Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting epidemic evolution on contact networks from partial observations

The massive employment of computational models in network epidemiology calls for the development of improved inference methods for epidemic forecast. For simple compartment models, such as the Susceptible-Infected-Recovered model, Belief Propagation was proved to be a reliable and efficient method to identify the origin of an observed epidemics. Here we show that the same method can be applied to predict the future evolution of an epidemic outbreak from partial observations at the early stage of the dynamics. The results obtained using Belief Propagation are compared with Monte Carlo direct sampling in the case of SIR model on random (regular and power-law) graphs for different observation methods and on an example of real-world contact network. Belief Propagation gives in general a better prediction that direct sampling, although the quality of the prediction depends on the quantity under study (e.g. marginals of individual states, epidemic size, extinction-time distribution) and on the actual number of observed nodes that are infected before the observation time.
Modeling and digital control of a high-power full-bridge isolated DC-DC buck converter designed for a two-stage grid-tie PV inverter

This paper describes a grid-tie photovoltaic (PV) inverter composed of an isolated full-bridge buck DC-DC converter with high-frequency transformer and a cascaded DC-AC full-bridge inverter connected to the grid. Emphasis is given on the modeling and digital control design of the DC-DC converter with the polynomial pole placement method. Simulation results are presented and a inverter prototype is currently being built.
Parental training for incarcerated fathers: effects on attitudes, self-esteem, and children's self-perceptions.

The effects of parent education programs on the parenting attitudes and abilities of 30 U.S. male inmates and on the self-perceptions of their children (aged 8-17 years) were examined. Inmates were pre- and post-tested with the Adult-Adolescent Parenting Inventory and the Index of Self-Esteem. The children were administered the Self-Perception Profile for Children or the Self-Perception Profile for Adolescents. Participants in the experimental group completed a 6-week program including parental training and behavior-management training. The control group's 6-week program consisted of viewing family-related videotapes, answering questions, and discussing the contents of the videotapes. Parent education improved the attitudes of inmates toward appropriate parenting but did not significantly change their children's self-perceptions.
Does Dopamine Still Have a Leading Role in Advanced Parkinson’s Disease after Subthalamic Stimulation?

The role of endogenous dopamine in severe Parkinson’s disease is often underestimated. We report on a case of acute general motor worsening induced by the ingestion of fluphenazine in a parkinsonian patient successfully treated with STN DBS. Other etiologies were ruled out. Clinical improvement was gradual and fully reversible 4 days after discontinuation of the antidopaminergic drug. We suggest that residual striatal and extrastriatal dopaminergic pathways still play a paramount role in mediating central neurotrasmissions that may take part in STN DBS’s mechanism of action.
VirHKey: a VIRtual Hyperbolic KEYboard with gesture interaction and visual feedback for mobile devices

The VirHKey is a new text entry method for mobile devices using a simple Unistroke-like alphabet. Gesture recognition is accomplished not through pattern recognition but through sequences of flicks with low required angular accuracy: 2p/5 in radians. This means that the full stroke path is unimportant and recognition is highly deterministic, enabling good accuracy. All during the interaction, an optional visual feedback is provided at least for the learning stage. This is done with a focus and context display based on the hyperbolic geometry. To illustrate the possibilities of the VirHKey, a prototype application was developed and usability tests demonstrated the overall good performances of the proposition with a text entry rate from 18 to 25 words per minute and a high satisfaction of users.
Useful Pattern Mining on Time Series - Applications in the Stock Market

We present the architecture of a “useful pattern” mining system that is capable of detecting thousands of different candlestick sequence patterns at the tick or any higher granularity levels. The system architecture is highly distributed and performs most of its highly compute-intensive aggregation calculations as complex but efficient distributed SQL queries on the relational databases that store the time-series. We present initial results from mining all frequent candlestick sequences with the characteristic property that when they occur then, with an average at least 60% probability, they signal a 2% or higher increase (or, alternatively, decrease) in a chosen property of the stock (e.g. close-value) within a given time-window (e.g. 5 days). Initial results from a first prototype implementation of the architecture show that after training on a large set of stocks, the system is capable of finding a significant number of candlestick sequences whose output signals (measured against an unseen set of stocks) have predictive accuracy which varies between 60% and 95% depended on the type of pattern.
Immunoinformatics Aided Prediction of Cytotoxic T Cell Epitope of Respiratory Syncytial Virus

