Genomic medicine and neurological disease

“Genomic medicine” refers to the diagnosis, optimized management, and treatment of disease—as well as screening, counseling, and disease gene identification—in the context of information provided by an individual patient’s personal genome. Genomic medicine, to some extent synonymous with “personalized medicine,” has been made possible by recent advances in genome technologies. Genomic medicine represents a new approach to health care and disease management that attempts to optimize the care of a patient based upon information gleaned from his or her personal genome sequence. In this review, we describe recent progress in genomic medicine as it relates to neurological disease. Many neurological disorders either segregate as Mendelian phenotypes or occur sporadically in association with a new mutation in a single gene. Heritability also contributes to other neurological conditions that appear to exhibit more complex genetics. In addition to discussing current knowledge in this field, we offer suggestions for maximizing the utility of genomic information in clinical practice as the field of genomic medicine unfolds.     

The Futility of Futility: Death Causation is the ��Elephant in the Room�� in Discussions about Limitation of Medical Treatment

The term “futility” has been widely used in medical ethics and clinical medicine for more than twenty years now. At first glance it appears to offer a clear-cut categorical characterisation of medical treatments at the end of life, and an apparently objective way of making decisions that are seen to be emotionally painful for those close to the patient, and ethically, and also potentially legally hazardous for clinicians. It also appears to deal with causation, because omission of a futile treatment cannot surely be a cause of death. The problem is that futility can be argued to be a “false friend”, in that it gives an appearance of representing a reliable conceptual basis, in ethics, for limitation of medical treatment—usually in the context of dying—without actually doing so. In fact, the concept of futility is a conflation of clinical judgement about outcomes of treatment and the quality or even value of life, and has really failed to contribute much to the advancement of decision-making and hence care at the end-of-life. It also has the capacity to medicalise the personal space. Deliberations about the likely outcomes of medical treatment are necessary, and medical expertise is pivotal. However, futility is argued to have a better future in partnership with a broad social action agenda about the process of dying, such as that articulated in health promoting palliative care, as a basis for better “death-ways” in the 21st century (Kellehear 2005). Medicine needs to more honest and upfront about its limits, as death is, after all, the elephant in everybody's room.     

An economic perspective on personalized medicine

The concept of personalized medicine not only promises to enhance the life of patients and increase the quality of clinical practice and targeted care pathways, but also to lower overall healthcare costs through early-detection, prevention, accurate risk assessments and efficiencies in care delivery. Current inefficiencies are widely regarded as substantial enough to have a significant impact on the economies of major nations like the US and China, and, therefore the world economy. A recent OECD report estimates healthcare expenditure for some of the developed western and eastern nations to be anywhere from 10% to 18%, and growing (with the US at the highest). Personalized medicine aims to use state-of-the-art genomic technologies, rich medical record data, tissue and blood banks and clinical knowledge that will allow clinicians and payors to tailor treatments to individuals, thereby greatly reducing the costs of ineffective therapies incurred through the current trial and error clinical paradigm. Pivotal to the field are drugs that have been designed to target a specific molecular pathway that has gone wrong and results in a diseased condition and the diagnostic tests that allow clinicians to separate responders from non-responders. However, the truly personalized approach in medicine faces two major problems: complex biology and complex economics; the pathways involved in diseases are quite often not well understood, and most targeted drugs are very expensive. As a result of all current efforts to translate the concepts of personalized healthcare into the clinic, personalized medicine becomes participatory and this implies patient decisions about their own health. Such a new paradigm requires powerful tools to handle significant amounts of personal information with the approach to be known as “P4 medicine”, that is predictive, preventive, personalized and participatory. P4 medicine promises to increase the quality of clinical care and treatments and will ultimately save costs. The greatest challenges are economic, not scientific.     

Chronic Homework in Emerging Borderlands of Healthcare

The task of caring for those with chronic illnesses has gained a new centrality in health care at a global level. We introduce the concept of “chronic homework” to offer a critical reflection on the treatment of chronic illnesses in three quite different national and local contexts: Uganda, Denmark, and the United States. A major challenge for clinicians, patients, and family caregivers is how to navigate the task of moving health care from clinic to home. By “chronic homework,” we refer to the work patients and families are expected to carry out in their home contexts as part of the treatment of chronic conditions. Families and patients spend time receiving training by clinical experts in the various tasks they are to do at home. While this “colonization” of the popular domain could easily be understood from a Foucauldian perspective as yet another emerging mode of governmentality, this a conceptualization can oversimplify the way specific practices of homework are re-imagined and redirected by patients and significant others in their home surroundings. In light of this re-invention of homework in local home contexts, we foreground another conceptual trope, describing chronic homework as a borderland practice.     

