cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Identification of complex functional relations among genes through association rule learning
Creators: name: Percudani, Riccardo
name: Doniselli, Nicola
name: Palù, Alessandro Dal
name: Cravedi, Pietro
Publisher: name: F1000Research
Year: 2015

description: The analysis of correlated and anti-correlated phylogenetic profiles is a widely used method to predict functional associations among genes. As previously pointed out, these methods corresponds to pairwise logic implications between genes of the type A → B or A → not B, respectively, i.e. the presence of gene A in a genome implies the presence of B, or the presence of gene A implies the absence of B. However, for the presence of analogous proteins, alternative pathways, and pathway branching points, the evolutionary and functional associations among genes can be far more complex than pairwise relations (1). No general algorithms have been implemented for the discovery of complex logic implications involving three or more genes. Here we describe the adaptation of the widely used Apriori algorithm of association rule learning (2,3) to the identification of complex patterns of gene presence/absence across genomes. As a proof of principle of the application of this data mining technique, we report on the identification of a missing gene in purine catabolism through the identification of an association rule relating six different genes involved in the pathway.

1. Bowers, et. al. Science (80). 306, 2246–2249 (2004).
2. Agrawal, R. & Srikant, R. in Proc. 20th Int. Conf. Very Large Data Bases 487–499 (1994).
3. Borgelt, C. Wiley Interdiscip. Rev. Data Min. Knowl. Discov. 2, 437–456 (2012).
Hopf algebras in dynamical systems theory
Creators: name: Carinena, J. F.
name: Ebrahimi-Fard, K.
name: Figueroa, H.
name: Gracia-Bondia, J. M.
Publisher: name: arXiv
Year: 2007
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 16W25, 16W30, 37B55, 37C10

description: The theory of exact and of approximate solutions for non-autonomous linear differential equations forms a wide field with strong ties to physics and applied problems. This paper is meant as a stepping stone for an exploration of this long-established theme, through the tinted glasses of a (Hopf and Rota-Baxter) algebraic point of view. By reviewing, reformulating and strengthening known results, we give evidence for the claim that the use of Hopf algebra allows for a refined analysis of differential equations. We revisit the renowned Campbell-Baker-Hausdorff-Dynkin formula by the modern approach involving Lie idempotents. Approximate solutions to differential equations involve, on the one hand, series of iterated integrals solving the corresponding integral equations; on the other hand, exponential solutions. Equating those solutions yields identities among products of iterated Riemann integrals. Now, the Riemann integral satisfies the integration-by-parts rule with the Leibniz rule for derivations as its partner; and skewderivations generalize derivations. Thus we seek an algebraic theory of integration, with the Rota-Baxter relation replacing the classical rule. The methods to deal with noncommutativity are especially highlighted. We find new identities, allowing for an extensive embedding of Dyson-Chen series of time- or path-ordered products (of generalized integration operators); of the corresponding Magnus expansion; and of their relations, into the unified algebraic setting of Rota-Baxter maps and their inverse skewderivations. This picture clarifies the approximate solutions to generalized integral equations corresponding to non-autonomous linear (skew)differential equations.
description: International Journal of Geometric Methods in Modern Physics, in press
The Hamiltonian approach to General Relativity and CMB primordial spectrum
Creators: name: Barbashov, B. M.
name: Pervushin, V. N.
name: Zakharov, A. F.
name: Zinchuk, V. A.
Publisher: name: arXiv
Year: 2006
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Approaches to solutions of problems of the energy, time, Hamiltonian operator quantization of the General Relativity, the creation of the Universe from vacuum are considered in the frame of reference associated with the CMB radiation in order to describe parameters of this radiation in terms of the parameters of the Standard Model of elementary particles.
description: 10 pages, An invitated lecture at the XXVIII 42nd Karpacz Winter School of Theoretical Physics, Ladek, Poland, 6-11 February 2006, "Current mathematical topics in gravitation and cosmology", references added
Fast, faithful, frequency-domain effective-one-body waveforms for compact binary coalescences
Creators: name: Gamba, Rossella
name: Bernuzzi, Sebastiano
name: Nagar, Alessandro
Publisher: name: arXiv
Year: 2020
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: The inference of binary neutron star properties from gravitational-wave observations requires the generation of millions of waveforms, each one spanning about three order of magnitudes in frequency range. Thus, waveform models must be efficiently generated and, at the same time, be faithful from the post-Newtonian quasi-adiabatic inspiral up to the merger regime. A simple solution to this problem is to combine effective-one-body waveforms with the stationary phase approximation to obtain frequency-domain multipolar approximants valid from any low frequency to merger. We demonstrate that effective-one-body frequency-domain waveforms generated in post-adiabatic approximation are computationally competitive with current phenomenological and surrogate models, (virtually) arbitrarily long, and faithful up to merger for any binary parameter. The same method can also be used to efficiently generate intermediate mass binary black hole inspiral waveforms detectable by space-based interferometers.
Probing Quantum Phase Transition in Macroscopic Qubit Array via circuit QED architecture
Creators: name: Wang, Y. D.
name: Xue, Fei
name: Sun, C. P.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Quantum Physics (quant-ph)
subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: We demonstrate a universal physical mechanism to probe the macroscopic quantum phase transition based on circuit QED architecture. We found that, with certain parameters, the Josephson junction qubit array behaves as an antiferromagnetic Ising model in transverse field and the coupled transmission line resonator serves as a bosonic quantum probe. Our investigation shows that, at the critical point, the drastic broadening of the spectrum of the probe indicates the quantum phase transition.
description: 4 pages, 4 figures
IgTools: a toolkit for construction of antibody repertoire using immunosequencing data
Creators: name: Safonova, Yana
name: Starostina, Ekaterina
name: Shlemov, Alexander
Publisher: name: F1000Research
Year: 2015

