Miracle-dz/UniFAR-FTUs huggingface dataset:
Commun Nonlinear

It is of great interests in identifying dynamical properties of human sleep signals using electroencephalographic (EEG) measures. Multiscale entropy (MSE) is effective in quantifying the degree of unpredictability of time series in different time scales. To understand the superior coarse-graining approach for the EEG analysis, we therefor use different moments to coarse-grain a time series
GPFlow: an intuitive environment for web-based scientific workflow

Increasingly scientists are using collections of software tools in their research. These tools are typically used in concert, often necessitating laborious and error-prone manual data reformatting and transfer. We present an intuitive workflow environment to support scientists with their research. The workflow, GPFlow, wraps legacy tools, presenting a high level, interactive web-based front end to scientists. The workflow backend is realized by a commercial grade workflow engine (Windows Workflow Foundation). The workflow model is inspired by spreadsheets and is novel in its support for an intuitive method of interaction enabling experimentation as required by many scientists, e.g. bioinformaticians. We apply GPFlow to two bioinformatics experiments and demonstrate its flexibility and simplicity. Copyright © 2007 John Wiley & Sons, Ltd.
Integrating Language Generation with Speech Synthesis in a Concept to Speech System

Concept To Speech (CTS) systems are closely related to two other types of systems: Natural Language Generation (NLG) and Speech Synthesis (SS). In this paper, we propose a new architecture for a CTS system. A Speech Integrating Markup Language (SIML) is designed as an general interface for integrating NLG and SS. We also present a CTS system for a multimedia presentation generation application. We discuss how to extend the current CTS system based on the new architecture. Currently, only limited semantic, syntactic and prosodic features are covered inour prototype system. 1 I n t r o d u c t i o n Currently, there are two ways to develop a ConceptTo-Speech (CTS) system. The first is to design a monolithic CTS system for a specific application. This design involves a specific NLG module and an SS module, often developed for the application, where discourse, semantic and syntactic information produced by the NLG module can be used directly by CTS algorithms to determine either system specific parameters for a TextTo-Speech system, or phonological parameters for a vocal tract model (e.g., (Young and Fallside, 1979)). One advantage of this design is its efficiency, but features from the two systems are usually so intertwined that the interface of the CTS algorithms are system dependent. Another design is to keep NLG and SS as independent as possible, thus allowing reuse of the current NLG tools and TTS systems for other applications. The typical design is equivalent to "NLG plus Text-ToSpeech( TTS)" where the common interface between NLG and TTS is plain text. One advantage of this is in a its simplicity and adaptability. No change is necessary for existing NLG tools and TTS systems, but it suffers from a serious problem in that it loses useful information. All discourse, semantic and syntactic information is lost when the internal representation of NLG is converted to the text output and clearly this could be useful in determining prosody. In this paper, we want to maintain the autonomy of NLG and SS so that they are reusable for different applications, yet flexible enough to easily integrate without losing useful information. We propose a new architecture in which the common interface is not plain text, but a Speech Integrating Markup Language (SIML). We show how this architecture can be used in a multimedia presentation application where a prototype SIML was designed for this purpose.
STATE ENCODING FOR LOW POWER IN VLSI

: - Since their introduction in the 1985, _eld programmable gate arrays (FPGAs) have become increasingly important to the electronics industry. They have the potential for higher performance and lower power consumption than microprocessors and compared with application speci_c integrated circuits (ASICs), offer lower non-recurrent engineering (NRE) costs, reduced development time, easier debugging and reduced risk. In this paper an efficient multiplier-less technique is presented to design and implement a high speed CIC decimator for wireless applications like SDR and GSM. The Cascaded Integrator Comb is a commonly used decimation filter which performs sample rate conversion (SRC) using only additions/subtractions. The implementation is based on efficient utilization of embedded LUTs of the target device to enhance the speed of proposed design. It is an efficient method used to design and implement CIC decimator because the use of embedded LUTs not only increases the speed but also saves the resources on the target device. The importance of cryptography applied to security in electronic data transactions has acquired an essential relevance during the last few years. A proposed FPGA-based implementation of the Advanced Encryption Standard (AES) algorithm is presented in this paper. The design has been coded by Very high speed integrated circuit Hardware Descriptive Language. All the results are synthesized and simulated using Xilinx ISE and ModelSim software respectively. This implementation is compared with other works to show the efficiency.
Modelling naturalistic argumentation in research literatures : representation and interaction design issues

