Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of sparse signals under finite-alphabet constraints

In this paper, we solve the problem of detecting the entries of a sparse finite-alphabet signal from a limited amount of data, for instance obtained by compressive sampling. While existing methods either rely on the sparsity property, the finite-alphabet property, or none of those properties to solve the under-determined system of linear equations, we capitalize on both the sparsity and the finite-alphabet features of the signal. The problem is first formulated in a Bayesian framework to incorporate the prior knowledge of sparsity, which is then shown to be solvable using sphere decoding (SD) or semi-definite relaxation (SDR) for efficient Boolean programming. A few toy simulations show how our method can outperform existing works.
Association of the PPARγ2 Pro12Ala polymorphism with increased risk of cardiovascular diseases.

This meta-analysis investigated the correlation between the PPARγ2 Pro12Ala polymorphism and cardiovascular disease (CVD). Electronic database and manual searches were conducted to retrieve studies published relevant to the PPARγ2 Pro12Ala polymorphism and CVD. Rigorous inclusion and exclusion criteria were employed for selection of high-quality patients-control studies. Statistical data analyses on allelic, dominant, homozygous, heterozygous, and recessive inheritance models were performed using the R 3.1. 0 and Stata 12.0 software. We enrolled 12 case-control studies consisting of 10,189 patients with CVD [1070 with myocardial infarction (MI), 7849 with coronary artery disease (CAD), and 1270 with acute coronary syndromes (ACS)] and 17,899 controls. The results of meta-analyses revealed that the PPARγ2 Pro12Ala (rs1801282) polymorphism was correlated with a higher risk of CVD under both allelic and dominant models, while no statistical significance was found under homozygous, heterozygous, or recessive models. Subgroup analysis based on disease showed that the PPARγ2 Pro12Ala (rs1801282) polymorphism was correlated with a higher risk of MI under both allelic and dominant models, while no statistical significance was found for association with CAD or ACS under allele or dominant models. Furthermore, under homozygous, heterozygous, and recessive models, the PPARγ2 Pro12Ala (rs1801282) polymorphism had no statistically significant association with MI, CAD, or ACS. The results of this meta-analysis suggest that the PPARγ2 Pro12Ala (rs1801282) polymorphism might be correlated with a higher risk of CVD, particularly MI, and could serve as an important early indicator for CVD.
Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches

MOTIVATION The deluge of biological information from different genomic initiatives and the rapid advancement in biotechnologies have made bioinformatics tools an integral part of modern biology. Among the widely used sequence alignment tools, BLAST and PSI-BLAST are arguably the most popular. PSI-BLAST, which uses an iterative profile position specific score matrix (PSSM)-based search strategy, is more sensitive than BLAST in detecting weak homologies, thus making it suitable for remote homolog detection. Many refinements have been made to improve PSI-BLAST, and its computational efficiency and high specificity have been much touted. Nevertheless, corruption of its profile via the incorporation of false positive sequences remains a major challenge. RESULTS We have developed a simple and elegant approach to resolve the problem of model corruption in PSI-BLAST searches. We hypothesized that combining results from the first (least-corrupted) profile with results from later (most sensitive) iterations of PSI-BLAST provides a better discriminator for true and false hits. Accordingly, we have derived a formula that utilizes the E-values from these two PSI-BLAST iterations to obtain a figure of merit for rank-ordering the hits. Our verification results based on a 'gold-standard' test set indicate that this figure of merit does indeed delineate true positives from false positives better than PSI-BLAST E-values. Perhaps what is most notable about this strategy is that it is simple and straightforward to implement.
The poweRlaw package: a general overview

The poweRlaw package provides code to ﬁt heavy tailed distributions, including discrete and continuous power-law distributions. Each model is ﬁtted using a maximum likelihood procedure and cut-oﬀ value, x min , is estimated by minimising the Kolmogorov-Smirnoﬀ statistic.
Sentiment analysis of user comments for one-class collaborative filtering over ted talks