description: The analysis of concentrations of circulating antibodies in serum (antibody repertoire) is a fundamental, yet poorly studied, problem in immunoinformatics. Here we present IgTools, a collection of tools for construction and analysis of antibody repertoire using immunosequencing data. IgTools includes IgRepertoireConstructor, IgSimulator, IgQUAST, and Ig reperoire evolution analyzer. IgRepertoireConstructor and IgSimulator are freely available at Github. IgQUAST and Ig reperoire evolution analyzer will be released in fall 2015.
Exploiting a large scale biodata management system to support NGS variant detection studies
Creators: name: Cuccuru, Gianmauro
name: Uva, Paolo
name: Atzeni, Rossano
name: Fotia, Giorgio
Publisher: name: F1000Research
Year: 2015

description: Tracing, analysing and updating the results of data processing protocols can significantly improve turn-around time and reproducibility when systematically dealing with any large scale NGS based clinical study. We present an infrastructure to automate and track all data-related procedures and clinical information at the CRS4 high-throughput sequencing platform, which is the largest in Italy (20 TB of raw sequencing data every ten days). To allow automated data processing this facility is directly interconnected to the CRS4 computational resources (3000 cores, 4.5 PB storage). Our infrastructure has been recently used in a clinical exome sequencing program for mutation identification in patients with syndromic intellectual disability, a large group of disorders with variable phenotypes. An average of 60 million or 100bp paired-end reads were generated per sample, with a mean 100-fold coverage across 62Mb of target regions. Sequences were automatically processed according to the GATK Best Practices, annotated and filtered by allele frequency and predicted impact to select likely pathogenic variants from an average of 170,000 variants per family. One of the core components of the CRS4 infrastructure is OMERO.biobank, a robust, extensible and scalable traceability biodata management system. This component provides a way to store, query and retrieve a full description of biomedical datasets, the computational procedures that derived them, and the graph of dependencies between datasets. These functionalities are essential to support dataset traceability, reproducibility and update.
The power of quantum neural networks
Creators: name: Abbas, Amira
name: Sutter, David
name: Zoufal, Christa
name: Lucchi, Aurélien
name: Figalli, Alessio
name: Woerner, Stefan
Publisher: name: arXiv
Year: 2020
Subjects: subject: Quantum Physics (quant-ph)
subject: Machine Learning (cs.LG)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Fault-tolerant quantum computers offer the promise of dramatically improving machine learning through speed-ups in computation or improved model scalability. In the near-term, however, the benefits of quantum machine learning are not so clear. Understanding expressibility and trainability of quantum models-and quantum neural networks in particular-requires further investigation. In this work, we use tools from information geometry to define a notion of expressibility for quantum and classical models. The effective dimension, which depends on the Fisher information, is used to prove a novel generalisation bound and establish a robust measure of expressibility. We show that quantum neural networks are able to achieve a significantly better effective dimension than comparable classical neural networks. To then assess the trainability of quantum models, we connect the Fisher information spectrum to barren plateaus, the problem of vanishing gradients. Importantly, certain quantum neural networks can show resilience to this phenomenon and train faster than classical models due to their favourable optimisation landscapes, captured by a more evenly spread Fisher information spectrum. Our work is the first to demonstrate that well-designed quantum neural networks offer an advantage over classical neural networks through a higher effective dimension and faster training ability, which we verify on real quantum hardware.
description: 25 pages, 10 figures
Quasiclassical Coarse Graining and Thermodynamic Entropy
Creators: name: Gell-Mann, Murray
name: Hartle, James
Publisher: name: arXiv
Year: 2006
Subjects: subject: Quantum Physics (quant-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Our everyday descriptions of the universe are highly coarse-grained, following only a tiny fraction of the variables necessary for a perfectly fine-grained description. Coarse graining in classical physics is made natural by our limited powers of observation and computation. But in the modern quantum mechanics of closed systems, some measure of coarse graining is inescapable because there are no non-trivial, probabilistic, fine-grained descriptions. This essay explores the consequences of that fact. Quantum theory allows for various coarse-grained descriptions some of which are mutually incompatible. For most purposes, however, we are interested in the small subset of ``quasiclassical descriptions'' defined by ranges of values of averages over small volumes of densities of conserved quantities such as energy and momentum and approximately conserved quantities such as baryon number. The near-conservation of these quasiclassical quantities results in approximate decoherence, predictability, and local equilibrium, leading to closed sets of equations of motion. In any description, information is sacrificed through the coarse graining that yields decoherence and gives rise to probabilities for histories. In quasiclassical descriptions, further information is sacrificed in exhibiting the emergent regularities summarized by classical equations of motion. An appropriate entropy measures the loss of information. For a ``quasiclassical realm'' this is connected with the usual thermodynamic entropy as obtained from statistical mechanics. It was low for the initial state of our universe and has been increasing since.
description: 17 pages, 0 figures, revtex4, Dedicated to Rafael Sorkin on his 60th birthday, minor corrections
Tabu search method for RNA partial degradation problem
Creators: name: Rybarczyk, Agnieszka
name: Kasprzak Marta
name: Blazewicz Jacek
Publisher: name: F1000Research
Year: 2015

