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1
Newman, Abraham L. Sequencing, Layering, and Feedbacks in Global Regulation. Edited by Orfeo Fioretos, Tulia G. Falleti, and Adam Sheingate. Oxford University Press, 2016. http://dx.doi.org/10.1093/oxfordhb/9780199662814.013.38.
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From banking standards to data privacy, regulation has entered the lexicon of international affairs. Unlike trade or currencies, however, there are few formal treaty-based international organizations resolving disputes or setting the rules for the world. Instead, global regulation is frequently shaped by informal networks of regulators or at times by the extraterritorial extension of domestic law by large markets. Drawing on work from historical institutionalism, this chapter argues that the global politics of regulation is in important respects the product of domestic and international institutions interacting over time and across space. In developing three mechanisms—relative sequencing, cross-national layering, and transnational feedbacks —the chapter argues that historical institutionalism helps address lacunae in extant approaches to global regulation.
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Bantekas, Ilias. Sequencing Peace and Justice in Post-Conflict Africa. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780198810568.003.0005.
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This chapter discusses the extent to which there is any conflict or harm in the ICC Prosecutor’s involvement in cases undergoing mediation by the international community, most of which are currently in Africa. The ICC Prosecutor’s discretion, as per the Court’s Statute, to hold a prosecution in abeyance in anticipation of the outcomes of mediating efforts which aim at ending a conflict is at best ambivalent. Recent practice suggests that stakeholders engaged in ending long-running African conflicts prefer the Prosecutor to decline to exercise jurisdiction in order to encourage the parties to reach some agreement. For obvious reasons, discussions on such matters are often held confidentially and not in the context of official debates. The African experience with the peace–justice nexus shows that the peace-versus-justice debate has not been resolved in favour of any camp.
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Sadleir, Lynette G., Jozef Gecz, and Ingrid E. Scheffer. Epilepsies That Occur Predominantly in Girls. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780199937837.003.0041.
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Availability of DNA sequencing has led to an increase in the number of children being identified with mutations in specific genes in specific epilepsy phenotypes. The presence of mutations that cause epilepsy only in females is one of the discoveries revealed in the sequencing era. Mutations in PCDH19 and CDKL5 are distinctive and identifiable forms of female-only epilepsy, and clinicians should consider PCDH19 in normal girls presenting with clusters of afebrile or febrile seizures in the first 3 years of life, and CDKL5 in girls or boys presenting with severe developmental delay within the first 6 months of life followed by intractable seizures including spasms within the first 2 years.
4
Walsh, Richard A. Siblings with Instability. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780190607555.003.0015.
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Over the past 5 years, there has been a shift in the approach to searching for a genetic diagnosis in familial ataxic syndromes. Whereas in the past, a limited but expensive search through a selection of commercially available genes using Sanger sequencing was performed, there is now widespread availability of gene panels utilizing next-generation sequencing techniques. This is an efficient and powerful approach that may achieve a diagnosis in more than 30% of patients with a familial ataxia that remain undiagnosed. However, accurate phenotyping remains critical to allow interpretation of sequence variants of uncertain significance, to identify biomarkers that may be useful to monitor future therapies, and to assist with the identification of underlying pathophysiology.
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Purcell, Shaun M. Genetic Methodologies and Applications. Edited by Dennis S. Charney, Eric J. Nestler, Pamela Sklar, and Joseph D. Buxbaum. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190681425.003.0001.
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Mental illness is highly heritable, yet it has been difficult historically to identify the specific genes that comprise that risk. This difficulty resides in the fact that the genetic risk for all common mental disorders is polygenic, with perhaps hundreds of genetic variations, each of small effect, contributing to the overall risk. Despite these challenges, the field has made dramatic advances over the past decade in beginning to understand the genetic basis of mental illness. This chapter provides an overview of the experimental approaches used, beginning with epidemiology and population genetics to define the heritability of an illness, to classic studies of large families and linkage disequilibrium analysis, to genome-wide investigations including genome-wide association studies (GWAS), exome sequencing, and whole genome sequencing. Increasingly, these genetic advances are being understood within the biological context of disease pathophysiology.
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Maher, Christopher J., and Elaine R. Mardis. Genomic Landscape of Cancer. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780190238667.003.0004.
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The study of cancer genomics has advanced rapidly during the last decade due to the development of next generation or massively parallel technology for DNA sequencing. The resulting knowledge is transforming the understanding of both inherited (germline) genetic susceptibility and the somatic changes in tumor tissue that drive abnormal growth and progression. The somatic alterations in tumor tissue vary depending on the type of cancer and its characteristic “genomic landscape.” New technologies have increased the speed and lowered the cost of DNA sequencing and have enabled high-volume characterization of RNA, DNA methylation, DNA-protein complexes, DNA conformation, and a host of other factors that, when altered, can contribute to the development and/or progression of the cancer. Technologic advances have greatly expanded research on somatic changes in tumor tissue, revealing both the singularity of individual cancer genomes and the commonality of genetic alterations that drive cancer in different tissues.
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Munro, Carol A., and Duncan Wilson. Fungal genomics and transcriptomics. Edited by Christopher C. Kibbler, Richard Barton, Neil A. R. Gow, Susan Howell, Donna M. MacCallum, and Rohini J. Manuel. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780198755388.003.0006.
