Miracle-dz/UniFAR-FTUs huggingface dataset:
Fuzzy C-means Method for Clustering Microarray Data

MOTIVATION Clustering analysis of data from DNA microarray hybridization studies is essential for identifying biologically relevant groups of genes. Partitional clustering methods such as K-means or self-organizing maps assign each gene to a single cluster. However, these methods do not provide information about the influence of a given gene for the overall shape of clusters. Here we apply a fuzzy partitioning method, Fuzzy C-means (FCM), to attribute cluster membership values to genes. RESULTS A major problem in applying the FCM method for clustering microarray data is the choice of the fuzziness parameter m. We show that the commonly used value m = 2 is not appropriate for some data sets, and that optimal values for m vary widely from one data set to another. We propose an empirical method, based on the distribution of distances between genes in a given data set, to determine an adequate value for m. By setting threshold levels for the membership values, genes which are tigthly associated to a given cluster can be selected. Using a yeast cell cycle data set as an example, we show that this selection increases the overall biological significance of the genes within the cluster. AVAILABILITY Supplementary text and Matlab functions are available at http://www-igbmc.u-strasbg.fr/fcm/
Peningkatan Kemampuan Problem Solving Mahasiswa Sebagai Calon Guru Fisika Menggunakan Socratic Dialogue

Mastery of the concepts of physics students can be measured by its ability to solve the problems of physics. Problem solving ability is one component that must be owned by the students as a physics teacher candidates. Based on the results of initial observations, it is known that the problem solving ability of students is still low, especially associated with the use of physics concepts to solve problems. Therefore, the ability of problem solving should be trained in teaching as a form of scaffolding for students. Scaffolding can be done through the method of Socratic dialogue which is the provision of structured questions to help students find answers to the problems of physics using the right concept. This type of research is the Classroom Action Research with two cycles were performed on physics student teachers in the subjects Physics 1 with a fluid material. Improved problem solving ability was measured using test items at the end of the cycle. The results qualitatively show their developments and increased activity in the classroom compared to learning before the action. These results are supported quantitatively by an increase in average test scores of the first cycle of 70.00 into 75.86 in the second cycle. Keywords : problem solving, socratic dialogue Penguasaan konsep fisika mahasiswa dapat diukur dari kemampuannya dalam memecahkan permasalahan fisika (problem solving) . Kemampuan problem solving merupakan salah satu komponen yang harus dimiliki oleh mahasiswa sebagai calon guru fisika. Berdasarkan hasil observasi awal, diketahui bahwa kemampuan problem solving mahasiswa masih rendah, khususnya terkait dengan penggunaan konsep fisika untuk memecahkan masalah. Oleh karena itu, kemampuan problem solving perlu dilatihkan dalam pembelajaran sebagai bentuk scaffolding bagi mahasiswa. Scaffolding dapat dilakukan melalui metode socratic dialogue yang merupakan pemberian pertanyaan terstruktur untuk membantu mahasiswa menemukan jawaban permasalahan fisika menggunakan konsep yang tepat. Jenis penelitian ini adalah Penelitian Tindakan Kelas (PTK) dengan 2 siklus yang dilakukan pada mahasiswa calon guru fisika pada matakuliah Fisika Dasar 1 dengan materi Fluida. Peningkatan kemampuan problem solving diukur menggunakan butir soal tes di akhir siklus. Hasil penelitian secara kualitatif menunjukkan adanya perkembangan dan peningkatan aktivitas di kelas dibandingkan dengan pembelajaran sebelum adanya tindakan. Hasil tersebut didukung secara kuantitatif melalui peningkatan rata-rata nilai tes dari siklus I sebesar 70,00 menjadi 75,86 pada siklus II. Kata Kunci: problem solving , socratic dialogue
On Corporate Social Responsibility, Sensemaking, and the Search for Meaningfulness Through Work

Corporate social responsibility (CSR) focuses on many types of stakeholders and outcomes, including stakeholders outside of the organization and outcomes that go beyond financial results. Thus, CSR expands the notion of work to go beyond a task, job, intraindividual, intraorganizational, and profit perspective and provides an ideal conduit for individuals to seek and find meaningfulness through work. We adopt a person-centric conceptualization of CSR by focusing on sensemaking as an underlying and unifying mechanism through which individuals are proactive and intentional agents who search for and find meaningfulness through work. Our conceptualization allows us to understand variability in CSR effects due to variability in employee sensemaking and the meaningfulness employees experience from CSR; highlight synergies across disconnected theories and streams of research originating in different disciplines and at the intraindividual, intraorganizational, and extraorganizational levels of analysis; and propose new research directions for the future in the form of propositions and research questions. By using sensemaking as a unifying underlying process, the proposed conceptualization explains how individuals find meaningfulness through work and, consequently, when and why employees experience CSR in a particular manner—resulting in more or less positive outcomes for themselves, their organizations, and external stakeholders. Our proposed model could also be used in other individual-level research domains that would benefit from (a) placing people and their search for meaningfulness center stage and (b) focusing on the role that same-level and cross-level interactions among intraindividual, intraorganizational, and extraorganizational sensemaking factors play in the process.
Dynamic Edge-Conditioned Filters in Convolutional Neural Networks on Graphs

