Miracle-dz/UniFAR-FTUs huggingface dataset:
Visualizing high dimensional datasets using parallel coordinates: Application to gene prioritization

In this paper, we introduce a visualization tool for interactive and efficient exploration of high dimensional data using parallel coordinates. An algorithm is developed to find an optimal permutation of dimensions, which allows the data miner to immediately see the most important features or irregularities in the dataset. This is implemented as a genetic algorithm based on the travelling salesman problem using maximal correlation as fitness. Other features of the tool include selection operators to group the data such as selection by intersection or by angle, orthogonal and density plots complementing the parallel coordinates plot, manual arrangement of permutation order of the dimensions, possibility to show all plots necessary to see all dimensional relations and displaying a certain number of standard deviations for each dimension separately. The tool is applied to multiple gene prioritization cases in search of genes that are relevant to certain genetic disorders. The used datasets are obtained with the MerKator and Endeavour tools and include a Breast cancer, Cataract, Charcoth-Marie-Tooth and Cardiomyopathy dataset, as well as a dataset relating 29 diseases with 22206 genes. Our tool, manual and data can be downloaded from http://www.toomas. be/parcoord/.
Effect of Chocolate and Yerba Mate Phenolic Compounds on Inflammatory and Oxidative Biomarkers in HIV/AIDS Individuals

Flavonoids in cocoa and yerba mate have a beneficial role on inflammation and oxidative disorders. Their effect on HIV individuals has not been studied yet, despite the high cardiovascular risk of this population. This study investigated the role of cocoa and yerba mate consumption on oxidative and inflammatory biomarkers in HIV+ individuals. A cross-over, placebo-controlled, double-blind, randomized clinical trial was conducted in 92 individuals on antiretroviral therapy for at least six months and at viral suppression. Participants were randomized to receive either 65 g of chocolate or chocolate-placebo or 3 g of yerba mate or mate-placebo for 15 days each, alternating by a washout period of 15 days. At baseline, and at the end of each intervention regimen, data regarding anthropometry, inflammatory, oxidative and immunological parameters were collected. High-sensitivity C-reactive protein, fibrinogen, lipid profile, white blood cell profile and thiobarbituric acid reactive substances were assessed. There was a difference between mean concentrations of HDL-c (ANOVA; p ≤ 0.05) among the different regimens: dark chocolate, chocolate-placebo, yerba mate and mate-placebo. When a paired Student t-test was used for comparisons between mean HDL-c at baseline and after each regimen, the mean concentration of HDL-c was higher after supplementation with dark chocolate (p = 0.008).
Delivery mechanisms and impact of microfinance training in indian self-help groups

We evaluate the effect of delivery mechanisms for training provided by facilitators of self- help groups. Indian self-help groups are unique in that they are mainly non-government organisation- formed microfinance groups but later funded by commercial banks. We correct for both membership and training endogeneity. Training impacts assets but not income. Underlying conditions that benefit training include better infrastructure (as in paved roads), linkage model type and training organiser. Copyright © 2011 John Wiley & Sons, Ltd. In a recent impact and sustainability study of the Self-Help Group (SHG) Bank Linkage Program, the National Council of Applied Economic Research (NCAER, 2008) finds that SHGs have significantly improved the access of the rural poor to financial services. The report also finds a considerable positive impact for the socio-economic conditions of SHG members. In addition to financial services, SHGs also provide both skill development and human capital training services to their members. This paper aims to explore the impact of the delivery of these training mechanisms. In com- plementarywork,BaliSwainandVarghese(2010) find that training positively impacts assets but not income. In this study, we examine whether the impact of training on assets and income depends on the delivery mechanism, namely, linkage model type, infrastructure and training organiser.
Trade Liberalization and Labor Market Adjustment in Brazil

We study the impact of the 1988-1994 trade liberalization in Brazil on the wage distribution. We explore three main channels through which trade liberalization could have affected the wage distribution: increasing returns to skilled workers due to Hecksher-Ohlin adjustments to trade policy, trade induced skill-biased technological change, and changes in industry wage premiums. Our results suggest the trade reform in Brazil did partially contribute to the growing skill premium through skill-biased technological change, which was partially instigated by the increased foreign competition. We also find that sector specific returns to skill increased by more in sectors with bigger tariff reductions. However, we find little support for Hecksher-Ohlin type adjustments to trade reform. Overall, the effects of trade reforms on wage inequality seem relatively small.
Gradient estimation for discrete-event systems by measure-valued differentiation