This paper characterises key weaknesses in the ability of current digital libraries to support scholarly inquiry, and as a way to address these, proposes computational services grounded in semiformal models of the naturalistic argumentation commonly found in research literatures. It is argued that a design priority is to balance formal expressiveness with usability, making it critical to co-evolve the modelling scheme with appropriate user interfaces for argument construction and analysis. We specify the requirements for an argument modelling scheme for use by untrained researchers, describe the resulting ontology, contrasting it with other domain modelling and semantic web approaches, before discussing passive and intelligent user interfaces designed to support analysts in the construction, navigation and analysis of scholarly argument structures in a Web-based environment.
of Gene Ontology in

— Semi-supervised clustering incorporating biological relevance as a prior knowledge has been favoured over the past decade. However, selection of prior knowledge has been a challenge. We generate prior knowledge from GO terms at different levels of GO hierarchy and use them to study their impact on the performance of subsequent clustering of microarray data by using MPCKMeans and GOFuzzy. We evaluate the performance by F-measure and the number of specific GO terms and transcription factors. The clustering result with prior knowledge generated from lower levels of GO hierarchy have higher F-measure and more number of specific GO terms and transcription factors. MPCKMeans with prior knowledge generated from multiple levels in the GO hierarchy outperforms GOFuzzy with prior knowledge from the first level in the GO hierarchy. A small amount (1-2%) of prior knowledge can improve semi-supervised clustering result substantially and the more specific prior knowledge is generally more efficient in guiding the semi-supervised clustering process.
On the true Cramer-Rao lower bound for the DA joint estimation of carrier phase and timing offsets

This paper concerns the Cramer-Rao lower bound (CRB) for the data-aided (DA) timing and/or phase recovery, i.e., the synchronization parameter acquisition is aided by a training sequence known to the receiver. For the DA parameter estimation, the CRB typically varies with the training sequence. This indicates that different training sequences offer fundamental different performance. We derive a closed-form formula of the CRB for timing and phase recovery with respect to any particular training sequence. The bound illustrates the close relation between the training sequence and the fundamental limit on timing and phase synchronization. It provides additional insights on the training sequence design.
BIOINFORMATICS ORIGINAL PAPER

Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A ﬁrst generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efﬁciently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼ 10–20 × faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package.
Journal of Computational and Graphical Statistics

This article considers a graphical model for ordinal variables, where it is assumed that the data are generated by discretizing the marginal distributions of a latent multivariate Gaussian distribution. The relationships between these ordinal variables are then described by the underlying Gaussian graphical model and can be inferred by estimating the corresponding concentration matrix. Direct estimation of the model is computationally expensive, but an approximate EM-like algorithm is developed to provide an accurate estimate of the parameters at a fraction of the computational cost. Numerical evidence based on simulation studies shows the strong performance of the algorithm, which is also illustrated on datasets on movie ratings and an educational survey.
Nutrition and management of dairy cows in dry period

U clanku su razmotreni važnost suhostaja kao pripreme krava za laktaciju i najvažniji cimbenici za uspjesnu hranidbu koji ukljucuju: stvaranje rezervi i prilagodbu probavnog sustava, mlijecnu žlijezdu i potrebe ploda. Ocjenjivanje kondicije naglaseno je kao izuzetno korisno za pravilno hranjenje i postupanje sa životinjama. Krmiva su, podijeljena na voluminozni i krepki dio, ukratko predstavljena sa svojim bitnim utjecajem. Po pojedinim fazama suhostaja objasnjeno je njihovo trajanje, postupak sa životinjama kao i posebnosti hranidbe. Kao zadnje, ali vrlo bitno, obrađene su pojedine bolesti vezane uz hranidbu. Iako glavni uzrok nekih navedenih bolesti nije hranidba, svrstane su ovdje jer se mogu uspjesno prevenirati ili cak lijeciti promjenom obroka.
Knowledge-Based Systems

Graph neural networks (GNNs) have drawn increasing attention in recent years and achieved remarkable performance in many graph-based tasks, especially in semi-supervised learning on graphs. However, most existing GNNs are based on the message-passing paradigm to iteratively aggregate neighborhood information in a single topology space. Despite their success, the expressive power of GNNs is limited by some drawbacks, such as inflexibility of message source expansion, negligence of node-level message output discrepancy, and restriction of single message space. To address these drawbacks, we present a novel message-passing paradigm, based on the properties of multi-step message source, node-specific message output, and multi-space message interaction. To verify its validity, we instantiate the new message-passing paradigm as a Dual-Perception Graph Neural Network (DPGNN), which applies a node-to-step attention mechanism to aggregate node-specific multi-step neighborhood information adaptively. Our proposed DPGNN can capture the structural neighborhood information and the feature-related information simultaneously for graph representation learning. Experimental results on six benchmark datasets with different topological structures demonstrate that our method outperforms the latest state-of-the-art models, which proves the superiority and versatility of our method. To our knowledge, we are the first to consider node-specific message passing in the GNNs.
Execution Management of Applications with Runtime Restrictions on Opportunistic Grids Environments