description: In the last few years, there has been observed a great interest in the RNA research due to the discovery of the role that RNA molecules play in the biological systems. They do not only serve as a template in protein synthesis or as adaptors in translation process but also influence and are involved in the regulation of gene expression. It was demonstrated that most of them are produced from the larger molecules due to enzyme cleavage or spontaneous degradation. In this work, we would like to present our recent results concerning the RNA degradation process. In our studies we used artificial RNA molecules designed according to the rules of degradation developed by Kierzek and co-workers. On the basis of the results of their degradation, we have proposed the formulation of the RNA Partial Degradation Problem (RNA PDP) and we have shown that the problem is strongly NP-complete. We would like to propose a new efficient heuristic algorithm based on tabu search approach that allows to reconstruct the cleavage sites of the given RNA molecule. The algorithm solves the problem with negative errors. Results of the computational experiment, which prove the quality and usefulness of the proposed method, are presented.
Varieties of dialgebras and conformal algebras
Creators: name: Kolesnikov, Pavel
Publisher: name: arXiv
Year: 2006
Subjects: subject: Quantum Algebra (math.QA)
subject: Rings and Algebras (math.RA)
subject: FOS: Mathematics

description: For a given variety Var of algebras we define the variety Var of dialgebras. This construction turns to be closely related with varieties of pseudo-algebras: every Var-dialgebra can be embedded into an appropriate pseudo-algebra of the variety Var. In particular, Leibniz algebras are exactly Lie dialgebras, and every Leibniz algebra can be embedded into current Lie conformal algebra.
description: v2: 20 pages
Using Artificial Neural Networks to extract the 21-cm Global Signal from the EDGES data
Creators: name: Choudhury, Madhurima
name: Chatterjee, Atrideb
name: Datta, Abhirup
name: Choudhury, Tirthankar Roy
Publisher: name: arXiv
Year: 2020
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: The redshifted 21-cm signal of neutral Hydrogen is a promising probe into the period of evolution of our Universe when the first stars were formed (Cosmic Dawn), to the period where the entire Universe changed its state from being completely neutral to completely ionized (Reionization). The most striking feature of this line of neutral Hydrogen is that it can be observed across an entire frequency range as a sky-averaged continuous signature, or its fluctuations can be measured using an interferometer. However, the 21-cm signal is very faint and is dominated by a much brighter Galactic and extra-galactic foregrounds, making it an observational challenge. We have used different physical models to simulate various realizations of the 21-cm Global signals, including an excess radio background to match the amplitude of the EDGES 21-cm signal. First, we have used an artificial neural network (ANN) to extract the astrophysical parameters from these simulated datasets. Then, mock observations were generated by adding a physically motivated foreground model and an ANN was used to extract the astrophysical parameters from such data. The $R^2$ score of our predictions from the mock-observations is in the range of 0.65-0.89. We have used this ANN to predict the signal parameters giving the EDGES data as the input. We find that the reconstructed signal closely mimics the amplitude of the reported detection. The recovered parameters can be used to infer the physical state of the gas at high redshifts.
description: Submitted to MNRAS
title: The American Samoa Longline Limited-entry Fishery Quarterly Report 1 July–30 September 2023
Creators: name: Pacific Islands Fisheries Science Center (U.S.). Fisheries Research and Monitoring Division
Publisher: name: NOAA National Marine Fisheries Service Pacific Islands Fisheries Science Center
publisherIdentifier: https://ror.org/02apffz65
publisherIdentifierScheme: ROR
Year: 2024

description: PIFSC data report ; DR-24-23
description: Effort and catch statistics for the American Samoa longline limited-entry fishery reported by fishers on electronic and paper logs are summarized for the third quarter of 2023 (1 July–30 September; PIFSC, 2024).
Re-evaluation of reflection seismology for archaeological investigation
Creators: name: Cross, Guy Matthew
Publisher: name: University of British Columbia
Year: 2009

