Does published orthodontic research account for clustering effects during statistical data analysis?

In orthodontics, multiple site observations within patients or multiple observations collected at consecutive time points are often encountered. Clustered designs require larger sample sizes compared to individual randomized trials and special statistical analyses that account for the fact that observations within clusters are correlated. It is the purpose of this study to assess to what degree clustering effects are considered during design and data analysis in the three major orthodontic journals. The contents of the most recent 24 issues of the American Journal of Orthodontics and Dentofacial Orthopedics (AJODO), Angle Orthodontist (AO), and European Journal of Orthodontics (EJO) from December 2010 backwards were hand searched. Articles with clustering effects and whether the authors accounted for clustering effects were identified. Additionally, information was collected on: involvement of a statistician, single or multicenter study, number of authors in the publication, geographical area, and statistical significance. From the 1584 articles, after exclusions, 1062 were assessed for clustering effects from which 250 (23.5 per cent) were considered to have clustering effects in the design (kappa = 0.92, 95 per cent CI: 0.67-0.99 for inter rater agreement). From the studies with clustering effects only, 63 (25.20 per cent) had indicated accounting for clustering effects. There was evidence that the studies published in the AO have higher odds of accounting for clustering effects [AO versus AJODO: odds ratio (OR) = 2.17, 95 per cent confidence interval (CI): 1.06-4.43, P = 0.03; EJO versus AJODO: OR = 1.90, 95 per cent CI: 0.84-4.24, non-significant; and EJO versus AO: OR = 1.15, 95 per cent CI: 0.57-2.33, non-significant). The results of this study indicate that only about a quarter of the studies with clustering effects account for this in statistical data analysis.

Investigation of a unique short open reading frame within the 3' untranslated region of the canine distemper virus matrix messenger RNA

Increasing evidence suggest that the long "untranslated" region (UTR) between the matrix (M) and the fusion (F) proteins of morbilliviruses has a functional role. In canine distemper virus (CDV), the F 5' UTR was recently shown to code for a long F signal peptide (Fsp). Subsequently, it was reported that the M/F UTRs combined with the long Fsp were synergistically regulating the F mRNA and protein expression, thereby modulating virulence. Unique to CDV, a short putative open reading frame (ORF) has been identified within the wild-type CDV-M 3' UTR (termed M2). Here, we investigated whether M2 was expressed from the genome of the virulent and demyelinating A75/17-CDV strain. An expression plasmid encoding the M2 ORF tagged both at its N-terminal (HA) and C-terminal domains (RFP), was first constructed. Then, a recombinant virus with its putative M2 ORF replaced by HA-M2-RFP was successfully recovered from cDNA (termed recA75/17(green)-HA-M2-RFP). M2 expression in cells transfected or infected with these mutants was studied by immunoprecipitation, immunofluorescence, immunoblot and flow cytometry analyses. Although fluorescence was readily detected in HA-M2-RFP-transfected cells, absence of red fluorescence emission in several recA75/17(green)-HA-M2-RFP-infected cell types suggested lack of M2 biosynthesis, which was confirmed by the other techniques. Consistent with these data, no functional role of the short polypeptide was revealed by infecting various cell types with HA-M2-RFP over-expressing or M2-knockout recombinant viruses. Thus, in sharp contrast to the CDV-F 5' UTR reported to translate a long Fsp, our data provided evidence that the CDV-M 3' UTR does not express any polypeptides.

Design, construction, and testing of a research quality electric machine testbed

With energy demands and costs growing every day, the need for improving energy efficiency in electrical devices has become very important. Research into various methods of improving efficiency for all electrical components will be a key to meet future energy needs. This report documents the design, construction, and testing of a research quality electric machine dynamometer and test bed. This test cell system can be used for research in several areas including: electric drives systems, electric vehicle propulsion systems, power electronic converters, load/source element in an AC Microgrid, as well as many others. The test cell design criteria, and decisions, will be discussed in reference to user functionality and flexibility. The individual power components will be discussed in detail to how they relate to the project, highlighting any feature used in operation of the test cell. A project timeline will be discussed, clearly stating the work done by the different individuals involved in the project. In addition, the system will be parameterized and benchmark data will be used to provide the functional operation of the system. With energy demands and costs growing every day, the need for improving energy efficiency in electrical devices has become very important. Research into various methods of improving efficiency for all electrical components will be a key to meet future energy needs. This report documents the design, construction, and testing of a research quality electric machine dynamometer and test bed. This test cell system can be used for research in several areas including: electric drives systems, electric vehicle propulsion systems, power electronic converters, load/source element in an AC Microgrid, as well as many others. The test cell design criteria, and decisions, will be discussed in reference to user functionality and flexibility. The individual power components will be discussed in detail to how they relate to the project, highlighting any feature used in operation of the test cell. A project timeline will be discussed, clearly stating the work done by the different individuals involved in the project. In addition, the system will be parameterized and benchmark data will be used to provide the functional operation of the system.