An opportunistic grid computing environment takes advantage of idle computing cycles of regular computers and workstations that can be spread across several administrative domains for running high performance applications. Opportunistic grids are usually constructed from personal computers that do not need to be dedicated for executing grid applications. The grid workload must coexist with local applications executions, submitted by the nodes regular users. Thus, its execution environment is typically dynamic, heterogeneous and unpredictable failures occur frequently. In addition, the resources of an opportunistic grid can be used at any time for the execution of local tasks, making it difficult to preview the conclusion of the tasks running on the grid nodes. These characteristics hinder the successful execution of applications for which there are time restrictions related to its completion. This paper presents a management mechanism specifically designed for opportunistic grid computing environments for handling the execution of applications with time deadlines set by users during their submission to the system. The proposed mechanism is based on a dynamic scheduling and rescheduling approach and was evaluated using a simulated model considering various typical scenarios of opportunistic grids. The results demonstrated the benefits of the proposed approach in comparison to traditional scheduling approaches applied in opportunistic grids. Keywords-opportunistic grids; application scheduling; soft deadline; simulation.
Conformance testing of VMEbus and Multibus II products

A system for testing VMEbus and Multibus II products is described. The system is mainly automated to reduce costs and ensure impartiality. A test campaign is explained in the sense of a walk through the test system, in the way of a customer-such as a manufacturer, reseller, or original equipment manufacturer-would see it. The focus is on testing bus interfaces because it is more complex than testing backplanes. <<ETX>>
Preservation of Historical Document Images using Phase-based Binarization

In this paper, a binarization model based on the phase of the ancient document images is proposed. Three features are derived from the phase information of an input document image which constitute the core of the binarization model. These three features are the maximum moment of phase congruency covariance, a locally weighted mean phase angle, and a phase preserving denoised image. The proposed binarization model consists of three standard steps: 1) preprocessing; 2) main binarization; and 3) postprocessing. In the preprocessing we try to bring a rough estimate of the binarized image and in main binarization steps, the features used are mainly derived from phase. In the postprocessing step, Gaussian and median filters are considered to remove Gaussian noise and salt and pepper
A co-produced community engagement workshop in South London to reduce psychosis related stigma

Background Early access to services is essential for those suffering a psychotic illness or at risk for the condition. Lack of knowledge of services and public stigma are major barriers to care and are associated with increased duration of untreated psychosis and delays in those at clinical high-risk for psychosis (CHR-P) from accessing support. Education and contact programmes have shown promise in reducing stigmatizing views, however, few have been co-produced and delivered by service users and clinical staff. A three-hour co-produced educational workshop was developed and delivered by service users and Outreach and Support in South London (OASIS) staff. The aim was to assess the feasibility of delivering a co-produced workshop to youth community workers, to see if it improved knowledge of psychosis, attitudes to mental health services and reduced stigma towards people with psychosis as well as seeing if the workshop increased community referrals to OASIS. Method Educational workshops were developed by community stakeholders and service users. Pre- and post-workshop questionnaires assessed knowledge of psychosis, attitudes towards mental health teams and stigma towards individuals with a psychotic disorder. Participants and service users views on the workshop were explored through two focus groups. Results 9 workshops were delivered to 75 community participants. Following the workshop participants questionnaire scores showed improvements in knowledge of psychosis, improved attitudes towards mental health teams and a reduction in stigmatizing views towards people with psychosis. The workshop was overwhelmingly well received with 97% agreeing with the statement that they learnt something valuable from the workshop. Referrals to the OASIS service increased by 22% following the workshops. Conclusion The co-produced educational workshop designed and delivered by service users and OASIS staff was successful in improving participants knowledge, attitudes and reducing stigma. We observed an increase in the rate of referrals to the OASIS service, although it is difficult to whether this was due to the workshops or to other outreach activities. Future research should examine whether these effects are long-lasting and explore online delivered workshops to reach more participants in the wider community.
Ursodeoxycholic acid for trans intestinal cholesterol excretion stimulation: a randomized placebo controlled cross-over study.

