Miracle-dz/UniFAR-FTUs huggingface dataset:
Quorum Sensing and Virulence of Pseudomonas aeruginosa during Lung Infection of Cystic Fibrosis Patients

Pseudomonas aeruginosa is the predominant microorganism in chronic lung infection of cystic fibrosis patients. The chronic lung infection is preceded by intermittent colonization. When the chronic infection becomes established, it is well accepted that the isolated strains differ phenotypically from the intermittent strains. Dominating changes are the switch to mucoidity (alginate overproduction) and loss of epigenetic regulation of virulence such as the Quorum Sensing (QS). To elucidate the dynamics of P. aeruginosa QS systems during long term infection of the CF lung, we have investigated 238 isolates obtained from 152 CF patients at different stages of infection ranging from intermittent to late chronic. Isolates were characterized with regard to QS signal molecules, alginate, rhamnolipid and elastase production and mutant frequency. The genetic basis for change in QS regulation were investigated and identified by sequence analysis of lasR, rhlR, lasI and rhlI. The first QS system to be lost was the one encoded by las system 12 years (median value) after the onset of the lung infection with subsequent loss of the rhl encoded system after 17 years (median value) shown as deficiencies in production of the 3-oxo-C12-HSL and C4-HSL QS signal molecules respectively. The concomitant development of QS malfunction significantly correlated with the reduced production of rhamnolipids and elastase and with the occurrence of mutations in the regulatory genes lasR and rhlR. Accumulation of mutations in both lasR and rhlR correlated with development of hypermutability. Interestingly, a higher number of mucoid isolates were found to produce C4-HSL signal molecules and rhamnolipids compared to the non-mucoid isolates. As seen from the present data, we can conclude that P. aeruginosa and particularly the mucoid strains do not lose the QS regulation or the ability to produce rhamnolipids until the late stage of the chronic infection.
Structural Evidence for Variable Oligomerization of the N-Terminal Domain of Cyclase-Associated Protein ( CAP )

Cyclase-associated protein (CAP) is a highly conserved and widely distributed protein that links the nutritional response signaling to cytoskeleton remodeling. In yeast, CAP is a component of the adenylyl cyclase complex and helps to activate the Ras-mediated catalytic cycle of the cyclase. While the N-terminal domain of CAP (NCAP) provides a binding site for adenylyl cyclase, the C-terminal domain (C-CAP) possesses actin binding activity. Our attempts to crystallize full-length recombinant CAP from Dictyostelium discoideum resulted in growth of orthorhombic crystals containing only the N-terminal domain (residues 42–227) due to auto-proteolytic cleavage. The structure was solved by molecular replacement with data at 2.2 Å resolution. The present crystal structure allows the characterization of a head-to-tail N-CAP dimer in the asymmetric unit and a crystallographic side-toside dimer. Comparison with previously published structures of N-CAP reveals variable modes of dimerization of this domain, but the presence of a common interface for the side-to-side dimer. Proteins 2005; 58:255–262. © 2004 Wiley-Liss, Inc.
A SYSTEM FOR DATA-DRIVEN CONCATENATIVE SOUND SYNTHESIS

In speech synthesis, concatenative data-driven synthesis methods prevail. They use a database of recorded speech and a unit selection algorithm that selects the segments that match best the utterance to be synthesized. Transferring these ideas to musical sound synthesis allows a new method of high quality sound synthesis. Usual synthesis methods are based on a model of the sound signal. It is very difficult to build a model that would preserve the entire fine details of sound. Concatenative synthesis achieves this by using actual recordings. This data-driven approach (as opposed to a rule-based approach) takes advantage of the information contained in the many sound recordings. For example, very naturally sounding transitions can be synthesized, since unit selection is aware of the context of the database units. The CATERPILLAR software system has been developed to allow data-driven concatenative unit selection sound synthesis. It allows high-quality instrument synthesis with high level control, explorative free synthesis from arbitrary sound databases, or resynthesis of a recording with sounds from the database. It is based on the new software-engineering concept of component-oriented software, increasing flexibility and facilitating reuse.
Performance Study for STC-OFDM Systems Based on IEEE802.11a Standard

