Edwin Southern developed a blotting technique for DNA in 1973, thereby creating a staple of molecular biology laboratory procedures still used after several decades. It became a seminal technology for studying the structure of DNA. The story of the creation and dissemination of this technology, which was not patented and was freely distributed throughout the scientific community, stands as a case study in open science. The Southern blot was developed at a time when attitudes about commercial intrusion into health research (...) were beginning to change and the practical value of molecular genetics was becoming apparent to industry. Interest from industry in fundamental molecular biological techniques meant that scientists began to think about commercial uses of their work even in otherwise "basic" research. The unpatented Southern blot is contrasted with later patented technologies, particularly microarray methods, which were created in the same environment by many of the same people, but which followed significant changes to UK policies encouraging commercialization of academic research and a norm shift friendlier to such commercialization within academic molecular biology. Professor Southern's personal experience illuminates how the technologies evolved, and his views provide insight into how scientists' attitudes about commercialization have changed. (shrink)

In this article we examine the history of the production of microarray technologies and their role in constructing and operationalizing views of human genetic difference in contemporary genomics. Rather than the “turn to difference” emerging as a post-Human Genome Project phenomenon, interest in individual and group differences was a central, motivating concept in human genetics throughout the twentieth century. This interest was entwined with efforts to develop polymorphic “genetic markers” for studying human traits and diseases. We trace the technological, (...) methodological and conceptual strategies in the late twentieth century that established single nucleotide polymorphisms as key focal points for locating difference in the genome. By embedding SNPs in microarrays, researchers created a technology that they used to catalog and assess human genetic variation. In the process of making genetic markers and array-based technologies to track variation, scientists also made commitments to ways of describing, cataloging and “knowing” human genetic differences that refracted difference through a continental geographic lens. We show how difference came to matter in both senses of the term: difference was made salient to, and inscribed on, genetic matter, as a result of the decisions, assessments and choices of collaborative and hybrid research collectives in medical genomics research. (shrink)

The Affymetrix GeneChip is a popular microarray platform for genome‐wide expression profiling and has been widely used in functional genomics especially in the classification of cancers. Due to the updating of genome data, much of the genome information with which the chips were designed is out‐of‐date and it has been reported that many of the genes/transcripts on the chips differ from their original definition when mapping the probes to the new genome information. Dai et al. have reported that the (...) updated definition can cause as much as 30–50% discrepancy in the genes selected as differentially expressed on a heart tissue expression profiling dataset. Understanding the nature of this difference is therefore very important for the utilization of the data. In this work, with a large cancer dataset as an example, we compared two major definitions and investigated their effects on classification, clustering, discovery of differentially expressed genes and gene‐set‐based analysis. Results show that the two definitions agree well on clustering and classification results but genes and gene sets discovered as differentially expressed or enriched can be very different. Discoveries based on the Affymetrix definition can cover most of those based on the new definition, but tend to have more false positives. BioEssays 28: 739–746, 2006. © 2006 Wiley Periodicals, Inc. (shrink)

The ethically controversial option of genetic population screening used to be restricted to a small number of rather rare diseases by methodological limitations which are now about to be overcome. With the new technology of DNA microarrays ("DNA chip"), emerging from the synthesis of microelectronics and molecular biology, methods are now at hand for the development of mass screening programmes for a wide spectrum of genetic traits. Thus, the DNA chip may be the key technology for a refined (...) preventive medicine as well as a new dimension of eugenics. The forthcoming introduction of the DNA chip technology into medical practice urgently requires an internationally consistent framework of ethical standards and legal limitations if we do not want it to become a new Pandora's box. (shrink)

The generation of patterns and the diversity of cell types in a multicellular organism require differential gene regulation. At the heart of this process are enhancers or cis‐regulatory modules (CRMs), genomic regions that are bound by transcription factors (TFs) that control spatio‐temporal gene expression in developmental networks. To date, only a few CRMs have been studied in detail and the underlying cis‐regulatory code is not well understood. Here, we review recent progress on the genome‐wide identification of CRMs with chromatin immunoprecipitation (...) of TF‐DNA complexes followed by microarrays (ChIP‐on‐chip). We focus on two computational approaches that have succeeded in predicting the expression pattern driven by a CRM either based on TF binding site preferences and their expression levels, or quantitative analysis of CRM occupancy by key TFs. We also discuss the current limits of these methods and highlight some of the key problems that have to be solved to gain a more complete understanding of the structure and function of CRMs. (shrink)

