Miracle-dz/UniFAR-FTUs huggingface dataset:
Hierarchical Clustering With Prototypes via Minimax Linkage

Agglomerative hierarchical clustering is a popular class of methods for understanding the structure of a dataset. The nature of the clustering depends on the choice of linkage—that is, on how one measures the distance between clusters. In this article we investigate minimax linkage, a recently introduced but little-studied linkage. Minimax linkage is unique in naturally associating a prototype chosen from the original dataset with every interior node of the dendrogram. These prototypes can be used to greatly enhance the interpretability of a hierarchical clustering. Furthermore, we prove that minimax linkage has a number of desirable theoretical properties; for example, minimax-linkage dendrograms cannot have inversions (unlike centroid linkage) and is robust against certain perturbations of a dataset. We provide an efficient implementation and illustrate minimax linkage’s strengths as a data analysis and visualization tool on a study of words from encyclopedia articles and on a dataset of images of human faces.
Deformations of nilpotent cones and Springer correspondences

Let $G = \mathop{Sp}( 2n )$ be the symplectic group over ${\Bbb Z}$. We present a certain kind of deformation of the nilpotent cone of $G$ with $G$-action. This enables us to make direct links between the Springer correspondence of ${\frak{sp}} _{2n}$ over ${\Bbb C}$, that over characteristic two, and our exotic Springer correspondence. As a by-product, we obtain a complete description of our exotic Springer correspondence.
Recombinant BCG Expressing Mycobacterium ulcerans Ag85A Imparts Enhanced Protection against Experimental Buruli ulcer

Buruli ulcer, an emerging tropical disease caused by Mycobacterium ulcerans (MU), is characterized by disfiguring skin necrosis and high morbidity. Relatively little is understood about the mode of transmission, pathogenesis, or host immune responses to MU infection. Due to significant reduction in quality of life for patients with extensive tissue scarring, and that a disproportionately high percentage of those affected are disadvantaged children, a Buruli ulcer vaccine would be greatly beneficial to the worldwide community. Previous studies have shown that mice inoculated with either M. bovis bacille Calmette–Guérin (BCG) or a DNA vaccine encoding the M. ulcerans mycolyl transferase, Ag85A (MU-Ag85A), are transiently protected against pathology caused by intradermal challenge with MU. Building upon this principle, we have generated quality-controlled, live-recombinant strains of BCG and M. smegmatis which express the immunodominant MU Ag85A. Priming with rBCG MU-Ag85A followed by an M. smegmatis MU-Ag85A boost strongly induced murine antigen-specific CD4+ T cells and elicited functional IFNγ-producing splenocytes which recognized MU-Ag85A peptide and whole M. ulcerans better than a BCG prime-boost vaccination. Strikingly, mice vaccinated with a single subcutaneous dose of BCG MU-Ag85A or prime-boost displayed significantly enhanced survival, reduced tissue pathology, and lower bacterial load compared to mice vaccinated with BCG. Importantly, this level of superior protection against experimental Buruli ulcer compared to BCG has not previously been achieved. These results suggest that use of BCG as a recombinant vehicle expressing MU antigens represents an effective Buruli ulcer vaccine strategy and warrants further antigen discovery to improve vaccine efficacy.
Back to Black: Values, Ideology and the Black Box of Political Radicalization

T his article focuses on the psychological drivers of anomic and violent behaviors described as ‘new radicalisms’ in the context of the Eurozone economic crisis. The authors make a conceptual and empirical distinction between the desire for change forward against the old (defined as radicalism) and the desire for change backward against the new (defined as reactionism). Using 2015 data from Greece, multinomial logit models test the role of core values that map on the desire for change against the new and the desire for change against the old as predictors of dormant and actualized anomic and violent behaviors. The findings support that desire for conservation triggered reactionist political engagement in Greece that spans across the left/right ideology spectrum.
Characterization of Dunaliella salina strains by flow cytometry: a new approach to select carotenoid hyperproducing strains

In the present work the characterization of different strains of Dunaliella salina from established cell culture collections and various isolates from solar saltworks located in the Canary Island, as well as one mutant, was carried out in order to assess the existence of intraspecific differences and to determine the potential productivity of each one. Morphological characteristics such as cellular size and cellular complexity and parameters linked to cellular physiology, such as pigment content or cellular growth rate, were determined by means of traditional techniques as well as flow cytometry. Results showed a high morphological and physiological intraspecific variability among the studied strains. Results suggest that the application of the lipidic dye Nile red allowed the development of a cytometric method faster than the traditional techniques to select carotenoid hyperproducing strains of microalgae.
PERSPECTIVE TAKING AND THREAT: DO THREATENING SITUATIONS HAVE AN EFFECT ON HELPING INTENTIONS AND PERCEIVED EXPECTATIONS?