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The advent of whole-genome sequencing has resulted in a range of platforms for large-scale analysis of the DNA (genomics), RNA (transcriptomics), protein (proteomics), and metabolite (metabolomics) content of cells. These inclusive ‘omics’ approaches have allowed for unparalleled insights into fungal biology. In this chapter we will discuss how genomics and transcriptomics have been used to broaden our understanding of the biology of human pathogenic fungi and their interactions with their hosts.
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Ingles, Jodie, Charlotte Burns, and Laura Yeates. Genetic counselling. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198784906.003.0145.
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Cardiac genetic counselling is an emerging but important subspecialty. The qualifications of cardiac genetic counsellors depend on the country of practice, but at a minimum they are Master’s-level trained health professionals with expertise in genetics, and are integral members of the multidisciplinary inherited cardiovascular disease clinic. Though the framework is diverse in different countries, key roles include investigation and confirmation of family history details, discussion of inheritance risks and facilitation of cardiac genetic testing, communication with at-risk relatives, and increasingly, curation of genetic test results. The use of next-generation sequencing technologies has seen a recent shift in the uptake of genetic testing, due to greater availability and lowered costs. As these gene tests become more comprehensive, including large panels of genes and even whole exome or whole genome sequencing, the need for cardiac genetic counsellors to provide informed consent, appropriate pre- and post-test genetic counselling, and ongoing curation of the variants identified is evident. Finally, given the improved understanding of the psychological implications of living with a cardiovascular genetic disease, cardiac genetic counsellors are integral in delivering psychosocial care and identifying patients requiring intervention with a clinical psychologist.
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Kirchman, David L. Genomes and meta-omics for microbes. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0005.
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The sequencing of entire genomes of microbes grown in pure cultures is now routine. The sequence data from cultivated microbes have provided insights into these microbes and their uncultivated relatives. Sequencing studies have found that bacterial genomes range from 0.18 Mb (intracellular symbiont) to 13 Mb (a soil bacterium), whereas genomes of eukaryotes are much bigger. Genomes from eukaryotes and prokaryotes are organized quite differently. While bacteria and their small genomes often grow faster than eukaryotes, there is no correlation between genome size and growth rates among the bacteria examined so far. Genomic studies have also highlighted the importance of genes exchanged (“horizontal gene transfer”) between organisms, seemingly unrelated, as defined by rRNA gene sequences. Microbial ecologists use metagenomics to sequence all microbes in a community. This approach has revealed unsuspected physiological processes in microbes, such as the occurrence of a light-driven proton pump, rhodopsin, in bacteria (dubbed proteorhodopsin). Genomes from single cells isolated by flow cytometry have also provided insights about the ecophysiology of both bacteria and protists. Oligotrophic bacteria have streamlined genomes, which are usually small but with a high fraction of genomic material devoted to protein-encoding genes, and few transcriptional control mechanisms. The study of all transcripts from a natural community, metatranscriptomics, has been informative about the response of eukaryotes as well as bacteria to changing environmental conditions.
10
Halliday, Catriona L., and Sarah E. Kidd. Cryptococcus species. Edited by Christopher C. Kibbler, Richard Barton, Neil A. R. Gow, Susan Howell, Donna M. MacCallum, and Rohini J. Manuel. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780198755388.003.0012.
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Cryptococcus neoformans and Cryptococcus gattii are the principal pathogenic species within the genus Cryptococcus and the causative agents of cryptococcosis. Although rare, the incidence of infection due to other Cryptococcus species previously regarded as saprophytes, has increased over the last 40 years. Irrespective of the infecting species, infections are acquired following inhalation from the environment, causing localised or disseminated disease. The severity of disease is dependent on the organism’s virulence factors and the host’s immune response, and the clinical manifestations are indistinguishable. Accurate identification of the pathogenic species relies on rDNA sequencing
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Archibald, John. Genomics: A Very Short Introduction. Oxford University Press, 2018. http://dx.doi.org/10.1093/actrade/9780198786207.001.0001.
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Genomics has transformed the biological sciences. From epidemiology and medicine to evolution and forensics, the ability to determine an organism’s complete genetic makeup has changed the way science is done and the questions that can be asked of it. Genomics: A Very Short Introduction explores the science of genomics and its rapidly expanding toolbox. Sequencing a human genome can now take only a few days and those of simple bacteria and viruses, a matter of hours. The resulting sequences can be used to better understand our biology in health and disease and to ‘personalize’ medicine. This VSI explains the implications for science and society today and in the future.
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Taberlet, Pierre, Aurélie Bonin, Lucie Zinger, and Eric Coissac. Environmental DNA. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198767220.001.0001.