Long noncoding RNAs have been described in cell lines and various whole tissues, but lncRNA analysis of development in vivo is limited. Here, we comprehensively analyze lncRNA expression for the adult mouse subventricular zone neural stem cell lineage. We utilize complementary genome-wide techniques including RNA-seq, RNA CaptureSeq, and ChIP-seq to associate specific lncRNAs with neural cell types, developmental processes, and human disease states. By integrating data from chromatin state maps, custom microarrays, and FACS purification of the subventricular zone lineage, (...) we stringently identify lncRNAs with potential roles in adult neurogenesis. shRNA-mediated knockdown of two such lncRNAs, Six3os and Dlx1as, indicate roles for lncRNAs in the glial-neuronal lineage specification of multipotent adult stem cells. Our data and workflow thus provide a uniquely coherent in vivo lncRNA analysis and form the foundation of a user-friendly online resource for the study of lncRNAs in development and disease. © 2013 Elsevier Inc. (shrink)

DNA arrays have become the preferred method for large-scale expression measurement. Such data are needed in view of the large amounts of sequence data available: expression levels in a number of different tissues or situations provide a first step toward functional characterisation of new entities revealed by DNA sequencing. Although the basic principle of measurement is in all cases based on hybridisation of a mixed probe derived from tissue RNA to large sets of DNA fragments representing many genes, a number (...) of different forms of implementation of this principle are at hand. They are briefly described and compared, emphasizing the important issue of sensitivity and sample requirements and the accessibility of the methods to academic scientists. When these factors are taken into account, it appears that, contrary to a largely prevalent impression, the “best” approach is not necessarily always provided by the widely advertised glass microarrays or oligonucleotide chips. BioEssays 21:781–790, 1999. © 1999 John Wiley & Sons, Inc. (shrink)

Old Havana: Spirit of the Living City artistically captures the architecture, people, and daily life of La Habana Vieja through the lenses of two visionary photographers and colleagues, one American and the other Cuban. Chip Cooper and Néstor Martí began collaborating in 2008, documenting the picturesque features of the oldest and most historically rich quarter in Cuba's capital city at the behest of Eusebio Leal Spengler, the historian of the city of Havana and the director of the Habana Vieja (...) restoration project. Cooper's and Martí's images highlight the spirit of change and renewal underlying the restoration of this international treasure and its revival as a vibrant business and residential area. Inspired by the work of twentieth century American photographer Walker Evans, Cooper and Martí, through perspectives both unique and deeply entwined, capture the humanity of the city, in a language at once universal and transcendent. (shrink)

We live in a reactionary culture where divisive issues arise, people on either side throw stones, and everyone ends up more entrenched in their opinions than in reaching common ground--or even exhibiting common courtesy! If there ever was a time for Christians to understand and communicate God's truth about controversial and polarizing issues, it is now. Believers must develop convictions based on research, reason, and biblical truth--and be able (and willing) to communicate these convictions with a love and respect that (...) reflects God's own heart. In Culture Shock, bestselling author, pastor, and radio personality Chip Ingram shows readers how they can bring light rather than heat to the most controversial and divisive issues of our day. Covering topics such as right and wrong, sex, homosexuality, abortion, politics, and the environment, Culture Shock is every engaged believer's must-have guidebook to replacing reactionary hate with revolutionary love. (shrink)

Examines the growing popularity of alternative medicine, and discusses the mind-body connection in healing.

