The focus of this study was to analyze the content, distribution, and comparative genome relationships of 996 chromosome bin-mapped expressed sequence tags accounting for 2266 restriction fragments on the homoeologous group 3 chromosomes of hexaploid wheat. Of these loci, 634, 884, and 748 were mapped on chromosomes 3A, 3B, and 3D, respectively. The individual chromosome bin maps revealed bins with a high density of mapped ESTs in the distal region and bins of low density in the proximal region of the (...) chromosome arms, with the exception of 3DS and 3DL. These distributions were more localized on the higher-resolution group 3 consensus map with intermediate regions of high-mapped-EST density on both chromosome arms. Gene ontology classification of mapped ESTs was not significantly different for homoeologous group 3 chromosomes compared to the other groups. A combined analysis of the individual bin maps using 537 of the mapped ESTs revealed rearrangements between the group 3 chromosomes. Approximately 232 of the consensus mapped ESTs matched sequences on rice chromosome 1 and revealed large- and small-scale differences in gene order. Of the group 3 mapped EST unigenes ∼21 and 32% matched the Arabidopsis coding regions and proteins, respectively, but no chromosome-level gene order conservation was detected. (shrink)

This paper forms an introduction to this issue, the contents of which arose directly or indirectly from a conference in May 2001 on Corruption of scientific integrity? — The commercialisation of academic science. The introduction, in recent decades, of business culture and values into universities and research institutions is incompatible with the openness which scientific and all academic pursuit traditionally require. It has given rise to a web of problems over intellectual property and conflict of interest which has even led (...) to corporate sponsors’ suppressing unfavourable results of clinical trials, to the detriment of patients’ health. Although there are those who see the norms of science developing to recognise the importance of instrumental science aiming at specific goals and of knowledge judged by its value in a context of application, none justifies the covert manipulation of results by vested interest. Public awareness of these problems is growing and creating a climate of opinion where they may be addressed. We suggest a way forward by the introduction of nationally and internationally-accepted guidelines for industrial collaboration which contain proper protections of the core purposes of universities and of the independence of their research. Some codes suggested for this purpose are discussed. We note that some universities are moving to adopt such codes of conduct, but argue the need for strong support from the government through its funding bodies. (shrink)

Evidence-based medicine has beendefined as the conscientious and judicious useof current best evidence in making clinicaldecisions. This paper will attempt to explicatethe terms ``conscientious'''' and ``judicious''''within the evidence-based medicine definition.It will be argued that ``conscientious'''' and``judicious'''' represent virtue terms derived fromvirtue ethics and virtue epistemology. Theidentification of explicit virtue components inthe definition and therefore conception ofevidence-based medicine presents an importantstarting point in the connection between virtuetheories and medicine itself. In addition, aunification of virtue theories andevidence-based medicine will illustrate theneed for (...) future research in order to combinethe fields of virtue-based approaches andclinical practice. (shrink)

This essay explores the role of informal logicand its application in the context of currentdebates regarding evidence-based medicine. This aim is achieved through a discussion ofthe goals and objectives of evidence-basedmedicine and a review of the criticisms raisedagainst evidence-based medicine. Thecontributions to informal logic by StephenToulmin and Douglas Walton are explicated andtheir relevance for evidence-based medicine isdiscussed in relation to a common clinicalscenario: hypertension management. This essayconcludes with a discussion on the relationshipbetween clinical reasoning, rationality, andevidence. It is argued that (...) informal logic hasthe virtue of bringing explicitness to the roleof evidence in clinical reasoning, and bringssensitivity to understanding the role ofdialogical context in the need for evidence inclinical decision making. (shrink)

This report describes the rationale, approaches, organization, and resource development leading to a large-scale deletion bin map of the hexaploid wheat genome. Accompanying reports in this issue detail results from chromosome bin-mapping of expressed sequence tags representing genes onto the seven homoeologous chromosome groups and a global analysis of the entire mapped wheat EST data set. Among the resources developed were the first extensive public wheat EST collection. Described are protocols for sequencing, sequence processing, EST nomenclature, and the assembly of (...) ESTs into contigs. These contigs plus singletons were used for selection of distinct sequence motif unigenes. Selected ESTs were rearrayed, validated by 5′ and 3′ sequencing, and amplified for probing a series of wheat aneuploid and deletion stocks. Images and data for all Southern hybridizations were deposited in databases and were used by the coordinators for each of the seven homoeologous chromosome groups to validate the mapping results. Results from this project have established the foundation for future developments in wheat genomics. (shrink)