This paper presents a reasonable program that use orthogonal frequency division multiplexing(OFDM) technology to reduce inter-symbol interference (ISI) to improve the performance of space-time coding (STC) under frequency selective fading channel. Analyze the STC-OFDM system under the combination of STC and OFDM technology based on IEEE802.11a wireless standards. Monte Carlo method is adopted in simulation. The simulation results show that the combination of STBC and OFDM technology is superior to the combination of VBLAST and OFDM technology; FFT points and the number of subcarriers of the system has a certain impact on performance; Random interleaver can improve the performance of system under multipath fading channel and get a reasonable robustness under a variety of channels.
An Elasticity-Aware Governance Platform for Cloud Service Delivery

In cloud service provisioning scenarios with a changing demand from consumers, it is appealing for cloud providers to leverage only a limited amount of the virtualized resources required to provide the service. However, it is not easy to determine how much resources are required to satisfy consumers expectations in terms of Quality of Service (QoS). Some existing frameworks provide mechanisms to adapt the required cloud resources in the service delivery, also called an elastic service, but only for consumers with the same QoS expectations. The problem arises when the service provider must deal with several consumers, each demanding a different QoS for the service. In such an scenario, cloud resources provisioning must deal with trade-offs between different QoS, while fulfilling these QoS, within the same service deployment. In this paper we propose an elasticity-aware governance platform for cloud service delivery that reacts to the dynamic service load introduced by consumers demand. Such a reaction consists of provisioning the required amount of cloud resources to satisfy the different QoS that is offered to the consumers by means of several service level agreements. The proposed platform aims to keep under control the QoS experienced by multiple service consumers while maintaining a controlled cost.
URDB: a universal reversible debugger based on decomposing debugging histories

Reversible debuggers have existed since the early 1970s. A novel approach, URDB, is introduced based on checkpoint/re-execute. It adds reversibility to a debugger, while still placing the end user within the familiar environment of their preferred debugger. The URDB software layer currently includes modes that understand the syntax for four debuggers: GDB for C/C++/Java/Fortran, Python (pdb), MATLAB, and Perl (perl -d). It does so by adding a thin URDB software layer on top of the DMTCP checkpoint-restart package. URDB passes native debugging commands between the end user and the underlying debugging session. URDB models the four common debugging primitives that form the basis for most debuggers: step, next, continue, break. For example, given a debugging history of the form [step, next, step], URDB's reverse-step produces a new history, [step, next]. Further, subtle algorithms are described for reverse-xxx. For example, reverse-step operates correctly when the last instruction of the history is next or continue. URDB calls DMTCP to create a checkpoint during a de-bugging session, and then replays the history from there. An essential novelty of this work is the extension of DMTCP to be the first checkpointing package capable of checkpointing a GDB sesssion to disk (through checkpointing the Linux ptrace system call). This was a significant barrier to earlier attempts toward checkpoint/re-execute for GDB. Support for the GDB debugger is important to any reversible debugger claiming universality. Experimental results are described for GDB, MATLAB, Python (pdb), and Perl.
Evaluating criminal networks with PEVNET

Evaluation of network visualization tools in software engineering is a tricky task. There are a number of factors, contradictions, and preferences of investigative analysts that are to be kept in consideration while designing the experiment. Complexity in data, computational overhead to reach the targeted information and scarcity of a standard platform may slow down the investigation process. In this research paper, we have made the evaluation of some of the new features of our proposed framework, PEVNET, by conducting an experiment. There were twenty four participants who had evaluated the system. The experiment was performed in two phases. In the first phase, a usability evaluation and qualitative feedback was carried out to check whether the PEVNET framework provided adequate results to the users. The qualitative feedback was performed by considering two aspects: the ease of use and the functionality. We have conducted an evaluation of the newly inducted features into PEVNET. These include the `Pie-chart feature', `Trend analysis Feature', `Graphical trend analysis feature', and `Encircle feature'. In the second phase, the comparison of the PEVNET had been performed against some other state-of-the-art tools. These tasks were to be performed in the groups of participants. We found that the participants of the PEVNET group performed the tasks faster, in respect to the respective features, as compared to the other techniques used in the experiment. Further, we have found that the network visualization of the PEVNET framework, based on the experimental results, had gotten satisfactory feedback from the majority of the participants. The case study of Chicago Narcotics datasets was used. We believe that by evaluating the PEVNET in this research paper, we will be able to check the effectiveness of our proposed features.
A DESIGN LANGUAGE AND TOOL FOR X-MACHINES SPECIFICATION