User-generated texts such as reviews, comments or discussions are valuable indicators of users' preferences. Unlike previous works which focus on labeled data from user-contributed reviews, we focus here on user comments which are not accompanied by explicit rating labels. We investigate their utility for a one-class collaborative filtering task such as bookmarking, where only the user actions are given as ground truth. We propose a sentiment-aware nearest neighbor model (SANN) for multimedia recommendations over TED talks, which makes use of user comments. The model outperforms significantly, by more than 25% on unseen data, several competitive baselines.
’ s repository of research publications and other research outputs Analysing online discussions in educational and work based settings Conference Item

Networked learning is becoming more and more about connectivity of learners or professionals and connectivity to resources available online and sometimes freely. Researchers are making use of these by designing online environments where this notion of connectivity and vast resources available to learners can be exploited. Many online discussion tools are available for use in educational settings. This paper discusses means of comparing the quality of interaction in these tools. We focus on the use of an online discussion tool called InterLoc (http://www.interloc.org.uk/). InterLoc is based on research by McAlister (2004) who designed a tool for online peer discussion that guides students’ dialogue towards more academic interactions and facilitates extended argument. A significant feature of the design of the tool is managed synchronous dialogue e.g. the use of sentence openers, and the facility to reply to earlier contributions. The design features of InterLoc ensure that it provides a collaborative argumentation environment for learners in higher education. We also demonstrate that it is possible to structure argumentation using InterLoc in different settings, both academic and workplace. One of our case studies was carried out with postgraduate distance learning students studying science communication and the participants were asked to consider the idea that everyone’s DNA should be kept on a data base to help fight crime. The second case study was in a health and social care setting and the participants were family-support workers of a London based charity, supporting families and individuals offering practical, emotional and financial help. They were asked to consider the case of a severely obese child whom social services are considering taking into care as the parents are unable to control his eating. The participants discussed what would be the best for the child. We used two methods of comparing the quality of interaction in these sessions: We analysed the transcripts of discussion sessions using content analysis and frequency of sentence openers and compared these analyses with those using Toulmin’s Argumentation Pattern (TAP). By comparing the results of these two analyses, we explored the possibility of using these measures as an indicator of the quality of the discussion taking place. Our findings have confirmed the potential of the InterLoc sentence opener analyses for future work.
Segment-Based Hidden Markov Models for Information Extraction

Hidden Markov models (HMMs) are powerful statistical models that have found successful applications in Information Extraction (IE). In current approaches to applying HMMs to IE, an HMM is used to model text at the document level. This modelling might cause undesired redundancy in extraction in the sense that more than one filler is identified and extracted. We propose to use HMMs to model text at the segment level, in which the extraction process consists of two steps: a segment retrieval step followed by an extraction step. In order to retrieve extraction-relevant segments from documents, we introduce a method to use HMMs to model and retrieve segments. Our experimental results show that the resulting segment HMM IE system not only achieves near zero extraction redundancy, but also has better overall extraction performance than traditional document HMM IE systems.
On nonlinear transformations of stochastic variables and its application to nonlinear filtering

A class of nonlinear transformation-based filters (NLTF) for state estimation is proposed. The nonlinear transformations that can be used include first (TT1) and second (TT2) order Taylor expansions, the unscented transformation (UT), and the Monte Carlo transformation (MCT) approximation. The unscented Kalman filter (UKF) is by construction a special case, but also nonstandard implementations of the Kalman filter (KF) and the extended Kalman filter (EKF) are included, where there are no explicit Riccati equations. The theoretical properties of these mappings are important for the performance of the NLTF. TT2 does by definition take care of the bias and covariance of the second order term that is neglected in the TT1 based EKF. The UT computes this bias term accurately, but the covariance is correct only for scalar state vectors. This result is demonstrated with a simple example and a general theorem, which explicitly shows the difference between TT1, TT2, UT, and MCT.
Endothelium-dependent hyperpolarization in isolated arteries taken from animals treated with NO-synthase inhibitors.

