Miracle-dz/UniFAR-FTUs huggingface dataset:
STEME: A Robust, Accurate Motif Finder for Large Data Sets

Motif finding is a difficult problem that has been studied for over 20 years. Some older popular motif finders are not suitable for analysis of the large data sets generated by next-generation sequencing. We recently published an efficient approximation (STEME) to the EM algorithm that is at the core of many motif finders such as MEME. This approximation allows the EM algorithm to be applied to large data sets. In this work we describe several efficient extensions to STEME that are based on the MEME algorithm. Together with the original STEME EM approximation, these extensions make STEME a fully-fledged motif finder with similar properties to MEME. We discuss the difficulty of objectively comparing motif finders. We show that STEME performs comparably to existing prominent discriminative motif finders, DREME and Trawler, on 13 sets of transcription factor binding data in mouse ES cells. We demonstrate the ability of STEME to find long degenerate motifs which these discriminative motif finders do not find. As part of our method, we extend an earlier method due to Nagarajan et al. for the efficient calculation of motif E-values. STEME's source code is available under an open source license and STEME is available via a web interface.
Human Time Estimation: On Differences between Methods

Using the same 8 standard intervals (ranging from 300 to 1000 msec. in 100-msec. steps), 16 male Ss made reproductions, verbal estimates, and productions in randomized blocks of trials according to a fixed complex order (sequence of methods, presentation of anchors). After presentation of anchors, significant differences between methods were still in evidence with respect to accuracy, intra-subject variability, and intersubject variability. The reliability of verbal estimates and of productions was decreased upon presentation of anchors, but in all methods, reliability increased over blocks of trials. Reliability of estimations and productions was significantly correlated with relative intersubject variability. As to association between judgments, verbal estimates and productions showed negative correlation while intercorrelations involving reproductions were not significant. A method involving a random-pertrial sequence of methods and standards is proposed for further studies.
Viscoelasticity Measurement and Identification of Viscoelastic Parametric Models

Generally speaking, the behaviour of viscoelastic material is more complicated than the behaviour proposed by classical models as Voigt, Maxwell or Zener. The stiffness of such materials is a frequency dependent complex function. Above 1000Hz, classical measurements techniques are unable to achieve accurate measurements of the stiffness. In this paper, a new Dynamical Mechanical Analysis (DMA) tester is presented. It allows the characterization of the shear stiffness of preloaded viscoelastic materials between 200 and 3500Hz and without using frequency-temperature equivalences. Then the Generalized Maxwell model is used to describe behaviours measured with the DMA tester. A new iterative identification method of the parameter of the Generalized Maxwell model is described. This identification method is based on the asymptotes of the model.Copyright © 2011 by ASME
A Selective-Relay Based Cooperative Spectrum Sensing Scheme without Dedicated Reporting Channels in Cognitive Radio Networks

Typically, each cooperative spectrum sensing process requires two phases: the primary user's signal detection phase, in which all cognitive users attempt to detect the presence of the primary user within a certain observation window (called signal detection overhead); and the initial detection result reporting phase, in which the cognitive users forward their detection results to a fusion center. To avoid interfering with the primary user in the reporting phase, previous research assumed that there is a common control channel (also known as dedicated reporting channel) between the cognitive users and fusion center, which, however, requires extra channel resources and introduces an additional complexity due to the dedicated channel resource management. In this paper, we propose a selective-relay based cooperative spectrum sensing scheme, which is able to control and reduce the interference from cognitive reporting users to primary user without the dedicated channel. We analyze the interference impact on the primary user and show that the interference induced by the reporting users is controllable and can be reduced to satisfy a given outage probability requirement of the primary transmissions. In addition, we investigate the receiver operating characteristics (ROC) of the traditional cooperative sensing scheme (with dedicated reporting channel) and the proposed scheme (without dedicated reporting channel) by jointly considering the signal detection and reporting phases. It is proven that, given a target detection probability, a unique optimal signal detection overhead exists to minimize an asymptotic overall false alarm probability in high SNR regions. We illustrate that, compared to the traditional scheme, the selective-relay based cooperative sensing scheme can save the dedicated channel resources without sacrificing ROC performance. Numerical results also show that, under a guaranteed overall detection probability, an overall false alarm probability can be minimized through an optimization of the signal detection overhead.
New strategies to improve results of mesh surgeries for vaginal prolapses repair – an update

