Miracle-dz/UniFAR-FTUs huggingface dataset:
Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture

Drosophila melanogaster has played a pivotal role in the development of modern population genetics. However, many basic questions regarding the demographic and adaptive history of this species remain unresolved. We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European population. Most genomes were sequenced above 25X depth from haploid embryos. Results indicated a pervasive influence of non-African admixture in many African populations, motivating the development and application of a novel admixture detection method. Admixture proportions varied among populations, with greater admixture in urban locations. Admixture levels also varied across the genome, with localized peaks and valleys suggestive of a non-neutral introgression process. Genomes from the same location differed starkly in ancestry, suggesting that isolation mechanisms may exist within African populations. After removing putatively admixed genomic segments, the greatest genetic diversity was observed in southern Africa (e.g. Zambia), while diversity in other populations was largely consistent with a geographic expansion from this potentially ancestral region. The European population showed different levels of diversity reduction on each chromosome arm, and some African populations displayed chromosome arm-specific diversity reductions. Inversions in the European sample were associated with strong elevations in diversity across chromosome arms. Genomic scans were conducted to identify loci that may represent targets of positive selection within an African population, between African populations, and between European and African populations. A disproportionate number of candidate selective sweep regions were located near genes with varied roles in gene regulation. Outliers for Europe-Africa FST were found to be enriched in genomic regions of locally elevated cosmopolitan admixture, possibly reflecting a role for some of these loci in driving the introgression of non-African alleles into African populations.
Metformin Inhibits Cytokine-Induced Nuclear Factor

AMP-activated protein kinase (AMPK) is tightly regulated by the cellular AMP:ATP ratio and plays a central role in regulation of energy homeostasis and metabolic stress. Metformin has been shown to activate AMPK. We hypothesized that metformin may prevent nuclear factor B (NFB) activation in endothelial cells exposed to inflammatory cytokines. Metformin was observed to activate AMPK, as well as its downstream target, phosphoacetyl coenzyme A carboxylase, in human umbilical vein endothelial cells (HUVECs). Metformin also dose-dependently inhibited tumor necrosis factor (TNF)–induced NFB activation and TNF–induced I B kinase activity. Furthermore, metformin attenuated the TNF–induced gene expression of various proinflammatory and cell adhesion molecules, such as vascular cell adhesion molecule-1, E-selectin, intercellular adhesion molecule-1, and monocyte chemoattractant protein-1, in HUVECs. A pharmacological activator of AMPK, 5-amino-4-imidazole carboxamide riboside (AICAR), dose-dependently inhibited TNFand interleukin-1 –induced NFB reporter gene expression. AICAR also suppressed the TNFand interleukin-1 –induced gene expression of vascular cell adhesion molecule-1, E-selectin, intercellular adhesion molecule-1, and monocyte chemoattractant protein-1 in HUVECs. The small interfering RNA for AMPK 1 attenuated metformin or AICAR–induced inhibition of NFB activation by TNF, suggesting a possible role of AMPK in the regulation of cell inflammation. In light of these findings, we suggest that metformin attenuates the cytokine-induced expression of proinflammatory and adhesion molecule genes by inhibiting NFB activation via AMPK activation. Thus, it might be useful to target AMPK signaling in future efforts to prevent atherogenic and inflammatory vascular disease. (Hypertension. 2006;47:1183-1188.)
Infection of an established mouse bone marrow cell line (JLS-V9) with Rauscher and Moloney murine leukemia viruses.

