Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying transcriptional regulatory sites in the human genome using an integrated system.

This work develops an integrated system which, after a set of genes are inputted, is able to predict transcriptional regulatory sites and to detect the co-occurrence of these regulatory sites. The system integrates several site detection methods such as known site matching, over-presented oligonucleotide detection and DNA motif discovery programs. User profiles and history pages enable users to trace the sequence analyses of these transcriptional regulatory sites. Two groups of co-regulated genes were used to test the proposed system. The results predicted by the proposed system consist of known site homologs and putative regulatory sites. By comparing these sites with previously published results, the proposed system is able to help biologists identify possible candidates for the regulatory sites from groups of co-regulated genes. The integrated system is now available at http://rgsminer. csie.ncu. edu.tw/.
Experiments on the DCASE Challenge 2016: Acoustic Scene Classification and Sound Event Detection in Real Life Recording

In this paper we present our work on Task 1 Acoustic Scene Classi- fication and Task 3 Sound Event Detection in Real Life Recordings. Among our experiments we have low-level and high-level features, classifier optimization and other heuristics specific to each task. Our performance for both tasks improved the baseline from DCASE: for Task 1 we achieved an overall accuracy of 78.9% compared to the baseline of 72.6% and for Task 3 we achieved a Segment-Based Error Rate of 0.76 compared to the baseline of 0.91.
Humanoid whole-body planning for loco-manipulation tasks

We consider the problem of planning whole-body motions for humanoids that must execute loco-manipulation tasks, i.e., manipulation tasks that implicitly require a locomotion phase. The proposed planner builds a tree in configuration-time space by concatenating feasible, collision-free whole-body motions that realize a succession of CoM movement primitives and, at the same time, the assigned manipulation task. To obtain fluid, natural motions we identify three zones of operation, i.e, locomotion, loco-manipulation and manipulation, and we carefully design a mechanism that allows to synchronize the two tasks. The proposed method has been implemented in V-REP for the NAO humanoid and successfully tested in various scenarios of increasing complexity.
Embedding virtual software-defined networks over distributed hypervisors for vDC formulation

We study how to embed virtual software-defined networks (vSDNs) cost-effectively over a substrate network with distributed network virtualization hypervisors (NVHs) for virtual datacenter (vDC) formulation to support Big Data applications. Specifically, we try to jointly optimize the embedding schemes of the control and data planes of each vSDN, i.e., to minimize the data plane's resource consumption and limit the number of NVHs used in the control plane simultaneously. We first formulate an integer linear programming (ILP) model to solve the problem exactly, and then design a heuristic to reduce the time complexity. Simulation results suggest that our proposed algorithms can embed vSDNs cost-effectively and significantly outperform the existing scheme based on global resource capacity (GRC).
UvA-DARE ( Digital Academic Repository ) How reliable is pooled analysis in political economy ? : the globalization-welfare state nexus revisited

Panel data analysis has become very popular in comparative political economy. However, in order to draw meaningful inferences from such data, one has to address specification and estimation issues carefully. This paper aims to demonstrate various pitfalls that typically occur in applied empirical work. To illustrate this, we refer to the debate on the globalization-welfare state nexus. We reexamine a model by Garrett and Mitchell (2001), a leading study in this regard. Utilizing a data set of 17 OECD countries and the time period 1961 to 1993, they find evidence that globalization and partisan composition have a significant impact on the extent of public activity. However, because they apply a dynamic specification in levels, they do not adequately take into account both the dynamic and spherical nature of the data. In contrast, we propose an autoregressive model in first differences that is shown to perform well in statistical terms. Further, we explicitly pay attention to the time pattern of the globalization-welfare state nexus. Substantively, we find evidence that government spending is primarily driven by the state of the domestic economy. Neither partisan effects nor the international economic environment have affected public expenditure considerably.
Low frequency parasitic effects in RF transistors and their impact on power amplifier performances

In this paper Low Frequency (LF) parasitic effects are assessed through three kinds of measurements. It is shown that LF S-parameters measurements allow to extract the thermal impedance of Heterojunction Bipolar Transistors (HBTs) and to put dispersive effects of AlGaN/GaN High Electron Mobility Transistors (HEMTs) into evidence. Large signal (RF pulsed and two tone intermodulation) confirm the impact of those parasitic effects on performances of Power Amplifiers.
Two Stage Fault Analysis against a Falsification Detection Cipher Minalpher

