cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
title: A Novel Multi‐Functional Thiophene‐Based Organic Cation as Passivation, Crystalline Orientation, and Organic Spacer Agent for Low‐Dimensional 3D/1D Perovskite Solar Cells
Creators: name: Semerci, Ali
name: Buyruk, Ali
name: Emin, Saim
name: Hooijer, Rik
name: Kovacheva, Daniela
name: Mayer, Peter
name: Reus, Manuel A.
name: Blätte, Dominic
name: Günther, Marcella
name: Hartmann, Nicolai F.
name: Lotfi, Soroush
name: Hofmann, Jan P.
name: Müller‐Buschbaum, Peter
name: Bein, Thomas
name: Ameri, Tayebeh
Publisher: name: Wiley-VCH
Year: 2024

description: Recently, the mixed‐dimensional (3D/2D or 3D/1D) perovskite solar cells using small organic spacers have attracted interest due to their outstanding long‐term stability. Here, a new type of thiophene‐based organic cation 2‐(thiophene‐2yl‐)pyridine‐1‐ium iodide (ThPyI), which is used to fabricate mixed‐dimensional 3D/1D perovskite solar cells, is presented. The ThPyI‐based 1D perovskitoid is applied as a passivator on top of a 3D methyl ammonium lead iodide (MAPI) to fabricate surface‐passivated 3D/1D perovskite films or added alone into the 3D perovskite precursor to generate bulk‐passivated 3D MAPI. The 1D perovskitoid acts as a passivating agent at the grain boundaries of surface‐passivated 3D/1D, which improves the power conversion efficiency (PCE) of the solar cells. Grazing incidence wide‐angle X‐ray scattering (GIWAXS) studies confirm that ThPyI triggers the preferential orientation of the bulk MAPI slabs, which is essential to enhance charge transport. Champion bulk‐passivated 3D and surface‐passivated 3D/1D devices yield 14.10% and 19.60% PCE, respectively. The bulk‐passivated 3D offers favorable stability, with 84% PCE retained after 2000 h without encapsulation. This study brings a new perspective to the design of organic spacers having a different binding motif and a passivation strategy to mitigate the impact of defects in hybrid 3D/1D perovskite solar cells.
Hardware-aware $in \ situ$ Boltzmann machine learning using stochastic magnetic tunnel junctions
Creators: name: Kaiser, Jan
name: Borders, William A.
name: Camsari, Kerem Y.
name: Fukami, Shunsuke
name: Ohno, Hideo
name: Datta, Supriyo
Publisher: name: arXiv
Year: 2021
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Emerging Technologies (cs.ET)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: One of the big challenges of current electronics is the design and implementation of hardware neural networks that perform fast and energy-efficient machine learning. Spintronics is a promising catalyst for this field with the capabilities of nanosecond operation and compatibility with existing microelectronics. Considering large-scale, viable neuromorphic systems however, variability of device properties is a serious concern. In this paper, we show an autonomously operating circuit that performs hardware-aware machine learning utilizing probabilistic neurons built with stochastic magnetic tunnel junctions. We show that $in \ situ$ learning of weights and biases in a Boltzmann machine can counter device-to-device variations and learn the probability distribution of meaningful operations such as a full adder. This scalable autonomously operating learning circuit using spintronics-based neurons could be especially of interest for standalone artificial-intelligence devices capable of fast and efficient learning at the edge.
A minimal regulatory network of extrinsic and intrinsic factors recovers observed patterns of CD4+‭ ‬T cell differentiation and plasticity
Creators: name: Martinez, Esther
name: Alvarez-Buylla, Elena
name: Villarreal, Carlos
name: Mendoza, Luis
Publisher: name: F1000Research
Year: 2015

