Assessing the Significance of Conserved Genomic Aberrations Using High Resolution Genomic Microarrays

Genomic aberrations recurrent in a particular cancer type can be important prognostic markers for tumor progression. Typically in early tumorigenesis, cells incur a breakdown of the DNA replication machinery that results in an accumulation of genomic aberrations in the form of duplications, deletions, translocations, and other genomic alterations. Microarray methods allow for finer mapping of these aberrations than has previously been possible; however, data processing and analysis methods have not taken full advantage of this higher resolution. Attention has primarily been given to analysis on the single sample level, where multiple adjacent probes are necessarily used as replicates for the local region containing their target sequences. However, regions of concordant aberration can be short enough to be detected by only one, or very few, array elements. We describe a method called Multiple Sample Analysis for assessing the significance of concordant genomic aberrations across multiple experiments that does not require a-priori definition of aberration calls for each sample. If there are multiple samples, representing a class, then by exploiting the replication across samples our method can detect concordant aberrations at much higher resolution than can be derived from current single sample approaches. Additionally, this method provides a meaningful approach to addressing population-based questions such as determining important regions for a cancer subtype of interest or determining regions of copy number variation in a population. Multiple Sample Analysis also provides single sample aberration calls in the locations of significant concordance, producing high resolution calls per sample, in concordant regions. The approach is demonstrated on a dataset representing a challenging but important resource: breast tumors that have been formalin-fixed, paraffin-embedded, archived, and subsequently UV-laser capture microdissected and hybridized to two-channel BAC arrays using an amplification protocol. We demonstrate the accurate detection on simulated data, and on real datasets involving known regions of aberration within subtypes of breast cancer at a resolution consistent with that of the array. Similarly, we apply our method to previously published datasets, including a 250K SNP array, and verify known results as well as detect novel regions of concordant aberration. The algorithm has been fully implemented and tested and is freely available as a Java application at http://www.cbil.upenn.edu/MSA

Reflecting on Pupil Learning to Promote Social Justice: A Catholic University’s Approach to Assessment

In contrast to current education policies that conceptualize pupil learning largely in terms of standardized exam scores, we offer an alternative view, one that conceives of pupil learning as a source of insight for pupils and teachers alike. Drawing on survey data and a qualitative study of the teacher candidate experience, we explore the following questions: In a teacher education program committed to promoting social justice, embracing an inquiry-into-practice stance, and affirming diversity by meeting the needs of diverse learners, how do teacher candidates assess pupil learning, in particular, how are their assessments influenced by these program themes? Further, how do they respond when dilemmas linked to pupil learning arise? Specifically, we focused on dilemmas two teacher candidates encountered that engendered a sense of “disequilibrium,” a feeling something was not quite right with their teaching. In turn, we consider how they responded”typically taking ownership of dilemmas and modifying their teaching, while occasionally distancing themselves from responsibility for pupil performance. To conclude, we discuss implications for teacher educators, and specifically for Catholic institutions of higher education that prepare teachers for both public and Catholic schools

Infant BMI or Weight-for-Length and Obesity Risk in Early Childhood

Weight-for-length (WFL) is currently used to assess adiposity under 2 years. We assessed WFL- versus BMI-based estimates of adiposity in healthy infants in determining risk for early obesity

Reflecting on Pupil Learning to Promote Social Justice: A Catholic University\u27s Approach to Assessment

In contrast to current education policies that conceptualize pupil learning largely in terms of standardized exam scores, we offer an alternative view, one that conceives of pupil learning as a source of insight for pupils and teachers alike. Drawing on survey data and a qualitative study of the teacher candidate experience, we explore the following questions: In a teacher education program committed to promoting social justice, embracing an inquiry-into-practice stance, and affirming diversity by meeting the needs of diverse learners, how do teacher candidates assess pupil learning, in particular, how are their assessments influenced by these program themes? Further, how do they respond when dilemmas linked to pupil learning arise? Specifically. we focused on dilemmas two teacher candidates encountered that engendered a sense of disequilibrium, a.feeling something was not quite right with their teaching. In turn, we consider how they responded - typically taking ownership of dilemmas and modifying their teaching, while occasionally distancing themselves from responsibility for pupil performance. To conclude, we discuss implications for teacher educators, and specifically for Catholic institutions of higher education that prepare teachers for both public and Catholic schools

Reflecting on Pupil Learning to Promote Social Justice: A Catholic University\u27s Approach to Assessment