One of the most essential phases of software development is the system specification. X-machines is an intuitive formal method which can be easily applied at this phase and also facilitate testing in order to prove the correctness of an implementation with respect to the specification. Although the X-Machine theory is already defined in detail mathematically, there is a lack of automated tools which can facilitate its use. In this paper, a brief introduction to the X-Machine theory is presented and a language for specifying X-Machines is defined, which could act as a communication protocol among various X-Machine tools. In addition, a proof tool is presented which checks special properties of X-Machines that are defined as prerequisites for the X-Machine testing algorithm.
Adaptive Phase Synchronisation Algorithm for Collaborative Beamforming in Wireless Sensor Networks

Collaborative beam forming (CB) is a cooperative technique that utilizes a group of distributed wireless nodes to collectively transmit a common message with proper phase weights to an intended direction. As a result, CB significantly extends the communication range of the sensor node in wireless sensor networks (WSNs). Each sensor node in CB has an independent local oscillator. It becomes a vital problem to achieve CB as the distributed nodes are unaware of their phase relationship. Therefore, an efficient phase synchronisation algorithm is needed as the distributed nodes are unaware of their phase relationship. In this paper, an iterative phase synchronisation algorithm using (1+1)-evolution strategy (ES) is proposed to achieve CB in WSNs. Evaluations have been carried out through simulation and the results show that the proposed algorithm is more energy efficient in comparison to the existing phase synchronisation algorithm.
Pneumococcal Lipoteichoic Acid (LTA) Is Not as Potent as Staphylococcal LTA in Stimulating Toll-Like Receptor 2

ABSTRACT Streptococcus pneumoniae is a leading cause of gram-positive sepsis, and lipoteichoic acid (LTA) may be important in causing gram-positive bacterial septic shock. Even though pneumococcal LTA is structurally distinct from the LTA of other gram-positive bacteria, the immunological properties of pneumococcal LTA have not been well characterized. We have investigated the ability of LTAs to stimulate human monocytes by using highly pure and structurally intact preparations of pneumococcal LTA and its two structural variants. The variants were pneumococcal LTA with only one acyl chain (LTA-1) and completely deacylated LTA (LTA-0). The target cells used in the study were peripheral blood mononuclear cells (PBMCs) and two model cell lines (CHO/CD14/TLR2 and CHO/CD14/TLR4) that express human CD25 protein in response to Toll-like receptor 2 (TLR2) and TLR4 stimulation, respectively. Intact pneumococcal LTA and LTA-1 stimulated PBMC and CHO/CD14/TLR2 cells in a dose-dependent manner but did not stimulate CHO/CD14/TLR4 cells. Pneumococcal LTA was about 100-fold less potent than Staphylococcus aureus LTA in stimulating the CHO/CD14/TLR2 cells and PBMCs. LTA-0 (or pneumococcal teichoic acid) stimulated neither CHO/CD14/TLR2 nor CHO/CD14/TLR4 cells even at high concentrations. Excess teichoic acid, LTA-0, antibodies to phosphocholine, or antibodies to TLR4 did not inhibit the LTA-induced TLR2 stimulation. However, antibodies to CD14, TLR1, or TLR2 suppressed tumor necrosis factor alpha (TNF-α) production by PBMCs in response to LTA or LTA-1. These results suggest that pneumococcal LTA with one or both acyl chains stimulates PBMCs primarily via TLR2 with the help of CD14 and TLR1.
Exploring Measures of “Readability” for Spoken Language: Analyzing linguistic features of subtitles to identify age-specific TV programs