Regarding security measures, several falsification detection ciphers have been proposed. On the other hand, a thread of fault analysis against cryptographic circuits has been noted. Fault analysis attacks use the characteristics of a circuit that is incorporated into the device, generate a fault, analyze internal information of the circuit from its output, and obtain secret keys. Therefore, to ensure the safety of future IoT devices, fault analysis against falsification detection ciphers must be investigated. The present study proposes a method of fault analysis against Minalpher, a typical falsification detection cipher. Simulation results verify the validity of the proposed method.
Quality metric for approximating subjective evaluation of 3-D objects

Many factors, such as the number of vertices and the resolution of texture, can affect the display quality of three-dimensional (3-D) objects. When the resources of a graphics system are not sufficient to render the ideal image, degradation is inevitable. It is, therefore, important to study how individual factors will affect the overall quality, and how the degradation can be controlled given limited resources. In this paper, the essential factors determining the display quality are reviewed. We then integrate two important ones, resolution of texture and resolution of wireframe, and use them in our model as a perceptual metric. We assess this metric using statistical data collected from a 3-D quality evaluation experiment. The statistical model and the methodology to assess the display quality metric are discussed. A preliminary study of the reliability of the estimates is also described. The contribution of this paper lies in: 1) determining the relative importance of wireframe versus texture resolution in perceptual quality evaluation and 2) proposing an experimental strategy for verifying and fitting a quantitative model that estimates 3-D perceptual quality. The proposed quantitative method is found to fit closely to subjective ratings by human observers based on preliminary experimental results.
Quantitative Modeling of a Gene's Expression from Its Intergenic Sequence

Modeling a gene's expression from its intergenic locus and trans-regulatory context is a fundamental goal in computational biology. Owing to the distributed nature of cis-regulatory information and the poorly understood mechanisms that integrate such information, gene locus modeling is a more challenging task than modeling individual enhancers. Here we report the first quantitative model of a gene's expression pattern as a function of its locus. We model the expression readout of a locus in two tiers: 1) combinatorial regulation by transcription factors bound to each enhancer is predicted by a thermodynamics-based model and 2) independent contributions from multiple enhancers are linearly combined to fit the gene expression pattern. The model does not require any prior knowledge about enhancers contributing toward a gene's expression. We demonstrate that the model captures the complex multi-domain expression patterns of anterior-posterior patterning genes in the early Drosophila embryo. Altogether, we model the expression patterns of 27 genes; these include several gap genes, pair-rule genes, and anterior, posterior, trunk, and terminal genes. We find that the model-selected enhancers for each gene overlap strongly with its experimentally characterized enhancers. Our findings also suggest the presence of sequence-segments in the locus that would contribute ectopic expression patterns and hence were “shut down” by the model. We applied our model to identify the transcription factors responsible for forming the stripe boundaries of the studied genes. The resulting network of regulatory interactions exhibits a high level of agreement with known regulatory influences on the target genes. Finally, we analyzed whether and why our assumption of enhancer independence was necessary for the genes we studied. We found a deterioration of expression when binding sites in one enhancer were allowed to influence the readout of another enhancer. Thus, interference between enhancer activities was a possible factor necessitating enhancer independence in our model.
Using minimum classification error training in dimensionality reduction

Dimensionality reduction is an important problem in pattern recognition. In a speech recognition system, the size of the feature set is normally large in the order of 40. Therefore, it is necessary to reduce the dimensionality of the feature space for efficient and effective speech recognition. Two popular methods to reduce the dimensionality of the feature space are linear discriminat analysis (LDA) and principal component analysis (PCA). This paper uses the minimum error classification (MCE) training algorithm for dimensionality reduction and presents an alternative MCE training algorithm that performs better on testing data than the conventional MCE training algorithm. The effects of the initial value of the transformation matrix on the performance of MCE have also been studied.
Crosstalk between Beclin-1-dependent autophagy and caspase-dependent apoptosis induced by tanshinone IIA in human osteosarcoma MG-63 cells