THE EXPERIENCE OF RESEARCH, GROWTH, DEVELOPMENT AND LEADERSHIP OF THE MiTEP PROGRAM

Chapter 1. The Action Research in this report was to focus on improving the reading comprehension of students with expository text in relation to identifying the main idea and supporting details. Students were given an expository text to read and identify main idea and 2 -3 supporting details as a pre assessment. Students were provided instruction and support in DRTA (Directed Reading Thinking Activity) and SQ3R (Survey, Question, Read, Recite, Review) methodology to identify the Main Idea and supporting details of a selected expository text for both pre & posttest. Results were compiled and analyzed on the effectiveness of the strategies by overall student growth in accurately identifying the Main Idea and being able to state at least 2 supporting details. Analysis of the data will show that the methods were effective in middle school students’ ability to read and extrapolate the necessary information from expository text. Chapter 2 is a reflective essay on the MiTEP Michigan Teacher Excellence Program and its impact on my teaching practices, lesson delivery and leadership development.

Selecting control genes for RT-QPCR using public microarray data

BACKGROUND: Gene expression analysis has emerged as a major biological research area, with real-time quantitative reverse transcription PCR (RT-QPCR) being one of the most accurate and widely used techniques for expression profiling of selected genes. In order to obtain results that are comparable across assays, a stable normalization strategy is required. In general, the normalization of PCR measurements between different samples uses one to several control genes (e.g. housekeeping genes), from which a baseline reference level is constructed. Thus, the choice of the control genes is of utmost importance, yet there is not a generally accepted standard technique for screening a large number of candidates and identifying the best ones. RESULTS: We propose a novel approach for scoring and ranking candidate genes for their suitability as control genes. Our approach relies on publicly available microarray data and allows the combination of multiple data sets originating from different platforms and/or representing different pathologies. The use of microarray data allows the screening of tens of thousands of genes, producing very comprehensive lists of candidates. We also provide two lists of candidate control genes: one which is breast cancer-specific and one with more general applicability. Two genes from the breast cancer list which had not been previously used as control genes are identified and validated by RT-QPCR. Open source R functions are available at http://www.isrec.isb-sib.ch/~vpopovic/research/ CONCLUSION: We proposed a new method for identifying candidate control genes for RT-QPCR which was able to rank thousands of genes according to some predefined suitability criteria and we applied it to the case of breast cancer. We also empirically showed that translating the results from microarray to PCR platform was achievable.

Learning Analytics: Challenges and Future Research Directions

In recent years, learning analytics (LA) has attracted a great deal of attention in technology-enhanced learning (TEL) research as practitioners, institutions, and researchers are increasingly seeing the potential that LA has to shape the future TEL landscape. Generally, LA deals with the development of methods that harness educational data sets to support the learning process. This paper provides a foundation for future research in LA. It provides a systematic overview on this emerging field and its key concepts through a reference model for LA based on four dimensions, namely data, environments, context (what?), stakeholders (who?), objectives (why?), and methods (how?). It further identifies various challenges and research opportunities in the area of LA in relation to each dimension.

