Miracle-dz/UniFAR-FTUs huggingface dataset:
Numerical Continuation Methods for Dynamical Systems: Path following and boundary value problems

Introduction Foreword Herbert B. Keller. 1. Lecture Notes on Numerical Analysis of Nonlinear Equations Eusebius J. Doedel. 2. Interactive Continuation Tools Willy Govaerts and Yuri A. Kuznetzov. 3. Higher-Dimensional Continuation Michael E. Henderson. 4. Computing Invariant Manifolds via the Continuation of Orbit Segments Bernd Krauskopf and Hinke M. Osinga. 5. The Dynamics of SQUIDs and Coupled Pendula Donald G. Aronson and Hans G. Othmer. 6. Global Bifurcation Analysis in Laser Systems Emilio Freire and Alejandro J. Rodriguez-Luis. 8. Periodic Orbit Continuation in Multiple Time Scale Systems John Guckenheimer and M. Drew Lamar. 9. Continuation of Periodic orbits in Symmetric Hamiltonian Systems Jorge Galan-Vioque aand Andre Vanderbauwhede. 10. Phase Conditions, Symmetries and PDE Continuation Wolf-Jurgen Beyn and Vera Thummler. 11. Numerical Computation of Coherent Structures Alan R. Champneys and Bjorn Sandstede. 12. Continuation and Bifurcation Analysis of Delay Differential Equations Dirk Roose and Robert Szalai. Index.
SU(4) skyrmions and activation energy anomaly in bilayer quantum Hall systems

The bilayer quantum Hall (QH) system has four energy levels in the lowest Landau level, corresponding to the layer and spin degrees of freedom. We investigate the system in the regime where all four levels are nearly degenerate and equally active. The underlying group structure is $\mathrm{SU}(4)$. At $\ensuremath{\nu}=1$ the QH state is a charge-transferable state between the two layers and the $\mathrm{SU}(4)$ isospin coherence develops spontaneously. Quasiparticles are isospin textures to be identified with $\mathrm{SU}(4)$ skyrmions. The skyrmion energy consists of the Coulomb energy, the Zeeman energy and the pseudo-Zeeman energy. The Coulomb energy consists of the self-energy, the capacitance energy and the exchange energy. At the balanced point only pseudospins are excited unless the tunneling gap is too large. Then, the $\mathrm{SU}(4)$ skyrmion evolves continuously from the pseudospin-skyrmion limit into the spin-skyrmion limit as the system is transformed from the balanced point to the monolayer point by controlling the bias voltage. Our theoretical result explains quite well the experimental data due to Murphyet al. [S. Q. Murphy, J. P. Eisenstein, G. S. Boebinger, L. N. Pfeiffer, and K. W. West, Phys. Rev. Lett. 72, 728 (1994)] and Sawada et al. [A. Sawada, D. Terasawa, N. Kumada, M. Morino, K. Tagashira, Z. F. Ezawa, K. Muraki, T. Saku, and Y. Hirayama, Physica E 18, 118 (2003); D. Terasawa, M. Morino, K. Nakada, S. Kozumi, A. Sawada, Z. F. Ezawa, N. Kumada, K. Muraki, T. Saku, and Y. Hirayama, Physica E 22, 52 (2004)] on the activation energy anomaly induced by applying parallel magnetic field.
That von Neumann Did Not Believe in a Physical Collapse

Many works intended to introduce interpretive issues in quantum mechanics present John von Neumann as having a view in which measurement produces a physical collapse in the system being measured. In this paper I argue that such a reading of von Neumann is inconsistent with what von Neumann actually says. I show that much of what he says makes no sense on the physical collapse reading, but falls into place if we assume he does not have such a view. I show that the physical collapse view is based on an understanding of ‘state’ which von Neumann does not share. 1. Introduction2. The standard reading of von Neumann3. The standard reading of von Neumann and Chapter VI4. The Chapter VI argument5. The Chapter V argument6. The Chapters III and IV argument7. Conclusion Introduction The standard reading of von Neumann The standard reading of von Neumann and Chapter VI The Chapter VI argument The Chapter V argument The Chapters III and IV argument Conclusion
PanPA: generation and alignment of panproteome graphs