ABSTRACT The use of meshes has become the first option for the treatment of soft tissue disorders as hernias and stress urinary incontinence and widely used in vaginal prolapse's treatment. However, complications related to mesh issues cannot be neglected. Various strategies have been used to improve tissue integration of prosthetic meshes and reduce related complications. The aim of this review is to present the state of art of mesh innovations, presenting the whole arsenal which has been studied worldwide since composite meshes, coated meshes, collagen's derived meshes and tissue engineered prostheses, with focus on its biocompatibility and technical innovations, especially for vaginal prolapse surgery.
Nitric oxide causes root apical meristem defects and growth inhibition while reducing PIN-FORMED 1 (PIN1)-dependent acropetal auxin transport

Nitric oxide (NO) is considered a key regulator of plant developmental processes and defense, although the mechanism and direct targets of NO action remain largely unknown. We used phenotypic, cellular, and genetic analyses in Arabidopsis thaliana to explore the role of NO in regulating primary root growth and auxin transport. Treatment with the NO donors S-nitroso-N-acetylpenicillamine, sodium nitroprusside, and S-nitrosoglutathione reduces cell division, affecting the distribution of mitotic cells and meristem size by reducing cell size and number compared with NO depletion by 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO). Interestingly, genetic backgrounds in which the endogenous NO levels are enhanced [chlorophyll a/b binding protein underexpressed 1/NO overproducer 1 (cue1/nox1) mirror this response, together with an increased cell differentiation phenotype. Because of the importance of auxin distribution in regulating primary root growth, we analyzed auxin-dependent response after altering NO levels. Both elevated NO supply and the NO-overproducing Arabidopsis mutant cue1/nox1 exhibit reduced expression of the auxin reporter markers DR5pro:GUS/GFP. These effects were accompanied by a reduction in auxin transport in primary roots. NO application and the cue1/nox1 mutation caused decreased PIN-FORMED 1 (PIN1)-GFP fluorescence in a proteasome-independent manner. Remarkably, the cue1/nox1-mutant root phenotypes resemble those of pin1 mutants. The use of both chemical treatments and mutants with altered NO levels demonstrates that high levels of NO reduce auxin transport and response by a PIN1-dependent mechanism, and root meristem activity is reduced concomitantly.
Mapping Peptidergic Cells in Drosophila: Where DIMM Fits In

The bHLH transcription factor DIMMED has been associated with the differentiation of peptidergic cells in Drosophila. However, whether all Drosophila peptidergic cells express DIMM, and the extent to which all DIMM cells are peptidergic, have not been determined. To address these issues, we have mapped DIMM expression in the central nervous system (CNS) and periphery in the late larval stage Drosophila. At 100 hr after egg-laying, DIMM immunosignals are largely congruent with a dimm-promoter reporter (c929-GAL4) and they present a stereotyped pattern of 306 CNS cells and 52 peripheral cells. We assigned positional values for all DIMM CNS cells with respect to reference gene expression patterns, or to patterns of secondary neuroblast lineages. We could assign provisional peptide identities to 68% of DIMM-expressing CNS cells (207/306) and to 73% of DIMM-expressing peripheral cells (38/52) using a panel of 24 markers for Drosophila neuropeptide genes. Furthermore, we found that DIMM co-expression was a prevalent feature within single neuropeptide marker expression patterns. Of the 24 CNS neuropeptide gene patterns we studied, six patterns are >90% DIMM-positive, while 16 of 22 patterns are >40% DIMM-positive. Thus most or all DIMM cells in Drosophila appear to be peptidergic, and many but not all peptidergic cells express DIMM. The co-incidence of DIMM-expression among peptidergic cells is best explained by a hypothesis that DIMM promotes a specific neurosecretory phenotype we term LEAP. LEAP denotes Large cells that display Episodic release of Amidated Peptides.
Enhanced schemes for L2 handover in IEEE 802.11 networks and their evaluations