To study the effects of chronic in vivo inhibition of NO synthase on endothelium-dependent hyperpolarization, cell-membrane potential (in individual vascular smooth-muscle cells) and changes in tension (in isolated rings) were recorded from isolated canine coronary arteries and guinea-pig carotid arteries and aortas. In coronary arteries taken from control dogs and contracted with U46619, acetylcholine- and bradykinin-induced endothelium-dependent relaxations, which were unaffected by short-term in vitro exposure to indomethacin but were inhibited partially by L-nitro-arginine (LNA). In coronary arteries taken from dogs treated over the long term in vivo with LNA (30 mg/kg on the first day and 20 mg/kg the 7 following days, i.v.), the response to acetylcholine and bradykinin was inhibited when compared with arteries from control dogs. Short-term in vitro exposure to LNA or indomethacin or both did not influence the effects of either agonist. In these arteries, the hyperpolarizing response to acetylcholine, observed in the presence of LNA and indomethacin, was enhanced, whereas that to bradykinin was partially inhibited. In the guinea pig isolated aorta, the relaxation to bradykinin was abolished by long-term in vivo treatment with L-nitro-arginine-methyl-ester (L-NAME; 1.5 mg/ml, in the drinking water for > or =4 days). In the isolated guinea pig carotid artery studied in the presence of LNA and indomethacin, acetylcholine induced a hyperpolarization that was not significantly affected by long-term in vivo treatment with L-NAME. These findings indicate that endothelium-dependent hyperpolarizations are maintained during long-term inhibition of NO synthase and probably act as a back-up mechanism to elicit endothelium-dependent relaxations.
Concealing complex policies with hidden credentials

Hidden credentials are useful in protecting sensitive resource requests, resources, policies, and credentials. We propose a significant performance improvement when implementing hidden credentials using Boneh/Franklin Identity Based Encryption. We also propose a substantially improved secret splitting scheme for enforcing complex policies, and show how it improves concealment of policies from nonsatisfying recipients.
Assumption, commitment rules for networks of asynchronously communicating agents

This report presents an assumption commitment speci cation technique and a re nement calculus for networks of agents communicating asynchronously via unbounded FIFO chan nels in the tradition of Kah Kel BDD We de ne two di erent types of explicit assumption commitment speci cations namely simple and general speci cations It is shown that semantically any deterministic agent can be uniquely characterized by a simple speci cation and any nondeterministic agent can be uniquely charac terized by a general speci cation We de ne two sets of re nement rules one for simple speci cations and one for general speci cations The rules are Hoare logic inspired In particular the feedback rules employ an invariant in the style of a traditional while rule Both sets of rules have been proved to be sound and also semantically complete with respect to a chosen set of composition operators Conversion rules allow the two logics to be combined This means that general speci cations and the rules for general speci cations have to be introduced only at the point in a system development where they are really needed The proposed speci cation formalism and re nement rules together with a number of related design principles presented in Bro d Bro a constitute a powerful design method which allows distributed systems to be developed in the same style as methods like Jon Mor allow for the design of sequential systems
Pruning error analysis for a class of curse-of-dimensionality free methods

In the context of computational nonlinear optimal control, curse-of-dimensionality (CoD) refers to the phenomenon of exponential growth of computational cost with respect to the dimension of state and input space. It is well-known that CoD is the major drawback of grid-based computational methods, which are consequently restricted their applications to low dimensional problems. Switching linear quadratic regulators (SLQR) is a class of nonlinear optimal control problems for which a CoD free method has been developed. However, it has been observed that this CoD free method suffers from a different form of computational complexity known as curse-of-complexity (CoC) which refers to the phenomenon that the number of quadratics necessary to represent the value functions of SLQR problems increases exponentially with respect to time horizon. Pruning is the key method of tackling this class of complexity at the cost of introducing pruning errors. This paper develops a framework that can be used to analyse pruning errors.
Performance improvement of V-BLAST through an iterative approach