description: During the last decade, archaeologists have widely accepted the use of geophysical exploration techniques, including magnetic, resistivity and electromagnetic methods, for pre-excavation site assessment. Although researchers were quick to recognize the potential of seismic techniques to provide cross-sectional images of the subsurface, early feasibility studies concluded that seismic methods were inappropriate due to restricted resolving power and the relatively small-scale nature of archaeological features. Unfortunately, this self-fulfilling prophesy endures and has largely discouraged subsequent attempts to exploit seismic methods for archaeological reconnaissance. Meanwhile, however, seismic technology has been revolutionized in connection with engineering, groundwater and environmental applications. Attention to detail in developing both instrumentation and data acquisition techniques has yielded a many-fold improvement in seismic resolving power. In light of these advances, this dissertation re-examines the potential of reflection seismology for archaeological remote sensing. It is not the objective of this dissertation to deliver an unequivocal pronouncement on the ultimate utility of reflection seismology for the investigation of archaeological sites. Rather, the goal has been to establish a sound theoretical foundation for objective evaluation of the method's potential and future development. In particular, a thorough theoretical analysis of seismic detection and resolution yields practical performance and identifies frequency response characteristics associated with optimum resolution. Findings have guided subsequent adaptation, development and integration of seismic instrumentation, resulting in a prototype system for high-resolution seismic imaging of the shallow subsurface. Finally, to assess system performance and the suitability of optimum offset data acquisition techniques, a full-scale subsurface model has been constructed, allowing direct comparison between experimental soundings and known subsurface structure. Results demonstrate the potential of reflection seismology to resolve near-surface features on the scale of archaeological interest. Moreover, despite conventional wisdom that the groundpenetrating radar method possesses vastly superior resolving power, acquisition of coincident radar soundings demonstrates that the two techniques provide comparable resolution.
Using the five practices model to promote statistical discourse
Creators: name: Groth, Randall E.
Publisher: name: Maryland Shared Open Access Repository
Year: 2015
Subjects: teaching statistics
classroom discussion
sampling
variability
informal solution stategies
comparing groups

description: Article first published online 9 June 2014.
description: Statistical tasks that can be solved in a variety of ways provide rich sites for classroom discourse. Orchestrating such discourse requires careful planning and execution. Stein, Engle, Smith, and Hughes (2008) suggested five practices to help teachers do so. The five practices can be used to structure conversations so that coherent classroom narratives about solutions to tasks may be formed. In this manuscript, two classroom examples that illustrate the five practices are offered. It is argued that employing the five practices can lead to higher quality classroom discussion than some commonly used arrangements.
Zero modes for the giant magnon
Creators: name: Minahan, J. A.
Publisher: name: arXiv
Year: 2007
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We explicitly construct the eight fermion zero mode solutions for the Hofman-Maldacena giant magnon. The solutions are naturally gauge fixed under the κ-symmetry. Substituting the solutions back into the Lagrangian leads to a simple expression that can be quantized directly. We also show how to construct the SU(2|2)\times SU(2|2) superalgebra from these zero modes. For completeness we also find the four bosonic zero mode solutions.
description: 14 pages; v2 references added; v3 minor changes, references added
Δικονομικές αξιώσεις δικαιούχων εγγραπτέων δικαιωμάτων στις περιπτώσεις ακινήτων με την ένδειξη «αγνώστου ιδιοκτήτη»:
Creators: name: Τσιλιγγερίδου, Μαγδαληνή Χρήστου
Publisher: name: Aristotle University of Thessaloniki
Year: 2014
Subjects: Κτηματολόγιο
άγνωστος ιδιοκτήτης
εκούσια δικαιοδοσία
Land registry
unknown owner
voluntary jurisdiction

