Miracle-dz/UniFAR-FTUs huggingface dataset:
Recombination analysis using directed graphical models.

In Strimmer and Moulton (2000), we described a method for computing the likelihood of a set of sequences assuming a phylogenetic network as an evolutionary hypothesis. That approach relied on converting a given graph into a directed graphical model or stochastic network from which all desired probability distributions could be derived. In particular, we investigated how to compute likelihoods using split-graphs (Huson 1998). However, in the presence of recombination, split-graphs may not provide an appropriate choice of the underlying graph. In this letter, we propose basing the stochastic network on an ancestral recombination graph (ARG) (Hudson 1983; Griffiths and Marjoram 1996, 1997). We show that our approach using directed graphical models extends in a straightforward fashion to ARGs, and we outline the computation of their likelihoods. In particular, we provide an example of an ARG whose likelihood is greater than that of a competing nonnested tree, even though the ARG has a smaller number of free parameters. Statistical phylogenetic analysis requires a model for the evolutionary relationships between the sequences in a given data set. For this purpose, directed acyclic graphs (DAGs) are suitable for describing the dependencies between the sequences. Several subclasses of DAGs can be easily derived from frequently used graphs such as trees, phylogenetic networks (Bandelt 1994), and split-graphs (Huson 1998). The latter two classes exhibit network-like structures for which the tree is a special case. Net-like models for sequence evolution can be particularly attractive when modeling statistical dependencies among sequences in the presence of recombination, where evolution is clearly non–tree-like. In order for a DAG-based phylogeny to provide a realistic model of recombination, we propose that the DAG should have at least the following properties:
MANAGEMENT CONTROL SYSTEMS, ORGANIZATION AND IMPACT ON PERFORMANCES: EVIDENCES FROM ITALY

The value creation is the primary goal of each organization and intellectual capital is certainly a key factor for long-term success. The intellectual capital variables have to be managed and measured within advanced management systems, in order to facilitate the communication and translation of strategy’s tangible and intangible elements into operational terms. This study focuses on a sample of medium-sized Italian firms and is based on multiple sources of evidence: the in-depth study of internal documents and interviews with corporate managers holding key positions within the organization. The research aims at investigating if managers identified, measured and monitored intellectual capital variables within advanced management accounting systems, over a period of 5 years. Because the strategy and the organizational structure are highly interdependent, this study also focuses on evaluation and incentive systems implemented within selected companies. Then, it was decided to analyze whether the use of managerial and organizational tools influence firms' performances. This research contributes to extend existing literature on intellectual capital and management systems: the results revealed that companies able to manage and monitor intellectual capital within advanced management tools, as well as implement evaluation and incentive systems, achieved higher and more stable performances. The main limit of this study is strictly related to the choice of these variables: in fact, company's performances are influenced by a significant number of factors, endogenous and exogenous to the organization. Future researches can involve a greater number of companies and organizational variables, in order to validate or confute the actual findings.
Microleakage Of Class II Bulk-fill And Conventional Resin Composite Restorations With And Without Enamel Preservation At Gingival Wall

Objectives: This in vitro study tested the hypothesis that preserving a thin enamel layer at the gingival margin and using bulk-fill resin composites could minimize microleakage of class II resin composite. Materials and Methods: Thirty-six human third molars were randomly divided into three groups of 12 specimens each: Filtek Bulk Fill Posterior Restorative in Capsules (BFC), Filtek Bulk Fill Posterior Restorative in Syringes (BFS) and Filtek Z350 XT (Z350). Teeth were prepared on two sides for a class II cavity (3 mm buccolingually x 2 mm mesiodistally at occlusal and 1.5 mm at coronal x 4 mm of axial depth) with 0.5 mm under the CEJ on one side (NP) and 0.5x1 mm of thin enamel at the gingival margin was preserved on the other side (EP). The teeth were then restored, thermocycled, immersed in 0.5% methylene blue solution for 24 hours and sectioned mesiodistally through the restorations. Dye penetration was evaluated at the gingival margin by three blinded examiners using a 0-4 ordinal scale. The Kruskal-Wallis test and Dunn test were used to compare differences in microleakage scores among the three restorative materials. Mann-Whitney U test was utilized to analyze the difference between enamel preserved (EP) and non-enamel preserved sides (NP) in the same restorative material. Tests were performed with the level of significance at α = 0.05. Results: Mann-Whitney U test showed that the “NP” groups had significantly higher microleakage score than the “EP” groups. The Kruskal-Wallis test revealed significant differences in microleakage scores among the three restorative materials (P < 0.05). Compared to “Z350”, the “EP” group, “BFC” and “BFS” had significantly less microleakage score (P = 0.001) (P = 0.028). The “NE” group, “BFC” had significantly less microleakage score than “Z350” (P = 0.001).
ETA-L EARNING FOR S TOCHASTIC G RADIENT MCMC