The aim of the present study was to ascertain whether or not autophagy is induced by tanshinone IIA (TanIIA), and to explore the crosstalk between autophagy and apoptosis in regards to the antitumor effects of TanIIA on MG-63 cells and the potential mechanism. MG-63 cells were cultured in vitro with various concentrations of TanIIA (0, 2.5, 5, 10 and 20 mg/l) for 0, 24, 48 and 72 h, respectively. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide MTT assay was used to evaluate the inhibition of the proliferation of osteosarcoma MG-63 cells by TanIIA or in the presence/absence of chloroquine (CQ). Autophagic vacuoles and characteristic autophagosomes were observed by transmission electron microscopy (TEM). TanIIA-induced autophagy in MG-63 cells was confirmed by GFP-LC3 punctate fluorescence. The expression levels of apoptosis-related proteins caspase-3, caspase-8, caspase-9 and cleaved-PARP and autophagy-related proteins LC3II/LC3I and Beclin-1 were detected by western blotting. FITC-Annexin V/propidium iodide (PI) staining, flow cytometry and Hoechst 33258 staining were used to analyze the apoptotic rate. Fluorescence intensity of reactive oxygen species (ROS) was examined under a fluorescence microscope using an analysis software system. Cell proliferation was obviously inhibited by TanIIA in a dose- and time-dependent manner. Generation of autophagy was triggered by TanIIA (0–20 mg/l) treatment, and in a Beclin-1-dependent manner. Compared with the control group, the apoptosis ratio following treatment with 2.5 mg/l TanIIA failed to achieve statistical significance. Expression of caspase-3, -8 and -9, and cleaved-PARP in the other groups was gradually enhanced in dose-dependent manner. Our analysis also suggested that the influence of autophagy on TanIIA cytotoxicity had a phase effect; with low-dose drugs and shorter treatment periods, autophagy functioned as a damage repair mechanism. In conrast, when the cells were treated with higher doses of TanIIA for longer treatment periods, autophagic cell death contributed to apoptosis. Furthermore, generation of ROS occurred in a dose-dependent manner and pretreatment with NAC, a selective ROS scavenger, blocked the coexistence of Beclin-1 autophagy and caspase-dependent apoptosis. In conclusion, our findings provide strong evidence that TanIIA may be a potential therapeutic drug against osteosarcoma. Moreover, its cytotoxity can be enhanced with ROS agonists.
The Crowding-Out Effect of Formal Insurance on Informal Risk Sharing Arrangements: An Experimental Study

An important issue with promoting formal insurance in the rural areas of developing countries that has been previously ignored is the interaction between formal insurance and preexisting informal risk sharing arrangements. This paper shows in theory that formal insurance will crowd out informal transfers even when individuals do not purchase insurance, which often makes the overall welfare impact of formal insurance negative. Our laboratory experiment indeed documents significant crowding-out effect. However, the overall welfare is improved when ex-ante income is equal but not when income inequality exists. The decision not to purchase formal insurance, the existence of ex-ante income inequality and altruistic motive are shown to reinforce the negative welfare impact of formal insurance.
Unsupervised Word Acquisition from Speech using Pattern Discovery

In this paper, we present an unsupervised method for automatically discovering words from speech using a combination of acoustic pattern discovery, graph clustering, and baseform searching. The algorithm we propose represents an alternative to traditional methods of speech recognition and makes use of the acoustic similarity of multiple realizations of the same words or phrases. On a set of three academic lectures on different subjects, we show that the clustering component of the algorithm is able to successfully generate word clusters that have good coverage of subject-relevant words. Moreover, we illustrate how to use the cluster nodes to retrieve the word identity of each cluster from a large baseform dictionary. Results indicate that this algorithm may prove useful for applications such as vocabulary initialization, speech summarization, or augmentation of existing recognition systems
Enhancing the soft proofing paradigm

The first part of this study is devoted to assessing the suitability of soft proofs as a surrogate for the final print in judging colour-reproduction quality. Two sets of psychophysical experiments were carried out. The first investigated whether the type of medium used to generate a stimulus influenced its appearance, while the second attempted to determine whether judgments made on the basis of hardcopy simulation are transferable to prints. The second part of this study is devoted to improve the accuracy of soft proofing by increasing the amount of information rendered on screen. We present a workflow that extends traditional colorimetry beyond simple colour appearance prediction to a higher dimensional representation, which includes gloss. The intention is to provide a full goniometric simulation of the spatial distribution of light reflected by a print based upon data gathered with simple and inexpensive instruments, glossmeters and spectrophotometers.
Surface Investigations of Aluminum in 2M Hydrochloric Acid Solution in the Presence of Potassium Iodate Inhibitor

The results of investigations by using optical, scanning electron microscopy (SEM) and energy dispersive X- ray spectroscopy (EDS) to study the surface morphology, the composition of adsorbed film formed on the surface of aluminum samples in 2M hydrochloric acid solution containing 100 ppm optimum KIO3 dose. The data reveal that the additive improves the surface morphology of aluminum, due to the marked layer enrichment of Al- surface by inhibitor components. Detailed studies were carried out to investigate the effect of oxygen in the inhibition process. The nature and strength of the passive film and the mechanism of its formation are explained based on detailed studies conducted under experimental conditions.
Group B–3:realization of Adaptive Locomotion Based on Dynamic Interaction between Body, Brain, and Environment

— The behavior of a robot is emerged from the interaction between body, control, and environmental dynamics. The research group B–3 aims to design body and control dynamics for emerging adaptive locomotion. We investigate three types of locomotion, biped, quadruped, and snake-like and developed robots. We also discuss on the lower control architecture for realizing reactive adaptive locomotion.
Observation of the superconducting proximity effect from kinetic-inductance measurements.