In contrast to current education policies that conceptualize pupil learning largely in terms of standardized exam scores, we offer an alternative view, one that conceives of pupil learning as a source of insight for pupils and teachers alike. Drawing on survey data and a qualitative study of the teacher candidate experience, we explore the following questions: In a teacher education program committed to promoting social justice, embracing an inquiry-into-practice stance, and affirming diversity by meeting the needs of diverse learners, how do teacher candidates assess pupil learning, in particular, how are their assessments influenced by these program themes? Further, how do they respond when dilemmas linked to pupil learning arise? Specifically. we focused on dilemmas two teacher candidates encountered that engendered a sense of disequilibrium, a.feeling something was not quite right with their teaching. In turn, we consider how they responded - typically taking ownership of dilemmas and modifying their teaching, while occasionally distancing themselves from responsibility for pupil performance. To conclude, we discuss implications for teacher educators, and specifically for Catholic institutions of higher education that prepare teachers for both public and Catholic schools

A dynamic network approach for the study of human phenotypes

The use of networks to integrate different genetic, proteomic, and metabolic datasets has been proposed as a viable path toward elucidating the origins of specific diseases. Here we introduce a new phenotypic database summarizing correlations obtained from the disease history of more than 30 million patients in a Phenotypic Disease Network (PDN). We present evidence that the structure of the PDN is relevant to the understanding of illness progression by showing that (1) patients develop diseases close in the network to those they already have; (2) the progression of disease along the links of the network is different for patients of different genders and ethnicities; (3) patients diagnosed with diseases which are more highly connected in the PDN tend to die sooner than those affected by less connected diseases; and (4) diseases that tend to be preceded by others in the PDN tend to be more connected than diseases that precede other illnesses, and are associated with higher degrees of mortality. Our findings show that disease progression can be represented and studied using network methods, offering the potential to enhance our understanding of the origin and evolution of human diseases. The dataset introduced here, released concurrently with this publication, represents the largest relational phenotypic resource publicly available to the research community.Comment: 28 pages (double space), 6 figure

Plasma-based assays distinguish hyperfibrinolysis and shutdown subgroups in trauma-induced coagulopathy

BACKGROUND Trauma patients with abnormal fibrinolysis have increased morbidity and mortality. Knowledge of mechanisms differentiating fibrinolytic phenotypes is important to optimize treatment. We hypothesized that subjects with abnormal fibrinolysis identified by whole blood viscoelastometry can also be distinguished by plasma thrombin generation, clot structure, fibrin formation, and plasmin generation measurements. METHODS Platelet-poor plasma (PPP) from an observational cross-sectional trauma cohort with fibrinolysis shutdown (% lysis at 30 minutes [LY30] \u3c 0.9, n = 11) or hyperfibrinolysis (LY30 \u3e 3%, n = 9) defined by whole blood thromboelastography were studied. Noninjured control subjects provided comparative samples. Thrombin generation, fibrin structure and formation, and plasmin generation were measured by fluorescence, confocal microscopy, turbidity, and a fluorescence-calibrated plasmin assay, respectively, in the absence/presence of tissue factor or tissue plasminogen activator (tPA). RESULTS Whereas spontaneous thrombin generation was not detected in PPP from control subjects, PPP from hyperfibrinolysis or shutdown patients demonstrated spontaneous thrombin generation, and the lag time was shorter in hyperfibrinolysis versus shutdown. Addition of tissue factor masked this difference but revealed increased thrombin generation in hyperfibrinolysis samples. Compared with shutdown, hyperfibrinolysis PPP formed denser fibrin networks. In the absence of tPA, the fibrin formation rate was faster in shutdown than hyperfibrinolysis, but hyperfibrinolysis clots lysed spontaneously; these differences were masked by addition of tPA. Tissue plasminogen activator–stimulated plasmin generation was similar in hyperfibrinolysis and shutdown samples. Differences in LY30, fibrin structure, and lysis correlated with pH. CONCLUSION This exploratory study using PPP-based assays identified differences in thrombin generation, fibrin formation and structure, and lysis in hyperfibrinolysis and shutdown subgroups. These groups did not differ in their ability to promote tPA-triggered plasmin generation. The ability to characterize these activities in PPP facilitates studies to identify mechanisms that promote adverse outcomes in trauma

The variable internal structure of the Mycoplasma penetrans attachment organelle revealed by biochemical and microscopic analyses: implications for attachment organelle mechanism and evolution

