Miracle-dz/UniFAR-FTUs huggingface dataset:
Complete game-theoretic characterization of SIS epidemics protection strategies

Defining an optimal protection strategy against viruses, spam propagation or any other kind of contamination process is an important feature for designing new networks and architectures. In this work, we consider decentralized optimal protection strategies when a virus is propagating over a network through a Susceptible Infected Susceptible (SIS) epidemic process. We assume that each node in the network can fully protect itself from infection at a constant cost, or the node can use recovery software, once it is infected. We model our system using a game theoretic framework. Based on this model, we find pure and mixed equilibria, and evaluate the performance of the equilibria by finding the Price of Anarchy (PoA) in several network topologies. Finally, we give numerical illustrations of our results.
Comparative Immunogenicity of HIV-1 gp140 Vaccine Delivered by Parenteral, and Mucosal Routes in Female Volunteers; MUCOVAC2, A Randomized Two Centre Study

Background Defining optimal routes for induction of mucosal immunity represents an important research priority for the HIV-1 vaccine field. In particular, it remains unclear whether mucosal routes of immunization can improve mucosal immune responses. Methods In this randomized two center phase I clinical trial we evaluated the systemic and mucosal immune response to a candidate HIV-1 Clade C CN54gp140 envelope glycoprotein vaccine administered by intramuscular (IM), intranasal (IN) and intravaginal (IVAG) routes of administration in HIV negative female volunteers. IM immunizations were co-administered with Glucopyranosyl Lipid Adjuvant (GLA), IN immunizations with 0.5% chitosan and IVAG immunizations were administered in an aqueous gel. Results Three IM immunizations of CN54 gp140 at either 20 or 100 μg elicited significantly greater systemic and mucosal antibodies than either IN or IVAG immunizations. Following additional intramuscular boosting we observed an anamnestic antibody response in nasally primed subjects. Modest neutralizing responses were detected against closely matched tier 1 clade C virus in the IM groups. Interestingly, the strongest CD4 T-cell responses were detected after IN and not IM immunization. Conclusions These data show that parenteral immunization elicits systemic and mucosal antibodies in women. Interestingly IN immunization was an effective prime for IM boost, while IVAG administration had no detectable impact on systemic or mucosal responses despite IM priming. Clinical Trials Registration EudraCT 2010-019103-27 and the UK Clinical Research Network (UKCRN) Number 11679
Efficient calculation of compound similarity based on maximum common subgraphs and its application to prediction of gene transcript levels

Properties of a chemical entity, both physical and biological, are related to its structure. Since compound similarity can be used to infer properties of novel compounds, in chemoinformatics much attention has been paid to ways of calculating structural similarity. A useful metric to capture the structural similarity between compounds is the relative size of the Maximum Common Subgraph (MCS). The MCS is the largest substructure present in a pair of compounds, when represented as graphs. However, in practice it is difficult to employ such a metric, since calculation of the MCS becomes computationally intractable when it is large. We propose a novel algorithm that significantly reduces computation time for finding large MCSs, compared to a number of state-of-the-art approaches. The use of this algorithm is demonstrated in an application predicting the transcriptional response of breast cancer cell lines to different drug-like compounds, at a scale which is challenging for the most efficient MCS-algorithms to date. In this application 714 compounds were compared.
Resource allocation for secure OFDMA communication systems

In this paper, resource allocation and scheduling in an orthogonal frequency division multiple access (OFDMA) downlink network is studied. The considered problem is modeled as an optimization problem which takes into account a multiple antenna eavesdropper and artificial noise generation for secure communications. Power, secrecy data rate, and subcarrier allocation are optimized for maximization of the average secrecy outage capacity (bit/s/Hz securely delivered to the users). The optimization problem is solved by using dual decomposition resulting in an efficient iterative resource allocation algorithm. Simulation results illustrate that the proposed iterative resource allocation and scheduling algorithm converges in a small number of iterations and guarantees a non-zero secrecy date rate even if the eavesdropper is closer to the base station than the desired users.
Mean Squared Error Matrix comparison of Least Squares and Stein-Rule Estimators for Regression Coefficients under Non-normal Disturbances

