Review by a local medical research ethics committee of the conduct of approved research projects,by examination of patients' case notes,consent forms,and research records and by interview.

OBJECTIVE: To monitor the conduct of medical research projects that have already been approved by the local medical research ethics committee. DESIGN: Follow up study of ethically approved studies (randomly selected from all the studies approved in the previous year) by examination of patients'' case notes, consent forms, and research records and by interview of the researchers at their workplace. SETTING: Tayside, Scotland (mixed rural and urban population). SUBJECTS: 30 research projects approved by Tayside local medical research ethics committee. MAIN OUTCOME MEASURES: Adherence to the agreed protocol, particularly for recruitment (obtaining and recording informed consent) and for specific requirements of the ethics committee, including notification of changes to the protocol and of adverse events. RESULTS: In one project only oral consent had been obtained, and in a quarter of the studies one or more consent forms were incorrectly completed. Inadequate filing of case notes in five studies and of consent forms in six made them unavailable for scrutiny. Adverse events were reported, but there was a general failure to report the abandoning or non-starting of projects in two studies the investigators failed to notify a change in the responsible researcher. CONCLUSIONS: Monitoring of medical research by local medical research ethics committees promotes and preserves ethical standards, protects subjects and researchers, discourages fraud, and has the support of investigators. We recommend that 10% of projects should undergo on-site review, with all others monitored by questionnaire. This would require about six person hours of time and a salary bill of 120 pounds per study monitored.     

An economic theory of patient decision-making

Patient autonomy, as exercised in the informed consent process, is a central concern in bioethics. The typical bioethicist's analysis of autonomy centers on decisional capacity--finding the line between autonomy and its absence. This approach leaves unexplored the structure of reasoning behind patient treatment decisions. To counter that approach, we present a microeconomic theory of patient decision-making regarding the acceptable level of medical treatment from the patient's perspective. We show that a rational patient's desired treatment level typically departs from the level yielding an absence of symptoms, the level we call ideal. This microeconomic theory demonstrates why patients have good reason not to pursue treatment to the point of absence of physical symptoms. We defend our view against possible objections that it is unrealistic and that it fails to adequately consider harm a patient may suffer by curtailing treatment. Our analysis is fruitful in various ways. It shows why decisions often considered unreasonable might be fully reasonable. It offers a theoretical account of how physician misinformation may adversely affect a patient's decision. It shows how billing costs influence patient decision-making. It indicates that health care professionals' beliefs about the 'unreasonable' attitudes of patients might often be wrong. It provides a better understanding of patient rationality that should help to ensure fuller information as well as increased respect for patient decision-making.     

Loglinear models for the robust design in mark-recapture experiments

The robust design is a method for implementing a mark-recapture experiment featuring a nested sampling structure. The first level consists of primary sampling sessions; the population experiences mortality and immigration between primary sessions so that open population models apply at this level. The second level of sampling has a short mark-recapture study within each primary session. Closed population models are used at this stage to estimate the animal abundance at each primary session. This article suggests a loglinear technique to fit the robust design. Loglinear models for the analysis of mark-recapture data from closed and open populations are first reviewed. These two types of models are then combined to analyze the data from a robust design. The proposed loglinear approach to the robust design allows incorporating parameters for a heterogeneity in the capture probabilities of the units within each primary session. Temporary emigration out of the study area can also be accounted for in the loglinear framework. The analysis is relatively simple; it relies on a large Poisson regression with the vector of frequencies of the capture histories as dependent variable. An example concerned with the estimation of abundance and survival of the red-back vole in an area of southeastern Québec is presented.     

A practical guide to DNA metabarcoding for entomological ecologists

1. DNA metabarcoding is a cost-effective species identification approach with great potential to assist entomological ecologists. This review presents a practical guide to help entomological ecologists design their own DNA metabarcoding studies and ensure that sound ecological conclusions can be obtained. 2. The review considers approaches to field sampling, laboratory work, and bioinformatic analyses, with the aim of providing the background knowledge needed to make decisions at each step of a DNA metabarcoding workflow. 3. Although most conventional sampling methods can be adapted to DNA metabarcoding, this review highlights techniques that will ensure suitable DNA preservation during field sampling and laboratory storage. The review also calls for a greater understanding of the occurrence, transportation, and deposition of environmental DNA when applying DNA metabarcoding approaches for different ecosystems. 4. Accurate species detection with DNA metabarcoding needs to consider biases introduced during DNA extraction and PCR amplification, cross-contamination resulting from inappropriate amplicon library preparation, and downstream bioinformatic analyses. Quantifying species abundance with DNA metabarcoding is in its infancy, yet recent studies demonstrate promise for estimating relative species abundance from DNA sequencing reads. 5. Given that bioinformatics is one of the biggest hurdles for researchers new to DNA metabarcoding, several useful graphical user interface programs are recommended for sequence data processing, and the application of emerging sequencing technologies is discussed.     

