Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling Virus Self-Assembly Pathways Using Computational Algebra and Geometry

We develop a tractable model for elucidating the assembly pathways by which an icosahedral viral shell forms from 60 identical constituent protein monomers. This poorly understood process a remarkable example of macromolecular self-assembly occuring in nature and possesses many features that are desirable while engineering self-assembly at the nanoscale. The model uses static geometric constraints to represent the driving (weak) forces that cause a viral shell to assemble and hold it together. The goal is to answer focused questions about the structural properties of a successful assembly pathway. Pathways and their properties are carefully defined and computed using computational algebra and geometry, specifically by crucial modifications to state of the art methods for geometric constraint decomposition. The model is analyzable and refinable and avoids expensive dynamics. It has a provably tractable and accurate computational simulation and that its predictions are roughly consistent with known information about viral shell assembly. Overall the paper’s new contributions are: (a) elucidation of a new model of virus assembly illustrating a strong, direct, mutually beneficial interplay between the concepts underlying macromolecular assembly and a wide variety of established as well as novel concepts from combinatorial and computational algebra, geometry and algebraic complexity; and (b) crucial modifications to existing geometric constraint decomposition methods to obtain a tractable and accurate simulation of the model. Organization of Paper –Introduction and Motivation –Geometric Constraints Background –The Virus Assembly Model: Pathways and Effort –A Tractable and Accurate Simulation supported in part by NSF-EIA 0218435.
Influence of haemorrhage on the pseudo-steady-state remifentanil concentration in a swine model: a comparison with propofol and the effect of haemorrhagic shock stage.

BACKGROUND The increase in remifentanil concentration during haemorrhagic shock and the difference between this effect and that for propofol are not fully understood. We investigated the influence of haemorrhage on the pseudo-steady-state remifentanil concentration in a porcine model and compared the changes with those for propofol. METHODS After infusion of remifentanil (0.5 µg kg⁻¹ min⁻¹) and propofol (6 mg kg⁻¹ h⁻¹ after 2 mg kg⁻¹ bolus infusion) for 60 min, nine swine [mean (standard deviation) body weight=26.3 (1.3) kg] were studied using a stepwise haemorrhage model (10% of estimated blood volume removed every 30 min until 1.5 h, and stepwise removal of 5% every 30 min thereafter until circulatory collapse). Haemodynamic and metabolic variables and plasma remifentanil and propofol concentrations were measured at every step. RESULTS A mean volume of 913 (82) ml of blood was drained before reaching circulatory collapse. The increases in plasma concentrations from the prehaemorrhagic value fitted the following equations: % increase in remifentanil=2.1 × cumulative blood loss (% of initial blood volume) and % increase in propofol = 0.7 × cumulative blood loss during compensated shock; and % increase in remifentanil = 27.4 × cumulative blood loss-897 and % increase in propofol = 9.5 × cumulative blood loss-306 during uncompensated shock. Remifentanil concentrations were highly correlated with the reciprocal of cardiac output. CONCLUSIONS During haemorrhage, the plasma remifentanil concentration showed a three-fold greater increase than that of propofol in administration by continuous infusion.
Beyond the remittances-driven economy: Notes as if the long run mattered

This paper discusses the causes and consequences of the current trend in which a principal driver of growth is inward remittances by workers deployed overseas. The main benefit of the phenomenon is an easing of the fiscal burden arising from the effectively large transfer from workers to the government. On the other hand, the “Dutch Disease” it causes takes a longterm toll on the tradables sector. The paper concludes that the fiscal payoffs from the phenomenon are best used by reinvesting these in the foundations of domestic competitiveness—particularly education and focused infrastructure—to offset the worst effects of the trend and prepare prudently for the time it ends or reverses.
Simultaneous Fault Diagnosis and Robust Activation Function Estimation of Linear Multiple-Models Considering the Bounded Modelling Uncertainty

In this paper, the main goal is to design an approach that performs fault detection and isolation in non linear systems. Fault diagnosis is established by regarding system as an interpolation of multiple LTI uncertainty models and not as a single global model. In multiple model framework, the purpose of the paper is the generation of a robust activation function of the representative linear model. The fault diagnosis method presented here is based on a bank of robust and decoupled parity spaces. The proposed method allows detection, isolation and estimation of multiple faults which appear simultaneously or in a sequential way. Robust model selection is obtained by considering the residual vector insensitive to faults, but sensitive to modelling uncertainty. Performances of the method are tested on a simulated example
Learning Analytics : The Coming Third Wave

What Is Learning Analytics? At its core, learning analytics (LA) is the collection and analysis of usage data associated with student learning. The purpose of LA is to observe and understand learning behaviors in order to enable appropriate interventions. The reports that an LA application generates can be very helpful for instructors (about student activities and progress), for students (feedback on their progress), and for administrators (e.g., aggregations of course and degree completion data). The main elements of LA include:
Bayesian modelling for matching and alignment of biomolecules