This paper proposes an iterative V-BLAST detection algorithm that improves the error performance over error propagation. Traditional detection algorithm cannot alleviate error propagation because the decision feedbacks from low-diversity substreams are used to decode high-diversity substreams. In our algorithm, we iteratively suppress the interference towards low-diversity substreams by using decisions from high-diversity substreams, and the system performance is highly improved over the traditional one, which is demonstrated via simulation results. Besides, existing algorithms combating error propagation operate in high complexity, while the complexity of our algorithm is proportional to the loop times, providing a tradeoff between performance and complexity.
cation in USENET Newsgroups : A Progress

We report on our investigations into topic classiica-tion with USENET newsgroups. Our framework is to determine the newsgroup that a new document should be posted to. We train our system by forming \meta-documents" that represent each topic. We discuss our experiments with this method, and provide evidence that choosing particular documents or words to use in these models degrades classiication accuracy. We also describe a technique called classiication-based retrieval for nding documents similar to a query document. Most work in classiication has involved articles taken oo of a newswire, or from a medical database(Lewis 1992). In these cases, correct topic labels are chosen by human experts. The domain of USENET news-group postings is another interesting testbed for clas-siication. The \labels" here are just the newsgroups to which the documents were originally posted. Since users of the Internet must make this classiication decision every time they post an article, this is a nice \real life" application of text categorization. Our approach is to create a model for each group, and then compare future documents to each model to nd the best match. Newsgroups have been studied in other projects. Mostly there has been work done in ltering. In this problem, users attempt to select documents from a large pool that match their interests or are similar to other documents. The SIFT project at Stanford(Yan & Garcia-Molina 1995) has users submit prooles of their interests. It then uses new documents as queries on the prooles. At CMU, the Newsweeder project(Lang 1995) has users rate new documents in terms of relevance , and attempts to learn these ratings to distinguish if future postings are relevant. We will address this problem using the techniques we tried for classii-cation. Our underlying system is SMART, developed by Salton(Salton 1971). SMART indexes a collection of text documents by rst removing stopwords, and then stemming words to join those with similar meanings. It then creates a vector for each document whose features represent the remaining terms. A query document is converted to a vector in the same manner, and then compared to each document in the collection by computing the cosine of the angle between the two vectors. Our job then is to create a set of metadocuments that represent each of the newsgroups we wish to classify. We then match a posting with the metadocument that gives the highest cosine similarity. There were three major approaches that …
Furin interacts with proMT1-MMP and integrin αV at specialized domains of renal cell plasma membrane

Matrix metalloproteinases (MMPs) and integrins are essential for cell and extracellular matrix homeostasis. Both membrane type-1 MMP (MT1-MMP) and the integrin αV subunit are fully activated upon cleavage at a furin recognition site. Furin is shuttled to the cell surface through the trans-Golgi network and endosomal system, and its only known role on plasma membrane consists in activation of opportunistic pathogenic entities. Here, we report findings about the interaction of furin with MT1-MMP and the integrinα V at the cell surface. By using in vivo gene delivery, western blotting and immunogold electron microscopy, we provide evidence of significant pools of furin and proMT1-MMP along the surface of cells lining basement membranes. Moreover, furin and integrin αV are frequently found associated with the slit diaphragm of renal podocytes and around endothelial fenestrations. ProMT1-MMP, by contrast, is concentrated at the slit diaphragm. Coimmunoprecipitations and double immunogold labelings indicate that furin interacts with proMT1-MMP and αV at points of insertion of the slit diaphragm. Our results suggest that these focalized complexes could trigger basement membrane proteolysis either directly by activation of proMT1-MMP or indirectly by promoting activation of proMMP2.
Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline

