Miracle-dz/UniFAR-FTUs huggingface dataset:
Designing Interactive Audiovisual Systems for Improvising Ensembles

Since 2009, I have been working on real-time audiovisual systems, used in many performances with improvising musicians. Real-time audio from a performance is analysed; the audio descriptors (along with data from gestural controllers) influence abstract animations that are based on generative systems and physics-based simulations. The musicians are in turn influenced by the visuals, essentially in a feedback loop. I will discuss technical and aesthetic design considerations for such systems and their integration into the practices of improvising ensembles, and share some experiences from musicians and audience members.
PINOKY: a ring that animates your plush toys

PINOKY is a wireless ring-like device that can be externally attached to any plush toy as an accessory that animates the toy by moving its limbs. A user is thus able to instantly convert any plush toy into a soft robot. The user can control the toy remotely or input the movement desired by moving the plush toy and having the data recorded and played back. Unlike other methods for animating plush toys, PINOKY is non-intrusive, so alterations to the toy are not required. In a user study, 1) the roles of plush toys in the participants' daily lives were examined, 2) how participants played with plush toys without PINOKY was observed, 3) how they played with plush toys with PINOKY was observed, and their reactions to the device were surveyed. On the basis of the results, potential applications were conceptualized to illustrate the utility of PINOKY.
Monopoly Pricing in the Presence of Social Learning

A monopolist offers a product to a market of consumers with heterogeneous quality preferences. Although initially uninformed about the product quality, they learn by observing past purchase decisions and reviews of other consumers. Our goal is to analyze the social learning mechanism and its effect on the seller's pricing decision. Consumers follow an intuitive non-Bayesian decision rule and, under some conditions, eventually learn the product's quality. We show how the learning trajectory can be approximated in settings with high demand intensity via a mean-field approximation that highlights the dynamics of this learning process, its dependence on the price, and the market heterogeneity with respect to quality preferences. Two pricing policies are studied: a static price, and one with a single price change. Finally, numerical experiments suggest that pricing policies that account for social learning may increase revenues considerably relative to policies that do not.
What Affects Clinicians’ Usage of Health Information Exchange?

Summary Background: The ability to electronically exchange health information among healthcare providers holds enormous promise to improve care coordination and reduce costs. Provider-to-provider data exchange is an explicit goal of the American Recovery and Reinvestment Act of 2009 and may be essential for the long-term success of the Affordable Care Act of 2010. However, little is known about what factors affect clinicians’ usage of health information exchange (HIE) functionality. Objective: To identify factors that affect clinicians’ HIE usage - in terms of frequency of contributing data to and accessing data from aggregate patient records - and suggest policies for fostering its usage. Methods: We performed a qualitative study using grounded theory by interviewing clinician-users and HIE staff of one operational HIE which supported aggregate patient record functionality. Fifteen clinicians were interviewed for one hour each about what factors affect their HIE usage. Five HIE staff were asked about technology and training issues to provide context. Interviews were recorded, transcribed and analyzed. Recruitment excluded clinicians with little or no familiarity with the HIE and was restricted to one community and a small number of specialties. Results: Clinicians were motivated to access the HIE by perceived improvements in care quality and time savings, but their motivation was moderated by an extensive list of factors including gaps in data, workflow issues and usability issues. HIE access intensities varied widely by clinician. Data contribution intensities to the HIE also varied widely and were affected by billing concerns and time constraints. Conclusions: Clinicians, EHR and HIE product vendors and trainers should work toward integrating HIE into clinical workflows. Policies should create incentives for HIE organizations to assist clinicians in using HIE, develop measures of HIE contributions and accesses, and create incentives for clinicians to contribute data to HIEs.
Effective implementation of a mapping swarm of robots

There are several driving factors involved in the development of a robotic swarm. On the hardware side, assembly should be adaptable, easily reproduced, and relatively inexpensive. Motors, mounts, wheels, and chassis material must be chosen as well as appropriate sensors. A workable communication protocol must be determined. Software should be concise and common to each robot in the swarm while meeting the requirements of the desired function.
Low-Abundance HIV Drug-Resistant Viral Variants in Treatment-Experienced Persons Correlate with Historical Antiretroviral Use