Motivation Compared to eukaryotes, prokaryote genomes are more diverse through different mechanisms, including a higher mutation rate and horizontal gene transfer. Therefore, using a linear representative reference can cause a reference bias. Graph-based pangenome methods have been developed to tackle this problem. However, comparisons in DNA space is still challenging due to this high diversity. In contrast, amino acids have higher similarity due to evolutionary constraints, resulting in conserved amino acids that, however, may be encoded by several synonymous codons. Coding regions cover the majority of the genome in prokaryotes. Thus, building panproteomes leverages the high sequence similarity while not losing much of the genome in non-coding regions. Results We present PanPA, a method that takes a set of multiple sequence alignments (MSAs) of proteins or protein clusters, indexes them, and builds a graph for each MSA. In the querying step, it can align DNA or amino acid sequences back to these graphs. We first showcase that PanPA generates correct alignments on a panproteome from 1,350 E. coli. To demonstrate that panproteomes allow longer phylogenetic distance comparison, we compare DNA and protein alignments from 1,073 S. enterica assemblies against E. coli reference genome, pangenome, and panproteome using BWA, GraphAligner, and PanPA respectively, where PanPA was able to produce around 22% more alignments. We also aligned DNA short-reads WGS sample from S. enterica against the E. coli reference with BWA and the panproteome with PanPA, where PanPA was able to find alignment for 69% of the reads compared to 5% with BWA Availability PanPA is available at https://github.com/fawaz-dabbaghieh/PanPA Contact fawaz@hhu.de, olga.kalinina@helmholtz-hzi.de Supplementary information Supplementary data are available at Bioinformatics online.
Egocentrism, Event Frequency, and Comparative Optimism: When what Happens Frequently is “More Likely to Happen to Me”

Three studies investigated the role of nonmotivated egocentric processes in comparative optimism (and pessimism). According to an egocentric-processes account, when people judge their com-parative likelihood of experiencing an event (e.g., “Compared to the average person, how likely are you to become wealthy? ”), they consider their own chances of experiencing the event more so than the referent's chances. This should produce higher comparative estimates when an event's absolute frequency is high rather than low—a prediction supported in Study 1, which manipulated event frequency through a novel, time frame manipulation. Study 2 empirically distinguished egocentrism from a related focalism account. In Study 3, comparative estimates were related to the perceived frequency of events, independent of the events' perceived desirability and controllability. Path analyses provided additional support for egocentrism, and systematic cases of comparative pessimism were observed as predicted by the egocentric-processes account.
The DfES Model for Best Practice Research Scholarships: tensions

I n September 2000, we began working with 17 secondary teachers on a programme of cooperative teacher research funded by the DfEE Best Practice Research Scholarship (BPRS) scheme.The DfEE’s expectations and their evaluation questions to date as to the role and purpose of such research define a particular model of the research process.This article explores the tensions inherent in this model and the potential conflict between the development of the teacher as researcher and the need to identify tangible practice outcomes. As a consequence of mounting criticism on the role and purpose of educational research (e.g. Hargreaves, 1999) there has been renewed interest in funding teachers to follow their own research questions. In 1996, the Teacher Training Agency (TTA) launched the Teacher Research Grant Pilot Scheme. Within a few years, the funding of such projects moved to the DfEE. In April 2000 Best Practice Research Scholarships (BPRS) were launched with a similar philosophy to that of the TTA. Such scholarships have continued to be funded by the DfES. The teacher as action-researcher has a long history but, through the TTA and DfES, BPRS offers a greater national emphasis on the development of the teacher as researcher. We applaud the initiative, and see it as an important approach towards the continuing professional development of teachers. Working with a group of teachers who have successfully bid for BPRS money, we have been sharply reminded of issues of how practice and research relate to each other. These issues are not new, they have been part of teacher education and professional development for a long time, particularly the question, ‘what counts as research? ’ Those of us who work within university education departments are familiar with the supposed dichotomies between research and curriculum development and the ‘worth’ attributed to publishing in professional journals or academic journals.
Are my Children Old Enough to Read these Books? Age Suitability Analysis

In general, books are not appropriate for all ages, so the aim of this work was to find an effective method of representing the age suitability of textual documents, making use of automatic analysis and visualization. Interviews with experts identified possible aspects of a text (such as 'is it hard to read? ') and a set of features were devised (such as linguistic complexity, story complexity, genre) which combine to characterize these age related aspects. In order to measure these properties, we map a set of text features onto each one. An evaluation of the measures, using Amazon Mechanical Turk, showed promising results. Finally, the set features are visualized in our age-suitability tool, which gives the user the possibility to explore the results, supporting transparency and traceability as well as the opportunity to deal with the limitations of automatic methods and computability issues.
A Survey on Homomorphic Encryption Schemes