Summary A cell line (JLS-V9) established from the bone marrow of normal weanling BALB/c mice has been shown to be susceptible to infection with either the Rauscher or Moloney murine leukemia viruses. The Rauscher- and Moloney-virus-infected cultures were designated JLS-V10 and JLS-V11, respectively. Both infected cultures were carried for 7 months without loss of infectivity. However, more recent bioassays of Rauscher virus from the JLS-V10 line have indicated a reduction of infectivity for BALB/c mice. Virus multiplication was evaluated both by electron microscopy and bioassays of cell free tissue culture fluids. The viruses were identified by serum neutralization and response of infected mice to the respective viruses, as well as electron microscopy. Cytopathogenic effects of the viruses have not been observed in either of the infected cultures.
HUMB: Automatic Key Term Extraction from Scientific Articles in GROBID

The Semeval task 5 was an opportunity for experimenting with the key term extraction module of GROBID, a system for extracting and generating bibliographical information from technical and scientific documents. The tool first uses GROBID's facilities for analyzing the structure of scientific articles, resulting in a first set of structural features. A second set of features captures content properties based on phraseness, informativeness and keywordness measures. Two knowledge bases, GRISP and Wikipedia, are then exploited for producing a last set of lexical/semantic features. Bagged decision trees appeared to be the most efficient machine learning algorithm for generating a list of ranked key term candidates. Finally a post ranking was realized based on statistics of cousage of keywords in HAL, a large Open Access publication repository.
Islands of Music Analysis, Organization, and Visualization of Music Archives

Islands of Music are a graphical user interface to music collections based on a metaphor of geographic maps, where islands represent music genres. Similar genres are located close to each other and the pieces of music are located accordingly. Islands of Music are intended to support the exploration of unknown music collections. The user can listen to the music by clicking on its representation on the map and can explore island after island according to his or her musical taste. Islands of Music could be utilized by music stores to assist their customers in finding something new to buy. They could also serve as interfaces to digital music libraries, or they could simply be used to organize one’s personal music collection at home. My thesis explores two main aspects related to music maps. One is how to compute the similarity of two pieces of music, so a whole music collection can be organized accordingly. The second aspect is how to present this information to the user in an intuitive way. The methods are illustrated and evaluated using a music collection consisting of 359 popular pieces from different genres with a total length of about 23 hours. This report briefly reviews related work in Section 2 and then presents the basic architecture of the system in Section 3. The results are briefly demonstrated in Section 4. Finally, in Section 5 some conclusions are drawn.
The Differential Effect of Cyclosporine on Hypnotic Response and Pain Reaction in Mice

BACKGROUND:The calcineurin inhibitor, cyclosporine, is widely used for preventing allograft rejection in organ transplantation. Systemically administered cyclosporine is prevented from entering into the brain by the action of P-glycoprotein, encoded by the multidrug resistant 1 (mdr1) gene. However, in many transplant recipients, cyclosporine administration causes postoperative neuropsychological side effects, such as confusion, depression, and anxiety. Recently, calcineurin-inhibitor-induced pain syndrome, characterized by severe pain in the lower limbs, has also been recognized in both organ and stem-cell transplantations. METHODS:In the present study, we developed behavioral models in wild-type and mdr1a knockout mice to reveal whether peripheral or central cyclosporine alters pain reactions and hypnotic sensitivities. Cyclosporine's central actions can be better evaluated in mdr1a knockout mice that lack P-glycoprotein. After intraperitoneal administration of cyclosporine, we examined tail-flick latency in the tail immersion test, or duration of loss of righting reflex in response to pentobarbital and ketamine. RESULTS:In wild-type mice, the highest dose of cyclosporine significantly prolonged the duration of loss of righting reflex in response to ketamine, but not to pentobarbital. On the other hand, the lower doses of cyclosporine significantly increased both pentobarbital- and ketamine-induced sleep durations in mdr1a knockout mice. Tail-flick latencies in the tail immersion test were significantly shortened in both wild-type and knockout mice by the administration of cyclosporine. CONCLUSIONS:Our results suggest that centrally accumulated cyclosporine enhances the hypnotic response to pentobarbital and ketamine, but peripheral cyclosporine induces hyperalgesia.
Crystal structures of substrate-bound and substrate-free cytochrome P450 46A1, the principal cholesterol hydroxylase in the brain

