Quality assurance in the 22991 EORTC ROG trial in localized prostate cancer: dummy run and individual case review.

INTRODUCTION: EORTC trial 22991 was designed to evaluate the addition of concomitant and adjuvant short-term hormonal treatments to curative radiotherapy in terms of disease-free survival for patients with intermediate risk localized prostate cancer. In order to assess the compliance to the 3D conformal radiotherapy protocol guidelines, all participating centres were requested to participate in a dummy run procedure. An individual case review was performed for the largest recruiting centres as well. MATERIALS AND METHODS: CT-data of an eligible prostate cancer patient were sent to 30 centres including a description of the clinical case. The investigator was requested to delineate the volumes of interest and to perform treatment planning according to the protocol. Thereafter, the investigators of the 12 most actively recruiting centres were requested to provide data on five randomly selected patients for an individual case review. RESULTS: Volume delineation varied significantly between investigators. Dose constraints for organs at risk (rectum, bladder, hips) were difficult to meet. In the individual case review, no major protocol deviations were observed, but a number of dose reporting problems were documented for centres using IMRT. CONCLUSIONS: Overall, results of this quality assurance program were satisfactory. The efficacy of the combination of a dummy run procedure with an individual case review is confirmed in this study, as none of the evaluated patient files harboured a major protocol deviation. Quality assurance remains a very important tool in radiotherapy to increase the reliability of the trial results. Special attention should be given when designing quality assurance programs for more complex irradiation techniques.

Use of DNA profiles for investigation using a simulated national DNA database: Part I. Partial SGM Plus profiles.

In traditional criminal investigation, uncertainties are often dealt with using a combination of common sense, practical considerations and experience, but rarely with tailored statistical models. For example, in some countries, in order to search for a given profile in the national DNA database, it must have allelic information for six or more of the ten SGM Plus loci for a simple trace. If the profile does not have this amount of information then it cannot be searched in the national DNA database (NDNAD). This requirement (of a result at six or more loci) is not based on a statistical approach, but rather on the feeling that six or more would be sufficient. A statistical approach, however, could be more rigorous and objective and would take into consideration factors such as the probability of adventitious matches relative to the actual database size and/or investigator's requirements in a sensible way. Therefore, this research was undertaken to establish scientific foundations pertaining to the use of partial SGM Plus loci profiles (or similar) for investigation.

Subgroup analyses in randomised controlled trials: cohort study on trial protocols and journal publications

OBJECTIVE: To investigate the planning of subgroup analyses in protocols of randomised controlled trials and the agreement with corresponding full journal publications. DESIGN: Cohort of protocols of randomised controlled trial and subsequent full journal publications. SETTING: Six research ethics committees in Switzerland, Germany, and Canada. DATA SOURCES: 894 protocols of randomised controlled trial involving patients approved by participating research ethics committees between 2000 and 2003 and 515 subsequent full journal publications. RESULTS: Of 894 protocols of randomised controlled trials, 252 (28.2%) included one or more planned subgroup analyses. Of those, 17 (6.7%) provided a clear hypothesis for at least one subgroup analysis, 10 (4.0%) anticipated the direction of a subgroup effect, and 87 (34.5%) planned a statistical test for interaction. Industry sponsored trials more often planned subgroup analyses compared with investigator sponsored trials (195/551 (35.4%) v 57/343 (16.6%), P<0.001). Of 515 identified journal publications, 246 (47.8%) reported at least one subgroup analysis. In 81 (32.9%) of the 246 publications reporting subgroup analyses, authors stated that subgroup analyses were prespecified, but this was not supported by 28 (34.6%) corresponding protocols. In 86 publications, authors claimed a subgroup effect, but only 36 (41.9%) corresponding protocols reported a planned subgroup analysis. CONCLUSIONS: Subgroup analyses are insufficiently described in the protocols of randomised controlled trials submitted to research ethics committees, and investigators rarely specify the anticipated direction of subgroup effects. More than one third of statements in publications of randomised controlled trials about subgroup prespecification had no documentation in the corresponding protocols. Definitive judgments regarding credibility of claimed subgroup effects are not possible without access to protocols and analysis plans of randomised controlled trials.