Proposal for an International Molybdenum Isotope Measurement Standard and Data Representation

Molybdenum isotopes are increasingly widely applied in Earth Sciences. They are primarily used to investigate the oxygenation of Earth's ocean and atmosphere. However, more and more fields of application are being developed, such as magmatic and hydrothermal processes, planetary sciences or the tracking of environmental pollution. Here, we present a proposal for a unifying presentation of Mo isotope ratios in the studies of mass-dependent isotope fractionation. We suggest that the δ98/95Mo of the NIST SRM 3134 be defined as +0.25‰. The rationale is that the vast majority of published data are presented relative to reference materials that are similar, but not identical, and that are all slightly lighter than NIST SRM 3134. Our proposed data presentation allows a direct first-order comparison of almost all old data with future work while referring to an international measurement standard. In particular, canonical δ98/95Mo values such as +2.3‰ for seawater and −0.7‰ for marine Fe–Mn precipitates can be kept for discussion. As recent publications show that the ocean molybdenum isotope signature is homogeneous, the IAPSO ocean water standard or any other open ocean water sample is suggested as a secondary measurement standard, with a defined δ98/95Mo value of +2.34 ± 0.10‰ (2s). Les isotopes du molybdène (Mo) sont de plus en plus largement utilisés dans les sciences de la Terre. Ils sont principalement utilisés pour étudier l'oxygénation de l'océan et de l'atmosphère de la Terre. Cependant, de plus en plus de domaines d'application sont en cours de développement, tels que ceux concernant les processus magmatiques et hydrothermaux, les sciences planétaires ou encore le suivi de la pollution environnementale. Ici, nous présentons une proposition de présentation unifiée des rapports isotopiques du Mo dans les études du fractionnement isotopique dépendant de la masse. Nous suggérons que le δ98/95Mo du NIST SRM 3134 soit définit comme étant égal à +0.25 ‰. La raison est que la grande majorité des données publiées sont présentés par rapport à des matériaux de référence qui sont similaires, mais pas identiques, et qui sont tous légèrement plus léger que le NIST SRM 3134. Notre proposition de présentation des données permet une comparaison directe au premier ordre de presque toutes les anciennes données avec les travaux futurs en se référant à un standard international. En particulier, les valeurs canoniques du δ98/95Mo comme celle de +2,3 ‰ pour l'eau de mer et de -0,7 ‰ pour les précipités de Fe-Mn marins peuvent être conservés pour la discussion. Comme les publications récentes montrent que la signature isotopique moyenne du molybdène de l'océan est homogène, le standard de l'eau océanique IAPSO ou tout autre échantillon d'eau provenant de l'océan ouvert sont proposé comme standards secondaires, avec une valeur définie du δ98/95 Mo de 2.34 ± 0.10 ‰ (2s).

SURVIVAL PREDICTION FOR BRAIN TUMOR PATIENTS USING GENE EXPRESSION DATA

Brain tumor is one of the most aggressive types of cancer in humans, with an estimated median survival time of 12 months and only 4% of the patients surviving more than 5 years after disease diagnosis. Until recently, brain tumor prognosis has been based only on clinical information such as tumor grade and patient age, but there are reports indicating that molecular profiling of gliomas can reveal subgroups of patients with distinct survival rates. We hypothesize that coupling molecular profiling of brain tumors with clinical information might improve predictions of patient survival time and, consequently, better guide future treatment decisions. In order to evaluate this hypothesis, the general goal of this research is to build models for survival prediction of glioma patients using DNA molecular profiles (U133 Affymetrix gene expression microarrays) along with clinical information. First, a predictive Random Forest model is built for binary outcomes (i.e. short vs. long-term survival) and a small subset of genes whose expression values can be used to predict survival time is selected. Following, a new statistical methodology is developed for predicting time-to-death outcomes using Bayesian ensemble trees. Due to a large heterogeneity observed within prognostic classes obtained by the Random Forest model, prediction can be improved by relating time-to-death with gene expression profile directly. We propose a Bayesian ensemble model for survival prediction which is appropriate for high-dimensional data such as gene expression data. Our approach is based on the ensemble "sum-of-trees" model which is flexible to incorporate additive and interaction effects between genes. We specify a fully Bayesian hierarchical approach and illustrate our methodology for the CPH, Weibull, and AFT survival models. We overcome the lack of conjugacy using a latent variable formulation to model the covariate effects which decreases computation time for model fitting. Also, our proposed models provides a model-free way to select important predictive prognostic markers based on controlling false discovery rates. We compare the performance of our methods with baseline reference survival methods and apply our methodology to an unpublished data set of brain tumor survival times and gene expression data, selecting genes potentially related to the development of the disease under study. A closing discussion compares results obtained by Random Forest and Bayesian ensemble methods under the biological/clinical perspectives and highlights the statistical advantages and disadvantages of the new methodology in the context of DNA microarray data analysis.