Legacy encryption systems depend on sharing a key (public or private) among the peers involved in exchanging an encrypted message. However, this approach poses privacy concerns. The users or service providers with the key have exclusive rights on the data. Especially with popular cloud services, control over the privacy of the sensitive data is lost. Even when the keys are not shared, the encrypted material is shared with a third party that does not necessarily need to access the content. Moreover, untrusted servers, providers, and cloud operators can keep identifying elements of users long after users end the relationship with the services. Indeed, Homomorphic Encryption (HE), a special kind of encryption scheme, can address these concerns as it allows any third party to operate on the encrypted data without decrypting it in advance. Although this extremely useful feature of the HE scheme has been known for over 30 years, the first plausible and achievable Fully Homomorphic Encryption (FHE) scheme, which allows any computable function to perform on the encrypted data, was introduced by Craig Gentry in 2009. Even though this was a major achievement, different implementations so far demonstrated that FHE still needs to be improved significantly to be practical on every platform. Therefore, this survey focuses on HE and FHE schemes. First, we present the basics of HE and the details of the well-known Partially Homomorphic Encryption (PHE) and Somewhat Homomorphic Encryption (SWHE), which are important pillars for achieving FHE. Then, the main FHE families, which have become the base for the other follow-up FHE schemes, are presented. Furthermore, the implementations and recent improvements in Gentry-type FHE schemes are also surveyed. Finally, further research directions are discussed. This survey is intended to give a clear knowledge and foundation to researchers and practitioners interested in knowing, applying, and extending the state-of-the-art HE, PHE, SWHE, and FHE systems.
AIMAC : An Auction-Inspired MAC Protocol

Much attention has been given over the past decade to examining the properties of ad-hoc wireless networks. Current trends, however, show that the proliferation of access point (AP) based wireless networks continues to grow, and impending deployments of large-scale AP-based networks in metropolitan areas (see [? ] and [? ]) speak volumes for their popularity. Given the continued spread of AP-based WiFi networks, it would be foolish to ignore the role an AP can play in enforcing MAC protocol adherence. As WiFi reaches wider and wider audiences, the potential for protocol-level misbehavior grows tremendously. Fortunately, AP-based and distributed solutions have been proposed to detect MAC-layer misbehavior. In the following sections, we first briefly review previous work in 802.11 MAC misbehavior. In light of this work, we next reconsider the role of the AP within the network. After recasting the AP as an auctioneer of channel resources, we propose an Auction-Inspired MAC protocol (AIMAC) that implicitly discourages greedy nodes from continually occupying the wireless channel (i.e. from misbehaving). Additionally, preliminary simulation results are given.
Scholarship in the postmodern era : new venues, new values, new visions

EDITOR S NOTES (Kenneth J. Zahorski). PART ONE: New Venues. 1. Beyond Scholarship Reconsidered: Toward an Enlarged Vision of the Scholarly Work of Faculty Members (R. Eugene Rice). 2. Transforming the Scholarly Process Through Information Technology (Wallace Hannum). 3. Nurturing Scholarship Through Holistic Faculty Development: A Synergistic Approach (Kenneth J. Zahorski). PART TWO: New Values. 4. New Conceptions of Scholarship for a New Generation of Faculty Members (Mary Deane Sorcinelli). 5. Engendering Trust Through Institutional Policies and Practices (Ann F. Lucas). 6. The Soul of Scholarship (Kina S. Mallard). PART THREE: New Visions. 7. Defining Scholarship for the Twenty First Century (Robert M. Diamond). 8. Student Faculty Collaborations, Undergraduate Research, and Collaboration as an Administrative Model (Ronald L. Dotterer). 9. Nurturing an Ethos of Community Engagement (Jerry Berberet). INDEX.
Classification of tweets for sentiment and trend analysis

Education and work-related reading have probably gone up and on-screen reading also increased considerably. A survey by the Pew Research Center in the year 2012 proved that the increase in ownership of tablet computers and electronic book reading devices, such as ipad, kindle fires, Nook, etc., the online book reading also increases considerably. A survey by National Literacy Trust during the year 2013 reported that more than 52% of students prefer to read electronic devices compared to 32% who preferred printed materials. The survey made by the Wall Street Journal, USA today and United Parcel Service (UPS) says that there is a rapid growth in online shopping during recent years. As online reading and online purchase have increased over the period, recommendation becomes mandatory for today's online world, an especially recommendation of books become most important for the student community, because of the availability of huge volume of books online. In order to gain the trusted recommendation people today depends on social networks. Twitter a social network is a popular microblogging service where users create tweets that sometimes express opinions about different topics which helps them to identify the current trends. The work proposed in this paper move towards recommending books based on trending topics from the trusted users obtained through provenance. The proposed work utilizes Naïve Bayesian technique and Moving Average (MA) method to identify the sentiments from tweets and trend respectively.
Face and Hair Region Labeling Using Semi-Supervised Spectral Clustering-Based Multiple Segmentations