Background Tuberculosis is a major cause of morbidity and mortality globally. Recent scholarly attention to public health ethics provides an opportunity to analyze several ethical issues raised by the global tuberculosis pandemic. Discussion Recently articulated frameworks for public health ethics emphasize the importance of effectiveness in the justification of public health action. This paper critically reviews the relationship between these frameworks and the published evidence of effectiveness of tuberculosis interventions, with a specific focus on the controversies engendered by the endorsement (...) of programs of service delivery that emphasize direct observation of therapy. The role of global economic inequities in perpetuating the tuberculosis pandemic is also discussed. Summary Tuberculosis is a complex but well understood disease that raises important ethical challenges for emerging frameworks in public health ethics. The exact role of effectiveness as a criterion for judging the ethics of interventions needs greater discussion and analysis. Emerging frameworks are silent about the economic conditions contributing to the global burden of illness associated with tuberculosis and this requires remediation. (shrink)

Potential ethical issues can arise during the process of epidemiological classification. For example, unnatural infant deaths are classified as accidental deaths or homicides. Societal sensitivity to the physical abuse and neglect of children has increased over recent decades. This enhanced sensitivity could impact reported infant homicide rates. Infant homicide and accident mortality rates in boys and girls in the USA from 1940 to 2005 were analysed. In 1940, infant accident mortality rates were over 20 times greater than infant homicide rates (...) in both boys and girls. After about 1980, when the ratio of infant accident mortality rates to infant homicide rates decreased to less than five, and the sum of infant accident and homicide rates became relatively constant, further decreases in infant accident mortality rates were associated with increases in reported infant homicide rates. These findings suggest that the dramatic decline of accidental infant mortality and recent increased societal sensitivity to child abuse may be related to the increased infant homicide rates observed in the USA since 1980 rather than an actual increase in societal violence directed against infants. Ethical consequences of epidemiological classification, involving the principles of beneficence, non-maleficence and justice, are suggested by observed patterns in infant accidental deaths and homicides in the USA from 1940 to 2005. (shrink)

This paper explores the relationship between concepts of probability and hermeneutics. It seeks to examine the relationship between subjective (Bayesian) views of probability and hermeneutic descriptions of understanding. It is argued that Gadamer'saccount of the prejudicial nature of understanding, derived from Heidegger'sanalysis of foreunderstanding, offers a provocative model of clinical reasoning. The implications of this model for evidence-based medicine are discussed in conclusion.

As health care embraces the tenets of evidence-based medicine it is important to ask questions about how evidence is produced and interpreted. This essay explores normative dimensions of evidence production, particularly around issues of setting the tolerable level of uncertainty of results. Four specific aspects are explored: what health care providers know about statistics, why alpha levels have been set at 0.05, the role of randomization in the generation of sufficient grounds of belief, and the role of observational studies. The (...) essay concludes with recommendations to acknowledge the value permeation of outcome measures and suggests that attention to reasoning and argument analysis can augment traditional evidence-based approaches in providing a robust critical approach to medical knowledge. (shrink)

Synaesthesia is a condition in which one type of stimulation evokes the sensation of another, as when the hearing of a sound produces photisms, i.e. mental percepts of colours. R is a 20 year old colour blind subject who, in addition to the relatively common grapheme-colour synaesthesia, presents a rarely reported cross modal perception in which a variety of visual stimuli elicit aura-like percepts of colour. In R, photisms seem to be closely related to the affective valence of stimuli and (...) typically bring out a consistent pattern of emotional responses. The present case study suggests that colours might be an intrinsic category of the human brain. We developed an empirical methodology that allowed us to study the subject's otherwise inaccessible phenomenological experience. First, we found that R shows a Stroop effect elicited by photisms despite the fact that he does not show a regular Stroop with real colours. Secondly, by manipulating the colour context we confirmed that colours can alter R's emotional evaluation of the stimuli. Furthermore, we demonstrated that R's auras may actually lead to a partially inverted emotional spectrum where certain stimuli bring out emotional reactions opposite to the normal ones. These findings can only be accounted for by considering R's subjective colour experience or qualia. Therefore the present paper defends the view that qualia are a useful scientific concept that can be approached and studied by experimental methods. (shrink)

RATIONALE, AIMS AND OBJECTIVES: This paper deals with the problem of surgical waiting lists and is aimed, in particular, at comparing two different prioritization approaches: (1) the clinical assessment of treatment urgency aimed at categorizing patients into urgency-related groups (URGs) with a given recommended maximum waiting time for treatment; and (2) the implementation of an original prioritization scoring algorithm aimed at determining the relative priority of each patient in the waiting list and the corresponding order of admission. METHODS: A modelling (...) exercise based on a cohort of 236 patients enrolled on the waiting list of a surgical department in an Italian public university hospital, from 1 January to 30 June 2004, is presented. The comparison is based on a measure called need-adjusted-waiting-days, which allows to take into proper account both urgency and priority. RESULTS: The results show that both methods should be implemented simultaneously for increasing the department's performance in terms of both efficiency--outcome gained from a given amount of resources--and equity--how patients are admitted according to their need. CONCLUSIONS: Waiting list prioritization should not be limited to classifying patients into URGs, but to using a scoring system as well, in order to schedule patient admissions in an explicit and transparent way. (shrink)