While human lives are endlessly variable, our most memorable positive moments are dominated by four elements: elevation, insight, pride, and connection. If we embrace these elements, we can conjure more moments that matter. What if a teacher could design a lesson that he knew his students would remember twenty years later? What if a manager knew how to create an experience that would delight customers? What if you had a better sense of how to create memories that matter for your (...) children? This book delves into some fascinating mysteries of experience: Why we tend to remember the best or worst moment of an experience, as well as the last moment, and forget the rest. Why 'we feel most comfortable when things are certain, but we feel most alive when they're not.' And why our most cherished memories are clustered into a brief period during our youth. Readers discover how brief experiences can change lives, such as the experiment in which two strangers meet in a room, and 45 minutes later, they leave as best friends. (What happens in that time?) Or the tale of the world's youngest female billionaire, who credits her resilience to something her father asked the family at the dinner table. (What was that simple question?) Many of the defining moments in our lives are the result of accident or luck -- but why would we leave our most meaningful, memorable moments to chance when we can create them? The Power of Moments shows us how to be the author of richer experiences."--Dust jacket flap. (shrink)

Using research into learning from sequences of examples, we generate predictions about what cultural products become widely distributed in the social marketplace of ideas. We investigate what we term the Repetition‐Break plot structure: the use of repetition among obviously similar items to establish a pattern, and then a final contrasting item that breaks with the pattern to generate surprise. Two corpus studies show that this structure arises in about a third of folktales and story jokes. An experiment shows that jokes (...) with this structure are more interesting than those without the initial repetition. Thus, we document evidence for how a cognitive factor influences the cultural products that are selected in the marketplace of ideas. (shrink)

It is no secret that Hegel, along with Vico, whom he never read, and Rousseau, whom he read with enthusiasm, regarded poetic meaning as historically prior to prosaic meaning - the figurative preceded the literal, the tropological antedated the logical per se. Indeed, Hegel went so far, in his Aesthetic, as to qualify poetry as “Man’s original grasp of truth”. Since, as we know, for Hegel the true is the whole, it would seem that this original grasp of the truth (...) would have to be accounted for in any speculative account of truth. (shrink)

We investigate 1 factor that influences the success of ideas or cultural representations by proposing that they have a habitat, that is, a set of environmental cues that encourages people to recall and transmit them. We test 2 hypotheses: (a) fluctuation: the success of an idea will vary over time with fluctuations in its habitat, and (b) competition: ideas with more prevalent habitats will be more successful. Four studies use subject ratings and data from newspapers to provide correlational support for (...) our 2 hypotheses, with a negative factoid, positive rumor, catchphrases, and variants of a proverb. Three additional experimental studies manipulate the topic of actual conversations and find empirical support for our theory, with catchphrases, proverbs, and slang. The discussion examines how habitat prevalence applies to a more extensive class of ideas and suggests how habitats may influence the process by which ideas evolve. (shrink)

Hegel has often been held by his critics to have failed in his efforts to achieve his professed goal to make of philosophy a science. Some of the major objections have been that he overlooked problems of finite, embodied existence, that he ignored the constitutive power of language, and that he did not make allowance for a creative unconscious. Wilfried Ver Eecke has written an oddly-titled work which traces the role of negation in the realms of child development, psychoanalysis, linguistics, (...) and Hegelian thought. In the course of his complex, nuanced study, he provides ample material for defending Hegel from these charges, even where he himself seems ambivalent about their validity. (shrink)

Desmond’s ambitious effort to re-conceive the problem of dialectic and otherness is both timely and provocative. Moving beyond the “generous hermeneutic” of Hegel exemplified in Art and the Absolute, Desmond develops more fully a discussion about the alleged “closure” of dialectical philosophies generally and Hegel’s philosophy specifically. Whereas Art and the Absolute tended to defend Hegel’s insights and achievements — at least in aesthetic theory — against a wide variety of critical approaches, the work under review attempts to engage seriously (...) the persistent charge of “closure” made against Hegelian speculative philosophy. Repeated by critics as various as Habermas, Heidegger, Lonergan, and Derrida, the charge is too widespread and too frequently levelled to ignore. At issue seems to be the very possibility of an “absolute” knowing. How is it possible to know absolutely without trimming up the edges of the knowable, dotting all i’s and crossing all t’s, and leaving nothing for future philosophers but the relationships of disciple, exegete, or rebel angel? It is of course arguable that the self-developing categorial criticism in terms of which Hegel develops his doctrine of absolute knowing renders such objections irrelevant, but Desmond does not opt for this strategy. Rather, in the development of his own original metaphysics of origin, Desmond attempts to “sublate” the Hegelian philosophy. (shrink)

In the decade since the late George Armstrong Kelly announced in the pages of this journal that Richard Winfield’s project has something significant to contribute to the debate over the contemporary relevance of Hegel’s systematic philosophy, Winfield has produced a number of works in support of that claim. These works have established Winfield as an important neo-Hegelian thinker.