This article describes Bayesian modelling for matching and alignment of biomolecules. One particular task where statistical modelling and inference can be useful in scientific understanding of protein structure is that of matching and alignment of two or more proteins. In this regard, statistical shape analysis potentially has something to offer in solving biomolecule matching and alignment problems. The article discusses the use of Bayesian methods for shape analysis to assist with understanding the three-dimensional structure of protein molecules, with a focus on the problem of matching instances of the same structure in the CoMFA (Comparative Molecular Field Analysis) database of steroid molecules. It introduces a Bayesian hierarchical model for pairwise matching and for alignment of multiple configurations before concluding with an overview of some advantages of the Bayesian approach to problems in protein bioinformatics, along with modelling and computation issues, alternative approaches, and directions for future research.
Proprioception : The Forgotten Sixth Sense Chapter : Robotic Devices and Proprioception

All book chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. However, users who aim to disseminate and distribute copies of this book as a whole must not seek monetary compensation for such service (excluded OMICS Group representatives and agreed collaborations). After this work has been published by OMICS Group, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source.
Convergence of European Transition Economies and the EU: What Do the Data Show?

This is an empirical study of the real income convergence among the fifteen European Union members and the eleven transition economies of Central and Eastern Europe. Debates and research on EU enlargement tends to concentrate on normative issues, so empirical studies constitute a small share of published work on the subject. This empirical investigation relies on available data on transition, and employs several econometric techniques including graphic analysis, classical cross-section regression and dynamic panel data estimations. Most estimation methods find positive convergence, but estimated rates of convergence vary considerably.
Search Engine Focused on Multiple Features of Scientific Articles

When starting new research or summarizing the results of research, it is necessary to review related work in the same research field. The research review requires several point of views such as ``problem'', ``method'', ``result''. Simple search by keywords is not effective to specify and narrow-down the scope of search for these meta purpose. In this paper, we focus on sentences to improve the efficiency of research survey with multiple viewpoints. We developed a search engine for scientific articles which classifies sentences by multiple viewpoints.
Regular expressions for language engineering

Many of the processing steps in natural language engineering can be performed using finite state transducers. An optimal way to create such transducers is to compile them from regular expressions. This paper is an introduction to the regular expression calculus, extended with certain operators that have proved very useful in natural language applications ranging from tokenization to light parsing. The examples in the paper illustrate in concrete detail some of these applications.
A Boundary Element Method for Substrate Cross-talk Analysis

An increasingly urgent topic for the realization of densely packed (mixed signal) integrated circuits is prevention of cross-talk via the substrate. Due to decreasing distances between components and increasing operating frequencies, the coupling between components and/or circuit blocks becomes stronger and affects the circuit behaviour more and more. This paper proposes a Boundary Element Method for calculating an admittance matrix for the substrate in order to analyze the parasitic coupling during layout verification. Some issues for the implementation in a layout extraction package, Space [3, 4], will be discussed. Finally, the paper will present relevant examples and comparison with results from the literature.
β-Catenin Activation Is Associated with Specific Clinical and Pathologic Characteristics and a Poor Outcome in Adrenocortical Carcinoma

Purpose: Activation of the Wnt/β-catenin signaling pathway is frequent in adrenocortical carcinoma (ACC) and might be associated with a more aggressive phenotype. The objective of this study was to assess the prognostic value of β-catenin immunohistochemistry and CTNNB1 (β-catenin gene)/APC (adenomatous polyposis coli gene) mutations in patients with resected primary ACC. Experimental design: In 79 patients with resected primary ACC from a French cohort (Cochin-COMETE), β-catenin expression was assessed on tumor specimens by immunohistochemistry. For patients with available DNA (n = 49), CTNNB1, and APC hotspot (mutation cluster region), were sequenced. Association between these results and the clinicopathologic characteristics of the ACC and overall and disease-free survival were studied. Results were confirmed on a tissue microarray from an independent multicentric cohort of 92 ACC from Germany (German-ENSAT cohort). Results: In the Cochin-COMETE cohort, the presence of a β-catenin nuclear staining was significantly associated with a higher ENSAT tumor stage (i.e., stages III and IV), higher Weiss score, more frequent necrosis, mitoses, and CTNNB1/APC mutations. β-Catenin nuclear staining and the presence of CTNNB1/APC mutations were both associated with decreased overall and disease-free survival, and were independent predictive factors of survival in multivariate analysis. The same results were observed in the German-ENSAT cohort. Conclusions: Wnt/β-catenin activation, confirmed by the presence of β-catenin nuclear staining, is an independent prognostic factor of overall and disease-free survival in patients with resected primary ACC. Clin Cancer Res; 17(2); 206–11. ©2010 AACR. Clin Cancer Res; 17(2); 328–36. ©2010 AACR.
Consensus Tracking for Multiagent Systems with Nonlinear Dynamics