By converting cholesterol to 24S-hydroxycholesterol, cytochrome P450 46A1 (CYP46A1) initiates the major pathway for cholesterol removal from the brain. Two crystal structures of CYP46A1 were determined. First is the 1.9-Å structure of CYP46A1 complexed with a high-affinity substrate cholesterol 3-sulfate (CH-3S). The second structure is that of the substrate-free CYP46A1 at 2.4-Å resolution. CH-3S is bound in the productive orientation and occupies the entire length of the banana-shaped hydrophobic active-site cavity. A unique helix B′–C loop insertion (residues 116–120) contributes to positioning cholesterol for oxygenation catalyzed by CYP46A1. A comparison with the substrate-free structure reveals substantial substrate-induced conformational changes in CYP46A1 and suggests that structurally distinct compounds could bind in the enzyme active site. In vitro assays were performed to characterize the effect of different therapeutic agents on cholesterol hydroxylase activity of purified full-length recombinant CYP46A1, and several strong inhibitors and modest coactivators of CYP46A1 were identified. Structural and biochemical data provide evidence that CYP46A1 activity could be altered by exposure to some therapeutic drugs and potentially other xenobiotics.
Theories in social psychology

List of Contributors. Acknowledgments. Introduction. Part I: Social Cognition: 1. Toward Freedom: Reactance Theory Revisited (Derek Chadee, University of the West Indies, St. Augustine). 2. Inconsistency in Cognition: Cognitive Dissonance (Paul R. Nail and Kurt A. Boniecki, University of Central Arkansas). 3. Attribution Theories: How People Make Sense of Behavior (Bertram F. Malle, Brown University). 4. The Elaboration Likelihood Model of Persuasion: Thoughtful and Non-Thoughtful Social Influence (Benjamin C. Wagner and Richard E. Petty, Ohio State University). Part II: Social Comparison: 5. Social Comparison: Motives, Standards, and Mechanisms (Katja Corcoran, Jan Crusius, and Thomas Mussweiler, University of Cologne). 6. Relative Deprivation: Understanding the Dynamics of Discontent (Jenny Carrillo, Planned Parenthood of Southern New England, Alexandra F. Corning, University of Notre Dame, Tara C. Dennehy, San Francisco State University, and Faye J. Crosby, University of California, Santa Cruz). Part III: Social Reinforcement: 7. Evaluating Fairness: Critical Assessment of Equity Theory (Denise M. Polk, West Chester University of Pennsylvania). 8. Interdependence in Social Interaction (Ann C. Rumble, Ohio University-Chillicothe). Part IV: Self: 9. Self-Categorization and Social Identification: Making Sense of Us and Them (Katharina Schmid, Miles Hewstone, New College, University of Oxford), and Ananthi Al Ramiah, University of Oxford). 10. Social Categorization Theories: From Culture to Cognition (Richard J. Crisp, University of Kent and Angela T. Maitner, University of Sharjah, United Arab Emirates). 11. Symbolic Interactionism: From Gestalt to Cybernetics (Andreas Schneider, Texas Tech University). 12. Impression Management: Influencing Perceptions of Self (Meni Koslowsky and Shani Pindek, Bar-Ilan University). Author Index. Subject Index.
Ontogenetic Variation in Digestion by the Herbivorous Lizard Ctenosaura pectinata

I tested the hypothesis that an animal with an ontogenetic diet shift must have different digestive efficiencies for foods that correspond to its diet shift, so that nutrient and energy extraction are maximized. The iguanine lizard Ctenosaura pectinata undergoes an ontogenetic diet shift from eating insects as a juvenile to plants as an adult. When fed six different pure foods from the natural diets of different age classes, C. pectinata assimilated nutrients and energy differently depending on food type and age class. Extraction of energy and nutrients in insect larvae was maximized by juvenile lizards. Calcium, phosphorus, and energy were readily assimilated from flowers and fruit by immature and adult lizards. Magnesium levels were highest in leaves and were extracted by immature and adult lizards, but xenobiotic effects of one plant leaf (Croton suberosus), eaten by adults, killed juvenile lizards. Although juvenile C. pectinata ate some flowers (Senna wislizenii) naturally, they were less efficient at digesting cell walls from these plant parts than were older lizards. Ontogenetic changes in ctenosaur digestive physiology were not the result of a trade‐off involving ecological costs of different foods; rather, each age class preferred a diet that maximized its physiological benefit.
Predictability and Transaction Costs: The Impact on Rebalancing Rules and Behavior

