Miracle-dz/UniFAR-FTUs huggingface dataset:
List of Additional Publications the Sequence Layer of Transcriptional Encoding Transcriptional Regulation at the Sequence Level the Structural Layer of Transcriptional Encoding Dna Organization and Compaction Transcriptional Regulation at the Structural Level Abnormalities in Transcriptional Encodin

" And don't it make you feel so sad Don't the blood rush to your feet To think that everything you do today Tomorrow is obsolete " Nick Cave – More news from nowhere Cover: A Hilbert curve displaying locations of nucleosomes (dark grey) and exons (medium grey) as well as their co-localizations (light grey) on human chromosome 16. List of papers This thesis is based on the following papers, which are referred to in the text by their Roman numerals. mixture modeling of nucleosome positioning in HepG2 cells and their regulatory dynamics in response to TGF-beta treatment. Manuscript. A segmental maximum a posteriori approach to genome-wide copy number profiling. Reprints were made with permission from the respective publishers. † These authors contributed equally to this work. A previously unrecognized microdeletion syndrome on chromosome 22 band q11.2 encompassing the BCR gene. (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. Hum Mutat 29: 398-408. 2008. Somatic mosaicism for copy number variation in differentiated human tissues. Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts.resolution analysis of DNA copy number alterations in NF1-associated malignant peripheral nerve sheath tumors using 32K BAC array. Genes Chromosomes Cancer 48: 897-907. Characterization of novel and complex genomic aberrations in glioblastoma using a 32K BAC array. genetic differences between matched primary and metastatic breast cancer provide an approach to identification of biomarkers for disease progression. genomic alterations in benign and malignant pheochromocytomas and paragangliomas revealed by whole-genome array comparative genomic hybridization analysis. Endocr Relat Cancer 17: 561-579. Abbreviations BAC bacterial artificial chromosome bp base pair cDNA complementary DNA CDS (protein-) coding sequence ChIP chromatin immunoprecipitation ChIP-chip ChIP measured on a microarray ChIP-seq ChIP measured with massively parallel sequencing CNV copy number variation CTD carboxy terminal domain DNA deoxyribonucleic acid Gb Giga base pairs GBM glioblastoma multiforme GTF general transcription factor HMM hidden Markov model IP immunoprecipitation kb kilo base pairs MCMC Markov chain Monte Carlo miRNA micro RNA MnaseI micrococcal nuclease I Mnase-seq MnaseI digested DNA measured with massively parallel sequencing mRNA messenger RNA ncRNA non-coding RNA NGS next-generation sequencing pdf probability distribution function PTM post-translational modification RNA ribonucleic acid RNAPII RNA polymerase II SMAP segmental maximum a posteriori SNR signal-to-noise ratio ssDNA single-stranded DNA SuMMIt Strand-based Mixture Modeling of protein-DNA Interactions TF transcription factor TFBS transcription factor binding site 13 Background Modern biological studies …
A proposed three dimensional hedonic model for intrinsic motivation on social tagging tools

In this article, we propose a three dimensional hedonic model for intrinsic motivation that has the potential to enhance users acceptance to online social tagging tools and social media in general. Our multi-layered model includes curiosity, explorability, and enjoyment as potential predictors for users' attitude and intention to use online social tagging tools. This conceptual model is based on a modified version of Technology Acceptance Model (TAM) as well as on an extensive review of motivation theory literature. The model forms the foundation for future empirical work in this area.
Generic Hopf Bifurcation from Lines of Equilibria without Parameters: I. Theory☆

Abstract Motivated by decoupling effects in coupled oscillators, by viscous shock profiles in systems of nonlinear hyperbolic balance laws, and by binary oscillation effects in discretizations of systems of hyperbolic balance laws, we consider vector fields with a one-dimensional line of equilibria, even in the absence of any parameters. Besides a trivial eigenvalue zero we assume that the linearization at these equilibria possesses a simple pair of nonzero eigenvalues which cross the imaginary axis transversely as we move along the equilibrium line. In normal form and under a suitable nondegeneracy condition, we distinguish two cases of this Hopf-type loss of stability, hyperbolic and elliptic . Going beyond normal forms we present a rigorous analysis of both cases. In particular, α - and ω -limit sets of nearby trajectories consist entirely of equilibria on the line.
Localization of a yeast early Golgi mannosyltransferase, Och1p, involves retrograde transport