This paper concerns the problem of consensus tracking for multiagent systems with a dynamical leader. In particular, it proposes the corresponding explicit control laws for multiple first-order nonlinear systems, second-order nonlinear systems, and quite general nonlinear systems based on the leader-follower and the tree shaped network topologies. Several numerical simulations are given to verify the theoretical results.
Guests’ Reactions to In-Room Sustainability Initiatives

Subtle energy saving changes in guest rooms did not diminish satisfaction, based on a study of 192 guests at an independent four-star hotel. Two changes were tested, a television with three energy settings and light-emitting diodes (LEDs) in place of the standard compact fluorescent lightings (CFLs). While overall satisfaction was not affected by these changes, some guests, notably those with high incomes, did react to the energy saving settings. Contrary to some studies, 45 percent of the guests agreed that they would pay a higher room rate to support sustainability programs. On balance, this study indicates that hotels can gain cost savings and improved sustainability by implementing judicious energy saving approaches without harming guest satisfaction. This article is based on a paper presented at the 2013 Quality in Service Conference (QUIS 13), in Karlstad, Sweden.
A knowledge structure for reusing abstract data types

A knowledge structure for a software library consisting of abstract data types (ADTs) is defined. Both automatically-derived and explicitly-defined relationships are used to impose a knowledge structure on the ADTs. ADTs are defined by an ADT descriptor and one or more ADT implementations. Performance characteristics and default implementations are provided to assist users in choosing among alternatives. An explanation is given as to how the knowledge structure helps users find ADTs of interest, browse through similar ADTs to investigate alternatives, and build and customize executable software components from ADTs in the library.
Exact best-case response time analysis of fixed priority scheduled tasks

We present a solution for exact calculation of the best-case response times of a periodic task set with fixed priorities. The solution is based on the identification of the best-case phasing of a low priority task compared to the higher priority tasks. This phasing occurs when the low priority task is released such that it finishes simultaneously with the releases of all the higher priority tasks, when these have experienced their maximum release jitter. A recurrence equation is applied to find the best-case response time. The dualism between worst-case and best-case response time calculation is characterized. The most important application of the solution is in the analysis of response jitter.
Chosen Problems of the Euro Zone Enlargement

An article investigates a problem of the euro introduction by new members of the European Union. It presents some potential benefits and costs of entry to European Monetary Union in the context of its present and future functioning. Then it discusses some advantages and disadvantages of postponing joining the euro-zone. Besides, potential meaning and consequences of giving a target date of introduction of the euro by a country and possible scenarios that can be taken at this way are presented in the paper. Since the 1st January 2007 Euroland comprises 13 countries. The finance ministers of EU member states have approved of Slovenia’s admission to the euro area. The application of Lithuania was rejected – European Commission and European Central Bank have judged that it has not fulfilled the inflation convergence criterion. With regard to this event, the article touches an issue of the need for reconsidering the Maastricht criteria which presently seem to be a source of many content-related and interpretation doubts. It also investigates the requirement for adjusting the convergence criteria to the fact that the euro-zone has already been in existence. * The first version of this article was presented at X International Conference of Doctoral Students from Czech, German and Polish Universities in Brno, Czech Republic, 12-14 September 2006 and Second Conference of Young Economist in Toruń, Contemporary Issues in Economy: Theory versus Reality, 17-18 November 2006. WYBRANE PROBLEMY ROZSZERZENIA STREFY EURO Adam P. Balcerzak, Dorota Górecka, Elżbieta Rogalska 1 Department of Microeconomics University of Warmia and Mazury in Olsztyn 2 Department of Econometrics and Statistics Nicolaus Copernicus University in Toruń 3 Department of Economics Nicolaus Copernicus University in Toruń S ł o w a k l u c z o w e: Unia Europejska, Unia Gospodarczo-Walutowa, kryteria konwergencji, nowe państwa członkowskie.
Comparison of SLM technique of PAPR reduction in OFDM with Non-linear companding technique

One of the challenging issues for Orthogonal Frequency Division Multiplexing (OFDM) system is its high Peak-to-Average Power Ratio (PAPR). That is the time domain OFDM signal which is a sum of several sinusoids leads to high peak to average power ratio (PAPR). Numbers of techniques have been proposed in the literature for reducing the PAPR in OFDM systems. In this paper comparison of SLM technique of PAPR reduction with Non linear companding technique in terms of various parameter such as coding gain, bit error rate and SNR.
2 Asynchronous Design Methodologies : An Overview