Summary - Choosing the performance criterion to be mean squared error matrix, we have compared the least squares and Stein-rule estimators for regression coefficients in a linear regression model when the disturbances are not necessarily normally distributed. It is shown that none of the two estimators dominates the other, except in the trivial case of merely one regression coefficient where least squares estimator is found to be superior in comparison to Stein-rule estimator.
In Vitro and In Vivo Properties of Ro 63-9141, a Novel Broad-Spectrum Cephalosporin with Activity against Methicillin-Resistant Staphylococci

ABSTRACT Ro 63-9141 is a new member of the pyrrolidinone-3-ylidenemethyl cephem series of cephalosporins. Its antibacterial spectrum was evaluated against significant gram-positive and gram-negative pathogens in comparison with those of reference drugs, including cefotaxime, cefepime, meropenem, and ciprofloxacin. Ro 63-9141 showed high antibacterial in vitro activity against gram-positive bacteria except ampicillin-resistant enterococci, particularly vancomycin-resistant strains of Enterococcus faecium. Its MIC at which 90% of the isolates tested were inhibited (MIC90) for methicillin-resistant Staphylococcus aureus (MRSA) was 4 μg/ml. Ro 63-9141 was bactericidal against MRSA. Development of resistance to the new compound in MRSA was not observed. Ro 63-9141 was more potent than cefotaxime against penicillin-resistant Streptococcus pneumoniae(MIC90 = 2 μg/ml). It was active against ceftazidime-susceptible strains of Pseudomonas aeruginosaand against Enterobacteriaceae except Proteus vulgaris and some isolates producing extended-spectrum β-lactamases. The basis for the antibacterial spectrum of Ro 63-9141 lies in its affinity to essential penicillin-binding proteins, including PBP 2′ of MRSA, and its stability towards β-lactamases. The in vivo findings were in accordance with the in vitro susceptibilities of the pathogens. These data suggest the potential utility of Ro 63-9141 for the therapy of infections caused by susceptible pathogens, including MRSA. Since insufficient solubility of Ro 63-9141 itself precludes parenteral administration in humans, a water-soluble prodrug, Ro 65-5788, is considered for development.
Multiple source localization using randomly distributed wireless sensor nodes

In this paper, we present a method to localize multiple sources using randomly distributed wireless sensor nodes. The principle of maximum power collection is used to obtain the beamforming weights which add the source signal constructively at the sensor outputs. The beamforming weights give the time difference of arrival (TDOA) for each of the sources from which the source location is subsequently computed using a hyperbolic estimator. Results show that the method successfully localizes multiple sources in noise.
Architecture recovery in ARES

Recovering the architecture of legacy systems requires more than just reverse engineering tools to generate some higherlevel descriptions of the system under study. Design decisions and logical groupings of functions have to be balanced with informal domain knowledge, domain standards and coding guidelines of the developers. Therefore, we combine domain aspects with coding aspects and use reverse engineering tools as one means of recovering the requested information to reason about the underlying architecture of the system. This reasoning is an alternating top-down and bottom-up approach. The’architecture recovery process we introduce is one part of the ESPRIT project ARES (Architectural Reasoning for Embedded Systems). ’
RWTH-PHOENIX-Weather: A Large Vocabulary Sign Language Recognition and Translation Corpus

This paper introduces the RWTH-PHOENIX-Weather corpus, a video-based, large vocabulary corpus of German Sign Language suitable for statistical sign language recognition and translation. In contrastto most available sign language data collections, the RWTH-PHOENIX-Weather corpus has not been recorded for linguistic research but for the use in statistical pattern recognition. The corpus contains weather forecasts recorded from German public TV which are manually annotated using glosses distinguishing sign variants, and time boundaries have been marked on the sentence and the gloss level. Further, the spoken German weather forecast has been transcribed in a semi-automatic fashion using a state-of-the-art automatic speech recognition system. Moreover, an additional translation of the glosses into spoken German has been created to capture allowable translation variability. In addition to the corpus, experimental baseline results for hand and head tracking, statistical sign language recognition and translation are presented.
Quality assessment of recent evidence‐based clinical practice guidelines for management of type 2 diabetes mellitus in adults using the AGREE II instrument