Clinical Proteomics: From Biomarker Discovery and Cell Signaling Profiles to Individualized Personal Therapy

The discovery of new highly sensitive and specific biomarkers for early disease detection and risk stratification coupled with the development of personalized “designer” therapies holds the key to future treatment of complex diseases such as cancer. Mounting evidence confirms that the low molecular weight (LMW) range of the circulatory proteome contains a rich source of information that may be able to detect early stage disease and stratify risk. Current mass spectrometry (MS) platforms can generate a rapid and high resolution portrait of the LMW proteome. Emerging novel nanotechnology strategies to amplify and harvest these LMW biomarkers in vivo or ex vivo will greatly enhance our ability to discover and characterize molecules for early disease detection, subclassification and prognostic capability of current proteomics modalities. Ultimately genetic mutations giving rise to disease are played out and manifested on a protein level, involving derangements in protein function and information flow within diseased cells and the interconnected tissue microenvironment. Newly developed highly sensitive, specific and linearly dynamic reverse phase protein microarray systems are now able to generate circuit maps of information flow through phosphoprotein networks of pure populations of microdissected tumor cells obtained from patient biopsies. We postulate that this type of enabling technology will provide the foundation for the development of individualized combinatorial therapies of molecular inhibitors to target tumor-specific deranged pathways regulating key biologic processes including proliferation, differentiation, apoptosis, immunity and metastasis. Hence future therapies will be tailored to the specific deranged molecular circuitry of an individual patient’s disease. The successful transition of these groundbreaking proteomic technologies from research tools to integrated clinical diagnostic platforms will require ongoing continued development, and optimization with rigorous standardization development and quality control procedures.     

Cancer proteomics

Conclusion The future of cancer diagnostics will be based on a panel of proteomic biomarkers. They could be used to detect cancer at an early stage, to predict and to direct therapies. Enzymes and related proteins are important biological molecules, which could serve as cancer biomarkers. These biomarkers could be intact or fragments of proteins. The challenge is to be able to find and validate these potential biomarkers as clinical diagnostics. With the advances in proteomic technologies, we are closer than ever to find these “new” enzyme molecules or fragments. The translation of newly discovered biomarkers could provide an opportunity to revolutionize the era of personalized medicine.     

Direct use values and passive use values: implications for conservation of large carnivores

We made a quantitative analysis of the responses of urban and rural residents in Sweden to arguments supporting and opposing conservation of large carnivores. The most important arguments in favour of conservation were: “I want them [the large carnivores] to exist in Sweden, even if I will never see any of them”, “Sweden should share the responsibility of conserving the large carnivores” and “We owe it [conservation of large carnivores] to future generations”. We found only small differences between rural and urban residents. For arguments opposing conservation, the difference between rural and urban areas was slightly greater. The most important arguments opposing conservation of large carnivores were: “They may have serious negative impact on livestock farming”, “They may have serious negative impact on reindeer husbandry” and “May inflict suffering on injured livestock”. We conclude that there seems to be less support for direct use values such as hunting, ecotourism or just experiencing large carnivores, this may imply that the minimum viable population size can be used as a long-term management goal for large carnivore populations, possibly with an exception for bears. We also conclude that a separate conservation or management plan is needed for each species, since the conflicts with human interests vary greatly between the different carnivore species.     

Personalized Mortality Prediction Driven by Electronic Medical Data and a Patient Similarity Metric

BackgroundClinical outcome prediction normally employs static, one-size-fits-all models that perform well for the average patient but are sub-optimal for individual patients with unique characteristics. In the era of digital healthcare, it is feasible to dynamically personalize decision support by identifying and analyzing similar past patients, in a way that is analogous to personalized product recommendation in e-commerce. Our objectives were: 1) to prove that analyzing only similar patients leads to better outcome prediction performance than analyzing all available patients, and 2) to characterize the trade-off between training data size and the degree of similarity between the training data and the index patient for whom prediction is to be made.ConclusionsThe present study provides crucial empirical evidence for the promising potential of personalized data-driven decision support systems. With the increasing adoption of electronic medical record (EMR) systems, our novel medical data analytics contributes to meaningful use of EMR data.     