Research in the clinical setting : a qualitative study of the value of play research in the continuing education of occupational therapists.

Occupational therapists have always recognized playas an important part of a child's life. However, until recently play has been viewed as a medium for reaching treatment goals, rather than as an activity that is valuable in and of itself. If occupational therapists think of playas the primary activity or occupation of childhood, then play should be a very important area of focus for paediatric clinicians. In order to assist children to become as independent as possible with play and to have fulfilling play experiences the occupational therapist needs to have a clear understanding of how to assess, set goals which lead towards competence in play, and promote play. Recent play literature has placed importance on play behaviours and looking at the relationship between the child and both the human and nonhuman environment. Believing that play and playfulness can and should be promoted, for children with physical disabilities, requires that therapists learn new assessment and intervention strategies. A new assessment tool, The Test of Playfulness, was developed by Bundy in 1994. It addressed play behaviours and environmental influences. The author, a co-investigator and eight occupational therapists were involved in a playfulness study using this test to compare the playfulness of children with physical disabilities with their able-bodied peers. After the study was completed the author questioned whether or not involvement in the playfulness study was enough of a change agent to bring about transformative learning in order to further the eight occupational therapists' education about play.This study investigated changes in either the therapists' thinking about play or their behaviour in their clinical practice. The study also examined the participants' retention of knowledge about the Test of Playfulness. The eight therapists who had been involved in the playfulness study (participants) were matched with eight therapists who had not been involved (nonparticipants). The therapists were interviewed 9 to 12 months after completion of the playfulness study. They were asked to describe various scenarios of play and open ended prompts were used to elicit the therapists' perceptions of play, good play, the role or value of play, environmental and gender influences on play, play assessment and intervention, and play research, for children with and without disabilities. The participants were also prompted to discuss their experience with the playfulness study. A self-report questionnaire was also completed at the end of the interview. The results of the study demonstrated that: (a) the play research project was a good format for continuing the participants' education about play; (b) their thinking had changed about play; (c) according to self report, they had used this new knowledge in their clinical practice; and (d) the participants remembered the items on the Test of Playfulness and could use them in describing various aspects of play. This study found that participating in a play research project had been an effective method of professional development. It also highlighted the need for increased awareness of the recent literature on play and the developing role of the occupational therapist in the assessment and intervention of play.

Evaluation of self-esteem before and after preceptorship experience for student nurses

seventy-eight diploma nursing students participated (from a class of 112 students) in completing the Coopersmith Self-Esteem Inventory administered by mailed questionnaire before and at the end of the preceptorship. Also a rating form was completed by 70 preceptors to determine how the observed level of self-confidence compared to self-reported self-esteem at the end of the preceptorship program. As well, four preceptors and five preceptees completed weekly diaries and six preceptors and six preceptees participated in weekly phone interviews with the investigator. Overall, self-esteem went up after the preceptorship. A comparison was made between the pretest and posttest using the t-test (dependent paired samples). Significant difference (p=.05) was demonstrated. Self-confidence ratings by preceptors were inaccurate as they had no relation to the self-reported self-esteem level of students. The diaries and interviews of preceptors and preceptees were a rich source of data as well.