An important skill for interpersonal communication is the ability to take the perspective of another person. Taking the perspective of a target can aid the perceiver in predicting the target’s mental states and subsequent behaviors. This can be especially important in threatening situations. How a member of an advantaged group believes that disadvantaged group members will react to a threatening situation may influence the advantaged member’s actions and beliefs. In the first study, female and male participants read information regarding gender while using three perspectives; their own perspective, predicting the other gender’s responses, or imagining their responses if they were the other gender. They estimated their career expectations while using their assigned perspective and their willingness to help women in the workplace while using their own perspective. The second study examined perspective taking in the political context. Participants were presented with a paragraph indicating that Independent voters were either in favor or against their political party. The participants indicated their future life expectations, willingness to compromise with the opposing party, and willingness to help a member of the opposing party. Both studies reported a similar pattern for expectations. Advantaged groups overestimated the negative effects of threat on the disadvantaged group, while disadvantaged groups overestimated the positive effects on the advantaged groups. Perspective taking increased helping intentions in Study 1 and showed mixed results in Study 2. The studies’ results were inconsistent with prior research and suggest that perspective taking may not produce positive results for groups who are disadvantaged. PERSPECTIVE TAKING AND THREAT: DO THREATENING SITUATIONS HAVE AN EFFECT ON HELPING INTENTIONS AND PERCEIVED EXPECTATIONS?
Artemisa: An open-source honeypot back-end to support security in VoIP domains

Voice over IP (VoIP) and the Session Initiation Protocol (SIP) are establishing themselves as strong players in the field of multimedia communications over IP, leveraged by low cost services and easy management. Nevertheless, the security aspects are not yet fully mastered. In this paper we present an open-source implementation of a VoIP SIP-specific honeypot named Artemisa. The honeypot is designed to connect to a VoIP enterprise domain as a back-end user-agent in order to detect malicious activity at an early stage. Moreover, the honeypot can play a role in the real-time adjustment of the security policies of the enterprise domain where it is deployed. We aim, by this contribution, to encourage the deployment of such honeypots at large scale and the collection of attack traces. We test the capacity of the honeypot to handle a series of known SIP attacks and present results from diverse scenarios.
Music and Children with Autism Spectrum Disorders: Potential Autonomic Mechanisms of Social Attention Improvement

Autism Spectrum Disorders (ASD) are an urgent health concern as new reports indicate approximately 1 in 110 children are affected by ASD (Centers for Disease Control and Prevention, 2009). Although children with ASD struggle with social interactions, quantitative meta-analyses have revealed that traditional social skill interventions only produce minimal effects (Bellini, Peters, Benner, & Hopf, 2007). Due to these minimal effects, this study diverged from the common understanding of social skill deficits and introduced an autonomic nervous system circuit as one root of social behavior problems. Children with ASD show a “fight-flight” (i.e., sympathetic) state at baseline and to unfamiliar individuals (e.g., Bal et al., 2010; Vaughan Van Hecke et al., 2009). Research indicates, however, that music has the ability to calm cardiovascular functioning (Iwanaga, Kobayashi, & Kawasaki, 2005) and improve social behaviors in children with ASD (Whipple, 2004). This study recruited participants (N = 23) between 4-7 years old with a previously diagnosed ASD. Each participant was assigned to a Music group, n = 11, or an Audiobook group, n = 12. The 90-minute experimental session consisted of a receptive vocabulary assessment and psychophysiological monitoring during a baseline video, social engagement task, listening period, and a recovery video. A soothed autonomic state was measured by increased high frequency heart rate variability and decreased heart rate. Results indicated a significant soothing effect for the Music group. Moreover, the Music group evidenced a significant increase in social attention (e.g., joint attention and sharing emotions) relative to the Audiobook group. Mediation analyses may reveal partial mediation for the soothed autonomic state on the relationship between group and social attention improvements. Thus, these results suggest that social skill interventions may not be targeting a core element of social deficits (i.e., over-aroused autonomic state).
The Dynamics of Germinal Centre Selection as Measured by Graph-Theoretical Analysis of Mutational Lineage Trees

We have developed a rigorous graph-theoretical algorithm for quantifying the shape properties of mutational lineage trees. We show that information about the dynamics of hypermutation and antigen-driven clonal selection during the humoral immune response is contained in the shape of mutational lineage trees deduced from the responding clones. Age and tissue related differences in the selection process can be studied using this method. Thus, tree shape analysis can be used as a means of elucidating humoral immune response dynamics in various situations.
Human endometrial cancer cell cultures for hormonal studies.