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Environmental DNA (eDNA), i.e. DNA released in the environment by any living form, represents a formidable opportunity to gather high-throughput and standard information on the distribution or feeding habits of species. It has therefore great potential for applications in ecology and biodiversity management. However, this research field is fast-moving, involves different areas of expertise and currently lacks standard approaches, which calls for an up-to-date and comprehensive synthesis. Environmental DNA for biodiversity research and monitoring covers current methods based on eDNA, with a particular focus on “eDNA metabarcoding”. Intended for scientists and managers, it provides the background information to allow the design of sound experiments. It revisits all steps necessary to produce high-quality metabarcoding data such as sampling, metabarcode design, optimization of PCR and sequencing protocols, as well as analysis of large sequencing datasets. All these different steps are presented by discussing the potential and current challenges of eDNA-based approaches to infer parameters on biodiversity or ecological processes. The last chapters of this book review how DNA metabarcoding has been used so far to unravel novel patterns of diversity in space and time, to detect particular species, and to answer new ecological questions in various ecosystems and for various organisms. Environmental DNA for biodiversity research and monitoring constitutes an essential reading for all graduate students, researchers and practitioners who do not have a strong background in molecular genetics and who are willing to use eDNA approaches in ecology and biomonitoring.
13
Kulkarni, Kunal, James Harrison, Mohamed Baguneid, and Bernard Prendergast, eds. Endocrinology. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780198729426.003.0007.
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The medical term ‘hormone’ was only introduced in 1905 to describe the chemical secretion from an endocrine gland. Since then, there has been tremendous progress in the field of endocrinology, as a result of advances in biochemistry, physiology, genetics, and molecular biology. Recently, advances in molecular biology, particularly sequencing of the human genome, have led to the unravelling of hormone receptor-post-receptor mechanisms. These discoveries have uncovered novel therapeutic targets for endocrine disease. This chapter covers recent clinical trials, in order to show the impact of some of the most crucial evidence in endocrinology in the late twentieth and twenty-first century.
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Julier, Alice P. Potlucks. University of Illinois Press, 2017. http://dx.doi.org/10.5406/illinois/9780252037634.003.0005.
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This chapter examines the social significance of potlucks. In the United States, the word potluck has come to mean a particular category of commensal events, where each participant brings a “dish to pass” to create a communal meal. As a social social event, the potluck represents a shift in both the form of the meal and the normative expectations of hospitality, away from formality and temporal sequencing. Because both emotional and material labor is shared at potlucks, people potentially construct different situated identities through these events than they might if orienting their social lives around more formal modes of entertaining. Potlucks are also about constructing temporary unities, bounded groups of informal and often heterogeneous people.
15
Bliss, Catherine. A Sociogenomic World. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780190465285.003.0006.
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This chapter discusses a paradigm shift in the genomic sciences wherein scientists have gone from ignoring race to studying it. It argues that the field has adopted a sociogenomic approach to race, in which scientists understand race as a muddled mix of genetic and social factors. Scientists responsible for seminal genome projects, who have faced pressure from the US public health establishment and an array of experts on race, now prioritize race-targeted research, minority recruitment, and analysis of genomic health disparities. As a result large-scale sequencing projects, pharmaceuticals, and postgenomic research have become ever more racialized, while race has taken on an irrevocably genomic imprimatur. This paradigm shift has occurred because of changes across a number of powerful social domains of expertise within science, medicine, and policy. This chapter thus draws upon events taking place in a variety of institutional, regulatory, and normative contexts.
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Riley, Peter. The role of the microbiology laboratory in antimicrobial stewardship. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780198758792.003.0010.
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Microbiology laboratories play an important role in antimicrobial stewardship at the level of individual patients and the population as a whole. When empiric therapy has been started, rapid results can lead to earlier targeted treatment. Accumulated results of susceptibility tests can be analysed and used to generate local or national guidelines on empiric treatment and prophylaxis. Several methods can be used to determine microbial identity and antimicrobial susceptibility, including traditional culture-based methods and newer molecular methods such as matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry, polymerase chain reaction (PCR), and whole-genome sequencing. These methods and potential advantages are reviewed. Before results are reported, expert rules are applied and results edited. At this point the laboratory can influence prescribing practices.
17
Ayala, Francisco J., and Camilo J. Cela-Conde. Neanderthals and modern humans. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780198739906.003.0011.
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This chapter deals with the similarities and differences between Homo neanderthalensis and Homo sapiens, by considering genetic, brain, and cognitive evidence. The genetic differentiation emerges from fossil genetic evidence obtained first from mtDNA and later from nuclear DNA. With high throughput whole genome sequencing, sequences have been obtained from the Denisova Cave (Siberia) fossils. Nuclear DNA of a third species (“Denisovans”) has been obtained from the same cave and used to define the phylogenetic relationships among the three species during the Upper Palaeolithic. Archaeological comparisons make it possible to advance a four-mode model of the evolution of symbolism. Neanderthals and modern humans would share a “modern mind” as defined up to Symbolic Mode 3. Whether the Neanderthals reached symbolic Mode 4 remains unsettled.
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Kotzer, Katrina E., and Sarah E. Kerr. Molecular Technologies and Test Issues. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190604929.003.0005.
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Molecular genetic testing has been around since the discovery and offering of clinical testing for the first gene sequenced. However, in recent years the methods and scope of molecular genetic testing have evolved significantly to encompass next-generation sequencing, multigene panels, and whole exome and genome testing. With this evolution in molecular methods, the nomenclature and variant evaluation and annotation processes are crucial for the systematic and standard interpretation of molecular test results. This chapter will provide the laboratory genetic counselor with information about the common sample types analyzed by molecular techniques for the purposes of genetic testing and the various methodologies available and their limitations. Guidelines are given for the standard approach to molecular variant reporting with respect to nomenclature and variant classification.
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Lurie, Peter. Queer Historiography in The Bridge. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780199797318.003.0005.