Rhapsodes of social science : Herodotus' performance of politeic inquiry

Herodotus' logos represents many examples ofthe relationship between political and paradigmatic authority, and the synthesis ofthese examples in a community characterized by free and equal speech. Herodotus' walkabout narrator sets forth an inquiry into knowledge-seeking he extends the isegoria principle from Athenian politics to the broader world. The History demonstrates (a) various modes of constructing meaning, (b) interacting notions ofhow people have lived and living questions as to how we ought to live, and (c) an investigation ofthe nature and limits ofhuman knowledge. Representing diverse wisdom, publicly and privately discovered and presented, Herodotus sets forth Solon's wise advice and law-making, the capital punishment of the learned Anacharsis, the investigative outrages of Cambyses and Psammetichus' more pious experiments. Their stories challenge and complement their communities' characters - the relative constraint under which the Egyptians and Persians make their investigations, the Scythians' qualified openness and the relative fearlessness and freedom in which the Greeks set forth their inquiries. Setting forth the investigator-storykeeper as a poetic historian, Herodotus shows that history as poetry thwarts natural decay by allowing custom to be reformed in an open milieu, and thus win through and survive. Despite the potential dangers that openness shares with tyranny, Herodotus' inquiry sets up a contest ofworld-views in which it is mutability that openness affords a community that ensures its survival.

Research in the clinical setting : a qualitative study of the value of play research in the continuing education of occupational therapists.

Occupational therapists have always recognized playas an important part of a child's life. However, until recently play has been viewed as a medium for reaching treatment goals, rather than as an activity that is valuable in and of itself. If occupational therapists think of playas the primary activity or occupation of childhood, then play should be a very important area of focus for paediatric clinicians. In order to assist children to become as independent as possible with play and to have fulfilling play experiences the occupational therapist needs to have a clear understanding of how to assess, set goals which lead towards competence in play, and promote play. Recent play literature has placed importance on play behaviours and looking at the relationship between the child and both the human and nonhuman environment. Believing that play and playfulness can and should be promoted, for children with physical disabilities, requires that therapists learn new assessment and intervention strategies. A new assessment tool, The Test of Playfulness, was developed by Bundy in 1994. It addressed play behaviours and environmental influences. The author, a co-investigator and eight occupational therapists were involved in a playfulness study using this test to compare the playfulness of children with physical disabilities with their able-bodied peers. After the study was completed the author questioned whether or not involvement in the playfulness study was enough of a change agent to bring about transformative learning in order to further the eight occupational therapists' education about play.

Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes.

Proteolytic processing of the CUX1 transcription factor generates an isoform, p110 that accelerates entry into S phase. To identify targets of p110 CUX1 that are involved in cell cycle progression, we performed genome-wide location analysis using a promoter microarray. Since there are no antibodies that specifically recognize p110, but not the full-length protein, we expressed physiological levels of a p110 isoform with two tags and purified chromatin by tandem affinity purification (ChAP). Conventional ChIP performed on synchronized populations of cells confirmed that p110 CUX1 is recruited to the promoter of cell cycle-related targets preferentially during S phase. Multiple approaches including silencing RNA (siRNA), transient infection with retroviral vectors, constitutive expression and reporter assays demonstrated that most cell cycle targets are activated whereas a few are repressed or not affected by p110 CUX1. Functional classes that were over-represented among targets included DNA replication initiation. Consistent with this finding, constitutive expression of p110 CUX1 led to a premature and more robust induction of replication genes during cell cycle progression, and stimulated the long-term replication of a plasmid bearing the oriP replicator of Epstein Barr virus (EBV).

The euchromatic and heterochromatic landscapes are shaped by antagonizing effects of transcription on H2A.Z deposition

A role for variant histone H2A.Z in gene expression is now well established but little is known about the mechanisms by which it operates. Using a combination of ChIP-chip, knockdown and expression profiling experiments, we show that upon gene induction, human H2A.Z associates with gene promoters and helps in recruiting the transcriptional machinery. Surprisingly, we also found that H2A.Z is randomly incorporated in the genome at low levels and that active transcription antagonizes this incorporation in transcribed regions. After cessation of transcription, random H2A.Z quickly reappears on genes, demonstrating that this incorporation utilizes an active mechanism. Within facultative heterochromatin, we observe a hyper accumulation of the variant histone, which might be due to the lack of transcription in these regions. These results show how chromatin structure and transcription can antagonize each other, therefore shaping chromatin and controlling gene expression.