Ethical obligation and legal requirements: On informed consent practices in Bangladesh

Informed consent to medical intervention is fundamental in both ethics and law. But in practice it is often not taken seriously in developing countries. This paper provides an appraisal of informed consent practices in Bangladesh. Following a review of the ethical and legal principles of informed consent, it assesses the degree to which doctors adhere to it in Bangladesh. Based on findings of non-compliance, it then investigates the reasons for such non-compliance through an appraisal of informed consent practices in Bangladesh and provides recommendations aimed at improving such practices. The significance of this paper lies in unveiling the interdependence between the ethical and legal traits of informed consent and their ramifications on strengthening the patient-oriented approach of duty to care.     

Evaluating the Consent Preferences of UK Research Volunteers for Genetic and Clinical Studies

Objectives

To establish the views of research volunteers on the consent process; to explore their views on the consent process in different research scenarios; to inform debate on emerging models of consent for participation in research.

Design, Setting and Participants

2,308 adult volunteers from the TwinsUK Registry (www.twinsuk.ac.uk) completed an online survey about their views on the consent process for use of their DNA and medical information in research. Their views on the re-consenting process in different scenarios were assessed.

Results

The majority of volunteers preferred to be informed of the identity of the main researcher of a study in which they are participating, which is contrary to current practice. Over 80% were willing to complete the consent process online instead of face to face. On the whole, respondents did not view their DNA differently from their medical information with regard to the consent process. Research participants were more willing to give broad consent to cover future research if their DNA was to be used by the original researcher than by another researcher, even if the disease under investigation varied, in contrast to the traditional ‘gold standard’ whereby specific consent is required for all new research projects.

Discussion

In some scenarios, research participants reported that they would be comfortable with not signing a new consent form for future research uses of their data and DNA, and are comfortable with secure, online consent processes rather than traditional face-to-face consent processes. Our findings indicate that the perceived relationship between research participants and researchers plays an important role in shaping preferences regarding the consent process and suggest that this relationship is not captured by traditional consent processes. We argue that the development of new formats of consent should be informed by empirical research on volunteers’ perceptions and preferences regarding the consent process.     

DNA supercoiling suppresses real-time PCR: a new approach to the quantification of mitochondrial DNA damage and repair

As a gold standard for quantification of starting amounts of nucleic acids, real-time PCR is increasingly used in quantitative analysis of mtDNA copy number in medical research. Using supercoiled plasmid DNA and mtDNA modified both in vitro and in cancer cells, we demonstrated that conformational changes in supercoiled DNA have profound influence on real-time PCR quantification. We showed that real-time PCR signal is a positive function of the relaxed forms (open circular and/or linear) rather than the supercoiled form of DNA, and that the conformation transitions mediated by DNA strand breaks are the main basis for sensitive detection of the relaxed DNA. This new finding was then used for sensitive detection of structure-mediated mtDNA damage and repair in stressed cancer cells, and for accurate quantification of total mtDNA copy number when all supercoiled DNA is converted into the relaxed forms using a prior heat-denaturation step. The new approach revealed a dynamic mtDNA response to oxidative stress in prostate cancer cells, which involves not only early structural damage and repair but also sustained copy number reduction induced by hydrogen peroxide. Finally, the supercoiling effect should raise caution in any DNA quantification using real-time PCR.     

Informed consent and public health

During the past 25 years, medical ethics has concentrated largely on clinical medicine and the treatment of individual patients. This focus permits a view of medical provision as a (quasi-) consumer good, whose distribution can be or should be contingent on individual choice. The approach cannot be extended to public health provision. Public health provision, including measures for limiting the spread of infectious diseases, is a public good and can be provided for some only if provided for many. The provision or non-provision of public goods cannot be contingent on individual informed consent, so must be in some respects compulsory. An adequate ethics of public health needs to set aside debates about informed consent and to consider the permissible limits of just compulsion for various types of public good. It will therefore gain more from engaging with work in political philosophy than with individualistic work in ethics.     