French interpretations of Hegel have been immensely influential in the past fifty years. One has only to think of the names Alexandre Kojève and Jean Hyppolite to begin to recognize the enormous debt which all students of Hegel owe to French scholarship in this period. Beyond the problems posed by the specific interpretations of Hegel advanced by Kojève and Hyppolite, however, there is also the task of beginning to assess the great influence upon subsequent French thought brought about by their (...) students, among whom are grouped a veritable pantheon of modern French thinkers. Maurice Merleau-Ponty, Alexandre Koyré, Raymond Aron, Maurice Blanchot, Jacques Lacan, and Georges Bataille, among others, all attended Kojèves’s lectures, while Michel Foucault and Jacques Derrida attended seminars with Hyppolite. (shrink)

Although DNA microarrays are now widely used in research settings, they have been slow to penetrate clinical practice in spite of their apparent advantages. This is due to the very different requirements for a clinical test in contrast to a research tool, and to a strict necessity for demonstrated clinical utility. There is a clear differentiation between two types of DNA array tests: “genomic” diagnostics, developed to ascertain the presence or absence of mutations, deletions or duplications, and for which clinical (...) evidence is already established, and tests using expression profiling for prognosis or predictive purposes, in which case the clinical correlate must be proven. Most array diagnostics currently used belong, understandably, to the “genomic” variety. It is to be expected that future improvements in tailored technology, as well as a logical trend towards measuring an ever‐increasing number of parameters, will ensure an important diagnostic role for DNA arrays in the coming decade. BioEssays 29:699–705, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

We argue that the most‐promising area of clinical application of microarrays in the foreseeable future is the diagnostics and monitoring of infectious diseases. Microarrays for the detection and characterization of human pathogens have already found their way into clinical practice in some countries. After discussing the persistent, yet often underestimated, importance of infectious diseases for public health, we consider the technologies that are best suited for the detection and clinical investigation of pathogens. Clinical application of microarray technologies for the (...) detection of mycobacteria, Bacillus anthracis, HIV, hepatitis and influenza viruses, and other major pathogens, as well as the analysis of their drug‐resistance patterns, illustrate our main thesis. BioEssays 30:673–682, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

Detection of genetic aberrations in prenatal samples, obtained through amniocentesis or chorion villus biopsy, is increasingly performed using chromosomal microarray (CMA), a technique that can uncover both aneuploidies and copy number variants throughout the genome. Despite the obvious benefits of CMA, the decision on implementing the technology is complicated by ethical issues concerning variant interpretation and reporting. In Belgium, uniform guidelines were composed and a shared database for prenatal CMA findings was established. This Belgian approach sparks discussion: it is (...) evidence-based, prevents inconsistencies and avoids parental anxiety, but can be considered paternalistic. Here, we reflect on the cultural and moral bases of the Belgian reporting system of prenatally detected variants. (shrink)

DNA microarrays are perfectly suited for comparing gene expression in different populations of cells. An important application of microarray techniques is identifying genes which are activated by a particular drug of interest. This process will allow biologists to identify therapies targeted to particular diseases, and, eventually, to gain more knowledge about the biological processes in organisms. Such an application is described in this paper. It is focused on diabetes and obesity, which is a genetically heterogeneous disease, meaning that multiple (...) defective genes are responsible for the diseases. The paper is divided in three parts, each dealing with a different problem addressed to our study. First we validate the data from our microarray experiment. We identified significant systematic sources of variability which are potentially issues for other microarray datasets. Second, we applied multiple hypothesis testing to identify differentially expressed genes. We found a set of genes which appear to change in expression level over time in response to a drug treatment. Third, we tried to address the problem of identification of co-expressed genes using cluster analysis. This last problem is still under discussion. (shrink)

