scholarly journals FARMS: A New Algorithm for Variable Selection

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Susana Perez-Alvarez ◽  
Guadalupe Gómez ◽  
Christian Brander
Keyword(s):  
Variable Selection ◽  
Immune Responses ◽  
Human Populations ◽  
Immune Reactivity ◽  
Genetic Studies ◽  
Genetic Characteristics ◽  
Explanatory Variables ◽  
Specific Outcome ◽  
Host Genetic ◽  
Complex Datasets

Large datasets including an extensive number of covariates are generated these days in many different situations, for instance, in detailed genetic studies of outbreed human populations or in complex analyses of immune responses to different infections. Aiming at informing clinical interventions or vaccine design, methods for variable selection identifying those variables with the optimal prediction performance for a specific outcome are crucial. However, testing for all potential subsets of variables is not feasible and alternatives to existing methods are needed. Here, we describe a new method to handle such complex datasets, referred to as FARMS, that combines forward and all subsets regression for model selection. We apply FARMS to a host genetic and immunological dataset of over 800 individuals from Lima (Peru) and Durban (South Africa) who were HIV infected and tested for antiviral immune responses. This dataset includes more than 500 explanatory variables: around 400 variables with information on HIV immune reactivity and around 100 individual genetic characteristics. We have implemented FARMS inRstatistical language and we showed that FARMS is fast and outcompetes other comparable commonly used approaches, thus providing a new tool for the thorough analysis of complex datasets without the need for massive computational infrastructure.

scholarly journals Antigen receptor repertoires of one of the smallest known vertebrates

2021 ◽  
Vol 7 (1) ◽  
pp. eabd8180
Author(s):  
Orlando B. Giorgetti ◽  
Prashant Shingate ◽  
Connor P. O’Meara ◽  
Vydianathan Ravi ◽  
Nisha E. Pillai ◽  
...  
Keyword(s):  
Immune Responses ◽  
Antigen Receptor ◽  
Fundamental Property ◽  
Cell Receptor ◽  
Immune Reactivity ◽  
Self Similarity ◽  
Frequency Distributions ◽  
Scale Free ◽  
Scale Free Networks ◽  
Incomplete Sampling

The rules underlying the structure of antigen receptor repertoires are not yet fully defined, despite their enormous importance for the understanding of adaptive immunity. With current technology, the large antigen receptor repertoires of mice and humans cannot be comprehensively studied. To circumvent the problems associated with incomplete sampling, we have studied the immunogenetic features of one of the smallest known vertebrates, the cyprinid fish Paedocypris sp. “Singkep” (“minifish”). Despite its small size, minifish has the key genetic facilities characterizing the principal vertebrate lymphocyte lineages. As described for mammals, the frequency distributions of immunoglobulin and T cell receptor clonotypes exhibit the features of fractal systems, demonstrating that self-similarity is a fundamental property of antigen receptor repertoires of vertebrates, irrespective of body size. Hence, minifish achieve immunocompetence via a few thousand lymphocytes organized in robust scale-free networks, thereby ensuring immune reactivity even when cells are lost or clone sizes fluctuate during immune responses.

scholarly journals Impact of Influenza A Virus Shutoff Proteins on Host Immune Responses

Vaccines ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 629
Author(s):  
Megan M. Dunagan ◽  
Kala Hardy ◽  
Toru Takimoto
Keyword(s):  
Immune Response ◽  
Immune Responses ◽  
Influenza A Virus ◽  
Influenza A ◽  
Human Populations ◽  
Lymphocyte Migration ◽  
Host Immune Responses ◽  
Mhc Molecules ◽  
The Impact

Influenza A virus (IAV) is a significant human pathogen that causes seasonal epidemics. Although various types of vaccines are available, IAVs still circulate among human populations, possibly due to their ability to circumvent host immune responses. IAV expresses two host shutoff proteins, PA-X and NS1, which antagonize the host innate immune response. By transcriptomic analysis, we previously showed that PA-X is a major contributor for general shutoff, while shutoff active NS1 specifically inhibits the expression of host cytokines, MHC molecules, and genes involved in innate immunity in cultured human cells. So far, the impact of these shutoff proteins in the acquired immune response in vivo has not been determined in detail. In this study, we analyzed the effects of PA-X and NS1 shutoff activities on immune response using recombinant influenza A/California/04/2009 viruses containing mutations affecting the expression of shutoff active PA-X and NS1 in a mouse model. Our data indicate that the virus without shutoff activities induced the strongest T and B cell responses. Both PA-X and NS1 reduced host immune responses, but shutoff active NS1 most effectively suppressed lymphocyte migration to the lungs, antibody production, and the generation of IAV specific CD4+ and CD8+ T cells. NS1 also prevented the generation of protective immunity against a heterologous virus challenge. These data indicate that shutoff active NS1 plays a major role in suppressing host immune responses against IAV infection.

