Assessing the Reproducibility of Clustering of Molecular Dynamics Conformations on Self-Organizing Maps

The goal of most clustering algorithms is to find the optimal number of clusters (i.e. fewest number of clusters). However, analysis of molecular conformations of biological macromolecules obtained from computer simulations may benefit from a larger array of clusters. The Self-Organizing Map (SOM) clustering method has the advantage of generating large numbers of clusters, but often gives ambiguous results. In this work, SOMs have been shown to be reproducible when the same conformational dataset is independently clustered multiple times (~100), with the help of the Cramérs V-index (C_v). The ability of C_v to determine which SOMs are reproduced is generalizable across different SOM source codes. The conformational ensembles produced from MD (molecular dynamics) and REMD (replica exchange molecular dynamics) simulations of the penta peptide Met-enkephalin (MET) and the 34 amino acid protein human Parathyroid Hormone (hPTH) were used to evaluate SOM reproducibility. The training length for the SOM has a huge impact on the reproducibility. Analysis of MET conformational data definitively determined that toroidal SOMs cluster data better than bordered maps due to the fact that toroidal maps do not have an edge effect. For the source code from MATLAB, it was determined that the learning rate function should be LINEAR with an initial learning rate factor of 0.05 and the SOM should be trained by a sequential algorithm. The trained SOMs can be used as a supervised classification for another dataset. The toroidal 10×10 hexagonal SOMs produced from the MATLAB program for hPTH conformational data produced three sets of reproducible clusters (27%, 15%, and 13% of 100 independent runs) which find similar partitionings to those of smaller 6×6 SOMs. The χ^2 values produced as part of the C_v calculation were used to locate clusters with identical conformational memberships on independently trained SOMs, even those with different dimensions. The χ^2 values could relate the different SOM partitionings to each other.

Development of a Chinese version WHO Self-Assessment Tool for Evaluating Health Promotion in Hospital

[Support Institutions:] Department of Administration of Health, University of Montreal, Canada Public Health School of Fudan University, Shanghai, China

Working Children: their Agency and self-organization

In recent years, ‘agency’ has appeared in academic writings as a new way of referring to active involvement from below in development interventions. The concept of ‘agency’ starts from the assumption that people are actually agents themselves, continuously acting in and reacting to circumstances. In child labour activism, this concept has been applied to working children in the understanding that, in order to improve their working conditions, children should be organised in organizations that are exclusively for and (ideally) run by working children. This paper aims to evaluate the extent to which child labourers can become agents of change through their own organizations. The paper will draw on two studies carried out by the IREWOC foundation. In 2002 a study was undertaken in Bolivia to give practical meaning to the concept of child agency. Secondly, in 2004/2005 an investigation was carried out on the functioning and impact of children’s organizations in Peru, Bolivia and Brazil. The applied research methods were mainly anthropological and used participant observation, (semi-) informal interviews and group interviewing with working children, their parents and adult representatives of the working children’s organizations. Both investigations show that in focussing on children as active participants, the structural constraints under which children have to live also need to be highlighted. One needs to understand how material poverty, mental deprivation and disempowerment help to shape resilience and defiance, but also anger, distrust and marginalisation.

Matlab self study tutorial - Graphing

These resources are designed to support students in gaining more confidence with using Matlab. The PDFs provide guidance and information; Objectives: Introduce basic syntax and data preparation for graphing with Matlab by providing some data, examples of code and some background documents. Outcomes: -how to write an m file script -the importance of syntax -how to load files -how to produce simple graphs -where to get help and further examples There are also some data files to provide example data for students to work with in producing Matlab resources.

Metacognitive knowledge and self-regulation: A qualitative lecture of students functioning in writing

This research emerges from the world-wide problematic concerning student's failure. It particularly analyzes the meta-cognitive competences in the writing process of this population. Based on Flavell's (1992) viewpoint about meta-cognition and the socio-cognitive approach of self-regulation, two variables were measured: meta-cognitive knowledge and self-regulation strategies. A qualitative study was conducted on a sample of 12 French students at first year university. This study uses a specific technique of interview known as "explicitation interview". The data analysis included the categorization, codification and quantification of the information obtained with the interviews. In conclusion, even though the students had metacognitive knowledge related to the written tasks, they did not show strategies that could help to go beyond the descriptive modality of written discourses by taking into account the readers' expectations. Their writing processes focused on transcription of ideas with little control on the planning and revision phases.

La influencia del autoconcepto en el rendimiento académico en estudiantes universitarios. 'The influence of self-concept on academic achievement in university students'.