ABSTRACT: The Respiratory Syncytial Virus (RSV) poses the threat of lower respiratory tract infection to the infants as well as elderlies. As there is no licensed vaccine, alternative vaccine candidates like Epitope-based vaccines can be considered as a potential candidate. Being conserved among strains and reported to elicit cytotoxic T cell (CTL) response, the fusion glycoprotein of RSV (RSV-FP) is a first-rate target for epitope based vaccine designing. As RSV specific CD8+ CTLs are the central cell of viral clearance, the epitopes capable to generate CTL response are desirable. In this study, available immunoinformatics tools are utilized with a target to predict epitopes on the RSV-FP that elicit strong (CTL) responses. We report seven nine-mer peptides that bind strongly with 17 different HLA, have 100% sequence conservancy and is projected to provide 76.03% population coverage worldwide. KEYWORDS: epitope based vaccine, RSV-F protein, CTL epitope, human respiratory syncytial virus, immunoinformatics.
A multi-objective decomposition-based evolutionary algorithm with enhanced variable space diversity control

Most Multi-objective Evolutionary Algorithms (MOEAs) operate without explicitly promoting the diversity of the variable space. Nevertheless, in the single-objective domain it has been shown that properly managing this kind of diversity might lead to higher-quality solutions. In this paper the diversity of the variable space is analyzed for several state-of-the-art MOEAs with well-known benchmarks, showing that in the long term, the diversity is lost in a subset of variables. This loss implies an important degradation of the performance. In order to show that increasing the diversity can solve these issues, MOEA/D with Enhanced Variable-Space Diversity (MOEA/D-EVSD) is proposed. This variant induces a gradual loss of diversity by altering the mating selection process. In addition, a final phase to properly intensify is included. The experimental validation was carried out with the Walking Fish Group (WFG) benchmark and several state-of-the-art MOEAs showing the benefits of the proposal. Particularly, WFG1 and WFG8, which are not properly solved by most state-of-the-art approaches, are readily solved by our proposal.
Real-time implementation of synthetic aperture vector flow imaging on a consumer-level tablet

In this work, a 2-D vector flow imaging (VFI) method based on synthetic aperture sequential beamforming (SASB) and directional transverse oscillation is implemented on a commercially available tablet. The SASB technique divides the beamforming process in two parts, whereby the required data rate between the probe and back-end can be reduced by a factor of 64 compared to conventional delay-and-sum focusing. The lowered data rate enables real-time wireless transfer for both B-mode and VFI data. In the present setup, element data were acquired from a straight vessel with the SARUS research scanner and processed by a first-stage beamformer in a fixed focus. The data were subsequently transferred to an HTC Nexus 9 tablet through an ASUS RT-AC68U Wi-Fi router to simulate a wireless probe. The second-stage beamforming of the B-mode and flow data and the velocity estimation were implemented on the tablet's built-in GPU (Nvidia Tegra K1) through the OpenGL ES 3.1 API. Real-time performance was achieved with rates up to 26 VFI frames per second (38 ms/frame) for concurrent processing and Wi-Fi transmission.
A Minimax Optimal Algorithm for Crowdsourcing

We consider the problem of accurately estimating the reliability of workers based on noisy labels they provide, which is a fundamental question in crowdsourcing. We propose a novel lower bound on the minimax estimation error which applies to any estimation procedure. We further propose Triangular Estimation (TE), an algorithm for estimating the reliability of workers. TE has low complexity, may be implemented in a streaming setting when labels are provided by workers in real time, and does not rely on an iterative procedure. We prove that TE is minimax optimal and matches our lower bound. We conclude by assessing the performance of TE and other state-of-the-art algorithms on both synthetic and real-world data.
rasta-plp 1 Tue Sep 22 10 : 25 : 24 1998 RASTA _ PLP