A number of problems can be formulated as prediction on graph-structured data. In this work, we generalize the convolution operator from regular grids to arbitrary graphs while avoiding the spectral domain, which allows us to handle graphs of varying size and connectivity. To move beyond a simple diffusion, filter weights are conditioned on the specific edge labels in the neighborhood of a vertex. Together with the proper choice of graph coarsening, we explore constructing deep neural networks for graph classification. In particular, we demonstrate the generality of our formulation in point cloud classification, where we set the new state of the art, and on a graph classification dataset, where we outperform other deep learning approaches.
How to Estimate Fat Mass in Overweight and Obese Subjects

Background. The prevalence of overweight and obesity is increasing and represents a primary health concern. Body composition evaluation is rarely performed in overweight/obese subjects, and the diagnosis is almost always achieved just considering body mass index (BMI). In fact, whereas BMI can be considered an important tool in epidemiological surveys, different papers stated the limitations of the use of BMI in single individuals. Aim. To assess the determinants of body composition in overweight and obese subjects. Methods. In 103 overweight or obese subjects (74 women, aged 41.5 ± 10 years, and 29 men, aged 43.8 ± 8 years), a multidimensional evaluation was performed including the assessment of body composition using Dual Energy X-Ray Absorptiometry (DXA), anthropometry, bioimpedance analysis (BIA), and biochemical parameters (total cholesterol, triacylglycerol, HDL- and LDL-cholesterol, free fatty acids and glycerol, glucose, insulin, C-reactive protein, plasma acylated and unacylated ghrelin, adiponectin, and leptin serum levels). Results. BMI does not represent the main predictor of FM estimated by DXA; FM from BIA and hip circumference showed a better association with FM from DXA. Moreover, models omitting BMI explained a greater part of variance. These data are confirmed by the predictive value analysis where BMI showed a performance similar to a “coin flip. ”
Shared Task System Description: Measuring the Compositionality of Bigrams using Statistical Methodologies

The measurement of relative compositionality of bigrams is crucial to identify Multi-word Expressions (MWEs) in Natural Language Processing (NLP) tasks. The article presents the experiments carried out as part of the participation in the shared task ‘Distributional Semantics and Compositionality (DiSCo)’ organized as part of the DiSCo workshop in ACLHLT 2011 . The experiments deal with various collocation based statistical approaches to compute the relative compositionality of three types of bigram phrases (Adjective-Noun, Verbsubject and Verb-object combinations). The experimental results in terms of both fine-grained and coarse-grained compositionality scores have been evaluated with the human annotated gold standard data. Reasonable results have been obtained in terms of average point difference and coarse precision.
“Having to Shift Everything We’ve Learned to the Side”: Expanding Research Methods Taught in Psychology to Incorporate Qualitative Methods

In Australia the tradition of conducting quantitative psychological research within a positivist framework has been challenged, with calls made for the inclusion of the full range of qualitative and quantitative methodologies within the undergraduate psychology curriculum. Despite this, the undergraduate psychology curriculum in most Australian universities retains a strong focus on teaching quantitative research methods. Limited research has examined attitudes toward qualitative research held by undergraduate psychology students taught within a positivist framework, and whether these attitudes are malleable and can be changed through teaching qualitative methodologies. Previous research has suggested that students from strong quantitative backgrounds experience some cognitive dissonance and greater difficulties in learning qualitative methods. In this article we examine 3rd year undergraduate psychology students’ attitudes to qualitative research prior to commencing and upon completion of a qualitative research unit. All students had previously completed two 13 weeks units of study in quantitative research methods. At Time 1, 63 students (84.1% female) completed online surveys comprising attitudinal measures. Key themes to emerge from student comments were that qualitative research was seen as an alternative approach, representing a paradigmatic shift that was construed by some students advantageous for meeting future professional and educative goals. Quantitative measures of attitudes to qualitative research were associated with general attitudes toward research, and psychology-specific epistemological beliefs. Changes in attitudes following completion of the qualitative research methods unit were in the hypothesized direction, but non-significant (small effect sizes). The findings increase our understanding of psychology students’ attitudes toward qualitative research and inform our recommendations for teaching research methods within the undergraduate psychology curriculum.
Interplay of Biomechanical, Energetic, Coordinative, and Muscular Factors in a 200 m Front Crawl Swim