Stochastic gradient Markov chain Monte Carlo (SG-MCMC) has become increasingly popular for simulating posterior samples in large-scale Bayesian modeling. However, existing SG-MCMC schemes are not tailored to any specific probabilistic model, even a simple modification of the underlying dynamical system requires significant physical intuition. This paper presents the first meta-learning algorithm that allows automated design for the underlying continuous dynamics of an SG-MCMC sampler. The learned sampler generalizes Hamiltonian dynamics with state-dependent drift and diffusion, enabling fast traversal and efficient exploration of energy landscapes. Experiments validate the proposed approach on learning tasks with Bayesian fully connected neural networks, Bayesian convolutional neural networks and Bayesian recurrent neural networks, showing that the learned sampler out-performs generic, hand-designed SG-MCMC algorithms, and generalizes to different datasets and larger architectures.
Evaluations of Capacity to Waive Miranda Rights

Minimal information is available regarding the frequency with which practitioners conduct evaluations of capacity to waive Miranda rights or what approaches they use in doing so. Grisso's Instruments for Assessing Understanding and Appreciation of Miranda Rights are the only published instruments designed specifically to assist practitioners in these evaluations. The instruments have been criticized for limited normative data in the test manual and the minimal guidance offered for interpreting results. A survey of practitioners was conducted to determine the nature and frequency of the use of these instruments. Of 401 respondents, 91% were engaged in forensic practice, and 26% had conducted evaluations of one's capacity to waive Miranda rights. Of those conducting Miranda evaluations, 44% had used Grisso's Miranda instruments. Practitioners' responses regarding the ways the instruments are used are reported. Suggestions are offered for informed practice, and related strengths and weaknesses of the instruments are identified.
CRITICAL EXPONENTS FOR TWO-DIMENSIONAL PERCOLATION

We show how to combine Kesten's scaling relations, the determination of critical exponents associated to the stochastic Loewner evolution process by Lawler, Schramm, and Werner, and Smirnov's proof of Cardy's formula, in order to determine the existence and value of critical exponents associated to percolation on the triangular lattice.
An Efficient Technique for Locating Multiple Narrow-Band Ultrasound Targets in Chorus Mode

A basic problem in time of arrival (TOA)-based locating systems using narrow-band ultrasound (NBU) is how to improve the location update rate for tracking multiple targets. It is challenging because each ongoing ultrasound (US) signal occupies the channel for a rather long time because the slow propagation speed in air and it is hard to encode information in the narrow-band US. In this paper, we investigate to allow multiple NBU targets to transmit signals concurrently and to determine their locations by signal processing, which is called locating in chorus mode. The key observation is the signal interference characteristics of the concurrently chorusing targets. Based on it, the necessary and sufficient conditions for the receivers to determine the TOAs from multiple concurrently transmitting targets are investigated. However, because NBU cannot encode the target's ID, the detected TOAs are lacking labels of the target ID, causing ambiguities in location estimation. We exploited both historical consistence and self-consistence methods to narrow down the possible IDs of the TOAs and proposed probabilistic particle filter algorithm to disambiguate the motion trajectories of targets based on the targets' motion pattern consistency. A prototype of chorus-mode NBU locating system was developed. Extensive evaluations of both simulations and prototype experiments showed the effectiveness of the proposed theories and algorithms. In the testbed experiment, chorus locating provided 300% refreshing rate improvements compared with exclusive locating method, while the accuracy is still kept.
Tumor‐Derived Epigenetic Changes in the Plasma and Serum of Liver Cancer Patients: Implications for Cancer Detection and Monitoring