A unified DNA sequence and non‐DNA sequence mapping model of complex traits

Increasing evidence shows that quantitative inheritance is based on both DNA sequence and non‐DNA sequence variants. However, how to simultaneously detect these variants from a mapping study has been unexplored, hampering our effort to illustrate the detailed genetic architecture of complex traits. We address this issue by developing a unified model of quantitative trait locus (QTL) mapping based on an open‐pollinated design composed of randomly sampling maternal plants from a natural population and their half‐sib seeds. This design forms a two‐level hierarchical platform for a joint linkage‐linkage disequilibrium analysis of population structure. The EM algorithm was implemented to estimate and test DNA sequence‐based effects and non‐DNA sequence‐based effects of QTLs. We applied this model to analyze genetic mapping data from the OP design of a gymnosperm coniferous species, Torreya grandis, identifying 25 significant DNA sequence and non‐DNA sequence QTLs for seedling height and diameter growth in different years. Results from computer simulation show that the unified model has good statistical properties and is powerful for QTL detection. Our model enables the tests of how a complex trait is affected differently by DNA‐based effects and non‐DNA sequence‐based transgenerational effects, thus allowing a more comprehensive picture of genetic architecture to be charted and quantified.     

‘VAGUE OVIEDO’: AUTONOMY,CULTURE AND THE CASE OF PREVIOUSLY COMPETENT PATIENTS

The paper examines the ethical and legal challenges of making decisions for previously competent patients and the role of advance directives and legal representatives in light of the Oviedo Convention. The paper identifies gaps in the Convention that result in conflicting instructions in cases of a disagreement between the expressed prior wishes of a patient, and the legal representative. The authors also examine the legal and moral status of informally expressed prior wishes of patients unable to consent. The authors argue that positivist legal reasoning is insufficient for a consistent interpretation of the relevant provisions of the Convention and argue that ethical argumentation is needed to provide guidance in such cases. Based on the ethical arguments, the authors propose a way of reconciling the apparent inconsistencies in the Oviedo Convention. They advance a culturally sensitive approach to the application of the Convention at the national level. This approach understands autonomy as a broader, relational consent and emphasizes the social and cultural embeddedness of the individual. Based on their approach, the authors argue that there exists a moral obligation to respect the prior wishes of the patient even in countries without advance directives. Yet it should be left to the national legislations to determine the extent of this obligation and its concrete forms.     

Unexpected foraminiferal diversity revealed by small-subunit rDNA analysis of Antarctic sediment

Studies of benthic Foraminifera typically rely on the morphological identification of dried specimens. This approach can introduce sampling bias against small, delicate, or morphologically ambiguous forms. To overcome this limitation, we extracted total DNA from sediment followed by PCR using group- and species-specific primers. Phylogenetic analyses revealed that approximately ninety percent of the PCR products represented previously undescribed sequence types that group with undersampled members of the allogromiid Foraminifera. We also used a modification of this technique to track individual species in sediment fractions too fine for normal morphological identification, and to confirm species placement of morphologically ambiguous foraminiferans. We were able to identify the DNA of several large foraminiferal species in fine fractions in a seasonally-dependent manner, indicating that in some seasons the majority of the standing stock of these species exists as gametes/juveniles. The approach outlined here represents a powerful strategy for exploring the total diversity of benthic foraminiferal communities.     

Integration of DNA sample collection into a multi-site birth defects case-control study