Objective: The Trans Intestinal Cholesterol Excretion (TICE) pathway is a potential therapeutic target to reduce plasma low-density lipoprotein (LDL) cholesterol levels. TICE encompasses the direct excretion of cholesterol by enterocytes into feces. In mice TICE has been shown to be stimulated by a hydrophilic bile acid pool, resulting in increased fecal neutral sterols (FNS) loss and reduced plasma cholesterol levels. We investigated whether treatment with a hydrophilic bile acid ursodeoxycholic acid (UDCA) - would increase FNS in humans as a proxy for TICE. Approach and Results: We performed a randomized double-blind placebo controlled cross-over trial in 20 male participants aged >18 years, with plasma LDL cholesterol levels greater than or equal to 2.6mmol/L. After a run-in period of ezetimibe 20mg once daily for three weeks, patients were randomized to UDCA 600mg or placebo orally once daily for two weeks. After a three week wash-out, patients underwent the alternate treatment. At baseline, mean (SD) age, BMI, and plasma LDL cholesterol were 59 +/- 11.3 years, 26.4 +/- 3.1 kg/m2, and 3.9 +/- 0.8 mmol/L, respectively. After UDCA treatment, the plasma bile acid hydrophobicity index was reduced compared to placebo (-115.88% versus +1.85%, p<0.001). The FNS did not change (-5.8% versus +18.8% , p=0.51) and treatment with UDCA increased LDL cholesterol with 0.39 mmol/L (+10.95% versus -3.24%, p=0.002) when compared with placebo. Conclusion: UDCA in combination with ezetimibe increased plasma bile acid hydrophilicity in hypercholesterolaemic subjects, but did not result in increased FNS or decreased LDL cholesterol. This suggests that TICE is not stimulated by an increase in the hydrophilicity of the bile acid pool in humans.
Memory layout techniques for variables utilizing efficient DRAM access modes in embedded system design

The delay of memory access is one of the major bottlenecks in embedded systems' performance. In software compilation, it is known that there are high variations in memory access delay depending on the ways of storing/retrieving the variables in code to/from the memories. In this paper, we propose effective storage assignment techniques for variables to maximize the use of memory bandwidth. Specifically, we study the problem of DRAM memory layout for storing the nonarray variables in code to achieve a maximum utilization of page and/or burst modes for the memory accesses. The contributions of our work are, for each page and burst modes: 1) we prove that the problem is NP-hard and 2) we propose an exact formulation of the problem and efficient memory layout algorithms, called Solve-MLP for the page mode and Solve-MLB for the burst mode. From experiments with a set of benchmark programs, we confirm that our proposed techniques use on average 28.2% and 10.1% more page accesses and 82.9% and 107% more burst accesses than those by the order of first use and the technique of Panda et al. in Proc. Int. Conf. Computer-Aided Design, 1997, and Panda et al. in ACM Trans. Design Automation Electron. Syst. , 1997, respectively.
Elevated plasma levels of vascular endothelial cell markers in patients with hypercholesterolemia

Hypercholesterolemia is associated with an increased incidence of vascular complications. To assess the actual degree of activation of coagulation systems and vascular disorders in hypercholesterolemia, plasma levels of vascular endothelial cell markers, such as thrombomodulin (TM), tissue‐type plasminogen activator, plasminogen activator inhibitor‐l (PAl‐l), and von Willebrand factor, were measured in 51 patients with hypercholesterolemia. We also investigated the effects of Pravastatin, an inhibitor of 3‐hydroxy‐3‐methylglutaryl coenzyme A reductase, on plasma lipid, lipoprotein a, and hemostatic markers. The mean plasma levels of thrombin‐antithrombin III complex (TAT), fibrinopeptide A (FPA), TM, and PAl‐I were significantly elevated in hypercholesterolemia. Of the hemostatic markers, only TM was significantly increased in patients with ischemic heart diseases (IHD). The mean concentration of total cholesterol and levels of TAT, FPA, PAI‐I, and TM were significantly reduced after the Pravastatin treatment. The PIC/TAT ratio was significantly increased in non‐IHD patients after treatment, this was not the case in IHD patients. These findings suggested the presence of a thrombogenic state and vascular endothelial cell disorders in hypercholesterolemia; such a state might well be related to hypofibrinolysis. © 1993 Wiley‐Liss, Inc.