A method is described for observing the proximity effect in a thin-film-superconductor--normal-metal bilayer. The superconducting film must be thin compared to its penetration depth. The kinetic inductance of the superconducting film alone is then proportional to {lambda}{sup 2}({ital T})/{ital d}. It is found that in a bilayer the temperature dependence of the kinetic inductance deviates significantly from this dependence at low temperatures. The kinetic inductance may be measured in a nondestructive manner using the two-coil mutual-inductance technique. Bilayers of NbN/Al and Nb/Cu have both exhibited the effect, whereas a bilayer in which the proximity coupling was purposefully suppressed had the same temperature dependence as the superconducting film alone. The effect is analyzed in terms of a spatially varying penetration depth through the film thickness, and the observations are found to be in qualitative agreement with the predictions of the model. A more exact fitting will require improved theoretical models for the proximity effect.
Detection of Psychological Stress Using a Hyperspectral Imaging Technique

The detection of stress at early stages is beneficial to both individuals and communities. However, traditional stress detection methods that use physiological signals are contact-based and require sensors to be in contact with test subjects for measurement. In this paper, we present a method to detect psychological stress in a non-contact manner using a human physiological response. In particular, we utilize a hyperspectral imaging (HSI) technique to extract the tissue oxygen saturation (StO2) value as a physiological feature for stress detection. Our experimental results indicate that this new feature may be independent from perspiration and ambient temperature. Trier Social Stress Tests (TSSTs) on 21 volunteers demonstrated a significant difference $p\< 0.005$ and a large practical discrimination (d 1/4 1.37) between normalized baseline and stress StO2 levels. The accuracy for stress recognition from baseline using a binary classifier was 76.19 and 88.1 percent for the automatic and manual selections of the classifier threshold, respectively. These results suggest that the StO2 level could serve as a new modality to recognize stress at standoff distances.
Design space exploration for multicore architectures: a power/performance/thermal view

Multicore architectures are ruling the recent microprocessor design trend. This is due to different reasons: better performance, thread-level parallelism bounds in modern applications, ILP diminishing returns, better thermal/power scaling (many small cores dissipate less than a large and complex one); and, ease and reuse of design.This paper presents a thorough evaluation of multicore architectures. The architecture we target is composed of a configurable number of cores, a memory hierarchy consisting of private L1 and L2, and a shared bus interconnect. We consider parallel shared memory applications. We explore the design space related to the number of cores, L2 cache size and processor complexity, showing the behavior of the different configurations/applications with respect to performance, energy consumption and temperature. Design tradeoffs are analyzed, stressing the interdependency of the metrics and design factors. In particular, we evaluate several chip floorplans. Their power/thermal characteristics are analyzed and they show the importance of considering thermal effects at the architectural level to achieve the best design choice.
Cloud Mobile Media: Opportunities, challenges, and directions

Three recent developments - increasing adoption of smart phones and tablets as desired platforms for infotainment, increased access to mobile broadband networks globally, and availability of public Clouds - are aligning to possibly enable a new generation of truly ubiquitous multimedia services on mobile devices: Cloud Mobile Media (CMM) services. Such services will be able to avail of the elasticity of cloud computing and ubiquity of cloud storage, and thereby not constrained either by mobile device capabilities, or availability of content. In this paper, we look at early trends in CMM services, and opportunities and benefits for new CMM services in the near future. We analyze the possible impact of such services, and issues that need to be addressed to make CMM services viable, including response time, user experience, energy, privacy, cost and scalability. We provide several directions for possible solutions, which include developing response time management techniques, scalable cloud media application, and cloud user experience measurement techniques. We also propose extending the Cloud beyond the traditional Internet to the edge of the wireless networks.
CRM Evaluation

Customer Relationship Management (CRM)1 has been discussed in the literature since the nineties. IT evaluation on the other hand dates back to the eighties starting with a more contemporary approach (Farbey et al. 1999, p. 191). As reported by earlier works, the success rate of CRM implementation projects is up to today still not satisfactory (Becker et al. 2009; Finnegan and Currie 2009). Reasons for failing the expectations of involved parties are diverse, but can be summarized under the three dimensions: people, process and technology (Figure 1). Due to the described quality problems and the speed of evaluation results becoming outdated, new CRM solutions or updated versions of established products continuously enter the market.