scholarly journals Immunogenicity of Heterologous Prime-Boost Regimens Involving Recombinant Adenovirus Serotype 11 (Ad11) and Ad35 Vaccine Vectors in the Presence of Anti-Ad5 Immunity

2005 ◽  
Vol 79 (15) ◽  
pp. 9694-9701 ◽  
Author(s):  
Angelique A. C. Lemckert ◽  
Shawn M. Sumida ◽  
Lennart Holterman ◽  
Ronald Vogels ◽  
Diana M. Truitt ◽  
...  
Keyword(s):  
Immune Responses ◽  
Recombinant Adenovirus ◽  
Human Populations ◽  
Vaccine Vectors ◽  
Adenovirus Serotype ◽  
Immunodeficiency Virus ◽  
High Prevalence ◽  
Boost Vaccine ◽  
Serotype 5 ◽  
Cellular Immune

ABSTRACT The high prevalence of preexisting immunity to adenovirus serotype 5 (Ad5) in human populations will likely limit the immunogenicity and clinical utility of recombinant Ad5 (rAd5) vector-based vaccines for human immunodeficiency virus type 1 and other pathogens. A potential solution to this problem is to utilize rAd vaccine vectors derived from rare Ad serotypes such as Ad35 and Ad11. We have previously reported that rAd35 vectors were immunogenic in the presence of anti-Ad5 immunity, but the immunogenicity of heterologous rAd prime-boost regimens and the extent that cross-reactive anti-vector immunity may limit this approach have not been fully explored. Here we assess the immunogenicity of heterologous vaccine regimens involving rAd5, rAd35, and novel rAd11 vectors expressing simian immunodeficiency virus Gag in mice both with and without anti-Ad5 immunity. Heterologous rAd prime-boost regimens proved significantly more immunogenic than homologous regimens, as expected. Importantly, all regimens that included rAd5 were markedly suppressed by anti-Ad5 immunity. In contrast, rAd35-rAd11 and rAd11-rAd35 regimens elicited high-frequency immune responses both in the presence and in the absence of anti-Ad5 immunity, although we also detected clear cross-reactive Ad35/Ad11-specific humoral and cellular immune responses. Nevertheless, these data suggest the potential utility of heterologous rAd prime-boost vaccine regimens using vectors derived from rare human Ad serotypes.

scholarly journals Potential Use of Salivary Markers for Longitudinal Monitoring of Inflammatory Immune Responses to Vaccination

2016 ◽  
Vol 2016 ◽  
pp. 1-12 ◽  
Author(s):  
Pei Wen Lim ◽  
Johan Garssen ◽  
Elena Sandalova
Keyword(s):  
Immune Responses ◽  
Time Course ◽  
Dynamic Range ◽  
Inflammatory Responses ◽  
Literature Survey ◽  
Inflammatory Biomarkers ◽  
Immune Reactivity ◽  
Kinetics Of ◽  
Potential Use ◽  
Full Dynamic Range

Vaccination, designed to trigger a protective immune response against infection, is a trigger for mild inflammatory responses. Vaccination studies can address the question of inflammation initiation, levels, and resolution as well as its regulation for respective studied pathogens. Such studies largely based on analyzing the blood components including specific antibodies and cytokines were usually constrained by number of participants and volume of collected blood sample. Hence, blood-based studies may not be able to cover the full dynamic range of inflammation responses induced by vaccination. In this review, the potential of using saliva in addition to blood for studying the kinetics of inflammatory response studies was assessed. Saliva sampling is noninvasive and has a great potential to be used for studies aimed at analysing the magnitude, time course, and variance in immune responses, including inflammation after vaccination. Based on a literature survey of inflammatory biomarkers that can be determined in saliva and an analysis of how these biomarkers could help to understand the mechanisms and dynamics of immune reactivity and inflammation, we propose that the saliva-based approach might have potential to add substantial value to clinical studies, particularly in vulnerable populations such as infants, toddlers, and ill individuals.

scholarly journals The microbiota plays a critical role in the reactivity of lung immune components to innate ligands