Multiple genetic abnormalities have now been recognized to be involved in the development of hepatocellular carcinoma (HCC). 1 Aberrant methylation of the p16 gene, a tumor suppressor gene that encodes the cell cycle regulator, has been frequently detected in patients with solid tumors including HCC.2,3 Recently, we have found tumor-derived p16 methylation in the plasma/serum of HCC patients by methylation-specific polymerase chain reaction (MSP). 3 To evaluate the potential implications of p16 hypermethylation for the noninvasive detection of HCC and the monitoring of tumor recurrence, we applied the p16 methylation assay to plasma/serum samples from a larger cohort of HCC patients. In this study, we analyzed p16 promoter methylation status in HCC tumors and peripheral blood samples from 45 HCC patients using MSP and correlated the findings with the clinical outcomes of patients.
Differences in Motor Evoked Potentials Induced in Rats by Transcranial Magnetic Stimulation under Two Separate Anesthetics: Implications for Plasticity Studies

Repetitive transcranial magnetic stimulation (rTMS) is primarily used in humans to change the state of corticospinal excitability. To assess the efficacy of different rTMS stimulation protocols, motor evoked potentials (MEPs) are used as a readout due to their non-invasive nature. Stimulation of the motor cortex produces a response in a targeted muscle, and the amplitude of this twitch provides an indirect measure of the current state of the cortex. When applied to the motor cortex, rTMS can alter MEP amplitude, however, results are variable between participants and across studies. In addition, the mechanisms underlying any change and its locus are poorly understood. In order to better understand these effects, MEPs have been investigated in vivo in animal models, primarily in rats. One major difference in protocols between rats and humans is the use of general anesthesia in animal experiments. Anesthetics are known to affect plasticity-like mechanisms and so may contaminate the effects of an rTMS protocol. In the present study, we explored the effect of anesthetic on MEP amplitude, recorded before and after intermittent theta burst stimulation (iTBS), a patterned rTMS protocol with reported facilitatory effects. MEPs were assessed in the brachioradialis muscle of the upper forelimb under two anesthetics: a xylazine/zoletil combination and urethane. We found MEPs could be induced under both anesthetics, with no differences in the resting motor threshold or the average baseline amplitudes. However, MEPs were highly variable between animals under both anesthetics, with the xylazine/zoletil combination showing higher variability and most prominently a rise in amplitude across the baseline recording period. Interestingly, application of iTBS did not facilitate MEP amplitude under either anesthetic condition. Although it is important to underpin human application of TMS with mechanistic examination of effects in animals, caution must be taken when selecting an anesthetic and in interpreting results during prolonged TMS recording.
Prevalence of Risk Factors for Coronary Artery Disease in Pennsylvania (USA) Firefighters