In simulation of complex stochastic systems, such as Discrete-Event Systems (DES), statistical distributions are used to model the underlying randomness in the system. A sensitivity analysis of the simulation output with respect to parameters of the input distributions, such as the mean and the variance, is therefore of great value. The focus of this article is to provide a practical guide for robust sensitivity, respectively, gradient estimation that can be easily implemented along the simulation of a DES. We study the Measure-Valued Differentiation (MVD) approach to sensitivity estimation. Specifically, we will exploit the “modular” structure of the MVD approach, by firstly providing measure-valued derivatives for input distributions that are of importance in practice, and subsequently, by showing that if an input distribution possesses a measure-valued derivative, then so does the overall Markov kernel modeling the system transitions. This simplifies the complexity of applying MVD drastically: one only has to study the measure-valued derivative of the input distribution, a measure-valued derivative of the associated Markov kernel is then given through a simple formula in canonical form. The derivative representations of the underlying simple distributions derived in this article can be stored in a computer library. Combined with the generic MVD estimator, this yields an automated gradient estimation procedure. The challenge in automating MVD so that it can be included into a simulation package is the verification of the integrability condition to guarantee that the estimators are unbiased. The key contribution of the article is that we establish a general condition for unbiasedness which is easily checked in applications. Gradient estimators obtained by MVD are typically phantom estimators and we discuss the numerical efficiency of phantom estimators with the example of waiting times in the G/G/1 queue.
Path planning for autonomous vehicles driving over rough terrain

This paper presents a multiresolutional architecture of planners for obstacle avoidance in outdoor mobility. The planner makes use of off-line dynamical simulations results to efficiently find paths that avoid obstacles. The trajectories are generated by sets of steering velocity commands. This approach of building the search space for the planner results in realistic cost and trajectories for the vehicle. An implementation of the planner was developed and tested in a vehicle at the National Institute of Standards and Technology (NIST) with promising results.
Maximization of Network Survivability under Malicious and Epidemic Attacks

Due to the Internet's scalability and connectivity, enterprises and organizations increasingly rely upon it to provide services for customers. However, attackers intelligently attack enterprises and organizations through continuous vulnerability exploitation and advanced malware. Recently, assailants have applied the characteristics of fast propagation and epidemic attack infection to launch more deliberate attacks, by using obtained network topology information. This paper examines malicious and epidemic attacks, taking into account various defense mechanisms. Attackers are assumed to only have incomplete information regarding the target network, which raises the difficulty of solving this problem and renders the nature of the problem non-deterministic. Our purpose is to help defenders evaluate average network survivability when making defense-related decisions. This scenario is modeled as a mathematical formulation, and through our simulation results, meaningful and useful defense guidelines are proposed.
INVESTIGATION OF CAVITY REFLEX ANTENNA USING CIRCULAR PATCH TYPE FSS SUPERSTRATE

Cavity re∞ex antenna (CRA) employing a circular patch type FSS (Frequency Selective Surface) superstrate is investigated. Analysis in terms of gain, bandwidth (impedance and gain) and radiation pattern has been presented. The aim of this work was to study low proflle CRA having very thin superstrate sizes. In this CRA a circular patch antenna is used as a feeding source. The circular patch type FSS possesses some unique properties favorable for thin superstrate sizes. In practice when the excitation source of the CRA is a probe-fed microstrip antenna with flnite ground plane, substrate and superstrate, cross-polarization increases. In the presented design, the cross polar level has been reduced by choosing the optimum air gap and superstrate geometrical and electrical properties. A CRA with circular patch type FSS ofiers better performance both in terms of gain and impedance bandwidth for, thin superstrates (0:008‚0) while giving a gain of 13dBi and considerably reduced crosspolar level. The proposed antenna exhibit nearly equal E-plane and H-plane radiation pattern. Measurement results are provided to support the simulated results (by Ansoft HFSS). The circular patch type FSS is easy to fabricate and can be embedded into the host proflle.
Asynchronous States and the Emergence of Synchrony in Large Networks of Interacting Excitatory and Inhibitory Neurons

We investigate theoretically the conditions for the emergence of synchronous activity in large networks, consisting of two populations of extensively connected neurons, one excitatory and one inhibitory. The neurons are modeled with quadratic integrate-and-fire dynamics, which provide a very good approximation for the subthreshold behavior of a large class of neurons. In addition to their synaptic recurrent inputs, the neurons receive a tonic external input that varies from neuron to neuron. Because of its relative simplicity, this model can be studied analytically. We investigate the stability of the asynchronous state (AS) of the network with given average firing rates of the two populations. First, we show that the AS can remain stable even if the synaptic couplings are strong. Then we investigate the conditions under which this state can be destabilized. We show that this can happen in four generic ways. The first is a saddle-node bifurcation, which leads to another state with different average firing rates. This bifurcation, which occurs for strong enough recurrent excitation, does not correspond to the emergence of synchrony. In contrast, in the three other instability mechanisms, Hopf bifurcations, which correspond to the emergence of oscillatory synchronous activity, occur. We show that these mechanisms can be differentiated by the firing patterns they generate and their dependence on the mutual interactions of the inhibitory neurons and cross talk between the two populations. We also show that besides these codimension 1 bifurcations, the system can display several codimension 2 bifurcations: Takens-Bogdanov, Gavrielov-Guckenheimer, and double Hopf bifurcations.
Improved lock-time in all-digital phase-locked loops due to binary search acquisition