Given the relatively limited coverage area of 802.11 access points, stations moving inside WLAN are often required to perform a handover. The time needed for a STA to switch from one AP to another is too long for real-time applications to continue operating seamlessly, even if no layer 3 handover is to occur ulteriorly. Many solutions have been proposed for improving the layer 2 handover latency, but we have observed a lack of performance analysis and comparison of the different algorithms. In this article we present two new schemes that aim to enhance L2 handover mechanisms. The main characteristic of these new methods is to reduce the discovery time. We then provide an evaluation of four algorithms in order to analyse and compare solutions in six different scenarios
The Incidence and Predictors of Thromboembolic Events in Patients with Lung Cancer

Patients with lung cancer experience elevated risk of venous thromboembolism. Cancer patients with thrombosis have a shorter life expectancy and the occurrence of VTE worsens the quality of life and may delay, interrupt, or completely halt the cancer therapy. In a large cohort of lung cancer patients we monitored the incidence of venous thromboembolism and we identified groups of patients with the highest risk of venous thromboembolism suitable for antithrombotic prophylaxis, which could favourably affect their morbidity and mortality.
Classes of service under perfect competition and technological change: a model for the dynamics of the internet?

Certain services may be provided in a continuous, one-dimensional, ordered range of different qualities and a customer requiring a service of quality q can only be offered a quality superior or equal to q. Only a discrete set of different qualities will be offered, and a service provider will provide the same service (of fixed quality b) to all customers requesting qualities of service inferior or equal to b. Assuming all services (of quality b) are priced identically, a monopolist will choose the qualities of service and the prices that maximize profit but, under perfect competition, a service provider will choose the (inferior) quality of service that can be priced at the lowest price. Assuming significant economies of scale, two fundamentally different regimes are possible: either a number of different classes of service are offered (DC regime), or a unique class of service offers an unbounded quality of service (UC regime). The DC regime appears in one of two sub-regimes: one, BDC, in which a finite number of classes is offered, the qualities of service offered are bounded and requests for high-quality services are not met, or UDC in which an infinite number of classes of service are offered and every request is met. The types of the demand curve and of the economies of scale, and not the pace of technological change, determine the regime and the class boundaries. The price structure in the DC regime obeys very general laws.
Contention-aware task and communication co-scheduling for network-on-chip based Multiprocessor System-on-Chip

To satisfy the ever increasing performance requirement of applications, Multiprocessor System-on-Chip (MPSoC) plays an irreplaceable role in embedded system these days. It is significant to effectively optimize communication for achieving maximum parallelism on MPSoC, especially on Network-on-Chip (NoC) based architectures. The problem of how to make an arbitration of communication congestion is remained unsolved. In this paper, we propose a reasonable Unified Priority-Based Scheduling (UPS) algorithm for task and communication co-scheduling with communication contention, which is based on a novel Task Communication Graph (TCG) model of an application. The proposed method is more accurate and effective to describe the overall process of applications. The experimental results show that the performance is improved by 31.1% on average of scheduling generated by our algorithm. It verifies that the proposed method in this paper can improve the performance of contention-aware task and communication scheduling on NoC-based MPSoC architecture.
Large-scale Top-down Proteomics of the Human Proteome: Membrane Proteins, Mitochondria, and Senescence*