This study aimed to determine the relative contribution of selected biomechanical, energetic, coordinative, and muscular factors for the 200 m front crawl and each of its four laps. Ten swimmers performed a 200 m front crawl swim, as well as 50, 100, and 150 m at the 200 m pace. Biomechanical, energetic, coordinative, and muscular factors were assessed during the 200 m swim. Multiple linear regression analysis was used to identify the weight of the factors to the performance. For each lap, the contributions to the 200 m performance were 17.6, 21.1, 18.4, and 7.6% for stroke length, 16.1, 18.7, 32.1, and 3.2% for stroke rate, 11.2, 13.2, 6.8, and 5.7% for intracycle velocity variation in x, 9.7, 7.5, 1.3, and 5.4% for intracycle velocity variation in y, 17.8, 10.5, 2.0, and 6.4% for propelling efficiency, 4.5, 5.8, 10.9, and 23.7% for total energy expenditure, 10.1, 5.1, 8.3, and 23.7% for interarm coordination, 9.0, 6.2, 8.5, and 5.5% for muscular activity amplitude, and 3.9, 11.9, 11.8, and 18.7% for muscular frequency). The relative contribution of the factors was closely related to the task constraints, especially fatigue, as the major changes occurred from the first to the last lap.
Central and satellite colours in galaxy groups: a comparison of the halo model and SDSS group catalogues

Current analytic and semi-analytic dark matter halo models distinguish between the central galaxy in a halo and the satellite galaxies in halo substructures. It is expected that galaxy properties are correlated with host halo mass, and that central galaxies tend to be the most luminous, massive and reddest galaxies in haloes while the satellites around them are fainter and bluer. Using a recent halo-model description of the colour dependence of galaxy clustering (Skibba & Sheth), we investigate the colours of central and satellite galaxies predicted by the model and compare them to those of two galaxy group catalogues constructed from the Sloan Digital Sky Survey (SDSS; Yang et al.; Berlind et al.). In the model, the environmental dependence of galaxy colour is determined by that of halo mass, and the predicted colour mark correlations were shown to be consistent with SDSS measurements. The model assumes that satellites tend to follow a colour–magnitude sequence that approaches the red sequence at bright luminosities; the model's success suggests that bright satellites tend to be ‘red and dead’ while the star formation in fainter ones is in the process of being quenched. In both the model and the SDSS group catalogues, we find that at fixed luminosity or stellar mass, central galaxies tend to be bluer than satellites. In contrast, at fixed group richness or halo mass, central galaxies tend to be redder than satellites, and galaxy colours become redder with increasing mass. We also compare the central and satellite galaxy colour distributions, as a function of luminosity and as a function of richness, in the model and in the two group catalogues. Except for faint galaxies and small groups, the model and both group catalogues are in very good agreement.
Success Factors for Team Project Courses

Team project courses are important elements in most computer science and software engineering programs. For many students, the team project course represents the only non-trivial software development experience before graduation. The team project should be used to introduce them to important project and process issues that otherwise are very difficult to teach. Sloppy documentation, poor project planning and tracking or ineffective communication will eventually affect the teams and teach the students a important lessons for their future work. In this paper, we investigate how students select, carry out and complete their projects. The results show that students tend to select mainstream projects with good specifications and that certain project types are less suitable for the course. The results also show that process related deliverables are crucial to the final outcome of the projects. Among the hardest, but also most important, deliverables we find the project plan
Intraspecies Competition for Niches in the Distal Gut Dictate Transmission during Persistent Salmonella Infection

In order to be transmitted, a pathogen must first successfully colonize and multiply within a host. Ecological principles can be applied to study host-pathogen interactions to predict transmission dynamics. Little is known about the population biology of Salmonella during persistent infection. To define Salmonella enterica serovar Typhimurium population structure in this context, 129SvJ mice were oral gavaged with a mixture of eight wild-type isogenic tagged Salmonella (WITS) strains. Distinct subpopulations arose within intestinal and systemic tissues after 35 days, and clonal expansion of the cecal and colonic subpopulation was responsible for increases in Salmonella fecal shedding. A co-infection system utilizing differentially marked isogenic strains was developed in which each mouse received one strain orally and the other systemically by intraperitoneal (IP) injection. Co-infections demonstrated that the intestinal subpopulation exerted intraspecies priority effects by excluding systemic S. Typhimurium from colonizing an extracellular niche within the cecum and colon. Importantly, the systemic strain was excluded from these distal gut sites and was not transmitted to naïve hosts. In addition, S. Typhimurium required hydrogenase, an enzyme that mediates acquisition of hydrogen from the gut microbiota, during the first week of infection to exert priority effects in the gut. Thus, early inhibitory priority effects are facilitated by the acquisition of nutrients, which allow S. Typhimurium to successfully compete for a nutritional niche in the distal gut. We also show that intraspecies colonization resistance is maintained by Salmonella Pathogenicity Islands SPI1 and SPI2 during persistent distal gut infection. Thus, important virulence effectors not only modulate interactions with host cells, but are crucial for Salmonella colonization of an extracellular intestinal niche and thereby also shape intraspecies dynamics. We conclude that priority effects and intraspecies competition for colonization niches in the distal gut control Salmonella population assembly and transmission.
“At the extremities of life” – Service user experiences of helpful help in mental health crises

