Spanning Trees and bootstrap reliability estimation in correlation based networks

We introduce a new technique to associate a spanning tree to the average linkage cluster analysis. We term this tree as the Average Linkage Minimum Spanning Tree. We also introduce a technique to associate a value of reliability to links of correlation based graphs by using bootstrap replicas of data. Both techniques are applied to the portfolio of the 300 most capitalized stocks traded at New York Stock Exchange during the time period 2001-2003. We show that the Average Linkage Minimum Spanning Tree recognizes economic sectors and sub-sectors as communities in the network slightly better than the Minimum Spanning Tree does. We also show that the average reliability of links in the Minimum Spanning Tree is slightly greater than the average reliability of links in the Average Linkage Minimum Spanning Tree.Comment: 17 pages, 3 figure

Pediatric resident and faculty attitudes toward self-assessment and self-directed learning: a cross-sectional study

<p>Abstract</p> <p>Background</p> <p>The development of self-assessment and self-directed learning skills is essential to lifelong learning and becoming an effective physician. Pediatric residents in the United States are now required to use Individualized Learning Plans (ILPs) to document self-assessment and self-directed learning. A better understanding of resident and faculty attitudes and skills about self-assessment and self-directed learning will allow more successful integration of lifelong learning into residency education. The objective of this study was to compare faculty and resident attitudes, knowledge and skills about self-assessment, self-directed learning and ILPs.</p> <p>Methods</p> <p>Survey of pediatric residents and faculty at a single institution. Respondents rated their attitudes, knowledge, and self-perceived skills surrounding self-assessment, self-directed learning and ILPs.</p> <p>Results</p> <p>Overall survey response rate was 81% (79/97); 100% (36/36) residents and 70% (43/61) faculty. Residents and faculty agreed that lifelong learning is a necessary part of being a physician. Both groups were comfortable with assessing their own strengths and weaknesses and developing specific goals to improve their own performance. However, residents were less likely than faculty to continuously assess their own performance (44% vs. 81%; p < 0.001) or continuously direct their own learning (53% vs. 86%; p < 0.001). Residents were more likely than faculty to believe that residents should be primarily responsible for directing their own learning (64% vs. 19%; p < 0.0001), but at the same time, more residents believed that assigned clinical (31% vs. 0%; p < 0.0001) or curricular (31% vs. 0%; p < 0.0001) experiences were sufficient to make them competent physicians. Interns were less likely than senior residents to have a good understanding of how to assess their own skills (8% vs. 58%; p = 0.004) or what it means to be a self-directed learner (50% vs. 83%; p = 0.04).</p> <p>Qualitative comments indicated that while ILPs have the potential to help learners develop individualized, goal-directed learning plans based on strengths and weaknesses, successful implementation will require dedicated time and resident and faculty development.</p> <p>Conclusion</p> <p>These findings suggest that training and experience are necessary for physicians to understand the role of self-directed learning in education. Deliberate practice, for example by requiring residents to use ILPs, may facilitate self-directed, lifelong learning.</p

Recruitment and follow-up of adolescent and young adult cancer survivors: the AYA HOPE Study

IntroductionCancer is rare in adolescents and young adults (AYA), but these patients have seen little improvement in survival in contrast to most other age groups. Furthermore, participation in research by AYAs is typically low. We conducted a study to examine the feasibility of recruiting a population-based sample of AYA survivors to examine issues of treatment and health outcomes.MethodsIndividuals diagnosed in 2007-08 and age 15-39 at the time of diagnosis with acute lymphocytic leukemia, Hodgkin lymphoma, non-Hodgkin lymphoma, germ cell cancer or sarcoma were identified by 7 Surveillance, Epidemiology, and End-Results (SEER) cancer registries, mailed surveys within 14 months after diagnosis and again a year later, and had medical records reviewed.Results525 (43%) of the eligible patients responded, 39% refused and 17% were lost to follow-up. Extensive efforts were required for most potential respondents (87%). 76% of respondents completed the paper rather than online survey version. In a multivariate model, age, cancer site, education and months from diagnosis to the first mailing of the survey were not associated with participation, although males (p  &lt;  0.01), Hispanics and non-Hispanic blacks (p  &lt;  0.001) were less likely to participate. 91% of survivors completing the initial survey completed the subsequent survey.DiscussionDespite the response rate, those who participated adequately reflected the population of AYA cancer survivors. The study demonstrates that cancer registries are valuable foundations for conducting observational, longitudinal population-based research on AYA cancer survivors.Implications for cancer survivorsAchieving a reasonable response rate in this population is possible, but requires extensive resources

PepShell : visualization of conformational proteomics data

Proteins are dynamic molecules; they undergo crucial conformational changes induced by post-translational modifications and by binding of cofactors or other molecules. The characterization of these conformational changes and their relation to protein function is a central goal of structural biology. Unfortunately, most conventional methods to obtain structural information do not provide information on protein dynamics. Therefore, mass spectrometry-based approaches, such as limited proteolysis, hydrogen-deuterium exchange, and stable-isotope labeling, are frequently used to characterize protein conformation and dynamics, yet the interpretation of these data can be cumbersome and time consuming. Here, we present PepShell, a tool that allows interactive data analysis of mass spectrometry-based conformational proteomics studies by visualization of the identified peptides both at the sequence and structure levels. Moreover, PepShell allows the comparison of experiments under different conditions, including different proteolysis times or binding of the protein to different substrates or inhibitors

Endophytic Bacillus spp. from medicinal plants inhibit mycelial growth of Sclerotinia sclerotiorum and promote plant growth