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This chapter culminates my earlier discussion of several works’ regretful looks back on U.S. history with Hart Crane’s plaintive lament over the country’s signal historical events, tempered by his hopefulness for the republic’s future. It uses sexuality theory to argue against a teleological, progressive sequencing—both in my study’s rhetorical structure and in ways of tracing history’s unfolding. It suggests the importance of textual erotics of painful empathy in the reader’s encounter with an indigenous past in its early sections, before turning to in The Bridge’s critique of U.S. aerial history and maritime trade. The poem’s account of displaced historical subjects encompasses this alterity in the figure of its peripatetic speaker across its several sections and historical eras. The chapter ends with a coda about Crane’s suicide as a response to his New Critical peers’ rejection of his nonironic, non-Eliotonian vision and of what they saw as his “undisciplined” style and sexuality.
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Barker, Richard. The accelerating pace of biomedical advance. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780198737780.003.0002.
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Bioscience has progressed exponentially, in scientific advances and enabling technology. From quicker and much cheaper gene sequencing to the emergence of data-mining tools, the last 20 years has been unprecedented in exploitable advances brought by research. We have the tools and insights to trace disease from underlying genetics and epigenetics, through proteins that represent intervention options, to ways to create molecules, diagnostics, and devices based on those insights. The life sciences enterprise, once largely confined to Europe, the USA, and Japan, is now seeing major investment from emerging economies. We should be poised to reap the benefits of this rising tide of research with lives transformed and health systems revolutionized. However, the two million biological science papers published annully results in about 14 000 patents, only 5000 drugs in the pipeline, and a mere 30 or so actual medicines. Translation of life sciences research into usable products is hugely inefficient.
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LaGrave, Danielle, Patricia L. Devers Winters, and Geralyn Lambert-Messerlian. Prenatal Screening Technologies and Test Issues. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190604929.003.0007.
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Maternal serum screening began with the measurement of serum alpha fetal protein to detect open neural tube defects, which led to the implementation of routine serum-based prenatal screening in the second trimester for Down syndrome. Advances via combined and integrated screening allowed for the first-trimester detection of both Down syndrome and trisomy 18. Next-generation sequencing has enabled the identification of aneuploidies in circulating cell-free fetal DNA from the plasma fraction of maternal whole blood. This breakthrough in molecular genetic testing, commonly referred to as noninvasive prenatal testing, has revolutionized prenatal screening and testing for genetic disorders without posing additional risk to the pregnancy. This chapter reviews the history of maternal serum screening, the disorders it can detect, the methods of calculating patient-specific risk, and reasons for recalculation or adjustment of risk. This chapter also reviews of cell-free DNA-based testing for fetal aneuploidies, including its limitations and potential.
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Leslie, Vinjamuri. Part I Context, Challenges, and Constraints, 2 The ICC and the Politics of Peace and Justice. Oxford University Press, 2015. http://dx.doi.org/10.1093/law/9780198705161.003.0002.
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The indictment of sitting heads of state and rebel leaders during active armed conflict has radically altered the debate surrounding international justice. Despite the view now widely held that peace and justice are complementary rather than competing values, conflicts in the former Yugoslavia, Sudan, Libya, and Syria have brought home the reality that there are still significant barriers to achieving both peace and justice simultaneously, and that the prospects for enforcing justice are weak when perpetrators of atrocities remain powerful at home. Leading advocacy organizations and the ICC stress the role of international justice in delivering results, especially peace, the rule of law, and stability. This chapter discusses the shift in international justice advocacy from a principle or duty-based logic to one that is results-based. It argues that one way to promote justice may be to postpone it (e.g. through sequencing).
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de Koning, Tom J. Serine Deficiency. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780199972135.003.0023.
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Serine deficiency is a rare cause of intractable seizures and severe psychomotor retardation in infants and young children. However, in recent years it has become clear that serine deficiency in adolescents and adults can give rise to milder forms of seizure disorders and mild mental retardation or to a phenotype with severe progressive polyneuropathy. Serine deficiency can be diagnosed on the basis of low values of serine in plasma and CSF using routine amino acid analysis. However, with the introduction of next generation sequencing in clinical diagnostics the majority of patients are diagnosed through molecular testing of the three genes of the synthesis pathway. L-serine therapy is highly effective in the treatment of seizures and improvement of wellbeing and daily activities. Early diagnosis and timely treatment are important to prevent irreversible damage to the central or peripheral nervous system.
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Winchester, Robert, Darren D. O’Rielly, and Proton Rahman. Genetics of psoriatic arthritis. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198737582.003.0006.
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The psoriatic phenotype is clinically heterogeneous with psoriatic arthritis (PsA) itself being heterogeneous. Studies have consistently demonstrated that PsA has a strong genetic component and disease pathogenesis encompasses a complex interplay between genetic, immunological, and environmental factors. In this chapter, we will review the genetics of PsA including the major histocompatibility complex (MHC) region and non-MHC loci. We will detail how susceptibility genes can be grouped into barrier integrity, innate immune response, and adaptive immune response (particularly Th-17 lymphocyte signalling). We will articulate how these studies strongly support PsA as genetically different from PsV and that the genetic heterogeneity is likely attributed to different HLA susceptibility alleles within the MHC region that an individual carries. Furthermore, we will highlight new emerging technologies, in particular, next-generation sequencing, which may lead to new genetic discoveries in PsA.