Top-down proteomics is emerging as a viable method for the routine identification of hundreds to thousands of proteins. In this work we report the largest top-down study to date, with the identification of 1,220 proteins from the transformed human cell line H1299 at a false discovery rate of 1%. Multiple separation strategies were utilized, including the focused isolation of mitochondria, resulting in significantly improved proteome coverage relative to previous work. In all, 347 mitochondrial proteins were identified, including ∼50% of the mitochondrial proteome below 30 kDa and over 75% of the subunits constituting the large complexes of oxidative phosphorylation. Three hundred of the identified proteins were found to be integral membrane proteins containing between 1 and 12 transmembrane helices, requiring no specific enrichment or modified LC-MS parameters. Over 5,000 proteoforms were observed, many harboring post-translational modifications, including over a dozen proteins containing lipid anchors (some previously unknown) and many others with phosphorylation and methylation modifications. Comparison between untreated and senescent H1299 cells revealed several changes to the proteome, including the hyperphosphorylation of HMGA2. This work illustrates the burgeoning ability of top-down proteomics to characterize large numbers of intact proteoforms in a high-throughput fashion.
High detection rate of clinically relevant genomic abnormalities in plasma cells enriched from patients with multiple myeloma

Multiple myeloma is a heterogeneous disease, which is characterized by the occurrence of specific genomic abnormalities that are both of diagnostic and prognostic relevance. Since the detection of these abnormalities through molecular‐genetic techniques is hampered by the overall low percentage of plasma cells present in primary bone marrow aspirates, we assessed the efficacy of these techniques in enriched plasma cell fractions from 61 multiple myeloma patients. Using interphase FISH, genomic abnormalities could be detected in 96% of the enriched samples as compared to 61% in the cultured whole bone marrow samples. We also found that microarray‐based genomic profiling of enriched plasma samples facilitates the detection of additional, possibly clinically relevant, genomic abnormalities. We conclude that the genomic delineation of enriched plasma cells from multiple myeloma patients results in a significantly increased detection rate of clinically relevant genomic abnormalities. In order to facilitate molecular‐genetic data interpretation, we recommend morphological assessment of plasma cell purity after enrichment. © 2012 Wiley Periodicals, Inc.
Realizing service migration in industry—lessons learned

In this paper, we present two descriptive case studies covering the re‐engineering and further evolution of adopting service‐oriented architecture (SOA) in the industry. The first case was carried out for a company in the transport sector with an application portfolio of over 700 systems. The second case study was conducted for an organization in the public sector. The goal of both case studies is to identify the possible benefits and drawbacks of realizing SOA in large organizations in order to obtain a better perspective on the real, rather than the assumed, benefits of SOA in practice. We describe how the two cases were developed and carried out, and discuss the experiences gained and lessons learned from adopting SOA in the two organizations. Based on these findings, we propose several directions for further research. Copyright © 2011 John Wiley & Sons, Ltd.
Research on the Influence Factor of the Value Chain Analysis by ICA

This paper introduced the ICA theory in the process of analyzing the entrepreneur mental factors which affect the value chain, and analyses the feasibility of applying ICA theory in the extraction of the entrepreneur mental factors. In the empirical study, we separated the main factors influencing value chain by the FastICA algorithm based on ICA theory, and the experimental results are in conformity with theory.It is feasible to sift Entrepreneur mental factors,the research results of this paper also provides a theoretical reference for the application of the ICA theory in value chain management and optimization.
A server-based approach for overrun management in multi-core real-time systems

This paper presents a server-based framework for task overrun management in multi-core real-time systems. Unlike most existing scheduling methods which usually assume a single upper bound of the Worst-Case Execution Time (WCET) for each task, our approach targets scenarios with task overruns. The main idea of our framework is to employ Synchronized Deferrable Servers (SDS) to deal with globally scheduled task overruns, while a partitioned scheduling approach is applied on regular task executions. Moreover, we provide a deterministic Worst-Case Response Time (WCRT) analysis focusing on hard timing constraints, along with a probabilistic analysis of Deadline Miss Ratio (DMR) for soft real-time applications. In the evaluation phase, we have implemented two types of experiments evaluating different timing constraints.
Run-time Repartitioning of Distributed Java Applications