description: Οι εκ των πρώτων κτηματολογικών εγγραφών αναφυόμενες αμφισβητήσεις ιδιοκτησιακών δικαιωμάτων, συνιστούν ιδιωτικές διαφορές, για τις οποίες απονέμεται από το Σύνταγμα δικαιοδοσία στα πολιτικά δικαστήρια. Ιδιαιτέρως επιζήμιες είναι οι συνέπειες από άποψη ουσιαστικού δικαίου στην περίπτωση των ακινήτων με την ένδειξη «αγνώστου ιδιοκτήτη», καθώς η διάταξη του αρ. 9 ν. 2664/98 ορίζει ότι αυτά «ανήκουν στην κυριότητα του Ελληνικού Δημοσίου μόλις καταστεί οριστική η πρώτη εγγραφή». Είναι πολύ πιθανό οι πρώτες κτηματολογικές εγγραφές να εμφανίζονται ανακριβείς. Το γεγονός αυτό μπορεί να οφείλεται σε διάφορους λόγους. Ανεξαρτήτως πάντως της αιτίας στην οποία οφείλεται η ανακρίβεια της πρώτης κτηματολογικής εγγραφής, καθώς ο νόμος δε διακρίνει, καθίσταται αναγκαία η διόρθωση των εγγραφών αυτών, προκειμένου να προστατευθούν τόσο τα συμφέροντα των αληθών δικαιούχων, αλλά και για να μπορέσει ο θεσμός του κτηματολογίου να υπηρετήσει τους σκοπούς του, ήτοι την αρχή της δημοσιότητας ως πρωτεύουσας αρχής τόσο του ιδιωτικού αλλά και του δημοσίου δικαίου, και ακολούθως τη διασφάλιση της δημόσιας πίστης και την προστασία των καλόπιστων συναλλασσομένων. Ο αληθής δικαιούχος, στις περιπτώσεις αυτές, δεν μένει ωστόσο απροστάτευτος, καθώς διαθέτει στο δικονομικό του οπλοστάσιο την αίτηση του αρ. 6 παρ. 3 ν. 2664/98 και, υπό προϋποθέσεις, τη διεκδικητική ή αναγνωριστική αγωγή του αρ. 6 παρ. 2 ν. 2664/98.
description: The first cadastral registrations nascent property rights disputes, constitute private disputes, which is awarded by the Constitution jurisdiction of to the civil courts. Particularly adverse are the consequences in terms of substantive law in the case of property marked "unknown owner" as the provision of ar. 9 n. 2664/98 states that these "owned by the Greek State when the first record is made final". It is very likely that the first cadastral registrations appear inaccurate. This may be due to various reasons. Regardless of the cause, however, which may be due to the inaccuracy of the first cadastral registration, since the law does not distinguish, it becomes necessary to correct these records and proper recording of registrable rights in order to protect both the interests of true beneficiaries, but also to enable the institution of land to serve its purposes, namely the principle of publicity as the most significant principal of both private and public law, and then to ensure public trust and the protection of bona fide transactions. The true beneficiary, in cases just mentioned, is not left unprotected, as he maintains in his procedural arsenal, the application of ar. 6 par. 3. n.2664/98 and, under certain conditions, the assertive or declaratory action of ar. 6 § 2 n. 2664/98.
Resource-Efficient Quantum Computing by Breaking Abstractions
Creators: name: Shi, Yunong
name: Gokhale, Pranav
name: Murali, Prakash
name: Baker, Jonathan M.
name: Duckering, Casey
name: Ding, Yongshan
name: Brown, Natalie C.
name: Chamberland, Christopher
name: Abhari, Ali Javadi
name: Cross, Andrew W.
name: Schuster, David I.
name: Brown, Kenneth R.
name: Martonosi, Margaret
name: Chong, Frederic T.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Quantum Physics (quant-ph)
subject: Systems and Control (eess.SY)
subject: FOS: Physical sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Building a quantum computer that surpasses the computational power of its classical counterpart is a great engineering challenge. Quantum software optimizations can provide an accelerated pathway to the first generation of quantum computing applications that might save years of engineering effort. Current quantum software stacks follow a layered approach similar to the stack of classical computers, which was designed to manage the complexity. In this review, we point out that greater efficiency of quantum computing systems can be achieved by breaking the abstractions between these layers. We review several works along this line, including two hardware-aware compilation optimizations that break the quantum Instruction Set Architecture (ISA) abstraction and two error-correction/information-processing schemes that break the qubit abstraction. Last, we discuss several possible future directions.
description: Invited paper by Proceedings of IEEE special issue
ImmuneRegulation: A web based tool for identifying human immune regulatory elements
Creators: name: Gümüş, Zeynep H.
name: Kalayci, Selim
name: Myvizhi Selvan
name: Ramos-Lopez, Irene
name: Cotsapas, Chris
name: Harris, Eva
name: Kim, Eun-Young
name: Montgomery, Ruth R.
name: Poland, Gregory
name: Bali Pulendran
name: Tsang, John S.
name: Klein, Robert J.
Publisher: name: F1000 Research Limited
Year: 2019