Resumen tomado de la publicación. Con el apoyo económico del departamento MIDE de la UNED. Incluye anexo con el cuestionario utilizado para la realización del estudio

Sexual presence and intentional dynamics: deviant and non-deviant sexual self-regulation from the first person stance

Child molesters (n=13) and sexually non-deviant subjects (n=29) were immersed with virtual characters depicting relevant sexual features while their sexual arousal and gaze behaviour were assessed to characterize their sexual preferences and intentional dynamics. Sexual arousal was measured using circumferential penile plethysmography (PPG). Gaze behaviour dynamics was derived from average gaze radial angular deviation (GRAD) and GRAD coefficient of variation (GRADCV). Results show distinct sexual arousal profiles according to sexual preferences and point towards the existence of specific gaze behaviour dynamics guided by sexual intentions. Theoretical interpretations are based on the ecological psychology of J.J. Gibson and the integrated theory of sexual offending (Ward, 2009; Ward & Beech, 2006). Theoretical underpinnings coming from these approaches are advocated as being especially well suited to explain how virtual reality can help probing into child molesters’ phenomenology as lived from the first-person stance.

Selecting valuable information to remember: age-related differences and similarities in self-regulated learning

It is often necessary to selectively attend to important information, at the expense of less important information, especially if you know you cannot remember large amounts of information. The present study examined how younger and older adults select valuable information to study, when given unrestricted choices about how to allocate study time. Participants were shown a display of point values ranging from 1–30. Participants could choose which values to study, and the associated word was then shown. Study time, and the choice to restudy words, was under the participant's control during the 2-minute study session. Overall, both age groups selected high value words to study and studied these more than the lower value words. However, older adults allocated a disproportionately greater amount of study time to the higher-value words, and age-differences in recall were reduced or eliminated for the highest value words. In addition, older adults capitalized on recency effects in a strategic manner, by studying high-value items often but also immediately before the test. A multilevel mediation analysis indicated that participants strategically remembered items with higher point value, and older adults showed similar or even stronger strategic process that may help to compensate for poorer memory. These results demonstrate efficient (and different) metacognitive control operations in younger and older adults, which can allow for strategic regulation of study choices and allocation of study time when remembering important information. The findings are interpreted in terms of life span models of agenda-based regulation and discussed in terms of practical applications. (PsycINFO Database Record (c) 2013 APA, all rights reserved)(journal abstract)

Triggering Solar-Powered Vehicle Activated Signs using Self Organising Maps with K-means

Solar-powered vehicle activated signs (VAS) are speed warning signs powered by batteries that are recharged by solar panels. These signs are more desirable than other active warning signs due to the low cost of installation and the minimal maintenance requirements. However, one problem that can affect a solar-powered VAS is the limited power capacity available to keep the sign operational. In order to be able to operate the sign more efficiently, it is proposed that the sign be appropriately triggered by taking into account the prevalent conditions. Triggering the sign depends on many factors such as the prevailing speed limit, road geometry, traffic behaviour, the weather and the number of hours of daylight. The main goal of this paper is therefore to develop an intelligent algorithm that would help optimize the trigger point to achieve the best compromise between speed reduction and power consumption. Data have been systematically collected whereby vehicle speed data were gathered whilst varying the value of the trigger speed threshold. A two stage algorithm is then utilized to extract the trigger speed value. Initially the algorithm employs a Self-Organising Map (SOM), to effectively visualize and explore the properties of the data that is then clustered in the second stage using K-means clustering method. Preliminary results achieved in the study indicate that using a SOM in conjunction with K-means method is found to perform well as opposed to direct clustering of the data by K-means alone. Using a SOM in the current case helped the algorithm determine the number of clusters in the data set, which is a frequent problem in data clustering.

The Purely Reflected Self

Belief in the concept of the self causes suffering. Unfortunately, although conceptual constructions like this may help to define our goal—the casting off of the belief in the self—this is a much more difficult thing to actualize and attain in daily practice. Our building blocks can form a neat tower, and we can climb to the top and gaze at the horizon, but they will topple, leaving us once again over our heads in the hedgerow. Buddha describes his teachings as a raft to ford the river of suffering in order to reach the far off bank of enlightenment: as one does not take the raft after crossing the river, so we must not lean on his teachings to make our way through life. So I intend here to abandon the raft for other accounts of existence written by other thinkers, and in this my purpose is twofold: First, in reading other interpretations we can gain new tools with which to study the architecture of the concept of the self, and second, in studying the history of the concept of self as it progresses through history we can better understand the non-inherentness of this problematic construct. I intend to examine the philosophies of self in the Chinese and European traditions, and their subsequent deconstructive traditions in order to achieve this goal.