A binary search algorithm for an improved settling time in phase-domain all-digital phase-locked loops (ADPLLs) is proposed. Therefore, an ADPLL structure for high-speed fractional-N frequency synthesis is adapted to extract the ratio between the reference and the output frequency in each reference cycle. A frequency detector compares the obtained ratio to the ideal value. The proposed control algorithm uses the frequency detector output to iteratively search for the desired tuning word. The binary search acquisition speeds-up the acquisition process significantly and suits digitally controlled oscillators with multiple varactor banks well. Behavioral simulations illustrate the proposed technique.
‘Free’ Enrichment and the Nature of Pragmatic Constraints

The contextualist approach to utterance interpretation posits processes of “free” pragmatic enrichment that supply unarticulated constituents of the explicit content of utterances. While this proposal is faithful to our intuitions about the truth conditions of utterances, and accommodates the optionality of these pragmatic effects, there remains a doubt about whether contextualism can account in any principled way for what pragmatically derived material enters into explicit content, and what does not. This gap in the theory leads to objections that the putative process of pragmatic enrichment would massively overgenerate interpretations of utterances, having no way to exclude from explicit content elements of meaning that are truth-conditionally irrelevant. Here I discuss how a derivational account can sort explicit content from implicatures, where the former is a result of “developing” the linguistically-encoded form, while implicatures are entirely inferred, from fully propositional premises. Using the idea that enrichment is constrained to the minimum necessary to inferentially warrant the implications of the utterance, I show how the derivational account can address existing examples of alleged overgeneration, and that these rest on a failure to properly appreciate that the occurrence of such “free” pragmatic processes depends on the details of the particular context in which the utterance was tokened. I conclude with a discussion of what kind of systematicity should be expected from an account of processes whose outcome is inevitably context-specific.
Identification and Characterization of a Sleep-Active Cell Group in the Rostral Medullary Brainstem

Early transection and stimulation studies suggested the existence of sleep-promoting circuitry in the medullary brainstem, yet the location and identity of the neurons comprising this putative hypnogenic circuitry remains unresolved. In the present study, we sought to uncover the location and identity of medullary neurons that might contribute to the regulation of sleep. Here we show the following in rats: (1) a delimited node of medullary neurons located lateral and dorsal to the facial nerve—a region we termed the parafacial zone (PZ)—project to the wake-promoting medial parabrachial nucleus; (2) PZ neurons express c-Fos after sleep but not after wakefulness and hence are sleep active; and (3) cell-body-specific lesions of the PZ result in large and sustained increases (50%) in daily wakefulness at the expense of slow-wave sleep (SWS). Using transgenic reporter mice [vesicular GABA/glycine transporter (Vgat)–GFP], we then show that >50% of PZ sleep-active neurons are inhibitory (GABAergic/glycinergic, VGAT-positive) in nature. Finally, we used a Cre-expressing adeno-associated viral vector and conditional Vgatlox/lox mice to selectively and genetically disrupt GABA/glycinergic neurotransmission from PZ neurons. Disruption of PZ GABAergic/glycinergic neurotransmission resulted in sustained increases (40%) in daily wakefulness at the expense of both SWS and rapid eye movement sleep. These results together reveal the location and neurochemical identity of a delimited node of sleep-active neurons within the rostral medullary brainstem.
The interplay of histone modifications – writers that read

Histones are subject to a vast array of posttranslational modifications including acetylation, methylation, phosphorylation, and ubiquitylation. The writers of these modifications play important roles in normal development and their mutation or misregulation is linked with both genetic disorders and various cancers. Readers of these marks contain protein domains that allow their recruitment to chromatin. Interestingly, writers often contain domains which can read chromatin marks, allowing the reinforcement of modifications through a positive feedback loop or inhibition of their activity by other modifications. We discuss how such positive reinforcement can result in chromatin states that are robust and can be epigenetically maintained through cell division. We describe the implications of these regulatory systems in relation to modifications including H3K4me3, H3K79me3, and H3K36me3 that are associated with active genes and H3K27me3 and H3K9me3 that have been linked to transcriptional repression. We also review the crosstalk between active and repressive modifications, illustrated by the interplay between the Polycomb and Trithorax histone‐modifying proteins, and discuss how this may be important in defining gene expression states during development.
Load-modifiable content-based Publish/Subscribe Architecture over structured peer-to-peer networks

