over 11 months, how the systemic expression of immunity genes changed in comparison to cohort-matched wild individuals in the originator population (total n = 299). We found that a range of innate (lyz, defbl2, il1r-like, tbk1)and adaptive (cd8a, igmh) immunity genes were up-regulated in captivity, accompanied by an increase in expression of the antioxidant enzyme, gpx4a. For some genes previously known to show seasonality in the wild, this appeared to be reduced in captive fishes. Captive fishes tended to express immunity genes, including igzh, foxp3b, lyz, defbl2, and il1r-like, more variably. Furthermore, although gene co-expression patterns (analyzed through gene-by-gene correlations and mutual information theory based networks) shared common structure in wild and captive fishes, there was also significant divergence. For one gene in particular, defbl2, high expression was associated with adverse health outcomes in captive fishes. Conclusion: Taken together, these results demonstrate widespread regulatory changes in the immune system in captive populations, and that the expression of immunity genes is more constrained in the wild. An increase in constitutive systemic immune activity, such as we observed here, may alter the risk of immunopathology and contribute to variance in health in vertebrate populations exposed to anthropogenic environments

The immunology of wild Rodents: Current Status and Future Prospects

Wild animals’ immune responses contribute to their evolutionary fitness. These responses are moulded by selection to be appropriate to the actual antigenic environment in which the animals live, but without imposing an excessive energetic demand which compromises other component of fitness. But, exactly what these responses are, and how they compare with those of laboratory animals, has been little studied. Here, we review the very small number of published studies of immune responses of wild rodents, finding general agreement that their humoral (antibody) responses are highly elevated when compared with those of laboratory animals, and that wild rodents’ cellular immune system reveals extensive antigenic exposure. In contrast, proliferative and cytokine responses of ex vivo-stimulated immune cells of wild rodents are typically depressed compared with those of laboratory animals. Collectively, these responses are appropriate to wild animals’ lives, because the elevated responses reflect the cumulative exposure to infection, while the depressed proliferative and cytokine responses are indicative of effective immune homeostasis that minimizes immunopathology. A more comprehensive understanding of the immune ecology of wild animals requires (i) understanding the antigenic load to which wild animals are exposed, and identification of any key antigens that mould the immune repertoire, (ii) identifying immunoregulatory processes of wild animals and the events that induce them, and (iii) understanding the actual resource state of wild animals, and the immunological consequences that flow from this. Together, by extending studies of wild rodents, particularly addressing these questions (while drawing on our immunological understanding of laboratory animals), we will be better able to understand how rodents’ immune responses contribute to their fitness in the wild

Development of SystemC Modules from HDL for System-on-Chip Applications

Designs are becoming bigger in size, faster in speed and larger in complexity with the emergence of System-on-Chip designs. Hardware components and embedded software co-exist in such designs making it necessary to describe designs at higher levels of abstraction. Describing designs at higher levels of abstraction enables faster simulation, hardware software co-simulation and architectural exploration. SystemC is a solution. Also the time to market can be reduced greatly if previously designed intellectually property (IP) described in a hardware description language (HDL) can be reused in SystemC. In this research SystemC modules were successfully developed and verified from Verilog using existing tools. Verilator is a tool that translates synthesizable Verilog into C++ or SystemC code with certain limitations. The generated SystemC code was simulated and compared against the simulation results of the original Verilog code. To add credibility several simple and a few large cores were transformed into SystemC and the simulation results of the Verilog and the SystemC code were compared. Pure SystemC code was synthesized using Synopsys’ SystemC Compiler and DC Shell and an area report based on the TSMC 0.18 technology was generated. The synthesis produced a Verilog code, which was simulated, and the simulations compared to the SystemC simulations Available VHDL to Verilog and vice-versa conversion tools were also investigated. Mentor Graphics’ HDL Designer and Ocean Logic’s VHDL to Verilog converter were used for this purpose. Simulation results before and after the conversions were compared

A software fault injection tool

Software testing is a very important phase in the software development life cycle. The quality and reliability of software are two major concerns of software testing. Developers assume that there are hidden bugs in software products because it is improbable to encounter all error paths of a complex system in a controlled test environment. Software has been an integral part of safety and mission critical systems. Software fault injection can help achieve this criterion. Fault injection involves deliberately inducing faults into software systems to observe their behavior in real time. This helps in identification of dependencies and improves fault tolerance algorithms and mechanisms. Compile time injection is an experimental-based approach to system's reliability and resilience. This approach requires injecting faults into source code of system under test and examining its behavior during the system's compilation phase. The goal of the project is to develop a software fault injection tool (C-SWFIT). This tool is capable of injecting faults during the pre-execution phase of a program/software and assessing fault injection effects. This tool is designed to be intuitive and easy to use by software developers looking to test software tolerance and resilience

2nd FIBRESHIP WORKSHOP - Breakout Session 4 - Regulatory and Standardisation

Presentation held at the second public workshop of the FIBRESHIP project, held at La Ciotat, France, on 25th of June 2019. &nbsp; The second public workshop of the FIBRESHIP project offered to the participants a chance to discuss the different composite materials solutions for shipbuilding as well as learn more about the latest technological advances of FIBRESHIP Project related to design, construction and operation of ships integrally built in composite materials. FIBRESHIP Consortium is looking for a niche in the future shipping market through promoting changes in the regulatory framework of IMO and generating guidelines and methodologies for designing, building and operating large-length vessels, laying the foundations of a new market based on composites technology in shipbuilding and shipping. &nbsp; This presentation is dedicated to the strategies of regulatory and standardization activities of the project, mainly focused on the fire challenges related to the use of composites in the shipping industry. Reddy Devalapalli (Lloyd&rsquo;s Register of Shipping) explained that a presentation in collaboration with RAMSSES project is being prepared for the next SDC of IMO in February 2020 as well as a info paper, to promote changes in the current regulatory frameworks which limit the use of Fibre Reinforced Plastic elements in the construction of large-length ship structures. In addition, Stephane Pabeouf from Bureau Veritas described the development of new performance criteria which will attempt to deal with the fire safety issues and structural performance of the new lightweight ships, being an essential part of the FIBRESHIP project. &nbsp

System-on-Chip Applications

have examined the final electronic copy of this thesis for form and content an