Ethical Care of the Self and the Teacher in the Pedagogical Relationship: Reflections Based on the Latest Foucault

Our conception of education is that it is the responsible action whereby man becomes human, trains and faces the challenges that life and the world present, as man enters a larger, shared cultural tradition and thus joins the world. However such sharing implies that we must not just rely on tradition, but remain open to new ideas. It is essential for schooling to preserve a field where the art of living intersects with the world for which future generations are being prepared. It is in this field of intersection that this essay seeks to discuss Michel Foucault's thought, care of the self and the role played by others in the acquisition of ethical attitudes pertaining to one's conduct in life. Through reconstructing Foucault's ideas, we elaborate on the hypothesis that, before morally shaping students, teaching them values, or aiding in their skill acquisition in the sense prevailing in schooling today, it is important to understand the notion of care of the self (and how the notion implies interaction with others for effective care of the self). Care of the self is vital for thoroughly understanding the relationships between ethics and education in school. We particularly examine how Foucault's ideas and his analysis of the teacher's role in shaping the student's life conduct can help educators rethink pedagogical action in an ethical sense and find within it a certain openness to the formation of attitudes in educators and students

Effects of Self-Assessment on Math Homework

In this action research study of my eighth grade differentiated Algebra students, I investigated the effects of students using self-assessment on their homework. Students in my class were unmotivated and failed test objectives consistently. I wanted students to see that they controlled their learning and could be motivated to succeed. Formative assessment tells students how they need to improve. Learning needs to happen before they can be assessed. Self-assessment is one tool that helps students know if they are learning. A rubric scoring guide, daily documentation sheet and feedback on homework and test correlations were used to help students monitor their learning. Students needed time to develop the skill to self-assess. Students began to understand the relationship between homework and performing well on tests by the end of the action research period. Early in the period, most students encountered difficulty understanding that they controlled their learning and did not think homework was important. By the end of the year, all students said homework was important and that it helped them on quizzes and tests. Motivating students to complete homework is difficult. Teaching them to self-assess and to keep track of their learning helps them stay motivated.

How Student Self-Assessment Influences Mastery Of Objectives

In this action research study of my classroom of 7th grade students, enrolled in Pre- Algebra (an 8th grade course), I investigated: rate of homework completion when not taken as part of the academic grade, cognizant self-assessment and its affect on mastery of objectives, and use of self-assessment to guide instruction and re-teaching of classroom objectives. I learned that without sufficient accountability homework completion rates drop with time. Similarly, students can be overconfident in their abilities but unmoved when their summative reports do not match their initial perceived formative benchmarks. Finally, due in part to our society’s reactive nature; students find it more practical to play catch-up rather than staying caught up. As a result of this research, I plan to create, with the help of the students, an accountability statute to help students stay caught up with their understanding of the objectives, as well as allow additional time and energy spent by both student and teacher to react in a timely manner to complete student knowledge within a day or two rather than a week or two later.

A Tool Box Half Full: How Social Science can Help Solve Human–Wildlife Conflict

There is a growing recognition among wildlife managers that focusing management on wildlife often provides a temporary fix to human–wildlife conflicts, whereas changing human behavior can provide long-term solutions. Human dimensions research of wildlife conflicts frequently focuses on stakeholders’ characteristics, problem identification, and acceptability of management, and less frequently on human behavior and evaluation of management actions to change that behavior. Consequently, little information exists to assess overall success of management. We draw on our experience studying human–bear conflicts, and argue for more human dimensions studies that focus on change in human behavior to measure management success. We call for help from social scientists to conduct applied experiments utilizing two methods, direct observation and self-reported data, to measure change in behavior. We are optimistic these approaches will help fill the managers’ tool box and lead to better integration of human dimensions into human–wildlife conflict management.

Older Breast Cancer Survivors: Factors Associated with Self-reported Symptoms of Persistent Lymphedema Over 7 years of Follow-up

Lymphedema of the arm is a common complication of breast cancer with symptoms that can persist over long periods of time. For older women (over 50% of breast cancer cases) it means living with the potential for long-term complications of persistent lymphedema in conjunction with the common diseases and disabilities of aging over survivorship. We identified women > or =65 years diagnosed with primary stage I-IIIA breast cancer. Data were collected over 7 years of follow-up from consenting patients' medical records and telephone interviews. Data collected included self-reported symptoms of persistent lymphedema, breast cancer characteristics, and selected sociodemographic and health-related characteristics. The overall prevalence of symptoms of persistent lymphedema was 36% over 7 years of follow-up. Having stage II or III (OR = 1.77, 95% CI: 1.07-2.93) breast cancer and having a BMI >30 (OR = 3.04, 95% CI: 1.69-5.45) were statistically significantly predictive of symptoms of persistent lymphedema. Women > or =80 years were less likely to report symptoms of persistent lymphedema when compared to younger women (OR = 0.44, 95% CI: 0.18-0.95). Women with symptoms of persistent lymphedema consistently reported worse general mental health and physical function. Symptoms of persistent lymphedema were common in this population of older breast cancer survivors and had a noticeable effect on both physical function and general mental health. Our findings provide evidence of the impact of symptoms of persistent lymphedema on the quality of survivorship of older women. Clinical and research efforts focused on risk factors for symptoms of persistent lymphedema in older breast cancer survivors may lead to preventative and therapeutic measures that help maintain their health and well-being over increasing periods of survivorship.