In this paper we present a mechanism for serializing the execution state of a distributed Java application that is programmed by means of an Object Request Broker such as Java RMI. To support capturing and reestablishment of distributed execution state, we developed a byte code transformer that adds this functionality to a Java application by extracting execution state from the application code. An important benefit of our mechanism is its portability. It can transparently be integrated into any legacy Java application. Furthermore, it does require no modifications to the Java Virtual Machine (JVM) or to the underlying Object Request Broker. Our mechanism can serve many purposes such as migrating execution state over the network or storing it on disk. In particular, we describe the implementation of a prototype for repartitioning distributed Java applications at runtime. Proper partitioning of distributed objects over the different machines is critical to the global performance of the distributed application. Methods for partitioning exist, and employ a graph-based model of the application being partitioned. Our mechanism enables then applying these methods at any point in an on-going distributed computation.
Phylogenetic evidence for the modular evolution of metazoan signalling pathways

Communication among cells was paramount to the evolutionary increase in cell type diversity and, ultimately, the origin of large body size. Across the diversity of Metazoa, there are only few conserved cell signalling pathways known to orchestrate the complex cell and tissue interactions regulating development; thus, modification to these few pathways has been responsible for generating diversity during the evolution of animals. Here, we summarize evidence for the origin and putative function of the intracellular, membrane-bound and secreted components of seven metazoan cell signalling pathways with a special focus on early branching metazoans (ctenophores, poriferans, placozoans and cnidarians) and basal unikonts (amoebozoans, fungi, filastereans and choanoflagellates). We highlight the modular incorporation of intra- and extracellular components in each signalling pathway and suggest that increases in the complexity of the extracellular matrix may have further promoted the modulation of cell signalling during metazoan evolution. Most importantly, this updated view of metazoan signalling pathways highlights the need for explicit study of canonical signalling pathway components in taxa that do not operate a complete signalling pathway. Studies like these are critical for developing a deeper understanding of the evolution of cell signalling. This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.
Approximate Maximum A Posteriori Inference with Entropic Priors

In certain applications it is useful to fit multinomial distributions to observed data with a penalty term that encourages sparsity. For example, in probabilistic latent audio source decomposition one may wish to encode the assumption that only a few latent sources are active at any given time. The standard heuristic of applying an L1 penalty is not an option when fitting the parameters to a multinomial distribution, which are constrained to sum to 1. An alternative is to use a penalty term that encourages low-entropy solutions, which corresponds to maximum a posteriori (MAP) parameter estimation with an entropic prior. The lack of conjugacy between the entropic prior and the multinomial distribution complicates this approach. In this report I propose a simple iterative algorithm for MAP estimation of multinomial distributions with sparsity-inducing entropic priors.
An LMI Approach to Fuzzy pole cluster for Regulating Wind Energy Conversion System

This paper addresses the design of fuzzy state feedback controller that has not only the ability to stabilize the fuzzy model/system but also to control the transient behavior and closed loop pole location for wind energy conversion system which present interesting control demands and exhibits intrinsic nonlinear characteristics. The proposed fuzzy controller is employed to regulate indirectly the power flow in the DC link by regulating the DC current. First, a Takagi-Sugeno fuzzy model is employed to represent a nonlinear system. Then a model-based fuzzy controller design utilizing the concept of parallel distributed compensation is developed. Additional constraints on the closed loop pole location are satisfied. Satisfactory time response and closed loop damping are achieved by forcing the closed loop poles into a suitable sub-region of the left half plane. These conditions are expressed in terms of linear matrix inequalities (LMI's) which can be solved very efficiently using convex optimization techniques. The design techniques are applied to a dynamic model of wind energy conversion system to illustrate the feasibility of the proposed solution