ABSTRACT Mental health services have recently undergone a transition from institution- to community-based care, and crisis resolution teams (CRTs) represent a community-based service that targets users experiencing an acute mental health crisis. The current study was undertaken to explore the service user experiences of helpful help provided by CRTs in a mental health crisis context. Semistructured in-depth interviews were conducted with 14 service users to elucidate how mental health crises are experienced as devastating and multilayered events. Suicidal thoughts and/or intentions were commonly reported, seemingly regardless of whether the crisis was related to a serious mental illness. The important issues relating to help that were emphasized by the participants in this study were practical support and help with daily structure, establishing a foundation of safety, and strengthening the sense of self. The authors elaborate in the discussion on how these different issues of help are connected, showing that practical help plays an important role in supporting self-worth and the sense of safety, but that practical and structural issues have been rarely addressed by CRTs, at least in the context of this study. Thus, a broadened and social contextual-oriented perspective on mental health crises is important in developing helping practices that are perceived as more recovery oriented and helpful.
Insights into the Function of the Unstructured N-Terminal Domain of Proteins 4.1R and 4.1G in Erythropoiesis

Membrane skeletal protein 4.1R is the prototypical member of a family of four highly paralogous proteins that include 4.1G, 4.1N, and 4.1B. Two isoforms of 4.1R (4.1R135 and 4.1R80), as well as 4.1G, are expressed in erythroblasts during terminal differentiation, but only 4.1R80 is present in mature erythrocytes. One goal in the field is to better understand the complex regulation of cell type and isoform-specific expression of 4.1 proteins. To start answering these questions, we are studying in depth the important functions of 4.1 proteins in the organization and function of the membrane skeleton in erythrocytes. We have previously reported that the binding profiles of 4.1R80 and 4.1R135 to membrane proteins and calmodulin are very different despite the similar structure of the membrane-binding domain of 4.1G and 4.1R135. We have accumulated evidence for those differences being caused by the N-terminal 209 amino acids headpiece region (HP). Interestingly, the HP region is an unstructured domain. Here we present an overview of the differences and similarities between 4.1 isoforms and paralogs. We also discuss the biological significance of unstructured domains.
Theory of Semiflexible Filaments and Networks

We briefly review the recent developments in the theory of individual semiflexible filaments, and of a crosslinked network of such filaments, both permanent and transient. Starting from the free energy of an individual semiflexible chain, models on its force-extension relation and other mechanical properties such as Euler buckling are discussed. For a permanently crosslinked network of filaments, theories on how the network responds to deformation are provided, with a focus on continuum approaches. Characteristic features of filament networks, such as nonlinear stress-strain relation, negative normal stress, tensegrity, and marginal stability are discussed. In the new area of transient filament network, where the crosslinks can be dynamically broken and re-formed, we show some recent attempts for understanding the dynamics of the crosslinks, and the related rheological properties, such as stress relaxation, yield stress and plasticity.
Telecommunication relay services as a tool for deaf political participation and citizenship

ABSTRACT It has long been recognised that deaf people experience barriers to political participation and that notions of citizenship do not take into account the needs of deaf sign language users. In light of an effort at the European level to increase the potential for deaf sign language users to participate in political processes through technology, this paper provides results from a survey study of deaf sign language users across Europe as to their preferences in using Telecommunications Relay Services (TRS), whether they would like to see the establishment of a pan-European multilingual TRS and if they would make use of such a service for the purposes of political participation. Responses from 74 deaf people across 14 European member states confirm that deaf people want to see such a service, and would be willing to use it in order to make contact with European institutions. Therefore, the establishment of such a service has the potential to contribute to improved access to, and increased willingness to engage in, democracy through telecommunications and thus enhance the citizenship status of deaf Europeans, and therefore enhance their political participation and access to information and communication in society.
Multifractal Fingerprints in the Visual Arts

The similarity in fractal dimensions of paint blobs in samples of gestural expressionist art implies that these pigment structures are statistically indistinguishable from one another. This conclusion suggests that such dimensions cannot be used as a finger-print for identifying the work of a single artist. To overcome this limitation, the authors have adopted the multifractal spectrum as an alternative tool for artwork analysis. For the pigment blobs, it is demonstrated that this spectrum can be used to isolate a construction paradigm or art style. Additionally, the fractal dimensions of edge structures created by luminance gradients on the canvas are analyzed, yielding a potential method for visual discrimination of fractally similar paintings