In this application note we explain how to use the ESPS program rasta_plp to compute features for use in automatic speech recognition systems, such as can be built by using the hidden Markov model tool kit HTK [1]. We also describe how to use rasta_plp to compute spectrograms that correspond to the auditory-based processing used by the ras a_plp program. Finally, we provide an introduction to the signal processing tec niques known as perceptual linear prediction (PLP) andrelative spectra (RASTA), and we list relevant literature references. Much of the backgrou information and description found here is based on the material containe references [2,3]
Efficient caching scheme for data access in disruption tolerant networks

Disruption Tolerant Networks (DTNs) are characterized by lack of continuous network connectivity because of the limits of radio communication range, sparsity of mobile nodes, shortage of energy resources. There are many researches about data forwarding in DTNs, while limited work on providing efficient data access. In this paper, we propose an efficient cooperative caching scheme, which enables the data query to be satisfied quickly. Our basic idea is to cache data at a set of Proper Nodes (PNs), which can be easily accessed by other nodes in the network. We present a novel algorithm to select the PNs. This algorithm ensures that the PNs are not clustered to damage the data access performance of the whole network. We evaluate our proposed cooperative caching scheme with extensive simulation by using the Sigcomm2009 trace records. The simulation results show that our proposed cooperative caching scheme significantly improves the performance of data access.
Dynamic Proliferation Assessment in Flow Cytometry

Dynamic proliferation assessment via flow cytometry is legitimately supposed to be the most powerful tool for recording cell cycle kinetics in‐vitro. The preeminent feature is a single cell–based multi‐informative analysis by temporal high‐resolution. Flow cytometric approaches are based on labeling of proliferating cells via thymidine substitution by a base analog (e.g., 5‐bromo‐2′‐deoxyuridine, BrdU) that is added to cell cultures either for a short period of time (pulse labeling) or continuously until cell harvesting. This unit describes the alternative use of the thymidine analog 5‐ethynyl‐2′‐deoxyuridine (EdU) in place of BrdU for three different applications: (1) dynamic proliferation assessment by EdU pulse cell labeling; (2) the same approach as (1) but in combination with live/dead cell discrimination; and (3) dynamic cell cycle analysis based on continuous cell labeling with EdU and Hoechst fluorochrome quenching. In contrast to the detection of BrdU incorporation, EdU‐positive cells can be identified by taking advantage of click chemistry, which facilitates a simplified and fast cell preparation. Further analysis options but also limitations of the utilization of EdU are discussed. Curr. Protoc. Cell Biol. 48:8.6. 1‐8.6. 23. © 2010 by John Wiley & Sons, Inc.
An integrated approach: advances in the use of Clostridium for biofuel

Almost 90% of our energy comes from fossil fuels, which are both limited and polluting, hence the need to find alternative sources. Biofuels can provide a sustainable and renewable source of energy for the future. Recent significant advances in genetic engineering and fermentation technology have made microbial bio-based production of chemicals from renewable resources more viable. Clostridium species are considered as promising micro-organisms for the production of a wide range of chemicals for industrial use. However, a number of scientific challenges still need to be overcome to facilitate an economically viable production system. These include the use of cheap non-food-based substrates, a better understanding of the metabolic processes involved, improvement of strains through genetic engineering and innovation in process technology. This paper reviews recent developments in these areas, advancing the use of Clostridium within an industrial context especially for the production of biofuels.
Contour Prediction with Long Short-Term Memory , Bi-Directional , Deep Recurrent Neural Networks