2020 ◽  
Author(s):  
Quentin Marquant ◽  
Daphné Laubreton ◽  
Carole Drajac ◽  
Elliot Mathieu ◽  
Edwige Bouguyon ◽  
...  
Keyword(s):  
Immune Responses ◽  
Critical Role ◽  
Innate Immune ◽  
Immune Reactivity ◽  
Innate Immune Responses ◽  
Plain Language ◽  
Pulmonary Tissue ◽  
Germ Free ◽  
Syncytial Virus

AbstractThe microbiota contributes to shaping efficient and safe immune defenses in the gut. However, little is known about the role of the microbiota in the education of pulmonary innate immune responses. Here, we tested whether the endogenous microbiota can modulate reactivity of pulmonary tissue to pathogen stimuli by comparing the response of specific pathogen-free (SPF) and germ-free (GF) mice. Using SPF and GF mice intranasally exposed to lipopolysaccharide (LPS), a component of Gram-negative bacteria, we observed earlier and greater inflammation in the pulmonary compartment of GF mice than that of SPF mice. Toll-like receptor 4 (TLR4) was more abundantly expressed in the lungs of GF mice than those of SPF mice at steady state, which could predispose the innate immunity of GF mice to strongly react to environmental stimuli. Lung explants were stimulated with different TLR agonists or infected with the human airways pathogen, respiratory syncytial virus (RSV), resulting in greater inflammation under almost all conditions for the GF explants. Finally, alveolar macrophages (AM) from GF mice presented a higher innate immune response upon RSV infection than those of SPF mice. Overall, these data suggest that the presence of microbiota in SPF mice induced a process of innate immune tolerance in the lungs by a mechanism which remains to be elucidated. Our study represents a step forward to establishing the link between the microbiota and the immune reactivity of the lungs.Plain Language summaryMicrobiota represents an important partner of immunologic system at the interface between immune cells and epithelium. It is well known, notably in the gut, that the microbiota contributes in shaping efficient and safe defenses. However, little is known about the role of the microbiota in the education of pulmonary innate immune responses. In this study, we postulate that endogenous microbiota could dampen an excessive reactivity of pulmonary tissue to external stimuli. Thus, we sought to study the innate immune reaction switched on by viral or bacterial ligands in respiratory tract cells coming from mice with or without microbiota (germ-free condition, GF). Altogether, our results show a higher inflammatory reaction in GF condition. This study represents a step forward to better establish the link between the microbiota and the reactivity of the lung tissue. Not only these data demonstrate that the microbiota educates the pulmonary innate immune system, but also contributes the emerging concept of using respiratory commensal bacteria as potential next-generation probiotics to prevent susceptibility to respiratory diseases.

scholarly journals Quantifying the prevalence of assortative mating in a human population

2019 ◽  
Author(s):  
Klaus Jaffe
Keyword(s):  
Assortative Mating ◽  
Genetic Relatedness ◽  
Random Mating ◽  
Human Populations ◽  
Genetic Composition ◽  
Genetic Studies ◽  
Maintenance Of Sex ◽  
Animal Populations ◽  
The Uk ◽  
First Time

AbstractFor the first time, empirical evidence allowed to construct the frequency distribution of a genetic relatedness index between the parents of about half a million individuals living in the UK. The results suggest that over 30% of the population is the product of parents mating assortatively. The rest is probably the offspring of parents matching the genetic composition of their partners randomly. High degrees of genetic relatedness between parents, i.e. extreme inbreeding, was rare. This result shows that assortative mating is likely to be highly prevalent in human populations. Thus, assuming only random mating among humans, as widely done in ecology and population genetic studies, is not an appropriate approximation to reality. The existence of assortative mating has to be accounted for. The results suggest the conclusion that both, assortative and random mating, are evolutionary stable strategies. This improved insight allows to better understand complex evolutionary phenomena, such as the emergence and maintenance of sex, the speed of adaptation, runaway adaptation, maintenance of cooperation, and many others in human and animal populations.

scholarly journals A Comprehensive Review and Update on the Pathogenesis of Inflammatory Bowel Disease

2019 ◽  
Vol 2019 ◽  
pp. 1-16 ◽  
Author(s):  
Qingdong Guan
Keyword(s):  
Inflammatory Bowel Disease ◽  
Immune Responses ◽  
Bowel Disease ◽  
Genetic Factors ◽  
Intestinal Inflammation ◽  
Adaptive Immune Responses ◽  
Adaptive Immune ◽  
Host Genetic ◽  
Inflammatory Bowel ◽  
Host Genetic Factors