A cell line of human endometrial adenocarcinoma (HEC-1), established by Kuramoto et al . in 1968, was studied. The presence of estradiol receptors in these cells was documented. The receptors were found to reside mainly in the nucleus, even when cells were grown in estrogen-free medium. Isolated nuclei from HEC cells could be labeled during incubations with [3H]estradiol at 0–4°. The induction of estradiol 17β-dehydrogenase by progestins, which has been demonstrated to occur in vivo and in vitro in normal proliferative endometrium, was attempted with these cells. The attempts were unsuccessful both when estradiol and medroxyprogesterone acetate were added to the culture medium and when they were injected into hamsters bearing adenomatous tumors resulting from the transplantation of HEC cells into the cheek pouch. Intact glands, free of stromal components, were obtained by collagenase treatment of specimens of well-differentiated endometrial carcinoma, followed by filtration through stainless steel sieves. An abundance of branched glands was evident by light microscopy. Epithelial cell monolayers were derived from these glands and examined by light and electron microscopy. The preparation of glands and epithelial cell monolayers from specimens of endometrial carcinoma may provide opportunities to evaluate the responsiveness of the neoplasm to progestins, a test of potential value for the prediction of the efficacy of progestin treatment in individual patients. This approach may obviate the problems of viability encountered during the maintenance of fragments of carcinomatous tissue in organ culture.
Proceedings in Applied Mathematics and Mechanics , 30 August 2007 Electron energy level calculations for semiconductor nanostructures

Although self-assembled quantum dots are grown on wetting layers, most simulations exclude the wetting layer. The neglected effects on the electronic structure of a pyramidal InAs quantum dot embedded in a GaAs matrix are investigated based on the effective one electronic band Hamiltonian, the energy and position dependent electron effective mass approximation, and a finite height hard-wall 3D confinement potential.
Prototype Theory and the Categorization of the English Tense System

This paper attempts to address an important concept--prototypicality ---in cognitive studies on the categorization of the English tense system, and raises the grammatical and functional approaches to the tense system to the level of universal cognition. On the theoretical basis of prototype theory, this research addresses the prototype of category TENSE, its cognitive features, and the mechanisms in the categorization of the system. It is argued that category TENSE, starting from the prototype of simple present tense, extends in the chained way of concatenation and expands in the polysemous way of radiation. It also suggests that vagueness exists in the boundary of the tense category. This vagueness in the boundary helps the extension and expansion of category TENSE. With family resemblance as the operating principle, chained metonymies and the interaction between metonymic and metaphoric mechanisms contribute in the categorization.
Enhancing decoding efficiency in poor readers via a word identification game

The effects of a word identification game aimed at enhancing decoding efficiency in poor readers were tested. Following a pretest-posttest-retention design with a waiting control group, 62 poor-reading Dutch second graders received a five-hour tablet intervention across a period of five weeks. During the intervention, participants practiced reading words and pseudowords while doing semantic categorization and lexical decision exercises in a gaming context. Prior to, directly after, and five weeks following the intervention, word-decoding efficiency was assessed using a standardized read-aloud test consisting of six lists of untrained words and pseudowords with three levels of difficulty: consonant-vowel-consonant items, consonant cluster items, and disyllabic items. Significant increases as a result of the brief gaming intervention were found for decoding efficiency on all six word lists. The game, which included repetition, immediate corrective feedback, and a semantics task, elicited transfer and retention effects.
Relation between nutrition, performances and nitrogen excretion in dairy cows

Reducing N excretion from individual cows is one way among others to better cope with the problem of the negative contribution of the dairy herd to the "Nitrogen cycle" on the farm. The objectives of this paper are first to quantify the effects of the main forage systems and protein feed- ing level on the amount of N excreted in relationship to their simultaneous effects on animal per- formances and efficiencies and then to examine the particularities of the grazing situation. N excre- tion depends primarily on the level of N intake i.e. on forage species, fertilisation, growth stage and protein supplementation and therefore varies between the main usual forage systems from 90 to 150 kg N per cow per year (i.e. 12 to 20 kg N per ton of milk). A simple method is proposed to cal- culate the load of excreta N from a dairy herd according to the specific pattern of feeding practices over the year. The effects of the level of metabolic protein supply over a wide range of dietary con- centrations (80-125 g PDI per UFL) were analysed from a set of 5 feeding trials. Through that range, excreta N were largely increased and productive responses were also important (but without any residual effect), not only for milk yield (+15 to +30%) but also for milk protein concentration (+2 g.kg -1 ) and feed efficiency (+10%). The simultaneous increase observed in feed intake (+1 to +3 kg DM) accounted for half of the productive responses and could explain why the nutritive bal- ance was hardly affected by protein levels, even in early lactation. Most of the productive parameters responded to increasing PDI levels according to laws of decreasing return that are given in the text. On the contrary, the relative N losses (excreta N per milk N) decreased curvilinearly with decreasing PDI levels reaching a minimal plateau. The concentration of 100 g PDI per UFL appears as a com- mon key value for both phenomena: higher PDI levels results only in small increases in productive performances whereas N losses increase sharply, and the reverse occurs with lower PDI levels. At graz- ing, the level of N fertilisation, through the increase in sward yield and N content, is the main deter- minant of productive performances and losses of excreta N per ha. The other factors of sward val- orisation such as stocking rate only have a moderate effect whereas the effect of concentrate supply could be low or high according to protein content. Total grazing days per ha is an integrative param- eter that accounts quite well for all these factors since it reflects both sward yield and herd valorisa- tion conditions. Roughly, each extra 100 grazing days induced by higher fertilisation increases N flows by 10-15 kg.ha -1 as milk and by 70-80 kg.ha -1 as excreta.
Dropout as a Bayesian Approximation: Appendix