description: ImmuneRegulation is an open-access web tool that enables exploration of immune regulatory elements in multiple cohorts. Users can interactively explore its massive repository in a single interface to identify associations between gene(s) of interest and their regulators. These regulators can explain cohort or cell type dependent genetic variations which may be critical in hypothesis generation.
ImmuneRegulation currently provides the largest centrally integrated resource available in the literature on regulation of whole blood and blood cell types in a single, user-friendly web interface. ImmuneRegulation runs on all modern web browsers as it utilizes only standard libraries and does not necessitate any external plug-ins. Query Browser guides users to construct their queries properly; multiple curated queries are provided for users to gain familiarity; multiple tutorials help explain different functionalities.
ImmuneRegulation is freely available at http://immuneregulation.mssm.edu.
A conjecture for the superintegrable chiral Potts model
Creators: name: Baxter, R. J.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We adapt our previous results for the ``partition function'' of the superintegrable chiral Potts model with open boundaries to obtain the corresponding matrix elements of e^{-αH}, where H is the associated hamiltonian. The spontaneous magnetization M_r can be expressed in terms of particular matrix elements of e^{-αH} S^r_1 \e^{-βH}, where S_1 is a diagonal matrix.We present a conjecture for these matrix elements as an m by m determinant, where m is proportional to the width of the lattice. The author has previously derived the spontaneous magnetization of the chiral Potts model by analytic means, but hopes that this work will facilitate a more algebraic derivation, similar to that of Yang for the Ising model.
description: 19 pages, one figure; Corrections made between 28 March 2008 and 28 April 2008: (1) 2.10: q to p; (2) 3.1: epsilon to 0 (not infinity); (3) 5.29: p to q; (4) p14: sub-head: p, q to q,p; (5) p15: sub-head: p, q to q,p; (6) 7.5 second theta to -theta ; (7) before 7.6: make more explicit definition of lambda_j. Several other typos fixed later
Entanglement Negativity at Measurement-Induced Criticality
Creators: name: Sang, Shengqi
name: Li, Yaodong
name: Zhou, Tianci
name: Chen, Xiao
name: Hsieh, Timothy H.
name: Fisher, Matthew P. A.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We propose entanglement negativity as a fine-grained probe of measurement-induced criticality. We motivate this proposal in stabilizer states, where for two disjoint subregions, comparing their "mutual negativity" and their mutual information leads to a precise distinction between bipartite and multipartite entanglement. In a measurement-only stabilizer circuit that maps exactly to two-dimensional critical percolation, we show that the mutual information and the mutual negativity are governed by boundary conformal fields of different scaling dimensions at long distances. We then consider a class of "hybrid" circuit models obtained by perturbing the measurement-only circuit with unitary gates of progressive levels of complexity. While other critical exponents vary appreciably for different choices of unitary gate ensembles at their respective critical points, the mutual negativity has scaling dimension 3 across remarkably many of the hybrid circuits, which is notably different from that in percolation. We contrast our results with limiting cases where a geometrical minimal-cut picture is available.
Multicritical continuous random trees
Creators: name: Bouttier, J.
name: Di Francesco, P.
name: Guitter, E.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Mathematical Physics (math-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Combinatorics (math.CO)
subject: Probability (math.PR)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We introduce generalizations of Aldous' Brownian Continuous Random Tree as scaling limits for multicritical models of discrete trees. These discrete models involve trees with fine-tuned vertex-dependent weights ensuring a k-th root singularity in their generating function. The scaling limit involves continuous trees with branching points of order up to k+1. We derive explicit integral representations for the average profile of this k-th order multicritical continuous random tree, as well as for its history distributions measuring multi-point correlations. The latter distributions involve non-positive universal weights at the branching points together with fractional derivative couplings. We prove universality by rederiving the same results within a purely continuous axiomatic approach based on the resolution of a set of consistency relations for the multi-point correlations. The average profile is shown to obey a fractional differential equation whose solution involves hypergeometric functions and matches the integral formula of the discrete approach.
description: 34 pages, 12 figures, uses lanlmac, hyperbasics, epsf
An ALMA survey of $λ$ Orionis disks: from supernovae to planet formation
Creators: name: Ansdell, Megan
name: Haworth, Thomas J.
name: Williams, Jonathan P.
name: Facchini, Stefano
name: Winter, Andrew
name: Manara, Carlo F.
name: Hacar, Alvaro
name: Chiang, Eugene
name: van Terwisga, Sierk
name: van der Marel, Nienke
name: van Dishoeck, Ewine F.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Protoplanetary disk surveys by the Atacama Large Millimeter/sub-millimeter Array (ALMA) are now probing a range of environmental conditions, from low-mass star-forming regions like Lupus to massive OB clusters like $σ$ Orionis. Here we conduct an ALMA survey of protoplanetary disks in $λ$ Orionis, a ~5 Myr old OB cluster in Orion, with dust mass sensitivities comparable to the surveys of nearby regions (~0.4 $M_\oplus$). We assess how massive OB stars impact planet formation, in particular from the supernova that may have occurred ~1 Myr ago in the core of $λ$ Orionis; studying these effects is important as most planetary systems, including our Solar System, are likely born in cluster environments. We find that the effects of massive stars, in the form of pre-supernova feedback and/or a supernova itself, do not appear to significantly reduce the available planet-forming material otherwise expected at the evolved age of $λ$ Orionis. We also compare a lingering massive "outlier" disk in $λ$ Orionis to similar systems in other evolved regions, hypothesizing that these outliers host companions in their inner disks that suppress disk dispersal to extend the lifetimes of their outer primordial disks. We conclude with numerous avenues for future work, highlighting how $λ$ Orionis still has much to teach us about perhaps one of the most common types of planet-forming environments in the Galaxy.
description: 21 pages, 8 figures, 3 tables. Accepted to AAS Journals
The Convex Hull Swampland Distance Conjecture and Bounds on Non-geodesics
Creators: name: Calderón-Infante, José
name: Uranga, Angel M.
name: Valenzuela, Irene
Publisher: name: arXiv
Year: 2020
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The Swampland Distance Conjecture (SDC) restricts the geodesic distances that scalars can traverse in effective field theories as they approach points at infinite distance in moduli space. We propose that, when applied to the subset of light fields in effective theories with scalar potentials, the SDC restricts the amount of non-geodesicity allowed for trajectories along valleys of the potential. This is necessary to ensure consistency of the SDC as a valid swampland criterium at any energy scale across the RG flow. We provide a simple description of this effect in moduli space of hyperbolic space type, and products thereof, and obtain critical trajectories which lead to maximum non-geodesicity compatible with the SDC. We recover and generalize these results by expressing the SDC as a new Convex Hull constraint on trajectories, characterizing towers by their scalar charge to mass ratio in analogy to the Scalar Weak Gravity Conjecture. We show that recent results on the asymptotic scalar potential of flux compatifications near infinity in moduli space precisely realize these critical amounts of non-geodesicity. Our results suggest that string theory flux compactifications lead to the most generic potentials allowing for maximum non-geodesicity of the potential valleys while respecting the SDC along them.
description: 35 pages, 6 figures
Chaplygin gas in light of recent Integrated Sachs--Wolfe effect data
Creators: name: Giannantonio, Tommaso
name: Melchiorri, Alessandro
Publisher: name: arXiv
Year: 2006
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We investigate the possibility of constraining Chaplygin dark energy models with current Integrated Sachs Wolfe effect data. In the case of a flat universe we found that generalized Chaplygin gas models must have an energy density such that $Ω_c >0.55$ and an equation of state $w 0.55$ and $w
description: 5 pages, 4 figures
Collective modes and superfluidity of a two-dimensional ultracold Bose gas
Creators: name: Singh, Vijay Pal
name: Mathey, Ludwig
Publisher: name: arXiv
Year: 2020
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The collective modes of a quantum liquid shape and impact its properties profoundly, including its emergent phenomena such as superfluidity. Here we present how a two-dimensional Bose gas responds to a moving lattice potential. In particular we discuss how the induced heating rate depends on the interaction strength and the temperature. This study is motivated by the recent measurements of Sobirey {\it et al.} arXiv:2005.07607 (2020), for which we provide a quantitative understanding. Going beyond the existing measurements, we demonstrate that this probing method allows to identify first and second sound in quantum liquids. We show that the two sound modes undergo hybridization as a function of interaction strength, which we propose to detect experimentally. This gives a novel insight into the two regimes of Bose gases, defined via the hierarchy of sounds modes.
description: Main text: 7 pages + 6 figures and Supplementary text: 5 pages + 4 figures
Dynamical deformation effects in subbarrier fusion of $^{64}$Ni+$^{132}$Sn
Creators: name: Umar, A. S.
name: Oberacker, V. E.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We show that dynamical deformation effects play an important role in fusion reactions involving the $^{64}$Ni nucleus, in particular the $^{64}$Ni+$^{132}$Sn system. We calculate fully microscopic interaction potentials and the corresponding subbarrier fusion cross sections.
description: 3 pages, 2 figures
Εθνική ταυτότητα και ιθαγένεια στο λόγο μαθητών μεταναστών και μη, σε ομάδες εστίασης:
Creators: name: Βενέτης, Παναγιώτης Γεωργίου
Publisher: name: Aristotle University of Thessaloniki
Year: 2014
Subjects: Εθνική ταυτότητα
Ιθαγένεια
Μετανάστες μαθητές
National identity
Citizenship
Immigrant students