Insect octopamine receptors: a new classification scheme based on studies of cloned Drosophila G-protein coupled receptors

Summary Insect octopamine receptors are G-protein coupled receptors. They can be coupled to second messenger pathways to mediate either increases or decreases in intracellular cyclic AMP levels or the generation of intracellular calcium signals. Insect octopamine receptors were originally classified on the basis of second messenger changes induced in a variety of intact tissue preparations. Such a classification system is problematic if more than one receptor subtype is present in the same tissue preparation. Recent progress on the cloning and characterization in heterologous cell systems of octopamine receptors from Drosophila and other insects is reviewed. A new classification system for insect octopamine receptors into “α-adrenergic-like octopamine receptors (OctαRs)”, “β-adrenergic-like octopamine receptors (OctβRs)” and “octopamine/tyramine (or tyraminergic) receptors” is proposed based on their similarities in structure and in signalling properties with vertebrate adrenergic receptors. In future studies on the molecular basis of octopamine signalling in individual tissues it will be essential to identify the relative expression levels of the different classes of octopamine receptor present. In addition, it will be essential to identify if co-expression of such receptors in the same cells results in the formation of oligomeric receptors with specific emergent pharmacological and signalling properties.     

Systems Approaches to Biology and Disease Enable Translational Systems Medicine

The development and application of systems strategies to biology and disease are transforming medical research and clinical practice in an unprecedented rate.In the foreseeable future,clinicians,medical researchers,and ultimately the consumers and patients will be increasingly equipped with a deluge of personal health information,e.g.,whole genome sequences,molecular profiling of diseased tissues,and periodic multi-analyte blood testing of biomarker panels for disease and wellness.The convergence of these practices will enable accurate prediction of disease susceptibility and early diagnosis for actionable preventive schema and personalized treatment regimes tailored to each individual.It will also entail proactive participation from all major stakeholders in the health care system.We are at the dawn of predictive,preventive,personalized,and participatory(P4) medicine,the fully implementation of which requires marrying basic and clinical researches through advanced systems thinking and the employment of high-throughput technologies in genomics,proteomics,nanofluidics,single-cell analysis,and computation strategies in a highly-orchestrated discipline we termed translational systems medicine.     

Facing Death,Gazing Inward: End-of-Life and the Transformation of Clinical Subjectivity in Thailand

In this article, I describe a new form of clinical subjectivity in Thailand, emerging out of public debate over medical care at the end of life. Following the controversial high-tech death of the famous Buddhist monk Buddhadasa, many began to denounce modern death as falling prey to social ills in Thai society, such as consumerism, technology-worship, and the desire to escape the realities of existence. As a result, governmental and non-governmental organizations have begun to focus on the end-of-life as a locus for transforming Thai society. Moving beyond the classic outward focus of the medical gaze, they have begun teaching clinicians and patients to gaze inward instead, to use the suffering inherent in medicine and illness to face the nature of existence and attain inner wisdom. In this article, I describe the emergence of this new gaze and its major conceptual components, including a novel idea of what it means to be ‘human,’ as well as a series of technologies used to craft this humanity: confession, “facing suffering,” and untying “knots” in the heart. I also describe how this new subjectivity has begun to change the long-stable Buddhist concept of death as taking place at a moment in time, giving way for a new concept of “end-of-life,” an elongated interval to be experienced, studied, and used for inner wisdom.     

The PhyloCode is fatally flawed, and the “Linnaean” System can easily be fixed

Promoters of the PhyloCode have mounted an intensive and deceptive publicity campaign. At the centerpiece of this campaign have been slogans such as that the Linnaean System will “goof you up,” that the PhyloCode is the “greatest thing since sliced bread,” and that systematists are “afraid” to propose new names because of “downstream consequences.” Aside from such subscientific spin and sloganeering, proponents of the PhyloCode have offered nothing real to back up claims of greater stability for their new system. They have also misled many into believing that the PhyloCode is the only truly phylogenetic system. The confusion that has been fostered involves several discrete arguments, concerning: a new “method” of “designating” names, rank-free taxonomy, uninomial nomenclature, and issues of priority. Claims that the PhyloCode produces a more stable nomenclature are false, as shown with the example of “paleoherbs.” A rank-free system of naming requires an annotated reference tree for even the simplest exchanges of information. This would be confusing at best and would cripple our ability to teach, learn, and use taxonomic names in the field or in publications. We would be confronted by a mass of polynomial names, tied together only by a tree graphic, with no agreed name (except a uninomial, conveying no hierarchy) to use for any particular species. The separate issue of stability in reference to rules of priority and rank can be easily addressed within the current codes, by implementation of some simple changes, as we will propose in this article. Thus there is no need to “scrap” the current Linnaean codes for a poorly reasoned, logically inconsistent, and fatally flawed new code that will only bring chaos.     