Abstract Introduction Firefighting is a physically demanding profession. Heart disease remains the number one killer of firefighters. Many firefighters have multiple risk factors, putting them at risk for sudden cardiac events. The purpose of this study was to describe the prevalence of risk factors for heart disease in a convenience sample of Pennsylvania (USA) firefighters. Methods A convenience sample of 160 firefighters in western Pennsylvania had height, weight, waist circumference, blood pressure, and body mass index (BMI) assessed, and then were surveyed to measure their knowledge of cardiovascular risk factors. Data analysis included subgroup comparisons of age, BMI, waist circumference, and exercise for their impact on health risks in the study cohort. In particular, the researchers were interested in understanding whether the knowledge of risk was associated with lower measures of risk. Results Eighteen firefighters (4%) reported a history of coronary artery disease (including stents/interventions). In this group, 69% to 82% correctly identified age, hypertension (HTN), high cholesterol, smoking, obesity, sedentary lifestyle, and family history as risk factors for coronary artery disease. Fourteen percent were smokers, 41% had HTN, 38% had pre-HTN with only 12% receiving treatment, and 13.5% were treated for high cholesterol. Fifty-eight percent exercised regularly. Conclusions While a majority of firefighters were able to identify risk factors for coronary artery disease, many could not. Eighteen (4%) had a history of coronary artery disease, including interventions. Many had several of the risk factors indicated, which highlights the need for an organized national approach to address the medical screening/evaluation, nutrition, and exercise components of firefighter fitness. RisaviBL, StaszkoJ. Prevalence of risk factors for coronary artery disease in Pennsylvania (USA) firefighters. Prehosp Disaster Med. 2016;31(1):102–107 .
EGF receptor ubiquitination is not necessary for its internalization

Ubiquitination of the EGF receptor (EGFR) has been implicated in EGF-induced receptor internalization, lysosomal degradation, and down-regulation. Mutation of EGFR ubiquitination sites identified by mass spectrometry yielded receptor mutants that are weakly ubiquitinated and not down-regulated by EGF. However, these EGFR mutants were normally internalized. To examine whether this internalization was mediated by the residual ubiquitination, systematic mutagenesis of lysine residues in the kinase domain of the EGFR was performed to generate a receptor mutant that is not ubiquitinated. Mutations of a number of lysines inhibited kinase activity of the EGFR, thus leading to the inhibition of receptor internalization. However, a mutant lacking 15 lysine residues (15KR), which was negligibly ubiquitinated and normally phosphorylated, was internalized at a rate similar to that of the wild-type EGFR. As in the case of the wild-type EGFR, internalization of the 15KR mutant depended on the presence of clathrin, Grb2 adaptor, and Cbl ubiquitin ligase. These data imply that EGFR ubiquitination is not necessary for its internalization by clathrin-coated pits. Interestingly, the reconstitution of two major ubiquitination sites in the 16KR receptor mutant, which had impaired kinase activity and slow internalization kinetics, resulted in a partial rescue of ubiquitination and a complete rescue of receptor internalization. This result suggests that ubiquitination of the kinase-impaired receptor can mediate its internalization by the clathrin pathway. Altogether these data emphasize the robustness of the EGFR internalization process, which can be controlled by multiple kinase- and ubiquitination-dependent and -independent mechanisms.
An interaction vocabulary. describing the how of interaction.

New technologies and opportunities in interaction design also come with new responsibilities. Besides the product's visual aesthetics, design needs to address the aesthetics of interaction. We discuss the various starting points of emerging approaches and then present an own approach to the How of interaction. We suggest an interaction vocabulary, i.e., a set of eleven dimensions of descriptive, non-judgmental, non-technology bound attributes of interaction. First insights from applying the vocabulary in design and evaluation studies and future research are discussed.
IDENTIFYING THE EFFICACY OF CENTRAL BANK INTERVENTIONS: EVIDENCE FROM AUSTRALIA

The endogeneity of exchange rates and intervention has long plagued studies of the effectiveness of central banks’ actions in foreign exchange markets. Researchers have either excluded contemporaneous intervention so that their explanators are predetermined, or obtained a small, and typically incorrectly signed, coefficient on contemporaneous intervention. Failing to account for the endogeneity, when central banks lean against the wind and trade strategically, will likely result in a large downward bias to the coefficient on contemporaneous intervention – explaining the negative coefficient frequently obtained. We use an alternative identification assumption – a change in the intervention policy of the Reserve Bank of Australia – that allows us to estimate, using simulated Generalised Method of Moments (GMM), a model that includes the contemporaneous impact of intervention. There are three main results. Our point estimates suggest that central bank intervention has an economically significant contemporaneous effect. A US$100 million purchase of the domestic currency will appreciate the exchange rate by 1.3 to 1.8 per cent. This estimate is remarkably similar to the calibration conducted by Dominguez and Frankel (1993c), who themselves noted their estimate was larger than previous empirical findings. Secondly, the vast majority of the effect of an intervention on the exchange rate is found to occur during the day in which it is conducted, with only a smaller impact on subsequent days. Finally, we confirm findings that Australian central bank intervention policy can be characterised as leaning against the wind.
Consensus of multiple second-order agents without velocity measurements