We consider the impact of transaction costs on the portfolio decisions of a long-lived agent with isoelastic preferences. In particular, we focus on how portfolio choice, rebalancing frequency and average cost incurred change over the lifecycle are affected by return predictability. Two types of costs are evaluated: proportional to the change in the holding of the risky asset and a fixed fraction of portfolio value. We find that realistic transaction costs can materially affect rebalancing behavior, creating no-trade regions that widen near the investor's terminal date. At the same time, realistic proportional and fixed costs have little effect on the midpoint of the no-trade region, unless liquidation costs differ across assets. Return predictability calibrated to U.S. stock returns is found to have large effects on rebalancing behavior relative to independent and identically distributed (i.i.d.) returns with the same unconditional distribution. For example, return predictability causes rebalancing frequency to increase, and cost incurred to increase by an order of magnitude, at all points in the investor's life. No-trade regions early in life are wider when returns are predictable than when they are not. Finally, we find that the nature of the return predictability, including the presence or not of return heteroscedasticity, can have large effects on rebalancing behavior.
The choice of forgiveness : Forgiveness of self and others focusing on situation and personality

Throughout the years research on forgiveness has expanded (Thompson et al., 2005). However it is only in recent years that forgiveness has been recognized as a concept with two components, forgiveness of self and others (Ross, Hertenstein & Wrobel, 2007). The aim of this study was to see how forgiveness of self and others differed, also taking into consideration variables such as situation and personality. One hundred participants completed a web-based questionnaire containing four forgiveness situations, the Heartland Forgiveness Scale and a personality test. The results from the forgiveness situations did not reveal any significant difference between forgiveness of self and others. However, the ratings of the Heartland Forgiveness Scale revealed that it was harder to forgive others. Also, it was found that participants differed in their forgiveness depending on what situation it was. In addition, individuals who scored low in the personality-type instability were less able to forgive others. It seems, therefore, that forgiveness of self and others do differ and also in the aspects of situation and personality.
Extensions of ordered theories by generic predicates

Given a theory T extending that of dense linear orders without endpoints (DLO), in a language ℒ ⊇ {<}, we are interested in extensions T′ of T in languages extending ℒ by unary relation symbols that are each interpreted in models of T′ as sets that are both dense and codense in the underlying sets of the models. There is a canonically “wild” example, namely T = Th(〈ℝ, <, +, ·〉) and T′ = Th(〈ℝ, <, +, · ℚ 〉). Recall that T is o-minimal, and so every open set definable in any model of T has only finitely many definably connected components. But it is well known that 〈ℝ, <, +, · ℚ 〉 defines every real Borel set, in particular, every open subset of any finite cartesian power of ℝ and every subset of any finite cartesian power of ℚ. To put this another way, the definable open sets in models of T are essentially as simple as possible, while T′ has a model where the definable open sets are as complicated as possible, as is the structure induced on the new predicate. In contrast to the preceding example, if ℝalg is the set of real algebraic numbers and T′ Th(〈ℝ, <, +, ·, 〈alg〉), then no model of T′ defines any open set (of any arity) that is not definable in the underlying model of T.
Power-spectrum normalization from the local abundance of rich clusters of galaxies