Using sensory weighting to model the influence of canal,otolith and visual cues on spatial orientation and eye movements

 The sensory weighting model is a general model of sensory integration that consists of three processing layers. First, each sensor provides the central nervous system (CNS) with information regarding a specific physical variable. Due to sensor dynamics, this measure is only reliable for the frequency range over which the sensor is accurate. Therefore, we hypothesize that the CNS improves on the reliability of the individual sensor outside this frequency range by using information from other sensors, a process referred to as “frequency completion.” Frequency completion uses internal models of sensory dynamics. This “improved” sensory signal is designated as the “sensory estimate” of the physical variable. Second, before being combined, information with different physical meanings is first transformed into a common representation; sensory estimates are converted to intermediate estimates. This conversion uses internal models of body dynamics and physical relationships. Third, several sensory systems may provide information about the same physical variable (e.g., semicircular canals and vision both measure self-rotation). Therefore, we hypothesize that the “central estimate” of a physical variable is computed as a weighted sum of all available intermediate estimates of this physical variable, a process referred to as “multicue weighted averaging.” The resulting central estimate is fed back to the first two layers. The sensory weighting model is applied to three-dimensional (3D) visual–vestibular interactions and their associated eye movements and perceptual responses. The model inputs are 3D angular and translational stimuli. The sensory inputs are the 3D sensory signals coming from the semicircular canals, otolith organs, and the visual system. The angular and translational components of visual movement are assumed to be available as separate stimuli measured by the visual system using retinal slip and image deformation. In addition, both tonic (“regular”) and phasic (“irregular”) otolithic afferents are implemented. Whereas neither tonic nor phasic otolithic afferents distinguish gravity from linear acceleration, the model uses tonic afferents to estimate gravity and phasic afferents to estimate linear acceleration. The model outputs are the internal estimates of physical motion variables and 3D slow-phase eye movements. The model also includes a smooth pursuit module. The model matches eye responses and perceptual effects measured during various motion paradigms in darkness (e.g., centered and eccentric yaw rotation about an earth-vertical axis, yaw rotation about an earth-horizontal axis) and with visual cues (e.g., stabilized visual stimulation or optokinetic stimulation). Received: 20 September 2000 / Accepted in revised form: 28 September 2001     

From “Lists of Traits” to “Open-Mindedness”: Emerging Issues in Cultural Competence Education

The incorporation of “culture” into U.S. biomedicine has been increasing at a rapid pace over the last several decades. Advocates for “cultural competence” point to changing patient demographics and growing health disparities as they call for improved educational efforts that train health providers to care for patients from a variety of backgrounds. Medical anthropologists have long been critical of the approach to “culture” that emerges in cultural competence efforts, identifying an essentialized, static notion of culture that is conflated with racial and ethnic categories and seen to exist primarily among exotic “Others.” With this approach, culture can become a “list of traits” associated with various racial and ethnic groups that must be mastered by health providers and applied to patients as necessary. This article uses an ethnographic examination of cultural competence training to highlight recent efforts to develop more nuanced approaches to teaching culture. I argue that much of contemporary cultural competence education has rejected the “list of traits” approach and instead aims to produce a new kind of health provider who is “open-minded,” willing to learn about difference, and treats each patient as an individual. This shift, however, can ultimately reinforce behavioral understandings of culture and draw attention away from the social conditions and power differentials that underlie health inequalities.     

Negotiating A Path To Efficacy At A Clinic Of Traditional Chinese Medicine

Chinese medicine emphasizes the underlying connection of the bodily, emotional, social, and environmental dimensions in illness experience and healing. The therapeutic process, characterized as tiao (attuning, balancing), targets the patient’s overall illness condition and experience including both physical and nonphysical aspects of suffering. This study, incorporating techniques of microanalysis as an ethnographic tool and using an actual recorded clinical interaction as data, analyzes how the path to effective healing is negotiated among multiple clinical realities at a clinic of Chinese medicine in Beijing. A close examination of interactive features of actual face-to-face communication between a doctor and a patient in a specific case of “stagnation of emotions” reveals that, for an illness recognized in Chinese medicine as originating from disordered emotions, adjustment of the patient’s perceptions of reality and social relations is particularly salient in the “attuning” process. Efficacy then should be understood as more than physiological changes produced by herbs, but also as emergent through an interactive event of clinical encounters. This study demonstrates empirically how the clinical process of Chinese medicine works to define and transform the patient’s emotions and experience.     