description: Σκοπός της διατριβής ήταν η μελέτη των παγιωμένων εκφράσεων της νεοελληνικής γλώσσας. Εξετάσαμε την ορολογία που χρησιμοποιείται για τις παγιωμένες εκφράσεις και τους ορισμούς που έχουν προταθεί. Στη συνέχεια παρουσιάσαμε αναλυτικά τα χαρακτηριστικά των παγιωμένων εκφράσεων, καθώς και τους περιορισμούς που ισχύουν όσον αφορά το λεξιλόγιο, τη γραμματική και τη σύνταξή τους. Ακόμη αναφερθήκαμε αναλυτικά στα μοντέλα κατανόησης των παγιωμένων εκφράσεων που έχουν προταθεί και μας απασχόλησε η κατανόηση των παγιωμένων εκφράσεων από τα παιδιά καθώς και η διδασκαλία τους σε ξενόγλωσσους. Ένα άλλο θέμα που θίξαμε ήταν η συγγραφή λεξικών παγιωμένων εκφράσεων και παρουσιάσαμε ορισμένα που έχουν γραφεί για την ελληνική. Ασχοληθήκαμε επιπλέον με την ιστορική διάσταση των παγιωμένων εκφράσεων της νέας ελληνικής και διαπιστώσαμε την παρουσία τους από την αρχαιότητα μέχρι σήμερα.
description: The aim of the present thesis was the study of frozen expressions (idioms) in Modern Greek. We examined the proposed terminology and the definitions given for frozen expressions. Then we presented the features of frozen expressions and the restrictions on vocabulary, grammar, and syntax. Furthermore, we analyzed the models concerning the comprehension of frozen expressions and we examined children’s ability to produce and understand frozen expressions as well as ways of teaching them to foreign learners. We also examined the compilation of dictionaries of frozen expressions and we presented selected Greek dictionaries written in the last two decades. Another aim of this study was to examine the historical dimension of frozen expressions.
Constraining quasar host halo masses with the strength of nearby Lyman-alpha forest absorption
Creators: name: Kim, Young-Rae
name: Croft, Rupert
Publisher: name: arXiv
Year: 2007
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Using cosmological hydrodynamic simulations we measure the mean transmitted flux in the Lyman alpha forest for quasar sightlines that pass near a foreground quasar. We find that the trend of absorption with pixel-quasar separation distance can be fitted using a simple power law form including the usual correlation function parameters r_{0} and γso that ( = \sum exp(-tau_eff*(1+(r/r_{0})^(-γ)))). From the simulations we find the relation between r_{0} and quasar mass and formulate this as a way to estimate quasar host dark matter halo masses, quantifying uncertainties due to cosmological and IGM parameters, and redshift errors. With this method, we examine data for ~3000 quasars from the Sloan Digital Sky Survey (SDSS) Data Release 3, assuming that the effect of ionizing radiation from quasars (the so-called transverse proximity effect) is unimportant (no evidence for it is seen in the data.) We find that the best fit host halo mass for SDSS quasars with mean redshift z=3 and absolute G band magnitude -27.5 is log10(M/M_sun) = 12.48^{+0.53}_{-0.89}. We also use the Lyman-Break Galaxy (LBG) and Lyman alpha forest data of Adelberger et al in a similar fashion to constrain the halo mass of LBGs to be log10(M/M_sun) = 11.13^{+0.39}_{-0.55}, a factor of ~20 lower than the bright quasars. In addition, we study the redshift distortions of the Lyman alpha forest around quasars, using the simulations. We use the quadrupole to monopole ratio of the quasar-Lyman alpha forest correlation function as a measure of the squashing effect. We find that this does not have a measurable dependence on halo mass, but may be useful for constraining cosmic geometry.
description: 10 pages, 11 figures, submitted to MNRAS
Life cycle of a bioinformatics workshop
Creators: name: Brazas, Michelle
name: Ouellette, Francis
Publisher: name: F1000Research
Year: 2015