RATIONALE, AIMS AND OBJECTIVES Type 2 diabetes mellitus (T2DM) is a worldwide and national public health problem that has a great impact on the population in Saudi Arabia. High-quality clinical practice guidelines (CPGs) are cornerstones in improving the health care provided for patients with diabetes. This study evaluated the methodological rigour, transparency, and applicability of recently published CPGs. METHODS Our group conducted a systematic search for recently published CPGs for T2DM. The searching and screening for Source CPGs were guided by tools from the ADAPTE methods with specific inclusion/exclusion criteria. Five reviewers using the second version of the Appraisal of Guidelines for Research and Evaluation (AGREE II) Instrument independently assessed the quality of the retrieved Source CPGs. RESULTS Domains of Scope and purpose and Clarity of presentation received the highest scores in all CPGs. Most of the assessed CPGs (86%) were considered with high overall quality and were recommended for use. Rigour of development and applicability domains were together highest in 3 CPGs (43%). The overall high quality of DM CPGs published in the last 3 years demonstrated the continuous development and improvement in CPG methodologies and standards. CONCLUSIONS Health care professionals should consider the quality of any CPG for T2DM before deciding to use it in their daily clinical practice. Three CPGs have been identified, using the AGREE criteria, as high-quality and trustworthy. Ideally, the resources provided by the AGREE trust including the AGREE II Instrument should be used by a clinician to scan through the large number of published T2DM CPGs to identify the CPGs with high methodological quality and applicability.
Inter-domain Gaussian Processes for Sparse Inference using Inducing Features

We present a general inference framework for inter-domain Gaussian Processes (GPs) and focus on its usefulness to build sparse GP models. The state-of-the-art sparse GP model introduced by Snelson and Ghahramani in [1] relies on finding a small, representative pseudo data set of m elements (from the same domain as the n available data elements) which is able to explain existing data well, and then uses it to perform inference. This reduces inference and model selection computation time from O(n3) to O(m2n), where m ≪ n. Inter-domain GPs can be used to find a (possibly more compact) representative set of features lying in a different domain, at the same computational cost. Being able to specify a different domain for the representative features allows to incorporate prior knowledge about relevant characteristics of data and detaches the functional form of the covariance and basis functions. We will show how previously existing models fit into this framework and will use it to develop two new sparse GP models. Tests on large, representative regression data sets suggest that significant improvement can be achieved, while retaining computational efficiency.
AIS Electronic Library (AISeL)

Open Source Software (“OSS”) has attracted significant research interest but research has focused on the development process (“supply side”) of OSS leaving the “demand-side” of OSS relatively unexplored. Further, extant OSS research is lacking in empirical studies. In this study we fill the gap with an empirical analysis of antecedents of perceived customer satisfaction with Linux, the most popular OSS product. We used Ordered Logit technique to analyze a dataset collected through a survey of business-technology professionals. Our results suggest that perceived customer satisfaction with Linux is positively influenced by duration of use and the quality of third party support. We also found a strong relationship between perceived satisfaction with Linux and prevalence of other OSS products in the organization. Further, we found that perceived customer satisfaction with Linux is lower for large firms and higher when the largest distribution of Linux is used. Interestingly, internal IT support capability was found to have no significant effect on perceived customer satisfaction with Linux. Our results contribute to research by verifying traditional customer satisfaction models in an OSS context and also by extending these models to include unique aspects of OSS. On practice side, this research provides directions to the OSS community for achieving higher customer satisfaction.
Resonating periodic waveguides as ultraresolution sensors in biomedicine