Although mycoplasmas have small genomes, many of them, including the HIV-associated opportunist Mycoplasma penetrans, construct a polar attachment organelle (AO) that is used for both adherence to host cells and gliding motility. However, the irregular phylogenetic distribution of similar structures within the mycoplasmas, as well as compositional and ultrastructural differences among these AOs, suggests that AOs have arisen several times through convergent evolution. We investigated the ultrastructure and protein composition of the cytoskeleton-like material of the M. penetrans AO with several forms of microscopy and biochemical analysis, to determine whether the M. penetrans AO was constructed at the molecular level on principles similar to those of other mycoplasmas, such as Mycoplasma pneumoniae and Mycoplasma mobile. We found that the M. penetrans AO interior was generally dissimilar from that of other mycoplasmas, in that it exhibited considerable heterogeneity in size and shape, suggesting a gel-like nature. In contrast, several of the 12 potential protein components identified by mass spectrometry of M. penetrans detergent-insoluble proteins shared certain distinctive biochemical characteristics with M. pneumoniae AO proteins, although not with M. mobile proteins. We conclude that convergence between M. penetrans and M. pneumoniae AOs extends to the molecular level, leading to the possibility that the less organized material in both M. pneumoniae and M. penetrans is the substance principally responsible for the organization and function of the AO

Can changes in spending on health and social care explain the recent mortality trends in Scotland? A protocol for an observational study

Introduction: There have been steady reductions in mortality rates in the majority of high-income countries, including Scotland, since 1945. However, reductions in mortality rates have slowed down since 2012–2014 in these nations; and have reversed in some cases. Deaths among those aged 55+ explain a large amount of these changing mortality trends in Scotland. Increased pressures on health and social care services have been suggested as one factor explaining these changes. This paper outlines a protocol for the approach to testing the extent to which health and social care pressures can explain recent mortality trends in Scotland. Although a slower rate of mortality improvements have affected people of all ages, certain ages have been more negatively affected than the others. The current analyses will be run by age-band to test if the service pressure-mortality link varies across age-group. Methods and analysis: This will be an observational ecological study based on the Scottish population. The exposures of interest will be the absolute (primary outcome) and percentage (secondary outcome) change in real terms per capita spending on social and healthcare services between 2011 and 2017. The outcome of interest will be the absolute (primary outcome) and percentage (secondary outcome) change in age-standardised mortality rate between 2012 and 2018 for men and women separately. The units of analysis will be the 32 local authorities and the 14 territorial health boards. The analyses will be run for both all age-groups combined and for the following age bands: <1, 1–15, 16–44, 45–64, 65–74, 75–84 and 85+. A series of descriptive analyses will summarise the distribution of health and social care expenditure and mortality trends between 2011 and 2018. Linear regression analysis will be used to investigate the direct association between health care spending and mortality rates. Ethics and dissemination: The data used in this study will be publicly available and aggregated and will not be individually identifiable; therefore, ethical committee approval is not needed. This work will not result in the creation of a new data set. On completion, the study will be stored within the National Health Service research governance system. All of the results will be published once they have been shared with partner agencies

MTN-001: Randomized Pharmacokinetic Cross-Over Study Comparing Tenofovir Vaginal Gel and Oral Tablets in Vaginal Tissue and Other Compartments

Background: Oral and vaginal preparations of tenofovir as pre-exposure prophylaxis (PrEP) for human immunodeficiency virus (HIV) infection have demonstrated variable efficacy in men and women prompting assessment of variation in drug concentration as an explanation. Knowledge of tenofovir concentration and its active form, tenofovir diphosphate, at the putative vaginal and rectal site of action and its relationship to concentrations at multiple other anatomic locations may provide key information for both interpreting PrEP study outcomes and planning future PrEP drug development. Objective: MTN-001 was designed to directly compare oral to vaginal steady-state tenofovir pharmacokinetics in blood, vaginal tissue, and vaginal and rectal fluid in a paired cross-over design. Methods and Findings: We enrolled 144 HIV-uninfected women at 4 US and 3 African clinical research sites in an open label, 3-period crossover study of three different daily tenofovir regimens, each for 6 weeks (oral 300 mg tenofovir disoproxil fumarate, vaginal 1% tenofovir gel [40 mg], or both). Serum concentrations after vaginal dosing were 56-fold lower than after oral dosing (p<0.001). Vaginal tissue tenofovir diphosphate was quantifiable in ≥90% of women with vaginal dosing and only 19% of women with oral dosing. Vaginal tissue tenofovir diphosphate was ≥130-fold higher with vaginal compared to oral dosing (p<0.001). Rectal fluid tenofovir concentrations in vaginal dosing periods were higher than concentrations measured in the oral only dosing period (p<0.03). Conclusions: Compared to oral dosing, vaginal dosing achieved much lower serum concentrations and much higher vaginal tissue concentrations. Even allowing for 100-fold concentration differences due to poor adherence or less frequent prescribed dosing, vaginal dosing of tenofovir should provide higher active site concentrations and theoretically greater PrEP efficacy than oral dosing; randomized topical dosing PrEP trials to the contrary indicates that factors beyond tenofovir's antiviral effect substantially influence PrEP efficacy. Trial Registration: ClinicalTrials.gov NCT00592124