Background It is largely unknown how frequently low-abundance HIV drug-resistant variants at levels under limit of detection of conventional genotyping (<20% of quasi-species) are present in antiretroviral-experienced persons experiencing virologic failure. Further, the clinical implications of low-abundance drug-resistant variants at time of virologic failure are unknown. Methodology/Principal Findings Plasma samples from 22 antiretroviral-experienced subjects collected at time of virologic failure (viral load 1380 to 304,000 copies/mL) were obtained from a specimen bank (from 2004–2007). The prevalence and profile of drug-resistant mutations were determined using Sanger sequencing and ultra-deep pyrosequencing. Genotypes were interpreted using Stanford HIV database algorithm. Antiretroviral treatment histories were obtained by chart review and correlated with drug-resistant mutations. Low-abundance drug-resistant mutations were detected in all 22 subjects by deep sequencing and only in 3 subjects by Sanger sequencing. In total they accounted for 90 of 247 mutations (36%) detected by deep sequencing; the majority of these (95%) were not detected by standard genotyping. A mean of 4 additional mutations per subject were detected by deep sequencing (p<0.0001, 95%CI: 2.85–5.53). The additional low-abundance drug-resistant mutations increased a subject's genotypic resistance to one or more antiretrovirals in 17 of 22 subjects (77%). When correlated with subjects' antiretroviral treatment histories, the additional low-abundance drug-resistant mutations correlated with the failing antiretroviral drugs in 21% subjects and correlated with historical antiretroviral use in 79% subjects (OR, 13.73; 95% CI, 2.5–74.3, p = 0.0016). Conclusions/Significance Low-abundance HIV drug-resistant mutations in antiretroviral-experienced subjects at time of virologic failure can increase a subject's overall burden of resistance, yet commonly go unrecognized by conventional genotyping. The majority of unrecognized resistant mutations correlate with historical antiretroviral use. Ultra-deep sequencing can provide important historical resistance information for clinicians when planning subsequent antiretroviral regimens for highly treatment-experienced patients, particularly when their prior treatment histories and longitudinal genotypes are not available.
Robust prior-based Direction of Arrival estimation

In certain Direction of Arrival (DOA) scenarios some of the sources are approximately known a priori. It is then desirable to be able to exploit this prior knowledge when estimating the DOAs of the unknown sources. In this paper we modify an estimator utilizing exact angular prior knowledge of some sources such that the estimator is able to exploit prior knowledge with some uncertainty. We derive the corresponding Cramér-Rao lower bound and present numerical results showing that the estimator can benefit from prior information, even when it is inaccurate.
HDL cholesterol efflux capacity and incident cardiovascular events.

BACKGROUND It is unclear whether high-density lipoprotein (HDL) cholesterol concentration plays a causal role in atherosclerosis. A more important factor may be HDL cholesterol efflux capacity, the ability of HDL to accept cholesterol from macrophages, which is a key step in reverse cholesterol transport. We investigated the epidemiology of cholesterol efflux capacity and its association with incident atherosclerotic cardiovascular disease outcomes in a large, multiethnic population cohort. METHODS We measured HDL cholesterol level, HDL particle concentration, and cholesterol efflux capacity at baseline in 2924 adults free from cardiovascular disease who were participants in the Dallas Heart Study, a probability-based population sample. The primary end point was atherosclerotic cardiovascular disease, defined as a first nonfatal myocardial infarction, nonfatal stroke, or coronary revascularization or death from cardiovascular causes. The median follow-up period was 9.4 years. RESULTS In contrast to HDL cholesterol level, which was associated with multiple traditional risk factors and metabolic variables, cholesterol efflux capacity had minimal association with these factors. Baseline HDL cholesterol level was not associated with cardiovascular events in an adjusted analysis (hazard ratio, 1.08; 95% confidence interval [CI], 0.59 to 1.99). In a fully adjusted model that included traditional risk factors, HDL cholesterol level, and HDL particle concentration, there was a 67% reduction in cardiovascular risk in the highest quartile of cholesterol efflux capacity versus the lowest quartile (hazard ratio, 0.33; 95% CI, 0.19 to 0.55). Adding cholesterol efflux capacity to traditional risk factors was associated with improvement in discrimination and reclassification indexes. CONCLUSIONS Cholesterol efflux capacity, a new biomarker that characterizes a key step in reverse cholesterol transport, was inversely associated with the incidence of cardiovascular events in a population-based cohort. (Funded by the Donald W. Reynolds Foundation and others.).
High-level scenarios for the future of cognitive radio business