description: Why did the Bioinformatics.ca ‘Bioinformatics’, ‘Genomics’, and ‘Proteomics’ workshops disappear from the series? Will there be a forthcoming workshop in epigenetics or clinical informatics? Over the past sixteen years of continuing education workshops in bioinformatics, Bioinformatics.ca has seen the introduction and retirement of numerous workshops. Here we explore what the drivers are for the introduction of new workshops in bioinformatics and what the reasons are for either the transformation or retirement of a workshop. Understanding the factors that contribute to the lifecycle of a bioinformatics workshop is critical for continuing education programs, like Bioinformatics.ca, to stay viable, up to date, and relevant.
Η συμβολή της Ser – 125 της ευκαρυωτικής ριβοσωμικής πρωτεΐνης S5 στην κυτταρική της διαμετακίνηση:
Creators: name: Ράντου, Αναστασία Ευστρατίου
Publisher: name: Aristotle University of Thessaloniki
Year: 2014
Subjects: Βιοχημεία
Ριβόσωμα
Μικροσκοπία συνεστίασης
Biochemistry
Ribosome
Confocal analysis

description: Σκοπός της μεταπτυχιακής εργασίας ήταν η μελέτη της πιθανής συνεισφοράς της Ser – 125 στον μηχανισμό εισόδου της στον πυρήνα. Πραγματοποιήθηκε η μελέτη του αμινοξέος Thr – 14, που βρίσκεται στην ευρύτερη αμινοτελική περιοχή των 1 – 50 aa, για την οποία γνωρίζουμε ότι συνεργάζεται με την καρβοξυτελική της rpS5 αλλά επίσης ότι η μετάλλαξη του αμινοξέος Thr – 14 της rpS5 εμποδίζει την είσοδο της πρωτεΐνης στους πυρήνες. Στη συνέχεια, μελετήθηκε η ενδοκυτταρική μεταφορά της πρωτεΐνης από τον πυρήνα στο κυτταρόπλασμα. Για τον έλεγχο μεταφοράς της rpS5 από τον πυρήνα στο κυτταρόπλασμα χρησιμοποιήθηκε ο αναστολέας της καρυοφερίνης (πρωτεΐνη μεταφοράς) Crm1, η λεπτομυκίνη Β (LMB). Τέλος, καταλήξαμε στο συμπέρασμα ότι υφίσταται μια συνέργεια της αμινοτελικής και της καρβοξυτελικής περιοχής της rpS5 για την είσοδό της στον πυρήνα με πιθανή συμμετοχή του αμινοξέος Ser – 125, ότι η Thr – 14 ίσως συμβάλλει στην παραμονή της rpS5 στον πυρήνα και ότι η καρυοφερίνη Crm1 συντελλεί στην έξοδο της rpS5 από τον πυρήνα στο κυτταρόπλασμα.
description: The goal of this study is the investigation of the cellular translocation of ribosomal protein S5 (rpS5). In particular, we attempted to explore the way which is followed by the rpS5 in order to be exported from nucleus to cytoplasm, by taking into consideration previous results related to protein’s entrance from cytoplasm to the nucleus and further to the nucleoli with mechanisms that seems to be based on protein’s structure and not on known signals. The accumulation of GFP - rpS5 - T14 mutant in the cytoplasm clearly addresses the importance of T14 amino acids for wild type rpS5 protein’s entrance into the nucleus. A further exploration of S125 indicates its potential to support the entrance of rpS5 into the nucleoli. Taking into consideration the above finding as well as previous similar data, regarding protein’s endo – cellular traffic, we believe on the existence of cooperation between C – terminal and N – terminal region for its transfer from nucleus to cytoplasm. Additional, our experimental data indicate the involvement of nuclear transport receptor Crm1 (leptomycin inhibited) in protein’s export from nucleus to cytoplasm.
Back translated peptide k-mer search on disk
Creators: name: AKM Tauhidul Islam
name: Xinge Ji
name: Sakti Pramanik
name: Zhu, Qiang
name: Cole, James R.
Publisher: name: F1000Research
Year: 2015

description: In the past, genome sequence databases had used main memory indexing, such as the suffix tree, for fast sequence searches. With next generation sequencing technologies, the amount of sequence data being generated is huge and main memory indexing is limited by the amount of memory available. K-mer based techniques are becoming widely used for various genome sequence database applications. K-mer can also provide an excellent basis for creating efficient disk based indexing. In this paper, we have proposed a k-mer based database searching tool using box queries on BoND-Tree indexing. BoND-tree is quite efficient for indexing and searching in Non-Ordered Discrete Data Space (NDDS). We have conducted experiments on searching DNA databases using back translated protein query sequences and have compared with existing methods. The results are quite promising and justify significance of the proposed approach.