Principles for Incorporating Farmers in the Ethical Assessment of Genetically Modified Crops

A current advance within the agricultural industry is the use of genetic engineering to produce novel crops for food production. This technology raises questions about how societies should position themselves with respect to genetically modified (GM) crop development and implementation; namely, how should the potentials and risks of this technology be evaluated? We argue that current methods to evaluate the risks and benefits of GM crops are inadequate and not conducive to the strategic development of this technology, where a way to ameliorate technology assessments for GM crops is to include farmers in the research process of evaluating these crops prior to their commercialization. However, particularities concerning the ethical status of such research require special consideration and vigilance. For example, in such technology assessment initiatives, farmers would occupy both the roles of research participant and research investigator. Other particularities surface due to factors related to the nature of GM crops. These particularities are examined with reference to concepts drawn from the field of research ethics, namely informed consent, compensatory decisions, and issues of participant inclusion/exclusion.

Cinéma et sens de la ville : la ville idéelle

C’est principalement par le cinéma que nous connaissons et partageons le réel des villes, même celles dans lesquelles nous vivons. Par le cinéma, nous découvrons plus de villes que nous n’en visiterons jamais. Nous connaissons des villes que nous n'avons jamais vues. Nous apprenons à découvrir des villes que nous connaissons déjà. Nous avons en mémoire des villes qui n'existent pas. Que nous soyons spectateur ou créateur, les villes existent d'abord dans notre imaginaire. Percevoir, représenter et créer sont des actes complémentaires qui mobilisent des fonctions communes. Toute perception est conditionnée par le savoir et la mémoire, elle dépend de la culture. Toute représentation, si elle veut communiquer, doit connaître les mécanismes et les codes mémoriels et culturels du public auquel elle s’adresse. Le cinéma ne fait pas que reproduire, il crée et il a appris à utiliser ces codes et ces mécanismes, notamment pour représenter la ville. L’étude du cinéma peut ouvrir aux urbanistes et aux professionnels de l’aménagement, de nouveaux champs de scientificité sur le plan de la représentation et de la perception comme partage du réel de la ville. La ville et le cinéma doivent alors être vus comme un spectacle dans son acception herméneutique, et de ce spectacle il devient possible d’en faire émerger un paradigme; ou dit autrement, the basic belief system or worldview that guides the investigator, not only in choices of methods but in ontologically and episemologically fundamental ways. (Guba & Lincoln, 1994) Ce paradigme, que nous proposons de décrire, de modéliser et dont nous montrons les fonctions conceptuelles; nous le désignons comme la Ville idéelle.

Yeast RNase III triggers polyadenylation-independent transcription termination

Transcription termination of messenger RNA (mRNA) is normally achieved by polyadenylation followed by Rat1p-dependent 5'-3' exoribonuleolytic degradation of the downstream transcript. Here we show that the yeast ortholog of the dsRNA-specific ribonuclease III (Rnt1p) may trigger Rat1p-dependent termination of RNA transcripts that fail to terminate near polyadenylation signals. Rnt1p cleavage sites were found downstream of several genes, and the deletion of RNT1 resulted in transcription readthrough. Inactivation of Rat1p impaired Rnt1p-dependent termination and resulted in the accumulation of 3' end cleavage products. These results support a model for transcription termination in which cotranscriptional cleavage by Rnt1p provides access for exoribonucleases in the absence of polyadenylation signals.