Deep Neural Networks (DNNs) have been shown to provide state-of-the-art performance over other baseline models in the task of predicting prosodic targets from text in a speechsynthesis system. However, prosody prediction can be affected by an interaction of shortand long-term contextual factors that a static model that depends on a fixed-size context window can fail to properly capture. In this work, we look at a recurrent formulation of neural networks (RNNs) that are deep in time and can store state information from an arbitrarily large input history when making a prediction. We show that RNNs provide improved performance over DNNs of comparable size in terms of various objective metrics for a variety of prosodic streams (notably, a relative reduction of about 6% in F0 mean-square error accompanied by a relative increase of about 14% in F0 variance), as well as in terms of perceptual quality assessed through mean-opinion-score listening tests.
A 40-GHz static frequency divider with quadrature outputs in 80-nm CMOS

The implemented static frequency divider provides quadrature (Q) clock outputs and divides frequencies up to 44GHz. The core divider circuit consists of two current-mode logic (CML) latches and consumes 3.2mW from a 1.1-V supply. The divided outputs result in a peak-to-peak and rms jitter of 6.3 and 0.8ps, respectively, and the maximum phase mismatch between the in-phase (I) and Q-outputs amounts to 1ps at an input frequency of 40GHz. The high division frequency is achieved by employing resistive loads, inductive peaking, and optimizing the circuit layout for reduced parasitic capacitances in the latches. The core divider consumes a chip area of 30mumtimes40mum only
Adaptive Immune Responses Are Dispensable for Isolated Lymphoid Follicle Formation: Antigen-Naive, Lymphotoxin-Sufficient B Lymphocytes Drive the Formation of Mature Isolated Lymphoid Follicles 1

Isolated lymphoid follicles (ILFs) are recently appreciated members of the mucosal immune system. The architecture, composition, and inducible nature of these structures indicates that these structures are tertiary lymphoid structures. The process leading to the formation of tertiary lymphoid structures, lymphoid neogenesis, has been observed in a number of inflammatory and autoimmune conditions. Given this association, there is considerable interest in identifying the factors promoting lymphoid neogenesis, and understanding the steps in this process. Using murine ILF formation as a model, we have examined the roles of different cellular sources of lymphotoxin (LT) and the adaptive immune response in lymphoid neogenesis. In this study, we report that, although other cellular sources of LT may supplant B lymphocytes in the formation of immature ILFs (loosely organized clusters of B lymphocytes), LT-sufficient B lymphocytes are required for the progression of immature ILFs to mature ILFs (organized lymphoid aggregates with a follicle-associated epithelium). ILF formation occurs in the absence of T lymphocytes and Ag-specific B lymphocyte responses, and ILF B lymphocytes express elevated levels of LT in the absence of antigenic stimulation. Consistent with a role for chemokines inducing LT expression in Ag-naive B lymphocytes, and a chemokine-driven positive-feedback loop driving mature ILF formation, mature ILFs express elevated levels of B lymphocyte chemoattractant in the absence of Ag-specific B lymphocyte stimulation. These observations indicate that ILFs contain Ag-naive lymphocytes, and suggest that events occurring within ILFs shape subsequent immune responses mediated by these lymphocytes.
Reverse Intersystem Crossing in Rose Bengal. II. Fluence Dependence of Fluorescence Following 532 nm Laser Excitation ¶

A fluence‐dependent fluorescence technique was used to observe reverse intersystem crossing from a certain higher‐lying triplet state of rose bengal populated by a single pulse of 532 nm light. The quantum yield of reverse intersystem crossing from this state was determined to be 0.12 ± 0.02 for rose bengal in phosphate‐buffered saline. The importance of including molecular rotation effects in the analysis of fluorescence resulting from reverse intersystem crossing is discussed. Differences in the photochemical reactivity of upper triplet states in biological systems have been previously hypothesized to result from photophysical differences, particularly substantial differences in their reverse intersystem crossing yields. In this work this hypothesis is analyzed quantitatively, using numerical models of the population dynamics. These models suggest that reverse intersystem crossing alone cannot adequately explain the differences in biological response.
Software quality knowledge discovery: a rough set approach