Optical sensor technology based on subwavelength periodic waveguides is applied for tag-free, high-resolution biomedical and chemical detection. Measured resonance wavelength shifts of 6.4 nm for chemically attached Bovine Serum Albumin agree well with theory for a sensor tested in air. Reflection peak efficiencies of 90% are measured, and do not degrade upon biolayer attachment. Phase detection methods are investigated to enhance sensor sensitivity and resolution. Direct measurement of the resonant phase response is reported for the first time using ellipsometric measurement techniques.
Bluetongue virus VP6 protein binds ATP and exhibits an RNA-dependent ATPase function and a helicase activity that catalyze the unwinding of double-stranded RNA substrates

RNA-dependent ATPase and helicase activities have been identified associated with the purified VP6 protein of bluetongue virus, a member of the Orbivirus genus of double-stranded RNA (dsRNA; Reoviridae family) viruses. In addition, the protein has an ATP binding activity. RNA unwinding of duplexes occurred with both 3' and 5' overhang templates, as well as with blunt-ended dsRNA, an activity not previously identified in other viral helicases. Although little sequence similarity to other helicases was detected, certain similarities to motifs commonly attributed to such proteins were identified.
Relationship between blood pressure, cholesterolemia and serum apolipoprotein B in a large population sample: the Brisighella Heart Study

Objective: The objective is to evaluate the relationship between cholesterolemia, serum apolipoprotein B (apoB) level and blood pressure in a large sample of general population. Methods: The Brisighella Heart Study (BHS) is a prospective, population-based longitudinal epidemiological investigation. For this study, we analysed the data sampled in the 2008 BHS population survey, excluding those participants treated with antihypertensive and/or lipid lowering drugs (N: 2473). Results: In a sex, BMI, smoking habit, physical activity level and serum creatinine adjusted model, low-density lipoprotein-cholesterol (LDL-C) appears to be significantly related to SBP (P < 0.001), DBP (P = 0.026), and pulse pressure (PP) (P < 0.001). In individuals aged less than 52 years, LDL-C was significantly associated to SBP and DBP (P < 0.001), but not PP. In the same model, apoB appears to be mildly but significantly related to SBP (P < 0.001), DBP (P < 0.001), and PP (P < 0.001). In individuals aged less than 52 years, apoB was significantly associated to SBP (P < 0.001), DBP (P < 0.001), and PP (P < 0.001). In individuals aged 52 or more, nor LDL-C neither apoB were significantly associated to blood pressure. Including in the same model LDL-C and apoB, apoB excluded the predicting role of LDL-C as it regards the blood pressure either in the whole population sample and in the younger individuals. Conclusion: On the basis of our observation, either serum LDL-C and apoB are significantly related to the blood pressure level in a large sample of individuals untreated with antihypertensive and lipid-lowering drugs. This association is stronger in younger individuals than in elderly. ApoB seems to be a stronger predictor of either SBP, DBP and PP than LDL-C.
An Evaluation of the Efficacy of a Triple P-Positive Parenting Program Podcast Series

Objective: Parenting programs based on cognitive-behavioral and social learning principles are effective in changing child behavior problems and parenting styles. However, such programs typically have limited population reach. The current study aimed to evaluate the efficacy of a brief radio series that provided parenting advice based on the Triple P-Positive Parenting Program. Method: One hundred thirty-nine parents of children aged 2 to 10 years who had concerns about their child’s behavioral and/or emotional adjustment were recruited, randomly assigned to either an intervention or waitlist control group, and completed online self-report measures. Parents in the intervention group were given access to seven Triple P podcasts online over a period of 2 weeks. Results: Parents in the intervention group improved significantly more than parents in the control group, from pre- to postintervention, on measures of child behavioral problems and parenting style, self-efficacy, and confidence. These short-term intervention effects were maintained at the 6-month follow-up. Conclusion: These results suggest that brief radio and online parenting programs can be effective and have the potential to reach a large proportion of parents experiencing child behavior problems. Limitations, clinical significance, and future research suggestions are discussed.
n-grams of Seeds: A Hybrid System for Corpus-Based Text Summarization