To analyze the mechanism of integral membrane protein localization in the early Golgi apparatus of Saccharomyces cerevisiae, we have used Och1p, a cis-Golgi mannosyltransferase. A series of influenza virus hemagglutinin (HA) epitope-tagged fusion proteins was constructed in which invertase is appended to the Golgi-luminal carboxy terminus of full-length Och1p. Several constructs included a Kex2p cleavage site between the Och1p and invertase moieties to monitor transit to the Kex2p-containing TGN. Cells expressing an Och1p-invertase fusion do not secrete invertase, but those expressing an Och1p-Kex2p site-invertase fusion protein secrete high levels of invertase in a Kex2p-dependent manner. The Och1p-Kex2p site-invertase fusion protein is cleaved with a half-time of 5 min, and the process proceeds to completion. Before cleavage the protein receives glycosyl modifications indicative of passage through the medial- and trans-Golgi, therefore cleavage occurs after ordered anterograde transport through the Golgi to the TGN. Transit to distal compartments is not induced by the invertase moiety, since noninvertase fusion constructs encounter the same glycosyltransferases and Kex2p as well. The Och1p-HA moiety, irrespective of whether it is generated by cleavage of the fusion protein in the TGN or synthesized de novo, is degraded with a half-time of about 60 min. Thus, the half-time of degradation is 12-fold longer than the time required to reach the TGN. At steady state, de novo- synthesized and TGN-generated HA epitope-tagged Och1p reside in a compartment with a buoyant density identical to that of wild-type Och1p and distinct from that of the vacuole or the TGN. Finally, och1 null cells that express an Ochlp fusion construct known to rapidly encounter the TGN glycosylate invertase to the same extent as wild-type cells, indicating that they have phenotypically wild-type Och1p activity. These results lead us to propose a model for Och1p-HA localization that involves movement to distal compartments, at least as far as the TGN, followed by retrieval to the cis compartment, presumably by vesicular transport.
The power of special characters in prosodicword prediction for Chinese TTS

Prosodic word (PW) prediction in Chinese Text-To-Speech (TTS) can be formulated as a classification problem that one predicts the tag of every character boundary in a sentence is the PW boundary or not. In this paper, a set of new features called special characters are introduced and put into classifiers to address the PW prediction problem. Some characters often appear at the beginning or at the end of a PW, which make them a strong clue of a PWboundary. Besides, quite a lot of PWs have only one character, which make such characters special. We select a set of special single characters, special starting characters, and special ending characters to help predict PW boundaries. Some special lexical words are often taken as PWs, and we collect a list of such words for PW boundary prediction. Decision tree, Supporting Vector Machine (SVM), MultiLayer Perceptron, and Random Forests are employed as the classifiers. Other features like part-of-speech (POS) of characters, word length, etc. are also used for PW prediction. In our experiments, we got 90.5% and 91.3% accuracies on two corpora containing 8, 000 and 1, 349 sentences respectively, which proved the efficiency of the method.
Counting independent sets via Divide Measure and Conquer method

In this paper we give an algorithm for counting the number of all independent sets in a given graph which works in time $O^*(1.1394^n)$ for subcubic graphs and in time $O^*(1.2369^n)$ for general graphs, where $n$ is the number of vertices in the instance graph, and polynomial space. The result comes from combining two well known methods "Divide and Conquer" and "Measure and Conquer". We introduce this new concept of Divide, Measure and Conquer method and expect it will find applications in other problems. The algorithm of Bj\"orklund, Husfeldt and Koivisto for graph colouring with our algorithm used as a subroutine has complexity $O^*(2.2369^n)$ and is currently the fastest graph colouring algorithm in polynomial space.
Propositional Term Extraction over Short Text using Word Cohesiveness and Conditional Random Fields with Multi-Level Features