This paper aims to provide a systematic analysis and formal presentation of high-level scenarios for the future development of Cognitive Radio business ecosystem. It uses the Intuitive Logics as a methodology for constructing four equally probable scenarios in a matrix at the intersection of two identified major uncertainties. The paper shows the importance of using high-level scenarios as a guiding framework for understanding the causal-consequential relationships and actions of different stakeholders that may help in building the strategies for responding and further facilitating the development of Cognitive Radio.
Transition from ectothermy to endothermy: the development of metabolic capacity in a bird (Gallus gallus)

The evolution of endothermy is one of the most significant events in vertebrate evolution. Adult mammals and birds are delineated from their early ontogenetic stages, as well as from other vertebrates, by high resting metabolic rates and consequent internal heat production. We used the embryonic development of a bird (Gallus gallus) as a model to investigate the metabolic transition between ectothermy and endothermy. Increases in aerobic capacity occur at two functional levels that are regulated independently from each other: (i) upregulation of gene expression; and (ii) significant increases in the catalytic activity of the main oxidative control enzymes. Anaerobic capacity, measured as lactate dehydrogenase activity, is extremely high during early development, but diminishes at the same time as aerobic capacity increases. Changes in lactate dehydrogenase activity are independent from its gene expression. The regulatory mechanisms that lead to endothermic metabolic capacity are similar to those of ectotherms in their response to environmental change. We suggest that the phylogenetic occurrence of endothermy is restricted by its limited selective advantages rather than by evolutionary innovation.
Fleece and fiber analysis in the Xisqueta ovine breed.

El objetivo de este trabajo fue caracterizar el vellon de la raza autoctona Xisqueta, una raza catalana perteneciente al Tronco Iberico. Se tomaron muestras de lana de la parte media lateral en 21 ovejas adultas. El promedio de longitud absoluta de la fibra larga-gruesa fue de 12,4 cm, la de la fibra corta-fina, de 7,3 cm, y la de fibra kemp, de 1,5 cm. La cantidad de fibras largas-gruesas fue del 1,5%, y de cortas-finas, de 94,1%. El rendimiento de la lana al desengrasado isoalcoholico fue superior al 80%, que explica que el vellon presenta poca “suarda” y una mecha medianamente cerrada. El diametro promedio de la fibra fue de 30,6 μ; los histogramas de distribucion de las fibras confirman la existencia de un vellon monocapa. La Xisqueta queda englobada claramente dentro de las razas entrefinas. Del estudio comparativo con otras razas, la Xisqueta se incluye dentro de en un cluster que engloba razas del tronco entrefino Celtiberico, como son la Aranesa, Manchega y Ripollesa.
Initiation of Glycogen Synthesis in Yeast

The self-glucosylating proteins, Glg1p and Glg2p, are required for glycogen synthesis in Saccharomyces cerevisiae (Cheng, C., Mu., J., Farkas, I., Huang, D., Goebl M. G., and Roach, P. J. (1995) Mol. Cell. Biol. 15, 6632-6640). Glg2p was shown to be associated with carbohydrate in vivo and was released from the high molecular weight glycogen fraction by treatment with α-amylase. In addition, some Glg2p exists as a protein of Mr ∼43,000, whose proportion is increased in cells lacking glycogen synthase. Unlike the mammalian counterpart, glycogenin, the yeast Glg proteins appear to require multiple Tyr residues for functionality. In Glg2p, mutation of both Tyr230 and Tyr232 is necessary to suppress self-glucosylation of purified protein in vitro. The mutant protein is still capable of transferring glucose to an exogeneous acceptor, n-dodecyl β-D-maltoside. A small COOH-terminal region, conserved between Glg1p and Glg2p, is also important for function; mutation of Tyr367 or truncation at residue 362 impairs the ability of primed Glg2p to be elongated by glycogen synthase. Complete suppression of glycogen accumulation in vivo requires mutation of all three Tyr residues. In Glg1p, two Tyr residues are implicated, Tyr232 and Tyr600, mutation of both being required to eliminate glycogen accumulation in vivo.
Using Word Position in Documents for Topic Characterization