BACKGROUND: Advances in quantitative analysis and molecular genotyping have provided unprecedented opportunities to add biological sampling and genetic information to epidemiologic studies. The purpose of this article is to describe the incorporation of DNA sample collection into the National Birth Defects Prevention Study (NBDPS), an ongoing case-control study in an eight-state consortium with a primary goal to identify risk factors for birth defects. METHODS: Babies with birth defects are identified through birth defects surveillance systems in the eight participating centers. Cases are infants with one or more of over 30 major birth defects. Controls are infants without defects from the same geographic area. Epidemiologic information is collected through an hour-long interview with mothers of both cases and controls. We added the collection of buccal cytobrush DNA samples for case-infants, control-infants, and their parents to this study. RESULTS: We describe here the methods by which the samples have been collected and processed, establishment of a centralized resource for DNA banking, and quality control, database management, access, informed consent, and confidentiality issues. CONCLUSIONS: Biological sampling and genetic analyses are important components to epidemiologic studies of birth defects aimed at identifying risk factors. The DNA specimens collected in this study can be used for detection of mutations, study of polymorphic variants that confer differential susceptibility to teratogens, and examination of interactions among genetic risk factors. Information on the methods used and issues faced by the NBDPS may be of value to others considering the addition of DNA sampling to epidemiologic studies.     

Kinetic and segregational analysis of mitochondrial DNA recombination in yeast

A pair of yeast strains of opposite mating type was constructed to contain polymorphisms at three loci on the mitochondrial genome--the 21 S rRNA gene, var1, and cob--such that parental and recombinant forms of these genes could be easily detected by Southern blot analysis. These polymorphisms were used to measure in a single cross gene conversions at the 21 S rRNA and var1 loci and a reciprocal recombination at cob. For all three loci, recombination initiates at about the same time, 4 to 6 h after mixing cells, and increases with similar kinetics over a 24-h period. The segregation of parental and recombinant forms of these genes was then followed by pedigree analysis. The results, which show a high variance in the distribution of parental and recombinant forms of all three genes in cells derived from both the first bud and the mother zygote, are consistent with the segregation of a small number of mitochondrial DNA molecules from the zygote to diploid buds. Based on these results and previous experiments of this type, a limited "zone of mixing" of parental mitochondrial DNA molecules probably exists in the zygote. The extent of sampling from this zone, together with the intrinsic properties of the recombination events themselves, is likely to determine the observed pattern of recombination of mitochondrial DNA sequences at the population level.     

An approach that integrates patient education and informed consent in breast augmentation

Informed consent requires surgeons to provide information about all available alternatives and their associated risks and tradeoffs to every prospective breast augmentation patient. The informed patient and surgeon then make decisions based on the information the patient has received, clinical parameters that may affect those decisions, and the patient's willingness to accept specific risks and tradeoffs. During the authors' 22 years of clinical practice, substantial changes have occurred in the requirements for adequate informed consent and the methods of ensuring that patients receive it.The numbers of alternatives for augmentation and the relative benefits and risks of each method have changed substantially over the past two decades. Four specific areas of postoperative issues stimulated major changes in the authors' approach to patient education and informed consent: 1) questions or dissatisfaction with implant size postoperatively, 2) questions about financial responsibility for costs associated with untoward events requiring reoperation postoperatively including capsular contracture or other problems, 3) spouses or other concerned parties rendering opinions postoperatively when they had not been involved in the informed consent process, and 4) criteria for whether reoperations were indicated, how many were indicated, and when implant removal without replacement might be most logical.This paper describes an approach that integrates patient education and informed consent in stages by 1) providing detailed, highly specific written and verbal information, 2) utilizing a staged approach to education and informed consent that provides information and requires simultaneous, informed consent in stages, 3) repeating each critical topic at least two or three times during the process, requiring repetitive written documentation by the patient on at least three different occasions, 4) emphasizing patient accountability for choices selected, and 5) organizing the education and informed consent process so that it is clinically practical and also increases thoroughness and documentation while conserving surgeon time.This staged, integrated system of patient education and informed consent uses a comprehensive set of informed consent documents that are available for downloading from the Plastic and Reconstructive Surgery Web site (www.plasreconsurg.org).Before incorporating any of the informed consent documents or statements reported in this paper, each surgeon should seek review by the surgeon's malpractice insurance carrier and by appropriate legal counsel to ensure compliance with state and federal laws applicable to the surgeon's practice. These documents have evolved to prospectively address patient management issues that have occurred over the authors' 22-year experience in augmentation. The documents are not endorsed by ASPS and do not necessarily represent the views of ASPS.     