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Buxbaum, Joseph D. An Overview of the Genetics of Autism Spectrum Disorders. Oxford University Press, 2013. http://dx.doi.org/10.1093/med/9780199744312.003.0004.
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There is very good evidence for a strong genetic component to the autism spectrum disorders (ASDs), which include autistic disorder, Asperger syndrome, pervasive developmental disorder not otherwise specified, and Rett syndrome. At the same time, identifying the loci contributing to ASD risk has proven difficult because of extreme heterogeneity. However, in spite of these difficulties, many ASD loci have been identified and, even using current clinical measures, an etiological diagnosis can be given in upward of 20% of cases. With the introduction of “second-generation” sequencing, gene discovery in ASDs will accelerate. As genes are being discovered, functional analyses are leading to potential novel therapeutics, and there is great optimism for more effective treatments in ASDs arising from gene discovery. In the current review, some of the important findings in ASD genetics will be outlined, as will the next steps in ASD genetics.
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Bentham, James R. The genetics of congenital heart disease. Edited by José Maria Pérez-Pomares, Robert G. Kelly, Maurice van den Hoff, José Luis de la Pompa, David Sedmera, Cristina Basso, and Deborah Henderson. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198757269.003.0022.
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Congenital heart disease (CHD) is defined as a structural cardiac malformation resulting from an abnormality of development; 8% of CHD is inherited in a Mendelian fashion and 12% results from chromosomal imbalance. Recurrence risk and new research suggest that even the remaining 80% of patients without an identifiable familial or syndromic basis for disease may have an identifiable genetic cause. The potential to understand these mechanisms is increasing with the advent of new sequencing techniques which have identified multiple or single rare variants and/or copy number variants clustering in cardiac developmental genes as well as common variants that may also contribute to disease, for example by altering metabolic pathways. Work in model organisms such as mouse and zebrafish has been pivotal in identifying CHD candidate genes. Future challenges involve translating the discoveries made in mouse models to human CHD genetics and manipulating potentially protective pathways to prevent disease.
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Chaudhry, Bill, José Luis de la Pompa, and Nadia Mercader. The zebrafish as a model for cardiac development and regeneration. Edited by José Maria Pérez-Pomares, Robert G. Kelly, Maurice van den Hoff, José Luis de la Pompa, David Sedmera, Cristina Basso, and Deborah Henderson. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198757269.003.0029.
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The zebrafish has become an established laboratory model for developmental studies and is increasingly used to model aspects of human development and disease. However, reviewers and grant funding bodies continue to speculate on the utility of this Himalayan minnow. In this chapter we explain the similarities and differences between the heart from this distantly related vertebrate and the mammalian heart, in order to reveal the common fundamental processes and to prevent misleading extrapolations. We provide an overview of zebrafish including their husbandry, development, peculiarities of their genome, and technological advances, which make them a highly tractable laboratory model for heart development and disease. We discuss the controversies around morphants and mutants, and relate the development and structures of the zebrafish heart to mammalian counterparts. Finally, we give an overview of regeneration in the zebrafish heart and speculate on the role of the model organism in next-generation sequencing technologies.
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Jalloh, Charles Chernor, and Ilias Bantekas. Conclusion. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780198810568.003.0016.
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Africa has been at the forefront of contemporary global efforts towards ensuring greater accountability for international crimes. This work analyses the relationship and tensions between the International Criminal Court (ICC) and Africa. It traces the origins of the confrontation between African governments, acting individually or within the framework of the African Union, and the permanent Hague-based ICC. Topics examined include Africa, the ICC, and universal jurisdiction; the controversial use of the Prosecutor’s proprio motu power to initiate investigations in Africa; national implementation of the ICC statute in Africa; the complementarity principle; the sequencing of justice and peace; the question of immunity of sitting heads of state; the controversial role of the UN Security Council in referring and deferring situations under ICC investigation; the role of African domestic and traditional courts in the fight against impunity; and the recent withdrawal of some African states parties from the ICC.
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Renner, Tanya, Tianying Lan, Kimberly M. Farr, Enrique Ibarra-Laclette, Luis Herrera-Estrella, Stephan C. Schuster, Mitsuyasu Hasebe, Kenji Fukushima, and Victor A. Albert. Carnivorous plant genomes. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198779841.003.0011.
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Carnivorous plant genome research has focused on members of the Lamiales and Oxalidales; the most complete sequences are for Utricularia gibba and Cephalotus follicularis. The size-limited U. gibba genome highlights the importance of small-scale tandem duplications, which likely play roles in this species’ carnivorous adaptation. Sequencing of the C. follicularis genome detected adaptive changes that may explain the evolution of traits associated with attraction, trapping, digestion, and absorption. Functional consequences of genes putatively missing in the U. gibba genome, yet present in other angiosperms, may have influenced the evolution of polyploidy, physiology, and a rootless Bauplan. Additional draft nuclear genomes and transcriptomes are available for carnivorous Caryophyllales, Ericales, Lamiales, and Poales, but are limited in quantity and quality. Chloroplast genomes of carnivorous Lentibulariaceae have revealed interesting patterns of gene loss, alterations in the proportion of repeat DNA, and plastome-wide increases in substitution rates.