In this report we show how to use the position of words in a text for characterizing the topic of the text, and compare our method to measures that use frequency statistics that are independent of word position. We show that word position information produces words that are more suited for characterizing topics and at the same time relies on a vocabulary size that is as little as 10% of the size used by the other measures.
Major gene and multifactorial inheritance of mandibular prognathism

Mandibular prognathism typically shows familial aggregation. Various genetic models have been described and it is assumed to be a multifactorial and polygenic trait, with a threshold for expression. Our goal was to examine specific genetic models of the familial transmission of this trait. The study sample comprised of 2,562 individuals from 55 families. Complete family histories for each proband were ascertained and the affection status of relatives were confirmed by lateral cephalograms, photographs, and dental models. Pedigrees were drawn using PELICAN and complex segregation analysis was performed using POINTER. Parts of some pedigrees were excluded to create one founder pedigrees, so the total N was 2,050. Analysis showed more affected females than males (P = 0.030). The majority of the pedigrees suggest autosomal dominant inheritance. Incomplete penetrance was demonstrated by the ratio of affected/unaffected parents and siblings. The heritability of mandibular prognathism was estimated to be 0.316. We conclude that there is a major gene that influences the expression of mandibular prognathism with clear signs of Mendelian inheritance and a multifactorial component. © 2007 Wiley‐Liss, Inc.
Question answering for biology and medicine

Biomedical professionals have at their disposal a huge amount of data, such as literature, i.e. textual contents, or databases, i.e. structured contents. But when they have a question, they often have to deal with too many documents in order to efficiently find the appropriate answer in a reasonable time. We have developed a Question Answering system which aims to analyze the user's question, to retrieve the most relevant documents from MEDLINE, and to extract from these retrieved documents a list of candidate answers, ranked by confidence. These candidate answers are concepts issued from biomedical controlled vocabularies, such as the Medical Subject Headings (MeSH) for a first step, and are extracted from the most relevant documents with pattern matching strategies. For evaluation purposes, we apply the system on two biological databases, UniProt and DrugBank. From these resources, we generated two large benchmarks of 200 questions dealing respectively with diseases and proteins, and with diseases and drugs. For these 2 sets, the first candidate answer proposed by our system is respectively correct in 57% and in 68%, while respectively 70% and 75% of all answers to find are contained in the ten first proposed candidate answers. Despite the use of simple Information Extraction strategies, our system exploits the redundancy of information in literature in order to provide a powerful Question Answering system.
Spike Train Statistics and Dynamics with Synaptic Input from any Renewal Process: A Population Density Approach

In the probability density function (PDF) approach to neural network modeling, a common simplifying assumption is that the arrival times of elementary postsynaptic events are governed by a Poisson process. This assumption ignores temporal correlations in the input that sometimes have important physiological consequences. We extend PDF methods to models with synaptic event times governed by any modulated renewal process. We focus on the integrate-and-fire neuron with instantaneous synaptic kinetics and a random elementary excitatory postsynaptic potential (EPSP), A. Between presynaptic events, the membrane voltage, v, decays exponentially toward rest, while s, the time since the last synaptic input event, evolves with unit velocity. When a synaptic event arrives, v jumps by A, and s is reset to zero. If v crosses the threshold voltage, an action potential occurs, and v is reset to vreset. The probability per unit time of a synaptic event at time t, given the elapsed time s since the last event, h(s, t), depends on specifics of the renewal process. We study how regularity of the train of synaptic input events affects output spike rate, PDF and coefficient of variation (CV) of the interspike interval, and the autocorrelation function of the output spike train. In the limit of a deterministic, clocklike train of input events, the PDF of the interspike interval converges to a sum of delta functions, with coefficients determined by the PDF for A. The limiting autocorrelation function of the output spike train is a sum of delta functions whose coefficients fall under a damped oscillatory envelope. When the EPSP CV, AA, is equal to 0.45, a CV for the intersynaptic event interval, TT 0.35, is functionally equivalent to a deterministic periodic train of synaptic input events (CV 0) with respect to spike statistics. We discuss the relevance to neural network simulations.
Automatic Ordinals