Development and disease of the photoreceptor cilium

Primary cilia are microtubule-rich hair-like extensions protruding from the surface of most post-mitotic cells. They act as sensory organelles that help interpret various environmental cues. Mutations in genes encoding proteins involved in ciliogenesis or protein transport to the primary cilia lead to a wide variety of diseases commonly referred to as ciliopathies,which include primary ciliary dyskinesia, situs invertus, hydrocephalus, kidney diseases, respiratory diseases, and retinal degenerations. In the retina, the photoreceptor cells have a highly specialized primary cilium called the outer segment (OS), which is essential for photosensation. Development of the photoreceptor OS shares key regulatory mechanisms with ciliogenesis in other cell types. Accumulating evidence indicates that mutations that affect OS development and/or protein transport to the OS generally lead to photoreceptor degeneration, which can be accompanied by a range of other clinical manifestations due to the dysfunction of primary cilia in different cell types. Here, we review the general mechanisms regulating ciliogenesis, and present different examples of mutations affecting OS ciliogenesis and protein transport that lead to photoreceptor degeneration. Overall, we conclude that the genetic and molecular evidence accumulated in recent years suggest a clear link between the development and function of the primary cilium and various clinical conditions. Future studies aimed at uncovering the cellular and molecular mechanisms implicated in ciliogenesis in a wide variety of animal models should greatly increase our understanding of the pathophysiology of many human diseases, including retinal degenerations.

Computational prediction of neural progenitor cell fates

Understanding how stem and progenitor cells choose between alternative cell fates is a major challenge in developmental biology. Efforts to tackle this problem have been hampered by the scarcity of markers that can be used to predict cell division outcomes. Here we present a computational method, based on algorithmic information theory, to analyze dynamic features of living cells over time. Using this method, we asked whether rat retinal progenitor cells (RPCs) display characteristic phenotypes before undergoing mitosis that could foretell their fate. We predicted whether RPCs will undergo a self-renewing or terminal division with 99% accuracy, or whether they will produce two photoreceptors or another combination of offspring with 87% accuracy. Our implementation can segment, track and generate predictions for 40 cells simultaneously on a standard computer at 5 min per frame. This method could be used to isolate cell populations with specific developmental potential, enabling previously impossible investigations.

Étude des conceptions alternatives et des processus de raisonnement des étudiants de chimie du niveau collégial sur la molécule, la polarité et les phénomènes macroscopiques