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Marlow, Heather, ed. Evolutionary Development of Marine Larvae. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198786962.003.0002.
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Access to a growing number of marine invertebrates with genetic and genomic tools has broadened our understanding of the diversity of developmental mechanisms, informing our understanding of larval evolution by allowing the identification of shared or divergent programs for the formation of body plan patterning and organ formation. Two such genetic programs are the apical plate patterning network and the hox/parahox trunk and gut patterning network common to larval and adult forms, respectively. While mounting evidence supports an ancient origin at the base of the Bilateria for both adult and larval forms, it is clear that many distinct organs and structures have appeared independently and can be shifted between the larval and adult phase frequently. Future advances in our understanding of larval evolution are likely to emerge from exhaustive studies of marine invertebrate cell types by single-cell sequencing technologies and through the study of the genetic basis of the metamorphic transition.
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Tangen, Catherine M., Marian L. Neuhouser, and Janet L. Stanford. Prostate Cancer. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780190238667.003.0053.
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Prostate cancer is the most common solid tumor and the second leading cause of cancer-related mortality in American men. Worldwide, prostate cancer ranks second and fifth as a cause of cancer and cancer deaths, respectively. Despite the international burden of disease due to prostate cancer, its etiology is unclear in most cases. Established risk factors include age, race/ancestry, and family history of the disease. Prostate cancer has a strong heritable component, and genome-wide association studies have identified over 110 common risk-associated genetic variants. Family-based sequencing studies have also found rare mutations (e.g., HOXB13) that contribute to prostate cancer susceptibility. Numerous environmental and lifestyle factors (e.g., obesity, diet) have been examined in relation to prostate cancer incidence, but few modifiable exposures have been consistently associated with risk. Some of the variability in results may be related to etiological heterogeneity, with different causes underlying the development of distinct disease subgroups.
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Pezzella, Francesco, Mahvash Tavassoli, and David J. Kerr, eds. Oxford Textbook of Cancer Biology. Oxford University Press, 2019. http://dx.doi.org/10.1093/med/9780198779452.001.0001.
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The study of the biology of tumours has grown to become markedly interdisciplinary, involving chemists, statisticians, epidemiologists, mathematicians, bioinformaticians, and computer scientists alongside medical scientists. Oxford Textbook of Cancer Biology brings together the developments from different branches of research into one volume. Structured in seven sections, the book starts with a review of the development and biology of multicellular organisms, how they maintain a healthy homeostasis in an individual, and a description of the molecular basis of cancer development. The book then illustrates how, once cells become neoplastic, their signalling network is altered and pathological behaviour follows. Changes that cancer cells can induce in nearby normal tissue are explored, and the new relationship established between them and the stroma is explicated. Finally, the authors illustrate the contribution provided by high throughput techniques to map cancer at different levels, from genomic sequencing to cellular metabolic functions, and how information technology with its vast amounts of data are integrated with traditional cell biology to provide a global view of the disease. The book concludes by summarizing what we know to date about cancer, and in what direction our understanding of cancer is moving.
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Bakhtiar, Syeda Marriam, and Erum Dilshad, eds. Omics Technologies for Clinical Diagnosis and Gene Therapy: Medical Applications in Human Genetics. BENTHAM SCIENCE PUBLISHERS, 2022. http://dx.doi.org/10.2174/97898150795171220101.
Full textAbstract:
Genetic disorders have been the focus of scientists for a long time. The emergence of next-generation sequencing techniques has ushered a new era in genetics and several developments have occurred in human genetics. The scientific perspective has also been widened with omics technologies that allow researchers to analyze genetic sequences and their expression products. An integrated approach is being used not only for diagnosis but also for disease management and therapeutic purposes. This book highlights emerging areas of omics technology and its application in the diagnosis and management of human genetic disorders. The book covers three areas of research and implementation: 1) Diagnosis (covering conventional strategies to next-generation platforms). This section focuses on the role of in silico analysis, databases and multi-omics of single-cell which will help in designing better management strategies. 2) Disease Management and therapeutic interventions. This section starts with genetic counselling and progresses to more specific techniques such as pharmacogenomics and personalized medicine, gene editing techniques and their applications in gene therapies and regenerative medicine. 3) Case studies. This section discusses the applications and success of all the above-mentioned strategies on selected human disorders. This book serves as a handy reference for students and academics studying advanced omics techniques in biochemistry and molecular genetics as part of courses in life sciences, pharmacology and medicine.
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Lewis, Myles, and Tim Vyse. Genetics of connective tissue diseases. Oxford University Press, 2013. http://dx.doi.org/10.1093/med/9780199642489.003.0042.