Three key performance indexes of distributed publish/subscribe systems are latency, load balance and flow cost. In this paper, we propose Adaptable Publish/Subscribe Architecture (APSA) for content-based publish/subscribe system, and it is built on structured P2P networks. In APSA, We use subscriptions covering, merging and binding, and two-layer delivering tree strategies to balance the load and reduce latency, so as to get a good performance. The experimental results show that APSA can provide modifiable load balance with relative low latency and low network flow cost which fit for publish/subscribe systems.
A News-Utility Theory for Inattention and Rebalancing in Portfolio Choice *

Recent evidence suggests that investors are either inattentive to their portfolios or undertake puzzling rebalancing efforts. This paper develops a life-cycle portfolio-choice model in which the investor experiences loss-averse utility over news and can choose whether or not to look up his portfolio. I obtain three main predictions. First, the investor prefers to not look up and not rebalance his portfolio most of the time to avoid fluctuations in news utility. Such fluctuations cause a first-order decrease in expected utility because the investor dislikes bad news more than he likes good news. Consequently, the investor has a first-order willingness to pay a portfolio manager who rebalances actively on his behalf. Second, if the investor looks up his portfolio himself, he rebalances extensively to enjoy or delay the realization of good or bad news, respectively. Third, the investor would like to commit to being inattentive even more often because it reduces overconsumption. Quantitatively, I structurally estimate the preference parameters by matching participation and stock shares over the life cycle. My parameter estimates are in line with the literature, generate reasonable intervals of inattentiveness, and simultaneously explain consumption and wealth accumulation over the life cycle. JEL Codes: G02, G11, D03, D14, D91. *Most recent version: http://econgrads.berkeley. edu/mpagel/files/2013/10/PortfolioChoicePaper.pdf **I thank Adam Szeidl, Matthew Rabin, Nick Barberis, Ulrike Malmendier, Botond Koszegi, Brett Green, Martin Lettau, John Beshears, James Choi, Keith Chen, Max Kasy, Florian Peters, Aniko Oery, Sheng Li, Ana Rocca, Marco Schwarz, Lydia Ashton, Takeshi Murooka, Victoria Vanasco as well as seminar participants at UC Berkeley and UC Berkeley Haas for their helpful comments and suggestions. Financial support from the Psych-and-Econ group at UC Berkeley is gratefully acknowledged. All errors remain my own. 1 USC FBE FINANCE FACULTY RECRUITING FRIDAY, Feb. 14, 2014 10:30 am – 12:00 pm, Room: JKP-210
A New Framework: The Sociotechnical Approach to Nation Branding

This research applies the principles of alignment and collaboration of technical and social systems to assess if the principles of Sociotechnical Systems Theory advance the theory and practice of nation branding. Following a mixed-method and mixed-model approach, using interviews, questionnaire and documentary evidence the aim of this work is to empirically investigate if the Isle of Man’s nation brand is affected by sociotechnical alignment in its creation, implementation and outcomes. The findings evidence how deficiency in branding know-how, the usage of incorrect tools in the production of the nation brand and the neglect of the brand’s social system leads misalignment in both technical and social systems; ultimately affecting the outcomes of the nation brand. Through these findings, this research has important implications for the filed of nation branding by confirming that the principles of sociotechnical theory can advance both the theory and practice of nation branding. This is achieved through facilitating transparency, democracy and expediting coherence, synergy and civic engagement with the nation brand. In terms of originality and contribution to knowledge, this work represents the first application of sociotechnical theory to nation branding and demonstrates that a nation brand is a sociotechnical system where distinct forms of technical and socio misalignment exist. It also uncovers the relationship between forms of nation branding sociotechnical misalignment and how as a consequence of these links, variants of misalignment combine to create other forms of misalignment within the nation brand’s sociotechnical system.
Global artificial bee colony search algorithm for numerical function optimization

The standard artificial bee colony (ABC) algorithm as a relatively new swarm optimization method is often trapped in local optima in global optimization. In this paper, a novel search strategy of main three procedures of the ABC algorithm is presented. The solutions of the whole swarm are exploited based on the neighbor information by employed bees and onlookers in the ABC algorithm. According to incorporating all employed bees' historical best position information of food source into the solution search equation, the improved algorithm that is called global artificial bee colony search algorithm has great advantages of convergence property and solution quality. Some experiments are made on a set of benchmark problems, and the results demonstrate that the proposed algorithm is more effective than other population based optimization algorithms.