Plant growth promoting bacteria that are also capable of suppressing plant pathogenic fungi play an important role in sustainable agriculture. There is a critical need of conducting research to discover, characterize and evaluate efficacy of new strains of such bacteria in controlling highly aggressive plant pathogens. In this study, we isolated endophytic bacteria from medicinal plants of Bangladesh and evaluated their antagonistic capacity against an important phytopathogenic fungus Sclerotinia sclerotiorum. Growth promoting effects of those isolates on cucumber and rice seedlings also were assessed. Among 16 morphologically distinct isolates, BDR-2, BRtL-2, and BCL-1 significantly inhibited the growth of S. sclerotiorum through induction of characteristic morphological alterations in hyphae and reduction of mycelial dry weight. When cucumber and rice seeds were treated with these endophytic bacteria, seven isolates (BCL-1, BDL-1, BRtL-2, BRtL-3, BDR-1, BDR-2 and BBoS-1) enhanced seed germination, seedling vigor, seedling growth, and number of roots per plant at varying level compared to untreated controls. All isolates produced high levels of indole-3-acetic acid (6.3 to 63μg mL−1) in vitro. Two most potential isolates, BDR-2 and BRtL-2 were identified 34 as Bacillus amyloliquefaciens and B. subtilis, respectively based on the 16S rRNA gene sequencing. These results suggest that endophytic Bacillus species from native medicinal plants have great potential for using as natural plant growth promoter and biopesticides in sustainable crop production

What factors in rural and remote extended clinical placements may contribute to preparedness for practice, from the perspective of students and clinicians?

What factors in rural and remote extended clinical placements may contribute to preparedness for practice, from the perspective of students and clinicians? Michele Daly, David Perkins, Koshila Kumar, Chris Roberts and Malcolm Moore Background: Community based rural education opportunities have expanded in Australia, attracting more medical students to placements in rural and remote settings. Aim: To identify the factors in an integrated, community engaged rural placement that may contribute to preparedness for practice (P4P), from the perspective of students and clinicians Methods: Forty two semi-structured interviews with medical students, supervisors and clinicians analysed thematically. Results: Opportunities for clinical learning, personal and professional development and cultural awareness were reported by students and clinicians as key factors that contribute to preparedness for practice. Potential barriers in rural and remote settings included geographical and academic isolation, perceived educational risk and differing degrees of program engagement. Conclusions: A longitudinal clinical placement in a rural setting may enable development of enhanced competencies leading to P4P. A rural setting can help provide a unique experience through hands-on learning, enhanced personal and professional development opportunities and observation of the cultural and contextual impact on health

Minor Body Science with the Nancy Grace Roman Space Telescope

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Pupillary Stroop effects

We recorded the pupil diameters of participants performing the words’ color-naming Stroop task (i.e., naming the color of a word that names a color). Non-color words were used as baseline to firmly establish the effects of semantic relatedness induced by color word distractors. We replicated the classic Stroop effects of color congruency and color incongruency with pupillary diameter recordings: relative to non-color words, pupil diameters increased for color distractors that differed from color responses, while they reduced for color distractors that were identical to color responses. Analyses of the time courses of pupil responses revealed further differences between color-congruent and color-incongruent distractors, with the latter inducing a steep increase of pupil size and the former a relatively lower increase. Consistent with previous findings that have demonstrated that pupil size increases as task demands rise, the present results indicate that pupillometry is a robust measure of Stroop interference, and it represents a valuable addition to the cognitive scientist’s toolbox

Inversion of the balance between hydrophobic and hydrogen bonding interactions in protein folding and aggregation.

Identifying the forces that drive proteins to misfold and aggregate, rather than to fold into their functional states, is fundamental to our understanding of living systems and to our ability to combat protein deposition disorders such as Alzheimer's disease and the spongiform encephalopathies. We report here the finding that the balance between hydrophobic and hydrogen bonding interactions is different for proteins in the processes of folding to their native states and misfolding to the alternative amyloid structures. We find that the minima of the protein free energy landscape for folding and misfolding tend to be respectively dominated by hydrophobic and by hydrogen bonding interactions. These results characterise the nature of the interactions that determine the competition between folding and misfolding of proteins by revealing that the stability of native proteins is primarily determined by hydrophobic interactions between side-chains, while the stability of amyloid fibrils depends more on backbone intermolecular hydrogen bonding interactions

Progressive GAA·TTC Repeat Expansion in Human Cell Lines

Trinucleotide repeat expansion is the genetic basis for a sizeable group of inherited neurological and neuromuscular disorders. Friedreich ataxia (FRDA) is a relentlessly progressive neurodegenerative disorder caused by GAA·TTC repeat expansion in the first intron of the FXN gene. The expanded repeat reduces FXN mRNA expression and the length of the repeat tract is proportional to disease severity. Somatic expansion of the GAA·TTC repeat sequence in disease-relevant tissues is thought to contribute to the progression of disease severity during patient aging. Previous models of GAA·TTC instability have not been able to produce substantial levels of expansion within an experimentally useful time frame, which has limited our understanding of the molecular basis for this expansion. Here, we present a novel model for studying GAA·TTC expansion in human cells. In our model system, uninterrupted GAA·TTC repeat sequences display high levels of genomic instability, with an overall tendency towards progressive expansion. Using this model, we characterize the relationship between repeat length and expansion. We identify the interval between 88 and 176 repeats as being an important length threshold where expansion rates dramatically increase. We show that expansion levels are affected by both the purity and orientation of the repeat tract within the genomic context. We further demonstrate that GAA·TTC expansion in our model is independent of cell division. Using unique reporter constructs, we identify transcription through the repeat tract as a major contributor to GAA·TTC expansion. Our findings provide novel insight into the mechanisms responsible for GAA·TTC expansion in human cells