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The advent of genome-wide association studies (GWAS) has been an exciting breakthrough in our understanding of the genetic aetiology of autoimmune diseases. Substantial overlap has been found in susceptibility genes across multiple diseases, from connective tissue diseases and rheumatoid arthritis (RA) to inflammatory bowel disease, coeliac disease, and psoriasis. Major technological advances now permit genotyping of millions of single nucleotide polymorphisms (SNPs). Group analysis of SNPs by haplotypes, aided by completion of the Hapmap project, has improved our ability to pinpoint causal genetic variants. International collaboration to pool large-scale cohorts of patients has enabled GWAS in systemic lupus erythematosus (SLE), systemic sclerosis and Behçet's disease, with studies in progress for ANCA-associated vasculitis. These 'hypothesis-free' studies have revealed many novel disease-associated genes. In both SLE and systemic sclerosis, identified genes map to known pathways including antigen presentation (MHC, TNFSF4), autoreactivity of B and T lymphocytes (BLK, BANK1), type I interferon production (STAT4, IRF5) and the NFκB pathway (TNIP1). In SLE alone, additional genes appear to be involved in dysregulated apoptotic cell clearance (ITGAM, TREX1, C1q, C4) and recognition of immune complexes (FCGR2A, FCGR3B). Future developments include whole-genome sequencing to identify rare variants, and efforts to understand functional consequences of susceptibility genes. Putative environmental triggers for connective tissue diseases include infectious agents, especially Epstein-Barr virus; cigarette smoking; occupational exposure to toxins including silica; and low vitamin D, due to its immunomodulatory effects. Despite numerous studies looking at toxin exposure and connective tissue diseases, conclusive evidence is lacking, due to either rarity of exposure or rarity of disease.
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Schram, Frederick R., and Stefan Koenemann. Evolution and Phylogeny of Pancrustacea. Oxford University Press, 2021. http://dx.doi.org/10.1093/oso/9780195365764.001.0001.
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The understanding of arthropod phylogeny and evolution in the past three decades has undergone major changes. These have arisen from new sources of data applicable across several fields of study. Developments within ontogenetic studies not only in regard to gross patterns of embryology but also regarding a revolution in the application of development genetics continue to generate remarkable insights into crustaceomorph evolution. Phylogeny techniques of analysis and new sources of data derived from molecular sequencing have forced consideration of new hypotheses concerning the interrelationships of all the pancrustaceans, both crustaceomorphs and Hexapoda. Furthermore, it is not uncommon that this multiplicity of sources for new data from opposing research teams can result in different hypotheses for phylogenetic relationships. This situation should not be treated as a defect, or an impediment, but rather as a source for multiple alternative hypotheses—the bases for further data gathering and analyses. Also, one should never view consideration of fossils as a vexing source of noise. Here, too, consideration of multiple hypotheses has proven useful. Often, fossils can produce deeper understanding of the paleodiversity of body plans. Nevertheless, some fossil groups still remain as enigmas, such as Thylacocephala. But even fossils incompletely understood can help fill in gaps in knowledge of paleobiodiversity that can prove useful, for example, in analyzing the the origin and early evolution of Hexapoda. Old ideas about pancrustacean evolution have served the field well, but results derived from all data inputs should be embraced.
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Jalloh, Charles Chernor, and Ilias Bantekas, eds. The International Criminal Court and Africa. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780198810568.001.0001.
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Africa has been at the forefront of contemporary global efforts towards ensuring greater accountability for international crimes. But the continent’s early embrace of international criminal justice seems to be taking a new turn with the recent pushback from some African states claiming that the emerging system of international criminal law represents a new form of imperialism masquerading as international rule of law. This work analyses the relationship and tensions between the International Criminal Court (ICC) and Africa. It traces the origins of the confrontation between African governments, acting individually or within the framework of the African Union, and the permanent Hague-based ICC. Topics examined include Africa, the ICC, and universal jurisdiction; the controversial use of the prosecutor’s proprio motu power to initiate investigations in Africa; national implementation of the ICC statute in Africa; the complementarity principle; the sequencing of justice and peace; the question of immunity of sitting heads of state; the controversial role of the UN Security Council in referring and deferring situations under ICC investigation; the role of African domestic and traditional courts in the fight against impunity as well as the recent withdrawal of some African states parties from the ICC. Leading commentators offer valuable insights on the core legal and political issues that have bedevilled the relationship between the two sides and expose the uneasy interaction between international law and international politics.
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Vaheri, Antti, James N. Mills, Christina F. Spiropoulou, and Brian Hjelle. Hantaviruses. Oxford University Press, 2011. http://dx.doi.org/10.1093/med/9780198570028.003.0035.
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Hantaviruses (genus Hantavirus, family Bunyaviridae) are rodent- and insectivore-borne zoonotic viruses. Several hantaviruses are human pathogens, some with 10-35% mortality, and cause two diseases: hemorrhagic fever with renal syndrome (HFRS) in Eurasia, and hantavirus cardiopulmonary syndrome (HCPS) in the Americas. Hantaviruses are enveloped and have a three-segmented, single-stranded, negative-sense RNA genome. The L gene encodes an RNA-dependent RNA polymerase, the M gene encodes two glycoproteins (Gn and Gc), and the S gene encodes a nucleocapsid protein. In addition, the S genes of some hantaviruses have an NSs open reading frame that can act as an interferon antagonist. Similarities between phylogenies have suggested ancient codivergence of the viruses and their hosts to many authors, but increasing evidence for frequent, recent host switching and local adaptation has led to questioning of this model. Infected rodents establish persistent infections with little or no effect on the host. Humans are infected from aerosols of rodent excreta, direct contact of broken skin or mucous membranes with infectious virus, or rodent bite. One hantavirus, Andes virus, is unique in that it is known to be transmitted from person-to-person. HFRS and HCPS, although primarily affecting kidneys and lungs, respectively, share a number of clinical features, such as capillary leakage, TNF-, and thrombocytopenia; notably, hemorrhages and alterations in renal function also occur in HCPS and cardiac and pulmonary involvement are not rare in HFRS. Of the four structural proteins, both in humoral and cellular immunity, the nucleocapsid protein appears to be the principal immunogen. Cytotoxic T-lymphocyte responses are seen in both HFRS and HCPS and may be important for both protective immunity and pathogenesis. Diagnosis is mainly based on detection of IgM antibodies although viral RNA (vRNA) may be readily, although not invariably, detected in blood, urine and saliva. For sero/genotyping neutralization tests/RNA sequencing are required. Formalin-inactivated vaccines have been widely used in China and Korea but not outside Asia. Hantaviruses are prime examples of emerging and re-emerging infections and, given the limited number of rodents and insectivores thus far studied, it is likely that many new hantaviruses will be detected in the near future.