A PROCESS FOR ACHIEVING COMPARABLE DATA FROM HETEROGENEOUS DATABASES

The current state of health and biomedicine includes an enormity of heterogeneous data ‘silos’, collected for different purposes and represented differently, that are presently impossible to share or analyze in toto. The greatest challenge for large-scale and meaningful analyses of health-related data is to achieve a uniform data representation for data extracted from heterogeneous source representations. Based upon an analysis and categorization of heterogeneities, a process for achieving comparable data content by using a uniform terminological representation is developed. This process addresses the types of representational heterogeneities that commonly arise in healthcare data integration problems. Specifically, this process uses a reference terminology, and associated "maps" to transform heterogeneous data to a standard representation for comparability and secondary use. The capture of quality and precision of the “maps” between local terms and reference terminology concepts enhances the meaning of the aggregated data, empowering end users with better-informed queries for subsequent analyses. A data integration case study in the domain of pediatric asthma illustrates the development and use of a reference terminology for creating comparable data from heterogeneous source representations. The contribution of this research is a generalized process for the integration of data from heterogeneous source representations, and this process can be applied and extended to other problems where heterogeneous data needs to be merged.

Upper ocean vertical supply: A neglected primary factor controlling the distribution of neodymium concentrations of open ocean surface waters?

Neodymium (Nd) isotopes are an important geochemical tool to trace the present and past water mass mixing as well as continental inputs. The distribution of Nd concentrations in open ocean surface waters (0�100 m) is generally assumed to be controlled by lateral mixing of Nd from coastal surface currents and by removal through reversible particle scavenging. However, using 228Ra activity as an indicator of coastal water mass influence, surface water Nd concentration data available on key oceanic transects as a whole do not support the above scenario. From a global compilation of available data, we find that more stratified regions are generally associated with low surface Nd concentrations. This implies that upper ocean vertical supply may be an as yet neglected primary factor in determining the basin-scale variations of surface water Nd concentrations. Similar to the mechanism of nutrients supply, it is likely that stratification inhibits vertical supply of Nd from the subsurface thermocline waters and thus the magnitude of Nd flux to the surface layer. Consistently, the estimated required input flux of Nd to the surface layer to maintain the observed concentrations could be nearly two orders of magnitudes larger than riverine/dust flux, and also larger than the model-based estimation on shelf-derived coastal flux. In addition, preliminary results from modeling experiments reveal that the input from shallow boundary sources, riverine input, and release from dust are actually not the primary factors controlling Nd concentrations most notably in the Pacific and Southern Ocean surface waters.

The door of the tomb is open: Participatory action research to assess the impact of strengthened community capacity on maternal health care in rural Mali

This participatory action-research project addressed the hypothesis that strengthened community and women's capacity for self-development will lead to action to address maternal health problems and the prevention of maternal morbidity and mortality in Mali. Research objectives were: (1) to undertake a comparative cross-sectional study of the association of community capacity with improved maternal health in rural areas of Sanando, Mali, where capacity building interventions have taken place in some villages but not in others. (2) to describe women's maternal health status, access to and use of maternal health services given their residence in program or comparison communities.^ The participatory action research project was an integrated qualitative and quantitative study using participatory rural appraisal exercises, semi-structured group interviews and a cross-sectional survey.^ Factors related to community capacity for self-development were identified: community harmony; an understanding of the benefits of self-development; dynamic leadership; and a structure to implement collective activities.^ A distinct difference between the program and comparison villages was the commitment to train and support traditional birth attendants (TBAs). The TBAs in the program villages work in the context of the wider, integrated self-development program and, 10 years after their initial training, the TBAs continue to practice.^ Many women experience labor and childbirth alone or are attended by an untrained relative in both program and comparison villages. Nevertheless a significant change is apparent, with more women in program villages than in comparison villages being assisted by the TBAs. The delivery practices of the TBAs reveal the positive impact of their training in the "three cleans" (clean hands of the assistant, clean delivery surface and clean cord-cutting). The findings of this study indicate a significant level of unmet need for child spacing methods in all villages.^ The training and support of TBAs in the program villages yielded significant improvements in their delivery practices, and resulting outcomes for women and infants. However, potential exists for further community action. Capacities for self-development have not yet been directed toward an action plan encompassing other Safe Motherhood interventions, including access to family planning services and emergency obstetric care services. ^