This paper studies consensus problems of multiple second-order agents with time-varying topology. It is assumed that each possible interaction topology is strongly connected and balanced and each agent can only obtain the measurements of its position relative to its neighbors. A feasible protocol is proposed, and by applying the linear matrix inequality technique and the common Lyapunov function approach, some sufficient conditions for consensus are established. Simulations are provided to illustrate the effectiveness of the theoretical results.
Lazy-writer multivalued registers

We study wait-free constructions of multivalued regist ers from bits. Although atomic wait-free registers cannot solely be used to solve complex coordination problems such as consensus [3], they can be used for basic interprocess communication. Also, register constructions and associated impossibility results seem to have a nice combinatorial structure. Many constructions of multivalued regular (atomic) registers from regular (atomic) bits have been proposed. [2] start ed an analysis of complexity measures (time, space) for this class of constructions and developed a multivalued safe register from safe bits with optimal writer time complexity (the writer changes at most one shared bit per multivalued write). [I] developed a dual purpose writer-optimal algorithm implementing a multivalued regular (atomic) register from regular (atomic) bits, in which the writer traverses a complete graph of the proper size. The nodes of the graph logically represent the multiple values that the register can hold, and the edges of the graph represent bits that are changed when the writer “walks” from value to value. This algorithm is combinatorially elegant, but suffers from 0( kz ) space and reader time complexity; the best known lower bound is Ct( k ) for building a k-valued register in a writeroptimal fashion [2]. In this paper, we propose using the [1] algorithm in a modular fashion to yield multivalued registers with larger value sets and slightly worse writer time complexity, but improved space and reader time complexities. In all our algorithms, the writer and readers access shared bits in reverse orders, as in an early construction of [4]. All improvements over the [1] algorithm are with respect to space and reader time complexities. Our first algorithm uses the complete graph, but each node now is a shared bit representing one of two possible values that the register can hold. Thh results in the writer changing at most 2 bits per write and fourfold improvements over the [1] algorithm for a 2k-valued register. Our second algorithm implements a k“ -valued register with the writer changing at most 1 + [log nl bits per write, and space and reader time complexities of 0( k”+ 1 ), beating the [1] algorithm by a factor of kn–l. It works by multiple uses of the [1] algorithm, with recursive embedding of complete graphs within complete graphs.
Open innovation in small and micro enterprises

Open innovation has become a key strategic element to increase the generation and commercialization of innovations among big companies. Small and medium-sized firms (SMEs), that exhibit particular characteristics regarding organization, culture and strategy, have been more reluctant to adopt this approach. Thus little research exists on the adoption of open innovation among SMEs, and small and micro companies in particular. The paper presents the results of an explorative research design based upon semi-structured and narrative interviews that investigates particularities of small and micro firms regarding the sources of innovation, the strengths and weaknesses of their innovation process, and the potential of open innovation based on Web 2.0 technologies.
Matrix Co-Factorization on Compressed Sensing

In this paper we address the problem of matrix factorization on compressively-sampled measurements which are obtained by random projections. While this approach improves the scalability of matrix factorization, its performance is not satisfactory. We present a matrix co-factorization method where compressed measurements and a small number of uncompressed measurements are jointly decomposed, sharing a factor matrix. We evaluate the performance of three matrix factorization methods in terms of Cramer-Rao bounds, including: (1) matrix factorization on uncompressed data (MF); (2) matrix factorization on compressed data (CS-MF); (3) matrix co-factorization on compressed and uncompressed data (CS-MCF). Numerical experiments demonstrate that CS-MCF improves the performance of CS-MF, emphasizing the useful behavior of exploiting side information (a small number of uncompressed measurements).