This paper presents a hybrid system for automatic text summarization which combines statistical and knowledge-based methods. In particular, it demonstrates how two corpus-based learning and indexing algorithms, namely an n-gram and a seed-oriented approach, may be combined to bring out the best of both approaches. This system selects sentences from an input text to constract a highly compressed, generic, and informative summary. The hybrid algorithm described here was developed and tested with a corpus of movie reviews collected from several on-line data bases
Three‐dimensional models of cancer for pharmacology and cancer cell biology: Capturing tumor complexity in vitro/ex vivo

Cancers are complex and heterogeneous pathological “organs” in a dynamic interplay with their host. Models of human cancer in vitro, used in cancer biology and drug discovery, are generally highly reductionist. These cancer models do not incorporate complexity or heterogeneity. This raises the question as to whether the cancer models' biochemical circuitry (not their genome) represents, with sufficient fidelity, a tumor in situ. Around 95% of new anticancer drugs eventually fail in clinical trial, despite robust indications of activity in existing in vitro pre‐clinical models. Innovative models are required that better capture tumor biology. An important feature of all tissues, and tumors, is that cells grow in three dimensions. Advances in generating and characterizing simple and complex (with added stromal components) three‐dimensional in vitro models (3D models) are reviewed in this article. The application of stirred bioreactors to permit both scale‐up/scale‐down of these cancer models and, importantly, methods to permit controlled changes in environment (pH, nutrients, and oxygen) are also described. The challenges of generating thin tumor slices, their utility, and potential advantages and disadvantages are discussed. These in vitro/ex vivo models represent a distinct move to capture the realities of tumor biology in situ, but significant characterization work still remains to be done in order to show that their biochemical circuitry accurately reflects that of a tumor.
Computer Evolution of Chemotaxis in Model Nematodes

tration. Since each segment follows the one in front of it during sinusoidal locomotion, the nematode body is represented by head location and velocity, with head direction controlled by the action of 2 opposing neck muscles. Finally, the model neural circuit consists of 2 chemosensory neurons and 2 neck muscle neurons, each representing identified classes of neurons in C. elegans , whose synaptic connections are consistent with the known anatomical connectivity. This circuit is driven by a sinusoidal oscillation representing the nematode locomotion system. In order to set the electrophysiological parameters of the neural circuit model, an evolutionary algorithm was used. An evolutionary algorithm is a search technique loosely based on biological evolution [Mitchell, 1998]. A search begins with a random population of genetic strings that encode the unknown phenotypic characteristics of interest (here, the parameters of the neural circuit model). Each individual is then assigned a fitness based on the quality of its performance on the given task (here, the chemotactic success of the entire brain-body-environment model averaged over multiple trials). Individuals are then selected to serve as parents for the next generation with a probability related to their fitness. From the selected parents, a new generation of children are then produced by randomly swapping portions of 2 parents (crossover) and making small modifications (mutation). Once a new The nematode worm Caenorhabditis elegans is a remarkable organism for behavioral neuroscience. Not only does this millimeter-long soil-living animal exhibit a rich behavioral repertoire (including withdrawal reflexes, crawling, swimming, a variety of taxes, social feeding, egg-laying, habituation and associative conditioning), but it does so with a nervous system containing only 302 neurons, for which the anatomical connectivity is completely known from serial section electron microscopy [White et al., 1986]. Despite the small size and pressurized body of C. elegans , progress is also being made on electrophysiological analysis of its nervous system using genetic and developmental manipulations, optical imaging, and whole-cell patch-clamp techniques [Schafer, 2006]. However, we are still a very long way from knowing even which of the over 6,000 synaptic connections that make up this nervous system are excitatory or inhibitory. A recent paper by Izquierdo and Lockery [2010] in the Journal of Neuroscience demonstrates a new way to use computational techniques to compensate for missing electrophysiological data. The paper focuses on a model of salt klinotaxis, a recently-discovered form of chemotaxis in C. elegans in which orientation is continuously adjusted along a line of steepest ascent in a salt gradient [Iino and Yoshida, 2009]. The environment is modeled as a static cone-shaped gradient of salt concenPublished online: December 24, 2010