This paper presents a theoretical elaboration of the ethical framework of classical capitalism as formulated by Adam Smith in reaction to the dominant mercantilism of his day. It is seen that Smith's project was profoundly ethical and designed to emancipate the consumer from a producer and state dominated economy. Over time, however, the various dysfunctions of a capitalist economy — e.g., concentration of wealth, market power — became manifest and the utilitarian ethical basis of the system eroded. Contemporary capitalism, dominated (...) as it is by large corporations, entrenched political interests and persistent social pathologies, bears little resemblance to the system which Smith envisioned would serve the common man. Most critiques of capitalism are launched from a Marxian-based perspective. We find, however, that by illustrating the wide gap between the reality of contemporary capitalism and the model of amoral political economy developed by Smith, the father of capitalism proves to be the most trenchant critic of the current order. (shrink)

Synaesthesia is a condition in which one type of stimulation evokes the sensation of another, as when the hearing of a sound produces photisms, i.e. mental percepts of colours. R is a 20 year old colour blind subject who, in addition to the relatively common grapheme-colour synaesthesia, presents a rarely reported cross modal perception in which a variety of visual stimuli elicit aura-like percepts of colour. In R, photisms seem to be closely related to the affective valence of stimuli and (...) typically bring out a consistent pattern of emotional responses. The present case study suggests that colours might be an intrinsic category of the human brain. We developed an empirical methodology that allowed us to study the subject's otherwise inaccessible phenomenological experience. First, we found that R shows a Stroop effect (delayed response due to interference) elicited by photisms despite the fact that he does not show a regular Stroop with real colours. Secondly, by manipulating the colour context we confirmed that colours can alter R's emotional evaluation of the stimuli. Furthermore, we demonstrated that R's auras may actually lead to a partially inverted emotional spectrum where certain stimuli bring out emotional reactions opposite to the normal ones. These findings can only be accounted for by considering R's subjective colour experience or qualia. Therefore the present paper defends the view that qualia are a useful scientific concept that can be approached and studied by experimental methods. (shrink)

The objectives of this study were to develop a high-density chromosome bin map of homoeologous group 7 in hexaploid wheat, to identify gene distribution in these chromosomes, and to perform comparative studies of wheat with rice and barley. We mapped 2148 loci from 919 EST clones onto group 7 chromosomes of wheat. In the majority of cases the numbers of loci were significantly lower in the centromeric regions and tended to increase in the distal regions. The level of duplicated loci (...) in this group was 24% with most of these loci being localized toward the distal regions. One hundred nineteen EST probes that hybridized to three fragments and mapped to the three group 7 chromosomes were designated landmark probes and were used to construct a consensus homoeologous group 7 map. An additional 49 probes that mapped to 7AS, 7DS, and the ancestral translocated segment involving 7BS also were designated landmarks. Landmark probe orders and comparative maps of wheat, rice, and barley were produced on the basis of corresponding rice BAC/PAC and genetic markers that mapped on chromosomes 6 and 8 of rice. Identification of landmark ESTs and development of consensus maps may provide a framework of conserved coding regions predating the evolution of wheat genomes. (shrink)

The complex hexaploid wheat genome offers many challenges for genomics research. Expressed sequence tags facilitate the analysis of gene-coding regions and provide a rich source of molecular markers for mapping and comparison with model organisms. The objectives of this study were to construct a high-density EST chromosome bin map of wheat homoeologous group 2 chromosomes to determine the distribution of ESTs, construct a consensus map of group 2 ESTs, investigate synteny, examine patterns of duplication, and assess the colinearity with rice (...) of ESTs assigned to the group 2 consensus bin map. A total of 2600 loci generated from 1110 ESTs were mapped to group 2 chromosomes by Southern hybridization onto wheat aneuploid chromosome and deletion stocks. A consensus map was constructed of 552 ESTs mapping to more than one group 2 chromosome. Regions of high gene density in distal bins and low gene density in proximal bins were found. Two interstitial gene-rich islands flanked by relatively gene-poor regions on both the short and long arms and having good synteny with rice were discovered. The map locations of two ESTs indicated the possible presence of a small pericentric inversion on chromosome 2B. Wheat chromosome group 2 was shown to share syntenous blocks with rice chromosomes 4 and 7. (shrink)