La chimie est un sujet difficile étant donné ses concepts nombreux et souvent peu intuitifs. Mais au-delà de ces difficultés d’ordre épistémologique, l’apprentissage de la chimie peut être en péril lorsqu’il s’appuie sur des fondations instables, mêlées de conceptions alternatives. Les conceptions alternatives sont les représentations internes, tacites, des étudiants, qui sont en désaccord avec la théorie scientifiquement acceptée. Leur présence dans leur esprit peut nuire à la compréhension conceptuelle, et elle peut mener les étudiants à expliquer le comportement de la matière incorrectement et à faire des prédictions inexactes en chimie. Les conceptions alternatives sont réputées répandues et difficiles à repérer dans un cadre traditionnel d’enseignement. De nombreuses conceptions alternatives en chimie ont été mises en lumière par différents groupes de chercheurs internationaux, sans toutefois qu’une telle opération n’ait jamais été réalisée avec des étudiants collégiaux québécois. Le système d’éducation postsecondaire québécois représentant un contexte unique, une étude des difficultés particulières de ces étudiants était nécessaire pour tracer un portrait juste de la situation. De plus, des chercheurs proposent aujourd’hui de ne pas faire uniquement l’inventaire des conceptions, mais de s’attarder aussi à étudier comment, par quel processus, elles mènent à de mauvaises prédictions ou explications. En effet, ils soutiennent que les catalogues de conceptions ne peuvent pas être facilement utilisés par les enseignants, ce qui devrait pourtant être la raison pour les mettre en lumière : qu’elles soient prises en compte dans l’enseignement. Toutefois, aucune typologie satisfaisante des raisonnements et des conceptions alternatives en chimie, qui serait appuyée sur des résultats expérimentaux, n’existe actuellement dans les écrits de recherche. Plusieurs chercheurs en didactique de la chimie suggèrent qu’une telle typologie est nécessaire et devrait rendre explicites les modes de raisonnement qui mettent en jeu ces conceptions alternatives. L’explicitation du raisonnement employé par les étudiants serait ainsi la voie permettant de repérer la conception alternative sur laquelle ce raisonnement s’appuie. Le raisonnement est le passage des idées tacites aux réponses manifestes. Ce ne sont pas toutes les mauvaises réponses en chimie qui proviennent de conceptions alternatives : certaines proviennent d’un manque de connaissances, d’autres d’un agencement incorrect de concepts pourtant corrects. Comme toutes les sortes de mauvaises réponses d’étudiants sont problématiques lors de l’enseignement, il est pertinent de toutes les considérer. Ainsi, ces préoccupations ont inspiré la question de recherche suivante : Quelles conceptions alternatives et quels processus de raisonnement mènent les étudiants à faire de mauvaises prédictions en chimie ou à donner de mauvaises explications du comportement de la matière? C’est pour fournir une réponse à cette question que cette recherche doctorale a été menée. Au total, 2413 étudiants ont participé à la recherche, qui était divisée en trois phases : la phase préliminaire, la phase pilote et la phase principale. Des entrevues cliniques ont été menées à la phase préliminaire, pour explorer les conceptions alternatives des étudiants en chimie. Lors de la phase pilote, des questionnaires à choix multiples avec justification ouverte des réponses ont été utilisés pour délimiter le sujet, notamment à propos des notions de chimie les plus pertinentes sur lesquelles concentrer la recherche et pour mettre en lumière les façons de raisonner des étudiants à propos de ces notions. La phase principale, quant à elle, a utilisé le questionnaire à deux paliers à choix multiples « Molécules, polarité et phénomènes » (MPP) développé spécifiquement pour cette recherche. Ce questionnaire a été distribué aux étudiants via une adaptation de la plateforme Web ConSOL, développée durant la recherche par le groupe de recherche dont fait partie la chercheuse principale. Les résultats montrent que les étudiants de sciences de la nature ont de nombreuses conceptions alternatives et autres difficultés conceptuelles, certaines étant très répandues parmi leur population. En particulier, une forte proportion d’étudiants croient que l’évaporation d’un composé entraîne le bris des liaisons covalentes de ses molécules (61,1 %), que tout regroupement d’atomes est une molécule (78,9 %) et que les atomes ont des propriétés macroscopiques pareilles à celles de l’élément qu’ils constituent (66,0 %). D’un autre côté, ce ne sont pas toutes les mauvaises réponses au MPP qui montrent des conceptions alternatives. Certaines d’entre elles s’expliquent plutôt par une carence dans les connaissances antérieures (par exemple, lorsque les étudiants montrent une méconnaissance d’éléments chimiques communs, à 21,8 %) ou par un raisonnement logique incomplet (lorsqu’ils croient que le seul fait de posséder des liaisons polaires rend nécessairement une molécule polaire, ce qu’on observe chez 24,1 % d’entre eux). Les conceptions alternatives et les raisonnements qui mènent à des réponses incorrectes s’observent chez les étudiants de première année et chez ceux de deuxième année du programme de sciences, dans certains cas avec une fréquence diminuant entre les deux années, et dans d’autres, à la même fréquence chez les deux sous-populations. Ces résultats permettent de mitiger l’affirmation, généralement reconnue dans les écrits de recherche, selon laquelle les conceptions alternatives sont résistantes à l’enseignement traditionnel : selon les résultats de la présente recherche, certaines d’entre elles semblent en effet se résoudre à travers un tel contexte d’enseignement. Il demeure que plusieurs conceptions alternatives, carences dans les connaissances antérieures de base et erreurs de raisonnement ont été mises en lumière par cette recherche. Ces problèmes dans l’apprentissage mènent les étudiants collégiaux à faire des prédictions incorrectes du comportement de la matière, ou à expliquer ce comportement de façon incorrecte. Au regard de ces résultats, une réflexion sur l’enseignement de la chimie au niveau collégial, qui pourrait faire une plus grande place à la réflexion conceptuelle et à l’utilisation du raisonnement pour la prédiction et l’explication des phénomènes étudiés, serait pertinente à tenir.