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Kirchman, David L. Community structure of microbes in natural environments. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0004.
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Community structure refers to the taxonomic types of microbes and their relative abundance in an environment. This chapter focuses on bacteria with a few words about fungi; protists and viruses are discussed in Chapters 9 and 10. Traditional methods for identifying microbes rely on biochemical testing of phenotype observable in the laboratory. Even for cultivated microbes and larger organisms, the traditional, phenotype approach has been replaced by comparing sequences of specific genes, those for 16S rRNA (archaea and bacteria) or 18S rRNA (microbial eukaryotes). Cultivation-independent approaches based on 16S rRNA gene sequencing have revealed that natural microbial communities have a few abundant types and many rare ones. These organisms differ substantially from those that can be grown in the laboratory using cultivation-dependent approaches. The abundant types of microbes found in soils, freshwater lakes, and oceans all differ. Once thought to be confined to extreme habitats, Archaea are now known to occur everywhere, but are particularly abundant in the deep ocean, where they make up as much as 50% of the total microbial abundance. Dispersal of bacteria and other small microbes is thought to be easy, leading to the Bass Becking hypothesis that “everything is everywhere, but the environment selects.” Among several factors known to affect community structure, salinity and temperature are very important, as is pH especially in soils. In addition to bottom-up factors, both top-down factors, grazing and viral lysis, also shape community structure. According to the Kill the Winner hypothesis, viruses select for fast-growing types, allowing slower growing defensive specialists to survive. Cultivation-independent approaches indicate that fungi are more diverse than previously appreciated, but they are less diverse than bacteria, especially in aquatic habitats. The community structure of fungi is affected by many of the same factors shaping bacterial community structure, but the dispersal of fungi is more limited than that of bacteria. The chapter ends with a discussion about the relationship between community structure and biogeochemical processes. The value of community structure information varies with the process and the degree of metabolic redundancy among the community members for the process.
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Hukić, Mirsada, and Mirza Ponjavić. COVID-19 pandemic in Bosnia and Herzegovina: March – June 2020. Academy of Sciences and Arts of Bosnia and Herzegovina, 2020. http://dx.doi.org/10.5644/pi20.190.00.
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At the end of 2019 the world became aware of the existence of a new virus stemming from the Coronaviridae family and causing a specific disease – COVID-19. In less than three months, the virus and its consequences, developed from being a local public health problem in China to a daunting global problem we all had to face. On March 11, 2020 the World Health Organization (WHO) declared a pandemic of COVID-19. On the international scale, even in Bosnia and Herzegovina (BiH), the response of the professionals and scientists has been rapid, although not always consistently efficient enough. Despite the selfless cooperation of scientists and practitioners worldwide, countries with developed economies, good public health and a strong scientific system have had the advantage in the fight against the disease over developing countries. Despite the fact that by these criteria BiH is not one of the most resilient countries, so far, its response to the pandemic has seemed to be satisfactory. The Academy of Sciences and Arts of Bosnia and Herzegovina (ANUBiH) was one of the first institutions of the science system to respond to the pandemic. On the initiative and under the leadership of academician Mirsada Hukić, on March 22, 2020 the development of the project "Epidemic Location Intelligence System (ELIS)" and its Geoportal began on a voluntary basis, with the task of permanently monitoring the spread of COVID-19. Theoretical and professional parts of the project in the areas of medicine, public health and informatics were completed by April 2, 2020. Thanks to the support to the project by the Chairman of the Presidency of Bosnia and Herzegovina, Mr. Šefik Džaferović, the expert system received additional hardware support and was filled in time with data from across the country. This enabled the system to become operational as early as on April 8, 2020. The results of all these efforts are visible in this publication. Initially, the ELIS project was important for the epidemiological and public health area. The abundance of collected data and obtained virus samples enabled the extension of the project idea to the sequencing of viruses found in BiH and their typology. The transition of research to the clinical aspects of COVID-19 is the next phase in the development of the ELIS project. ANUBiH has already started the work on examining the economic and pedagogical consequences of COVID-19 in order to look at this medical phenomenon in the broadest possible context. All the results of ANUBiH in response to the epidemic challenges of COVID-19 are achieved due to the synergistic action of numerous individuals and institutions in different fields of science and public health in cooperation with government. Therefore, I believe that the ELIS project has shown the way to go in solving the burning problems of our society which we will encounter in the future.