We show that a neural network with arbitrary depth and non-linearities, with dropout applied before every weight layer, is mathematically equivalent to an approximation to a well known Bayesian model. This interpretation might offer an explanation to some of dropout's key properties, such as its robustness to overfitting. Our interpretation allows us to reason about uncertainty in deep learning, and allows the introduction of the Bayesian machinery into existing deep learning frameworks in a principled way. This document is an appendix for the main paper "Dropout as a Bayesian Approximation: Representing Model Uncertainty in Deep Learning" by Gal and Ghahramani, 2015.
Real-time face tracking and pose estimation with partitioned sampling and relevance vector machine

Tracking the pose of human face has long been an important research topic which has many important applications, and it is particularly challenging with a monocular camera because the depth information is lost due to the perspective projection. This work adopts particle filter with partitioned sampling to decompose the state space of face pose tracking into two subspaces for increasing the sampling efficiency, thus achieving satisfactory performance with fewer particles. The parameters in the first subspace describe the target on image plane, and the parameter in the second subspace is used for the estimate of the face pose in yaw angle direction. For the evaluation of each hypothesis in the second subspace, a statistical learning algorithm called relevance vector machine (RVM) is used to map a face containing image to the pose of the face. The training of RVM is tailored to each detected frontal face, and it takes less than half second, which is suitable for a real-time application. The learning based regression model also presents the insensitive ability to expression variation and unmodeled degree of freedom. The experimental results verify that the combination of particle filter and RVM can efficiently reduce the processing time and add robustness to the performance of the system, thus making this algorithm applicable to human-machine interface with low-cost webcams.
Representations of mental health and arts participation in the national and local British press, 2007–2015

We analysed news articles published in national and local British newspapers between 2007 and 2015 to understand (1) how mental health and arts participation were framed and (2) how the relationships between participants in arts initiatives were conceptualised. Using corpus-assisted qualitative frame analysis, we identified frames of recovery, stigma and economy. The recovery frame, which emphasised that mental illness can be treated similarly to physical illness, positioned arts participation as a form of therapy that can complement or substitute medication. The stigma frame presented arts participation as a mechanism for challenging social conceptions that mentally ill individuals are incapable of productive work. The economy frame discussed the economic burden of mentally ill individuals and portrayed arts participation as facilitating their return to employment. Using thematic analysis, which paid attention to the representation of social actors, we found that service users were identified as the prime beneficiaries of arts initiatives, and arts participation was conceptualised as a way to bring people with mental health issues together. We discuss these findings against existing research on media representations of mental health and the concept of ‘mutual recovery’ and suggest what wider concurrent developments in the areas of mental health and the media may account for the uncovered frames and themes.
Social connectedness and the transition from work to retirement.

OBJECTIVES Although there are numerous studies on the role of social connections in early working life, research that examines how social connectedness matters in the later stages of a career is scarce. The present study analyzes to what extent social connectedness affects the timing of the transition from work to retirement. METHODS We draw on data from the German Socioeconomic Panel Study (GSOEP) from the years 1985-2009 (N = 10,225), and we apply techniques of event history analysis. Social connectedness includes social gatherings with friends, relatives, and neighbors (informal participation) as well as engagement in voluntary and civic associations and local politics (formal participation). RESULTS The findings demonstrate that social connectedness matters for the transition from work to retirement, but its impact depends on the type of participation. Whereas informal participation results in earlier retirement, formal participation delays labor force withdrawal. DISCUSSION The findings suggest a trade-off between informal participation and work in later life, which leads people with frequent social contacts to opt for early retirement. By contrast, the fact that formal participation is associated with postponed retirement points to employment benefits of volunteering and civic engagement among older workers.