Propositional terms in a research abstract (RA) generally convey the most important information for readers to quickly glean the contribution of a research article. This paper considers propositional term extraction from RAs as a sequence labeling task using the IOB (Inside, Outside, Beginning) encoding scheme. In this study, conditional random fields (CRFs) are used to initially detect the propositional terms, and the combined association measure (CAM) is applied to further adjust the term boundaries. This method can extract beyond simply NP-based propositional terms by combining multi-level features and inner lexical cohesion. Experimental results show that CRFs can significantly increase the recall rate of imperfect boundary term extraction and the CAM can further effectively improve the term boundaries.
Encapsulating models and approximate inference programs in probabilistic modules

This paper introduces the probabilistic module interface, which allows encapsulation of complex probabilistic models with latent variables alongside custom stochastic approximate inference machinery, and provides a platform-agnostic abstraction barrier separating the model internals from the host probabilistic inference system. The interface can be seen as a stochastic generalization of a standard simulation and density interface for probabilistic primitives. We show that sound approximate inference algorithms can be constructed for networks of probabilistic modules, and we demonstrate that the interface can be implemented using learned stochastic inference networks and MCMC and SMC approximate inference programs.
Cluster Analysis of E-Commerce Customer Profiles Based on Trust Perception

Understanding how consumers perceive the market is a necessity for an E-commerce (EC) site's survival. The number of EC consumers has been increasing, and customerpsilas trust in EC has become a critical issue. The objective of our study was to apply a two-step cluster analysis in profiling EC consumerspsila demographic characteristics and perception of trust in EC. The findings suggest four clusters. The cluster of respondents most concerned with trust consisted of technical experts and engineers who were 30- to 39-year-old single males, and the cluster of respondents less concerned with trust consisted of above 60-year-old married unemployed and retired males.
Journal of Internet Banking and Commerce a Study of the Relationship between the Value Perception and Loyalty Intention toward an E-retailer Website

Chao Chao Chuang is a full-time instructor in Hsing Wu Institute of Technology. Her areas of interest are correlation of international financial markets, financial institution governance, portfolio management and e-commerce. Abstract The Internet has become an important channel for retailers to effectively reach their target customers or expand into new markets. Due to the low switching costs for customers and few entry barriers for competitors, competition in the online environment has become fierce. Value creation for consumers is important in the success of retaining customers. The Internet provides a new way for retailers to create value for a wider range of customers. Understanding how to offer value through the interaction between website attributes and visitors can help online retailers enhance customer loyalty intention to the site. This study examined the effects of three components of perceived value on customer loyalty intention to an e-retailer's website. Perceived value components-utilitarian value, trust, and hedonic value-were hypothesized to have direct and positive effects on customer loyalty intention toward an e-retailer's website. Data were collected from 243 students-2-2 through five different colleges and 418 office workers in the urban cities of Northern and Central Taiwan by using a paper-pencil survey. A Structural Equation Modeling technique was employed to test the research model. The result shows that trust and utilitarian value both had significant effects on e-loyalty intention; however, hedonic value did not appear to have a positive effect on e-loyalty.
Concentric Anchor Beacon Localization Algorithm for Wireless Sensor Networks

Many applications in wireless sensor networks require sensor nodes to obtain their absolute or relative geographical positions. Although various localization algorithms have been recently proposed, most of them require nodes to be equipped with range-determining hardware to obtain distance information. In this paper, we propose a concentric anchor beacon (CAB) localization algorithm for wireless sensor networks. CAB is a range-free approach and uses a small number of anchor nodes. Each anchor emits beacons at different power levels. From the information received by each beacon heard, nodes can determine in which annular ring they are located within each anchor. Each node uses the approximated center of intersection of the rings as its position estimate. We also propose two heuristics, namely CAB with equal area and CAB with equal width, to determine the transmitting power levels of the beacons. Simulation results show that the estimation error is reduced by half when anchors transmit beacons at two different power levels instead of at a single power level. CAB also gives a lower estimation error than some other range-free localization schemes (e.g., centroid and approximated point-in-triangulation) when the anchor-to-node range ratio is less than 4.
Tailoring nomograms on patients and institutions: The utility of Fagan's two-step nomogram