We prove that the injectively omega-tree-automatic ordinals are the ordinals smaller than $\omega^{\omega^\omega}$. Then we show that the injectively $\omega^n$-automatic ordinals, where $n>0$ is an integer, are the ordinals smaller than $\omega^{\omega^n}$. This strengthens a recent result of Schlicht and Stephan who considered in [Schlicht-Stephan11] the subclasses of finite word $\omega^n$-automatic ordinals. As a by-product we obtain that the hierarchy of injectively $\omega^n$-automatic structures, n>0, which was considered in [Finkel-Todorcevic12], is strict.
Role of Alcohol Consumption in Escalation to Violence

Abstract: No other drug has been associated with aggressive and violent behavior more than alcohol has. A major characteristic of the link between alcohol and social interactions is the very large variation in who becomes more aggressive while drinking and who does not. Tracing the origins of these individual differences has led to a focus on predispositions, such as the antisocial behavior of Type 2 alcoholics. Successful development of an experimental procedure to model heightened aggressive behavior after voluntary consumption of alcohol has facilitated the neurobiologic analysis of the link between alcohol and aggression. From a pharmacologic perspective, consumption of low to moderate doses of alcohol engenders heightened aggressive behavior in a significant minority of individuals before the circulation of appreciable amounts of the aldehyde metabolite. Ionophoric receptors such as NMDA, 5‐HT3 and GABAA have been identified in the brain as major sites of action for alcohol in the dose range that is relevant for engendering heightened aggression. Actions at the GABAA receptor complex that depend on particular GABAA subunits appear to be necessary for alcohol‐heightened aggression. Genes that encode the synthesis of these alpha and gamma subunits are potentially significant markers for those individuals that are prone to engage in heightened aggressive behavior after the consumption of alcohol. Of particular importance are the reciprocal interactions between GABA and serotonin. Activating specific serotonin receptor subtypes such as 5‐HT1B receptors reduces alcohol‐heightened aggressive behavior. How these GABAergic and serotonergic corticolimbic mechanisms for alcohol‐heightened aggression develop during the adolescent period remains an area of urgent study.
Automated point-neuron simplification of data-driven microcircuit models

A method is presented for the reduction of morphologically detailed microcircuit models to a point-neuron representation without human intervention. The simplification occurs in a modular workflow, in the neighborhood of a user specified network activity state for the reference model, the "operating point". First, synapses are moved to the soma, correcting for dendritic filtering by low-pass filtering the delivered synaptic current. Filter parameters are computed numerically and independently for inhibitory and excitatory input using a Green's function approach. Next, point-neuron models for each neuron in the microcircuit are fit to their respective morphologically detailed counterparts. Here, generalized integrate-and-fire point neuron models are used, leveraging a recently published fitting toolbox. The fits are constrained by currents and voltages computed in the morphologically detailed partner neurons with soma corrected synapses at three depolarizations about the user specified operating point. The result is a simplified circuit which is well constrained by the reference circuit, and can be continuously updated as the latter iteratively integrates new data. The modularity of the approach makes it applicable also for other point-neuron and synapse models. The approach is demonstrated on a recently reported reconstruction of a neocortical microcircuit around an in vivo-like working point. The resulting simplified network model is benchmarked to the reference morphologically detailed microcircuit model for a range of simulated network protocols. The simplified network is found to be slightly more sub-critical than the reference, with otherwise good agreement for both quantitative and qualitative validations.