We investigate whether measures of readability can be used to identify age-specific TV programs. Based on a corpus of BBC TV subtitles, we employ a range of linguistic readability features motivated by Second Language Acquisition and Psycholinguistics research. Our hypothesis that such readability features can successfully distinguish between spoken language targeting different age groups is fully confirmed. The classifiers we trained on the basis of these readability features achieve a classification accuracy of 95.9%. Investigating several feature subsets, we show that the authentic material targeting specific age groups exhibits a broad range of linguistics and psycholinguistic characteristics that are indicative of the complexity of the language used.
HIGHLY VARIABLE YOUNG MASSIVE STARS IN ATLASGAL CLUMPS

High-amplitude variability in young stellar objects (YSOs) is usually associated with episodic accretion events. It has not been observed so far in massive YSOs. Here, the high-amplitude variable star sample of Contreras Peña et al. has been used to search for highly variable (ΔK ≥ 1 mag) sources coinciding with dense clumps mapped using the 850 μm continuum emission by the ATLASGAL survey. A total of 18 variable sources are centered on the submillimeter clump peaks and coincide (<1″) with a 24 μm point or compact (<10″) source. Of these 18 sources, 13 can be fit by YSO models. The 13 variable YSOs (VYSOs) have luminosities of ∼103 L⊙, an average mass of 8 M⊙, and a range of ages up to 106 yr. A total of 11 of these 13 VYSOs are located in the midst of infrared dark clouds. Nine of the 13 sources have ΔK > 2 mag, significantly higher compared to the mean variability of the entire VVV sample. The light curves of these objects sampled between 2010 and 2015 display rising, declining, or quasi-periodic behavior but no clear periodicity. Light-curve analysis using the Plavchan method shows that the most prominent phased signals have periods of a few hundred days. The nature and timescale of variations found in 6.7 Ghz methanol maser emission in massive stars are similar to that of the VYSO light curves. We argue that the origin of the observed variability is episodic accretion. We suggest that the timescale of a few hundred days may represent the frequency at which a spiraling disk feeds dense gas to the young massive star.
DCU at WikipediaMM 2009: Document Expansion from Wikipedia Abstracts

In this paper, we describe our participation in the WikipediaMM task at CLEF 2009. Our main efforts concern the expansion of the image metadata from the Wikipedia abstracts collection DBpedia. Since the metadata is short for retrieval by query words, we decided to expand the metadata using a typical query expansion method. In our experiments, we use the Rocchio algorithm for document expansion. Our best run is in the 26th rank of all 57 runs which is under our expectation, and we think that the main reason is that our document expansion method uses all the words from the metadata documents which contain words which are unrelated to the content of the images. Compared with our text retrieval baseline, our best document expansion run improves MAP by 11.17%. As one of our conclusions, we think that the document expansion can play an effective factor in the image metadata retrieval task. Our content-based image retrieval uses the same approach as in our participation in ImageCLEF 2008.
Efficient Vaccine Distribution Based on a Hybrid Compartmental Model

To effectively and efficiently reduce the morbidity and mortality that may be caused by outbreaks of emerging infectious diseases, it is very important for public health agencies to make informed decisions for controlling the spread of the disease. Such decisions must incorporate various kinds of intervention strategies, such as vaccinations, school closures and border restrictions. Recently, researchers have paid increased attention to searching for effective vaccine distribution strategies for reducing the effects of pandemic outbreaks when resources are limited. Most of the existing research work has been focused on how to design an effective age-structured epidemic model and to select a suitable vaccine distribution strategy to prevent the propagation of an infectious virus. Models that evaluate age structure effects are common, but models that additionally evaluate geographical effects are less common. In this paper, we propose a new SEIR (susceptible—exposed—infectious šC recovered) model, named the hybrid SEIR-V model (HSEIR-V), which considers not only the dynamics of infection prevalence in several age-specific host populations, but also seeks to characterize the dynamics by which a virus spreads in various geographic districts. Several vaccination strategies such as different kinds of vaccine coverage, different vaccine releasing times and different vaccine deployment methods are incorporated into the HSEIR-V compartmental model. We also design four hybrid vaccination distribution strategies (based on population size, contact pattern matrix, infection rate and infectious risk) for controlling the spread of viral infections. Based on data from the 2009–2010 H1N1 influenza epidemic, we evaluate the effectiveness of our proposed HSEIR-V model and study the effects of different types of human behaviour in responding to epidemics.
Collaborative Filtering via Ensembles of Matrix