The number density of rich galaxy clusters still provides the most robust way of normalizing the power spectrum of dark matter perturbations on scales relevant to large-scale structure. We revisit this constraint in the light of several recent developments: (1) the availability of well-defined samples of local clusters with relatively accurate X-ray temperatures; (2) new theoretical mass functions for dark matter haloes, which provide a good fit to large numerical simulations; (3) more accurate mass–temperature relations from larger catalogues of hydrodynamical simulations; (4) the requirement to consider closed as well as open and flat cosmologies to obtain full multiparameter likelihood constraints for CMB and SNe studies. We present a new sample of clusters drawn from the literature and use this sample to obtain improved results on σ8, the normalization of the matter power spectrum on scales of 8 h−1 Mpc, as a function of the matter density and cosmological constant in a universe with general curvature. We discuss our differences with previous work, and the remaining major sources of uncertainty. Final results on the normalization, approximately independent of power spectrum shape, can be expressed as constraints on σ at an appropriate cluster normalization scale RCl. We provide fitting formulas for RCl and σ(RCl) for general cosmologies, as well as for σ8 as a function of cosmology and shape parameter Γ. For flat models we find approximately σ8≃(0.495−0.037+0.034)ΩM−0.60 for Γ=0.23, where the error bar is dominated by uncertainty in the mass–temperature relation.
The Representation and Recognition of Action Using Temporal Templates

A new view-based approach to the representation and recognition of action is presented. The basis of the representation is a temporal template | a static vector-image where the vector value at each point is a function of the motion properties at the corresponding spatial location in an image sequence. Using 18 aerobics exercises as a test domain, we explore the representational power of a simple, two component version of the templates: the rst value is a binary value indicating the presence of motion, and the second value is a function of the recency of motion in a sequence. We then develop a recognition method which matches these temporal templates against stored instances of views of known actions. The method automatically performs temporal segmentation, is invariant to linear changes in speed, and runs in real-time on a standard platform. We recently incorporated this technique into the KidsRoom: an interactive, narrative play-space for children.
Protofibrillar Intermediates of Amyloid β-Protein Induce Acute Electrophysiological Changes and Progressive Neurotoxicity in Cortical Neurons

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder that is thought to be caused in part by the age-related accumulation of amyloid β-protein (Aβ). The presence of neuritic plaques containing abundant Aβ-derived amyloid fibrils in AD brain tissue supports the concept that fibril accumulation per se underlies neuronal dysfunction in AD. Recent observations have begun to challenge this assumption by suggesting that earlier Aβ assemblies formed during the process of fibrillogenesis may also play a role in AD pathogenesis. Here, we present the novel finding that protofibrils (PF), metastable intermediates in amyloid fibril formation, can alter the electrical activity of neurons and cause neuronal loss. Both low molecular weight Aβ (LMW Aβ) and PF reproducibly induced toxicity in mixed brain cultures in a time- and concentration-dependent manner. No increase in fibril formation during the course of the experiments was observed by either Congo red binding or electron microscopy, suggesting that the neurotoxicity of LMW Aβ and PF cannot be explained by conversion to fibrils. Importantly, protofibrils, but not LMW Aβ, produced a rapid increase in EPSPs, action potentials, and membrane depolarizations. These data suggest that PF have inherent biological activity similar to that of mature fibrils. Our results raise the possibility that the preclinical and early clinical progression of AD is driven in part by the accumulation of specific Aβ assembly intermediates formed during the process of fibrillogenesis.
Autonomous Learning of User's Preferences Improved through User Feedback

Ambient Intelligent (AmI) environments are supposed to act proactively anticipating the user’s needs and preferences, therefore the capability of an AmI system to learn those elements out of daily life behaviour of those using the environment is very valuable. In this paper we present a system that discovers patterns related to user’s actions and improves them through user feedback. The core of this system is an algorithm which taking as starting point information collected by sensor discovers these patterns. Coupled with the algorithm, a language to represent those patterns has been developed. This system allows the user experiencing the AmI environment to verbally interact with the system and give his/her feedback about patterns that have been discovered. The speech based interaction provides a natural communication for the user and the simple protocol established makes the system available to users without sophisticated training.
Dynamical Models for Omni-directional Robots with 3 and 4 Wheels

Omni-directional robots are becoming more and more common in recent robotic applications. They offer improved ease of maneuverability and effectiveness at the expense of increased complexity. Frequent applications include but are not limited to robotic competitions and service robotics. The goal of this work is to find a precise dynamical model in order to predict the robot behavior. Models were found for two real world omni-directional robot configurations and their parameters estimated using a prototype that can have 3 or 4 wheels. Simulations and experimental runs are presented in order to validate the presented work.