The multiple segmentation (MS) scheme is considered to be a way to get a better spatial support for various shaped objects in image segmentation. The MS scheme assumes that the segmented regions (i.e., segments) can be treated as hypotheses for object support rather than mere partitionings of the image. As for attaining each segmentation in the MS scheme, one of the most popular methods is to employ spectral clustering (SC). When applied to image segmentation tasks, SC groups a set of pixels or small regions into unique segments. While it has been popularly used in image segmentation, it often fails to deal with images containing objects with complex boundaries. To split the image as close to the object boundaries as possible, some prior knowledge can be used to guide the clustering algorithm toward appropriate partitioning of the data. In semisupervised clustering, prior knowledge is often formulated as pairwise constraints. In this paper, we propose an MS technique combined with constrained SC to build a face and hair region labeler. To put it concretely, pairwise constraints modified to fit the problem of labeling face regions are added to SC and multiple segments are generated by the constrained SC. Then, the labeling is conducted by estimating the likelihoods for each segment to belong to the target object classes. Experiments are conducted on three datasets and the results show that the proposed scheme offers useful tools for labeling the face images.
Clostridium difficile: Association with Thrombocytosis and Leukocytosis

Background: Apart from leukocytosis, few laboratory markers suggestive of Clostridium difficile infections have been described. Methods: We retrospectively analyzed the association between thrombocytosis, leukocytosis and C difficile infections at the Atlanta Veterans Affairs Medical Center. Results: Of 162 patients with C difficile infection, 36 (22%) had thrombocytosis, and 97 (60%) had leukocytosis. C difficile toxin A ELISA was performed in 46/695 (6.6%) patients with thrombocytosis and was positive in 18 (39.1%). Leukocytosis was present in 16/18 (89%) of patients with positive C difficile toxin A ELISA and thrombocytosis, but also in 21/28 (75%) of patients with negative C difficile toxin A ELISA and thrombocytosis. Among patients with marked leukocytosis, C difficile toxin A was more frequently detected in those with concomitant thrombocytosis (P = 0.07). Conclusions: The presence of thrombocytosis may be helpful to improve the pretest probability for C difficile infections.
Thermal IR emissivity of oil films on sea surfaces at moderate winds

Oil slick detection, identification, and even quantization are of great interest in the context of oil spill countermeasures. As a first approximation, it can be assumed that at radar wavelengths, as the oil film thickness is much lower than the wavelength, the electromagnetic wave cannot “see” the thickness H [? ]; consequently, it could be concluded that the radar response is not significantly sensitive to H. By contrast, at infrared (IR) wavelengths, as the wavelength λ is in the same order as the oil film thickness H, the electromagnetic response sensitivity with respect to H can be hoped for. Then, the thermal IR emissivity of clean and contaminated seas is studied for this purpose. The phenomenon of multiple scattering at the same interface is not taken into account here, making the model applicable for moderate winds (corresponding to gentle surface slopes). By contrast, the phenomenon of multiple scattering inside the inner oil layer between the upper and lower interfaces is taken into account. Hereafter, the hydrodynamic modelling describing the surfaces is summed up in section 2, and the numerical results of the electromagnetic model based on the Geometric Optics (GO) approximation are presented in section 3.
Solubility of Cyclodextrins and Drug/Cyclodextrin Complexes

Cyclodextrins (CDs), a group of oligosaccharides formed by glucose units bound together in a ring, show a promising ability to form complexes with drug molecules and improve their physicochemical properties without molecular modifications. The stoichiometry of drug/CD complexes is most frequently 1:1. However, natural CDs have a tendency to self-assemble and form aggregates in aqueous media. CD aggregation can limit their solubility. Through derivative formation, it is possible to enhance their solubility and complexation capacity, but this depends on the type of substituent and degree of substitution. Formation of water-soluble drug/CD complexes can increase drug permeation through biological membranes. To maximize drug permeation the amount of added CD into pharmaceutical preparation has to be optimized. However, solubility of CDs, especially that of natural CDs, is affected by the complex formation. The presence of pharmaceutical excipients, such as water-soluble polymers, preservatives, and surfactants, can influence the solubilizing abilities of CDs, but this depends on the excipients’ physicochemical properties. The competitive CD complexation of drugs and excipients has to be considered during formulation studies.
Embedding in Neural Networks: A-Priori Design of Hybrid Computers for Prediction

The prediction of complex signals is among the most important applications of random recurrent Neural Networks (rRNN). Yet, no theory which completely describes prediction in rRNNs exists. As such, these systems remain "black boxes". Based on nearest neighbors theory and random nonlinear mapping, we fully describe the mechanisms employed by rRNNs solving this essential task. Our approach combines machine learning techniques (Reservoir Computing) and dynamical systems theory. We derive optimization cost functions which are (a) task specific, and (b) go far beyond the simple optimization of the prediction error. Going beyond, we demonstrate the consequences resulting from our theory. Based on our analysis of an rRNN stabilizing of an arrhythmic heart, we amend this system by a nonvolatile external FIFO memory. Furthermore, we are able a-priori specify the FIFO's properties, strongly reducing the previous training efforts of such systems.