Science through the internet: Researching, evaluating and citing websites

This article attempts to convey the joys and frustrations of skimming the Internet trying to find relevant information concerning an academic’s work as a scientist, a student or an instructor. A brief overview of the Internet and the “do’s and don’ts” for the neophyte as well for the more seasoned “navigator” are given. Some guidelines of “what works and what does not” and “what is out there” are provided for the scientist with specific emphasis for biologists, as well as for all others having an interest in science but with little interest in spending countless hours “surfing the net”. An extensive but not exhaustive list of related websites is provided.     

Traumatic Amputation: A Case of Laotian Indignation and Injustice

Culture is an essential variable of diagnosis and treatment. A cultural perspective draws attention to the social context within which symptoms arise, are given meaning, and are managed. Ethno-cultural work on illness narratives suggests that most people can provide culturally-based explanations for their symptoms. While these explanations are inconsistent with biomedical theory, they relieve patient distress by allowing the patient to create meaning for symptoms. Exploring the characteristics, context, and antecedents of the symptoms enables the patient to convey them to the clinician who may have a divergent explanation of sickness. This case study uses the Outline for Cultural Formulation of the DSM-IV created for clinicians to elicit a narrative account of the illness experience from the patient. Our study examines how the patient, a Laotian used social indignation (“Kwam khem keuang”) as an explanatory model for his ailment. He was diagnosed with post-traumatic stress disorder after having undergone a traumatic amputation. In the process of explaining his illness through a cultural idiom, the patient was able to reveal both personal and collective meaning of repressed anger and frustration, expressing them in a context that was acceptable to him. This cultural idiom allowed the patient to reflect upon the structure of the health care system and the specific context in which symptoms and their possible origins are recounted and explored. It also clarified to the treating clinicians some categories of experience and causal explanations that did not fit easily with western biomedical and psychiatric understanding. The case study illustrates how a cultural approach to illness from the patient’s perspective offers a reflexive stance on the clinician–patient interaction that allows for better patient care.     

Source-sink landscape theory and its ecological significance

Exploring the relationships between landscape pattern and ecological processes is the key topic of landscape ecology, for which, a large number of indices as well as landscape pattern analysis model were developed. However, one problem faced by landscape ecologists is that it is hard to link the landscape indices with a specific ecological process. Linking landscape pattern and ecological processes has become a challenge for landscape ecologists. “Source” and “sink” are common concepts used in air pollution research, by which the movement direction and pattern of different pollutants in air can be clearly identified. In fact, for any ecological process, the research can be considered as a balance between the source and the sink in space. Thus, the concepts of “source” and “sink” could be implemented to the research of landscape pattern and ecological processes. In this paper, a theory of sourcesink landscape was proposed, which include: (1) In the research of landscape pattern and ecological process, all landscape types can be divided into two groups, “source” landscape and “sink” landscape. “Source” landscape contributes positively to the ecological process, while “sink” landscape is unhelpful to the ecological process. (2) Both landscapes are recognized with regard to the specific ecological process. “Source” landscape in a target ecological process may change into a “sink” landscape as in another ecological process. Therefore, the ecological process should be determined before “source” or “sink” landscape were defined. (3) The key point to distinguish “source” landscape from “sink” landscape is to quantify the effect of landscape on ecological process. The positive effect is made by “source” landscape, and the negative effect by “sink” landscape. (4) For the same ecological process, the contribution of “source” landscapes may vary, and it is the same to the “sink” landscapes. It is required to determine the weight of each landscape type on ecological processes. (5) The sourcesink principle can be applied to non-point source pollution control, biologic diversity protection, urban heat island effect mitigation, etc. However, the landscape evaluation models need to be calibrated respectively, because different ecological processes correspond with different source-sink landscapes and evaluation models for the different study areas. This theory is helpful to further study landscape pattern and ecological process, and offers a basis for new landscape index design. __________ Translated from Acta Ecologica Sinica, 2006, 26(5): 1444–1449 [译自: 生态学报]     

Abstract mathematical molecular biology: II some relational consequences of the “one gene-one enzyme” hypothesis

Following the program outlined in a previous paper (Bull. Math. Biophysics,23, 237–260, 1961), a further abstract study is made of some simple relational systems which possess some properties of living organisms. It is shown that the “one gene-one enzyme” hypothesis leads to the conclusion that either all genes are built of the same chemical building blocks, or that at least all genes have a number of building blocks in common. A consistent relational application of the “one gene-one enzyme” hypothesis leads moreover to the conclusion that replication is not an inherent property of a gene. Rather there must be a set of enzymes which “copy” the genes. The number of enzymes in this set must be less than the number of genes and therefore the activity of those “copying” enzymes cannot be absolutely specific.