Advancements in women's reproductive health have been hindered by insufficient knowledge and the underrepresentation of women in research, leading to symptom‐focused care with poor outcomes. Modeling female reproductive biology and disease pathophysiology has been challenging due to the complexity and dynamic nature of the female organs. Here, we briefly review recent advancements made with a new in vitro microfluidic organ‐on‐a‐chip model of the human cervix (Cervix Chip) that faithfully mimics key features of the cervix, including mucus production and (...) physiological responses to hormonal, environmental, and microbial stimuli. We also discuss how this preclinical platform can provide a way to obtain unique insights into the role of mucosal immunity, genetic and risk factors, as well as microbiome and pathogen interactions in human cervix health and disease, while bridging knowledge gaps in fertility and pregnancy‐related conditions. By enabling preclinical drug screening and accelerating translational research, the Cervix Chip holds the potential to improve the development of therapeutics, diagnostics, and ultimately, the sexual and reproductive health of millions of women globally. (shrink)

In his highly regarded history of the rise of clinical trials in America, HarryMarks describes how their widespread adoption resulted largely fromthe efforts of ‘therapeutic reformers’ who sought to replace the individualexpertise of clinicians with the ‘science of controlled experiment’. Thetransition described by Marks resembles in many respects the transition fromthe ‘truth-to-nature’ objectivity of individual experts to a ‘mechanical’ formof objectivity portrayed by Daston and Galison. In particular,Marks details the passage from a regime of trust in expertise and experts to (...) aregime based on the mechanical generation of data, the elimination ofhuman judgement and the adoption of a ‘view from nowhere’ where individual and group idiosyncrasies are systematically suppressedthrough recourse to quantitative methods.[...]. (shrink)

The increasing flow of immigrants in many European countries and the growing presence of children from immigrant families in schools makes it relevant to study the development of prejudice in children. Parents play an important role in shaping children’s values and their attitudes toward members of other ethnic groups; an intergenerational transmission of prejudice has been found in a number of studies targeting adolescents. The present study aims to investigate the intergenerational transmission of ethnic prejudice in 3- to 9- year-old (...) children and its relations to parenting styles. Parents’ blatant and subtle ethnic prejudice and parenting style are measured together with children’s explicit and implicit ethnic prejudice in pupils and parents of preschool and primary schools in the region of Rome, Italy ( N = 318). Results show that parents’ subtle prejudice predicts children’s implicit prejudice regardless of the parenting style. Findings indicate that children might acquire prejudice by means of the parents’ implicit cognition and automatic behavior and educational actions. Implications for future studies and insights for possible applied interventions are discussed. (shrink)

Views on aging, such as self-perceptions of aging or age stereotypes are generated in early childhood and continue to develop throughout the entire lifespan. The ideas a person has about their own aging and aging in general influence their behavior toward older persons as well as their own actual aging, which is why VoA are already important in adolescence and young adulthood. The current study investigates VoA of young adults in different domains and how different family aspects are related to (...) VoA. From February to March 2021, N = 305 young adults [aged 18–30 years, Mage = 22.20 ] participated in an online survey, in which, in addition to sociodemographic variables and family aspects, self-perceptions of aging, age stereotypes, and the young adults’ ratings of their parents’ VoA were assessed. The results of stepwise regression analyses predicting the young adults’ VoA, revealed significant associations between the quality of contact with grandparents and the self-perceptions of aging of young adults. However, the frequency of contact was neither related to young adults’ self-perceptions of aging nor age stereotypes. Grandparents’ health status emerged as a significant moderator between the relationship of contact quality and the young adults’ self-perceptions of aging as continued growth and physical decline. Family climate was also found to be significantly related to young adults’ self-perceptions of aging. Similarities regarding VoA within the family were demonstrated, based on proxy report from the respondents. The results underline the importance of family aspects for the development of VoA in young adulthood, and the significance of interventions targeting these factors to combat ageism. (shrink)

A brief review and classification of technology in general begins the paper, followed by an application of the classification to two specific marathon case studies: the 2018 Boston marathon and the 2017 Nike Breaking2 Project marathon. Then concepts from an array of sport philosophers are discussed to suggest an explanation for why each of the case studies strikes us as problematic. The conclusion provides a reasonable explanation for our misgivings, as well as an indication of how we might evaluate sporting (...) endeavors in the face of increasing technological innovation. (shrink)