This paper presents a practical knowledge discovery approach to software quality and resource allocation that incorporated recent advances in rough set theory, parameterized approximation spaces and rough neural computing. In addition, this research utilizes the results of recent studies of software quality measurement and prediction. A software quality measure quantifies the extent, to which some specific attribute is present in a system. Such measurements are considered in the context of rough sets. This research provides a framework for making resource allocation decisions based on evaluation of various measurements of the complexity of software. Knowledge about software quality is gained when preprocessing during which, software measurements are analyzed using discretization techniques, genetic algorithms in deriving reducts, and in the derivation of training and testing sets, especially in the context of the rough sets exploration system (RSES) developed by the logic group at the Institute of Mathematics at Warsaw University. Experiments show that both RSES and rough neural network models are effective in classifying software modules.
Hypersensitive Inhibition of the Proliferation of Cells with Mutated DNA Repair-Related Genes by the Catalytic Topoisomerase II Inhibitor 20-O-IngenolEZ

We previously reported that many ingenol compounds derived from Euphoria kansui exhibit topoisomerase inhibitory activity. 20-O-ingenolEZ in these compounds exerted inhibitory effects on both topoisomerase II (topo II) activity and cell proliferative activity. Topoisomerase II inhibitors can be divided into the poison and catalytic inhibitor types and 20-O-ingenolEZ is a catalytic inhibitor and inhibits topo IIα through inhibition of ATPase activity, but induces topo II-mediated DNA damage and apoptosis in BLM-/- DT40 cells through the induction of the DNA damage checkpoint, similar to the poison type inhibitor adriamycin. The ATPase inhibitor of topo II ICRF-193 also showed poison-like characteristics in the same cell line. However, the inhibitory effects of ICRF-193 on the proliferation of BLM-/- DT40 cells differed from those of 20-O-ingenolEZ, as did the specificity of its inhibition of the proliferation of other cell lines. 20-O-ingenolEZ showed hypersensitive inhibition of the proliferation of MCF-7 cells and BLM-/- DT40 cells with mutated DNA repair-related genes.
Formation of Tetrahydrocurcumin by Reduction of Curcumin with Cultured Plant Cells of Marchantia Polymorpha

Cultured plant cells of Marchantia polymorpha, Nicotiana tabacum, Phytolacca americana, Catharanthus roseus, and Gossypium hirsutum were examined for their ability to reduce curcumin. Only M. polymorpha cells converted curcumin into tetrahydrocurcumin in 90% yield in one day. Time-course experiment revealed a two-step formation of tetrahydrocurcumin via dihydrocurcumin.
Effect of licorice versus bismuth on eradication of Helicobacter pylori in patients with peptic ulcer disease

Background: Different therapeutic regimens were used for eradication of Helicobacter pylori, based on the cost, effectiveness and patient's compliance. The aim of this study was the evaluation of licorice compared with bismuth in quadruple regimen on eradication of H. pylori in patients with peptic ulcer disease (PUD). Materials and Methods: In a double-blind clinical trial study, 60 patients with PUD and positive rapid urease test were enrolled. The patients were randomly allocated into two equal groups. In first group, licorice, amoxicillin, metronidazole and omeprazole and in the second (control) group, bismuth subsalicylate, amoxicillin, metronidazole and omeprazole were prescribed respectively, and 4 weeks after treatment, in order to evaluate H. pylori eradication, urea breath test was done in all patients. The outcome of the study was the preference usage of licorice as an effective medication for H. pylori eradication. Results: Mean age of the patients in the control and case groups were 40.8 ± 15.5 and 42.2 ± 15.8 years, respectively (P = 0.726). Seventeen (56.7%) patients in control group and 16 (53.3%) in the case group were female (P = 0.795). Both groups were similar based on frequency of gastric or duodenal ulcer. Response to treatment were seen in 20 (67%) and 17 (57%) patients of case and control groups, respectively (P > 0.05). Conclusion: Our study showed that licorice is as effective as bismuth in H. pylori eradication; therefore, in patients whom bismuth is contraindicated, licorice can be used safely instead.