Besides oncologic outcomes, functional outcomes (preservation of potency and early recovery of the pre-operative urinary continence) are the two main goals of radical prostatectomy. Tailoring the most appropriate but also the most conservative surgery in patients with low or intermediate risk prostate cancer is one of the hottest topic in urologic oncology nowdays. A number of nomograms, risk calculators and graphic tools have been developed to gather data from biopsy, blood samples and radiologic imaging and help clinicians to find the best balance between oncologic and functional goals. *Correspondence to: Tommaso Prayer Galetti, Department of Surgery, Oncology and Gastroenterology – Urology, University of Padova, Italy, Tel: +390498212720, Fax: +39.0498218758, E-mail: tommaso.prayer@aopd.veneto. it
Robust Perceptual Image Hashing Based on Ring Partition and NMF

This paper designs an efficient image hashing with a ring partition and a nonnegative matrix factorization (NMF), which has both the rotation robustness and good discriminative capability. The key contribution is a novel construction of rotation-invariant secondary image, which is used for the first time in image hashing and helps to make image hash resistant to rotation. In addition, NMF coefficients are approximately linearly changed by content-preserving manipulations, so as to measure hash similarity with correlation coefficient. We conduct experiments for illustrating the efficiency with 346 images. Our experiments show that the proposed hashing is robust against content-preserving operations, such as image rotation, JPEG compression, watermark embedding, Gaussian low-pass filtering, gamma correction, brightness adjustment, contrast adjustment, and image scaling. Receiver operating characteristics (ROC) curve comparisons are also conducted with the state-of-the-art algorithms, and demonstrate that the proposed hashing is much better than all these algorithms in classification performances with respect to robustness and discrimination.
Effect of simulated microgravity by head-down bed rest on T wave alternans

Reports of ventricular arrhythmias during spaceflights raise the question of whether microgravity increases sudden cardiac death risk. Our aim in this work was to study changes in T-wave alternans (TWA) during VO2 max stress tests before and after five days of -6° head-down bed rest (HDBR) simulating exposure to microgravity. Two HDBR campaigns were organized by the European Space Agency in MEDES (Toulouse, France) and DLR (Koln, Germany). High-resolution ECG signal was recorded in 19 male volunteers during VO2 max tests by bicycle exercise stress, the day before the beginning of HDBR (pre) and within 26 hours after the end of HDBR (post). ECG was analyzed for multilead TWA detection. In the MEDES campaign, 4 subjects at pre while 6 at post-HDBR presented TWA. In the DLR campaign, TWA was detected in all subjects both in pre and post-HDBR. Various TWA features were compared, but only the heart rate at the onset of TWA episodes from the beginning of the VO2 max test resulted in significant differences between pre and post, being always higher than 110 beats/min.
Formal methods for security protocols : three examples of the black-box approach

Security protocols are hard to design, even under the assumption of perfect cryptography. With the ‘classical’ Needham-Schroder protocol as leading example, three so-called black-box approaches to the formal verification of security protocols are sketched. BAN-logic is a light-weight method under the assumption of honest agents and a passive intruder. The Casper/FDR approach translates a high-level description of a security protocol, together with its security requirements and a particular instantiation into CSP, that can be machine-verified using the FDR model checker. In this approach the intruder is in control of the network and is allowed to participate as one of the agents. The same holds for the strand space approach. By focusing on the causal dependency of actions and message passing, one aims to prove security properties of general class of protocols instantiations at the same time.
Directing Gene Expression to Gustducin-Positive Taste Receptor Cells