We present a Matrix Factorization (MF) based approach for the Netflix Prize competition. Currently MF based algorithms are popular and have proved successful for collaborative filtering tasks. For the Netflix Prize competition, we adopt three different types of MF algorithms: regularized MF, maximum margin MF and non-negative MF. Furthermore, for each MF algorithm, instead of selecting the optimal parameters, we combine the results obtained with several parameters. With this method, we achieve a performance that is more than 6% better than the Netflix’s own system.
Rank Functions Based Inference System for Group Key Management Protocols Verification

Design and veriflcation of cryptographic protocols has been under investigation for quite sometime. However, most of the attention has been paid for two parties protocols. In group key management and distribution protocols, keys are computed dynamically through cooperation of all protocol participants. Therefore regular approaches for two parties protocols veriflcation cannot be applied on group key protocols. In this paper, we present a framework for formally verifying of group key management and distribution protocols based on the concept of rank functions. We deflne a class of rank functions that satisfy speciflc requirements and prove the soundness of these rank functions. Based on the set of sound rank functions, we provide a sound and complete inference system to detect attacks in group key management protocols. The inference system provides an elegant and natural proof strategy for such protocols compared to existing approaches. The above formalizations and rank theorems were implemented using the PVS theorem prover. We illustrate our approach by applying the inference system on a generic Di‐e-Hellman group protocol and prove it in PVS.
Implementation of a network based cloud load balancer

Cloud service providers offer their customers to rent or release hardware resources (CPU, RAM, HDD), which are isolated in virtual machine instances, on demand. Increased load on customer applications or web services require more resources than a physical server can supply, which enforces the cloud provider to implement some load balancing technique in order to scatter the load among several virtual or physical servers. Many load balancers exist, both centralized and distributed, with various techniques. In this paper we present a new solution for a low level load balancer (L3B), working on a network level of OSI model. When a network packet arrives, its header is altered in order to forward to some end-point server. After the server replies, the packet's header is also changed using the previously stored mapping and forwarded to the client. Unfortunately, the results of the experiments showed that this implementation did not provide the expected results, i.e., to achieve linear speedup when more server nodes are added.
Performance Analysis of TDMA Relay Protocols Over Nakagami- $m$ Fading

Several time-division multiple-access (TDMA) cooperative wireless relay protocols and their performances have recently been developed by Nabar, Bolcskei, and Kneubuhler. Their work, however, is limited to an upper bound-based performance analysis for Rayleigh fading. We thus provide an exact analysis of two of their protocols in single-relay and multiple-relay networks over independent identically distributed (i.i.d.) Nakagami-m fading channels. Our analysis is focused on an Alamouti-coded system with two-stage protocols, fixed-gain amplify-and-forward (AF) relays, and maximal ratio combiner (MRC) reception. The performance metrics are the capacity, the diversity order, and the symbol error rate (SER). The closed-form moment-generating function (MGF) of the total end-to-end signal-to-noise ratio (SNR) is derived. The MGF is then used to derive the diversity order and the SER of M-ary phase-shift keying (M-PSK) and M-ary quadrature amplitude modulation (M -QAM). It is found that the end-to-end SNR for relaying with orthogonal channels is higher than that of nonorthogonal relay channels. The diversity order of a multiple-relay network (n relays) in a Nakagami-m environment is shown to be (n + 1)m. The closed-form SER expressions for relay-destination links with high SNRs and static relay-destination links are derived. Numerical and simulation results are provided to verify the analysis.