Asynchronous design has been an active area of research since at least the mid 1950's, but has yet to achieve widespread use. We examine the benefits and problems inherent in asynchronous computations, and in some of the more notable design methodologies. These include Huffman asynchronous circuits, burst-mode circuits, micropipelines, template-based and trace theory-based delay-insensitive circuits, signal transition graphs, change diagrams, and compilation-based quasidelay-insensitive circuits.
An Optimization-based Routing Forwarding Algorithm in ICN

In dynamic routing construction of ICN, traditional CCN routing mechanism can improve the diversity and reliability of data forwarding. But it also brings problems in retrieval re dundancy, taking some load to the network. SoCCeR strategy uses ant colony algorithm to finish single-path routing of CCN in dist ribution, while it has defects in ant agency control and convergence feature. Therefore, based on rapid routing this paper proposes a service nodes selecting algorithm with optimized ACO algorithm. The algorithm integrates path time-delay and load of service node into optimized selecting algorithm of routers, which makes full used of the visiting feature of users to improve visiting quality and re duce request loss efficiency. In our method, the probabilist ic state forwarding rules are modified and adaptive pheromone updating formulas are introduced, to prevent ant agency to fall into search sta gnation, due to abnormal accumulation of pheromone density in current optimal path. So the routing algorithm is more responsive to the dynamic changes of network topology.
Towards a classification of Information Technology governance frameworks for the development of a IT GRC healthcare framework

The issues, opportunities and challenges of effectively governing an organization's Information Technology (IT) demands and resources have become a major concern of the Board and executive management in many organisations today. The Swiss healthcare is currently searching for methods and practices for the solution of operational planning and optimisation of IT processes. To make sure that the corporate hospital strategy leads to adequate business decisions an IT GRC Framework for Healthcare will be needed. This paper presents the first task — the classification of existing IT governance frameworks — within the development process. After the dissociation of IT management and corporate governance — a proposal for a classification scheme for IT governance frameworks is described and the application of the classification template is explained.
Lagrangian concordance of Legendrian knots

In this article, we define the notion of a Lagrangian concordance between two Legendrian knots analogous to smooth concordance in the Legendrian context. We show that Legendrian isotopic Legendrian knots are Lagrangian concordant. The focus is primarily on the algebraic aspects of the problem. We study the behavior of the classical invariants (namely the Thurston–Bennequin number and the rotation number) under this relation, and provide some examples of nontrivial Legendrian knots bounding Lagrangian surfaces in D 4. 57R17; 57M50
Efficient Computation and Representation of the Diffusion Echo

Diffusion gained an important role in image processing and computer vision problems. Each mathematically well-founded diffusion model proved its advantages especially in image smoothing. However, unlike the linear diffusion, nonlinear models require a strong mathematical intuition to understand the process. A visual description would yield a better interpretation within and in between various models. The diffusion echo is a good way to visualise diffusion processes. However, it is computationally expensive. The diffusion echo of a pixel in an image has the size of the image itself. Additionally, in nonlinear settings, the diffusion echo is also different for each pixel. Moreover, large stopping times are useful to analyse the image structures, which increases the computational burden further. To this end, this thesis exploits parallel programming on GPU with CUDA and Fast Explicit Diffusion (FED) schemes to compute diffusion echoes in an efficient way. With the implementation in this thesis, it is possible to compute 1024 segment-like diffusion echoes of an image of size 256× 256 in 160 sec. Furthermore, having thousands of segment-like diffusion echoes led us to analyse the image structures in a compact way. PCA is used to find significant eigenechoes to represent all diffusion echoes of an image. In our evaluation, the first 30 eigenechoes of 4096 diffusion echoes resulting from edge-enhancing diffusion of a 256× 256 image can represent all 65536 diffusion echoes of the image with the average MSE of 10.83. Inspired by the scale-space representation, we introduce a diffusion echo-driven segment scale-space. Each segment-like echo can be used as a coarse segment and traced back in time to improve localization. Besides the wide range of possible future work, the work in this thesis can help improving the existing diffusion models as well as designing new ones with more intuitive and better understanding.
Exploitation of ontologies for the management of clinical archetypes in ArchMS

An archetype is a formal model of a domain concept, expressed as a set of constraints based on a reference model and used in a particular domain. In clinical domains, an archetype is defined as a formal model of a clinical concept. Archetypes are considered by many researchers a fundamental tool for the achievement of semantic interoperability of electronic healthcare records. To date, different libraries of archetypes and a series of tools have been developed for archetype-based standards like ISO 13606 and openEHR. However, despite the importance of the semantics of the clinical content and the demonstrated usefulness of ontologies and semantic web technologies, the available platforms for managing archetypes do not exploit them. In this paper we present our archetype management system, which enables the semantic management of archetypes, performing a series of activities based on their OWL representation. The activities include the transformation of archetypes between standards, their validation or the recommendation of appropriate