We applied a computational pipeline based on comparative genomics to bacteria, and identified 22 novel candidate RNA motifs. We predicted six to be riboswitches, which are mRNA elements that regulate gene expression on binding a specific metabolite. In separate studies, we confirmed that two of these are novel riboswitches. Three other riboswitch candidates are upstream of either a putative transporter gene in the order Lactobacillales, citric acid cycle genes in Burkholderiales or molybdenum cofactor biosynthesis genes in several phyla. The remaining riboswitch candidate, the widespread Genes for the Environment, for Membranes and for Motility (GEMM) motif, is associated with genes important for natural competence in Vibrio cholerae and the use of metal ions as electron acceptors in Geobacter sulfurreducens. Among the other motifs, one has a genetic distribution similar to a previously published candidate riboswitch, ykkC/yxkD, but has a different structure. We identified possible non-coding RNAs in five phyla, and several additional cis-regulatory RNAs, including one in ε-proteobacteria (upstream of purD, involved in purine biosynthesis), and one in Cyanobacteria (within an ATP synthase operon). These candidate RNAs add to the growing list of RNA motifs involved in multiple cellular processes, and suggest that many additional RNAs remain to be discovered.
New inventory for measurement of parental rearing patterns: AN ENGLISH FORM OF THE EMBU

Despite the importance of measurement of parental rearing patterns in psychiatric research, there are almost no acceptable standardised inventories available. An English‐language version of the Swedish EMBU Inventory is presented, which has subscales measuring the degree to which each parent was abusive, depriving, punitive, shaming, rejecting, overprotective, overinvolved, tolerant, affectionate, performance‐oriented, guilt‐engendering, stimulating, favoured siblings, and favoured the subject. Results indicate high and comparable reliability and item‐scale correlations in the English version, and a similar factor structure. It would appear that the EMBU has both cross‐cultural reliability and stable structure in the English translation.
Preclinical Development Carfilzomib Interacts Synergistically with Histone Deacetylase Inhibitors in Mantle Cell Lymphoma Cells In Vitro and In Vivo

Interactions between the proteasome inhibitor carfilzomib and the histone deacetylase (HDAC) inhibitors vorinostat and SNDX-275 were examined in mantle cell lymphoma (MCL) cells in vitro and in vivo. Coadministration of very low, marginally toxic carfilzomib concentrations (e.g., 3–4 nmol/L) with minimally lethal vorinostat or SNDX-275 concentrations induced sharp increases in mitochondrial injury and apoptosis in multiple MCL cell lines and primary MCL cells. Enhanced lethality was associated with c-jun-NH,-kinase (JNK) 1/2 activation, increased DNA damage (induction of lH2A.X), and ERK1/2 and AKT1/2 inactivation. Coadministration of carfilzomib and histone deacetylase inhibitors (HDACI) induced a marked increase in reactive oxygen species (ROS) generation and G2–M arrest. Significantly, the free radical scavenger tetrakis (4-benzoic acid) porphyrin (TBAP) blocked carfilzomib/HDACI-mediated ROS generation, lH2A.X formation, JNK1/2 activation, and lethality. Genetic (short hairpin RNA) knockdown of JNK1/2 significantly attenuated carfilzomib/HDACI-induced apoptosis, but did not prevent ROS generation or DNA damage. Carfilzomib/HDACI regimens were also active against bortezomib-resistant MCL cells. Finally, carfilzomib/ vorinostat coadministration resulted in a pronounced reduction in tumor growth compared with single agent treatment in an MCL xenograft model associated with enhanced apoptosis, lH2A.X formation, and JNK activation. Collectively, these findings suggest that carfilzomib/HDACI regimens warrant attention in MCL. Mol Cancer Ther; 10(9); 1686–97. 2011 AACR.
A 60-GHz phase-locked loop with inductor-less prescaler in 90-nm CMOS

A 60-GHz phase-locked loop (PLL) with inductor-less prescaler is fabricated in a 90-nm CMOS process. The inductor-less prescaler has a smaller chip area than previously reported ones. The PLL operates from 61 to 63 GHz and consumes 78 mW from a 1.2 V supply. The phase noise at 100 kHz and 1 MHz offset from carrier are -72 and -80 dBc/Hz, respectively. The prescaler occupies 80 x 40 mum2. The active area of the PLL is 0.6 x 0.6 mm2.