Family refusal of emergency medical treatment in China: An investigation from legal,empirical and ethical perspectives

This paper is an analysis of the limits of family authority to refuse life saving treatment for a family member (in the Chinese medical context). Family consent has long been praised and practiced in many non-Western cultural settings such as China and Japan. In contrast, the controversy of family refusal remains less examined despite its prevalence in low-income and middle-income countries. In this paper, we investigate family refusal in medical emergencies through a combination of legal, empirical and ethical approaches, which is highly relevant to the ongoing discussion about the place of informed consent in non-Western cultures. We first provide an overview of the Chinese legislation concerning informed consent to show the significance of family values in the context of medical decision-making and demonstrate the lack of legal support to override family refusal. Next, we present the findings of a vignette question that investigated how 11,771 medical professionals and 2,944 patients in China responded to the family refusal of emergency treatment for an unconscious patient. In our analysis of these results, we employ ethical reasoning to question the legitimacy of family refusal of life-sustaining emergency treatment for temporarily incompetent patients. Last, we examine some practical obstacles encountered by medical professionals wishing to override family refusal to give context to the discussion.     

Bayesian analysis of case control polygenic etiology studies with missing data

Many genetic studies are based on analysing multiple DNA regions of cases and controls. Usually each is tested separately for association with disease. However, some diseases may require interacting polymorphisms at several regions, and most disease susceptibility is polygenic. In this paper, we develop new methods for determining combinations of polymorphisms that affect the risk of disease. For example, two different genes might produce normal proteins, but these proteins improperly function when they occur together. We consider a Bayesian approach to analyse studies where DNA data from cases and controls have been analysed for polymorphisms at multiple regions and a polygenic etiology is suspected. The method of Gibbs sampling is used to incorporate data from individuals who have not had every region analysed at the DNA sequence or amino acid level. The Gibbs sampling algorithm alternatively generates a sample from the posterior distribution of the sequence of combinations of polymorphisms in cases and controls and then uses this sample to impute the data that are missing. After convergence the algorithm is used to generate a sample from the posterior distribution for the probability of each combination in order to identify groups of polymorphisms that best discriminate cases from controls. We apply the methods to a genetic study of type I diabetes. The protein encoded by the TAP2 gene is important in T cell function, and thus may affect the development of autoimmune diseases such as insulin dependent diabetes mellitus (IDDM). We determine pairs of polymorphisms of genetic fragments in the coding regions of linked HLA genes that may impact the risk of IDDM.     

Genetic diversity and microgeographic differentiation of Yushan cane (Yushania niitakayamensis; Poaceae) in Taiwan

Yushan cane ( Yushania niitakayamensis ) is distributed in southeast Asia. In Taiwan, the species occurs in mountains 1000–3600 m above sea level. The species appears to spread mainly by rhizomes and flowers only rarely. Nine locations across its distribution range in Taiwan were sampled. Locations at higher altitudes generally consist of grassland and forest undergrowth habitats while those of lower altitudes generally consist of forest undergrowth only. Thus two sampling sites (montane grassland and forest undergrowth) were selected from each location at higher altitudes while only one sampling site was selected from each location at lower altitudes, resulting in a total of 13 sampling sites. Within each sampling site, 20 individual plants were sampled. The results of the cluster analysis and the principal coordinate analysis based on random amplified polymorphic DNA (RAPD) indicated that the populations are generally differentiated according to geographical separation and altitudinal differences that interrupt gene flow. The populations at higher altitudes, where the species is distributed somewhat contiguously, were found to be more similar genetically. Analysis of molecular variance ( AMOVA ) revealed that the among-location, between sampling sites within location, and among individuals within sampling site components accounted for 15.27%, 4.80% and 79.93% of the total variance, respectively. For locations with two sampling sites, two-level AMOVA revealed that the diversities between sampling sites (sun and shade habitats) within locations ranged from 2.91% to 7.99% of the total diversity. Random permutation tests revealed that these diversities were significant, implying that there is microgeographic differentiation due to habitat differences.     

Neonatal screening by DNA microarray: spots and chips

Newborn screening (NBS) is a public-health genetic screening programme aimed at early detection and treatment of pre-symptomatic children affected by specific disorders. It currently involves protein-based assays and PCR to confirm abnormal results. We propose that DNA microarray technology might be an improvement over protein assays in the first stage of NBS. This approach has important advantages, such as multiplex analysis, but also has disadvantages, which include a high initial cost and the analysis/storage of large data sets. Determining the optimal technology for NBS will require that technical, public health and ethical considerations are made for the collection and extent of analysis of paediatric genomic data, for privacy and for parental consent.