We have demonstrated that an 8.4 kb segment (GUS8.4) from the upstream region of the mouse α-gustducin gene acts as a fully functional promoter to targetlacZ transgene expression to the gustducin-positive subset of taste receptor cells (TRCs). The GUS8.4 promoter drove TRC expression of the β-galactosidase marker at high levels and in a developmentally appropriate pattern. The gustducin minimal 1.4 kb promoter (GUS1.4) by itself was insufficient to specify TRC expression. We also identified an upstream enhancer from the distal portion of the murine gustducin gene that, in combination with the minimal promoter, specified TRC expression of transgenes. Expression of the lacZ transgene from the GUS8.4 promoter and of endogenous gustducin was coordinately lost after nerve section and simultaneously recovered after reinnervation, confirming the functionality of this promoter. Transgenic expression of rat α-gustducin restored responsiveness of gustducin null mice to both bitter and sweet compounds, demonstrating the utility of the gustducin promoter.
Using System Dynamics to Construct Design Theory for Community Information Systems

Virtual communities are complex and evolving socio-technical systems. The design of community information systems requires much theoretical research to solve design problems. A design theory is a prescriptive theory which helps optimize design methods. Community IS design theory is still very young and fragmented, however. In the design theory development process, a mix of theory components is used to solve novel problems or existing problems more effectively and efficiently. We present a meta-model of IS development which focuses on the role of theory in IS design. We show how simulation via system dynamics could play an important role in a more systematic development of design theory for community information systems.
An effective feedback scheme for notification service based on IoT technology

Great demand on notification service has been increased in the IoT (Internet of things) environment. With the growing needs of information generated by IoT devices in everyday lives, the development of effective transmission technology on notification service is inevitable. In this paper, we propose an efficient feedback scheme to enhance the performance of notification system. The proposed approach capitalizes a new notion of feedback interval time to maximize the service efficiency by preventing from delivering unnecessary notification. The simulation result shows that the service performance is improved by reducing wasted notifications and average transmission time compared to the existing scheme.
The Impact of Spelling Errors on Patent Search

The search in patent databases is a risky business compared to the search in other domains. A single document that is relevant but overlooked during a patent search can turn into an expensive proposition. While recent research engages in specialized models and algorithms to improve the effectiveness of patent retrieval, we bring another aspect into focus: the detection and exploitation of patent inconsistencies. In particular, we analyze spelling errors in the assignee field of patents granted by the United States Patent & Trademark Office. We introduce technology in order to improve retrieval effectiveness despite the presence of typographical ambiguities. In this regard, we (1) quantify spelling errors in terms of edit distance and phonological dissimilarity and (2) render error detection as a learning problem that combines word dissimilarities with patent meta-features. For the task of finding all patents of a company, our approach improves recall from 96.7% (when using a state-of-the-art patent search engine) to 99.5%, while precision is compromised by only 3.7%.
An Experimental Study of Old and New Depth Measures

Data depth is a statistical analysis method that assigns a numeric value to a point based on its centrality relative to a data set. Examples include the half-space depth (also known as Tukey depth), convex-hull peeling depth and L1 depth. Data depth has significant potential as a data analysis tool. The lack of efficient computational tools for depth based analysis of large high-dimensional data sets, however, prevents it from being in widespread use. We provide an experimental evaluation of several existing depth measures on different types of data sets, recognize problems with the existing measures and suggest modifications. Specifically, we show how the L1 depth contours are not indicative of shape and suggest a PCA-based scaling that handles this problem; we demonstrate how most existing depth measures are unable to cope with multimodal data sets and how the newly suggested proximity graph depth addresses this issue; and we explore how depth measures perform when the underlying distribution is not elliptic. Our experimental tool is of independent interest: it is an interactive software tool for the generation of data sets and visualization of the performance of multiple depth measures. The tool uses a hierarchical render-pipeline to allow for diverse data sets and fine control of the visual result. With this tool, new ideas in the field of data depth can be evaluated visually and quickly, allowing researchers to assess and adjust current depth functions.