Inflammatory bowel disease (IBD) is a chronic and life-threating inflammatory disease of gastroenteric tissue characterized by episodes of intestinal inflammation. The pathogenesis of IBD is complex. Recent studies have greatly improved our knowledge of the pathophysiology of IBD, leading to great advances in the treatment as well as diagnosis of IBD. In this review, we have systemically reviewed the pathogenesis of IBD and highlighted recent advances in host genetic factors, gut microbiota, and environmental factors and, especially, in abnormal innate and adaptive immune responses and their interactions, which may hold the keys to identify novel predictive or prognostic biomarkers and develop new therapies.

Reactive arthritis and enteropathic arthropathy

2016 ◽  
Author(s):  
J. S. Hill Gaston
Keyword(s):  
Inflammatory Bowel Disease ◽  
Back Pain ◽  
Immune Responses ◽  
Reactive Arthritis ◽  
Inflammatory Back Pain ◽  
Hla B27 ◽  
Genetic Studies ◽  
Inflammatory Bowel ◽  
Disease Modifying ◽  
Crystal Induced Arthritis

Reactive arthritis (ReA), and enteropathic arthritis secondary to inflammatory bowel disease, are forms of spondyloarthritis, all of which share an association with HLA B27 and can involve both axial and peripheral joints. Genetic studies strongly implicate the cytokines IL-17 and IL-23 in their pathogenesis, and evidence for autoimmunity is lacking. ReA is triggered by particular bacteria, mainly affecting the gut and genitourinary tract, though infections are sometimes asymptomatic. Classically an acute oligo- or monoarthritis with enthesitis occurs, often with inflammatory back pain, though mild polyarthritis can also occur. Septic and crystal-induced arthritis are the principal differential diagnoses. Extra-articular features may aid diagnosis, which otherwise requires laboratory evidence of preceding infection. Bacterial components traffic to the joint (which is nevertheless sterile), and elicit local pro-inflammatory immune responses. Most ReA is self-limiting, but persistent cases may require disease-modifying anti-rheumatic drugs or even biologics.

Viral Disease in Hematology

Hematology ◽  
2000 ◽  
Vol 2000 (1) ◽  
pp. 409-423 ◽  
Author(s):  
Genoveffa Franchini ◽  
Richard F. Ambinder ◽  
Michèle Barry
Keyword(s):  
Leukemia Virus ◽  
Antiviral Treatment ◽  
Basic Research ◽  
Epidemiological Data ◽  
Viral Disease ◽  
Human Populations ◽  
Genetic Characteristics ◽  
Barr Virus ◽  
Ebv Infection ◽  
Human T Cell

As part of the international outreach of the American Society of Hematology, this review addresses some aspects of the genetics, biology, epidemiology, and clinical relevance of viruses that cause a variety of hematopoietic disorders in human populations. The viruses described here have a different pattern of geographical distribution, and the disease manifestations may vary according to environmental and/or genetic characteristics of the host. Epstein-Barr virus, a linear double-stranded DNA virus (herpesvirus), and the human T-cell leukemia virus, a retrovirus with a single-stranded diploid RNA genome, are associated among other diseases with lymphoma and leukemia/lymphoma, respectively. Both viruses cause a lifelong infection, but only a small percentage of infected individuals develop hematopoietic neoplasms. Epidemiological data suggest that the time of infection may be important in determining disease outcome in both HTLV-I and EBV infection. The pathogenic mechanisms used by these viruses are of most interest since they may recapitulate growth dysregulation steps also occurring in other hematopoietic malignancies.In Section I Dr. Franchini reviews the biology, genetics and diseases associated with HTLV-I and HTLV-II. In Section II, Dr. Ambinder reviews the biology of EBV infection and its relationship to the pathogenesis of Hodgkin's disease and other malignancies.In Section III, Dr. Barry reviews the viral hemorrhagic fevers caused by RNA viruses such as Arenaviridae, Bunyaviridae, Filoviridae, and Flaviviridae, which can lead to acute syndromes that can be fatal. However, prompt diagnosis is key for patient management as well as for limiting their spread to others. These syndromes have become the focus of public concern and represent not only a clinical challenge, since in most cases no specific antiviral treatment is available, but also a challenge for future basic research on their biology and pathogenesis since little is known at present.

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