description: CD4+ T cells orchestrate adaptive immune responses in vertebrates. These cells differentiate into several types depending on environmental signals and immunological challenges, as well as the lineage to which they belong. Once these cells are committed to a particular fate, they can alter their expression pattern and switch to different cell types, thus exhibiting cell plasticity that enables the immune system to dynamically adapt to novel challenges. How is such plasticity attained and what is the role of intracellular versus extracellular molecular components, as well as environmental cues, is still not well understood. We integrated the experimental data available on the molecular components involved CD4+ T cell differentiation into a large network, we then used formal methods to reduce the large network into a reduced network, that constitutes an intracellular regulatory core that includes transcription factors, signaling molecules, and that is able to attain the configurations characteristic of most CD4+ T cell types, as well as their transitions patterns in response to various signals. Our model provides a formal test of the insufficiency of the regulatory interactions among the core transcription factors, or intrinsic factors, to recover CD4+ T cell types. Using such regulatory network model we also recovered CD4+ T cell transition maps under contrasting micro-environments. Finally, we identified key components for cell differentiation and plasticity under contrasting immunogenic conditions. Our models may be useful to further explore the mechanism underlying the immunological system and may also be a useful tool for biomedical applications.
title: Pedestrian-Motorist Self-Reported Behavioral Intentions Toward Using Alternative and Standard Safety Infrastructure
Creators: name: Hood, Emma Sunshine
Publisher: name: Old Dominion University
publisherIdentifier: https://ror.org/04zjtrb98
publisherIdentifierScheme: ROR
Year: 2024

description: The increasing trend in pedestrian-motorist incidents on American roadways warrants a novel solution for improving roadway safety. Alternative crosswalk designs have piqued communities both in the United States and abroad. Designs range from slight changes in colors to extravagant illusions of the roadway falling beneath users. These crosswalk designs are not novel, literature on their efficacy as safety infrastructure is modest with mixed results. The purpose of the study was to expand the current literature on alternative crosswalk designs. The author hypothesized that the differences in behavioral intentions at alternative and standard safety infrastructure would be greater for younger male road users and these differences would diminish as road users got older. This study aimed to answer these questions by examining the relationship between behavioral intentions for pedestrians (going out of the way and walking a minute or more out of their way) and motorists (yielding for pedestrians) using three different crosswalk designs (continental, color aditivo, and colorful 3-dimensional). An online survey recruited 525 participants. Three well-known measures were used as covariates: the Balanced Inventory of Desirable Responding (BIDR), the Pedestrian Behavioral Questionnaire (PBQ), and the Driver Behavioral Questionnaire (DBQ). There were three major findings. Respondents had higher intentions of going out of the way and yielding at standard and 3-dimensional crosswalk designs compared to color aditivo designs (Cruz-Diez, 2024). This finding could be attributed to participants not recognizing color aditivo designs as crosswalks and could suggest that color changes to crosswalk designs should be consistent with existing road marking colors (e.g., primarily white, with yellow or red) and not varying color hues (i.e., greens and blues). Male’s age appeared to be a stronger predictor for intentions to yield, whereas, for females, age predicted intentions to go out of the way to cross traffic at all crosswalk designs. That is, older male motorists had higher intentions to yield. Similarly, as females got older, they had higher intentions to walk out of the way to use a crosswalk. Finally, for motorists the covariates for social desirability (BIDR) and intentional unsafe behaviors (DBQ) contributed medium to large effects in most analysis.
Load Balanced Onion Relay for Prevention of Traffic Analysis in Ad Hoc Networks
Creators: name: Lu, Mi
Publisher: name: figshare
Year: 2021
Subjects: subject: 100503 Computer Communications Networks
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: In this paper, an ad hoc network anonymous data forwardingmethod and an associated routing protocol to prevent traffic analysis is presented. This method assumes trusted closed group nodes and every node can play the role of onion relay for the anonymous data forwarding. The route discovery operation of the protocol adopts the load balancingconcept. The load balancing not only improves the throughput but also helps the prevention of the traffic analysis since the load cost for camouflage traffic can be reduce and the routes change dynamically. The performance of the proposed protocol is evaluated by simulation, and compared in several major aspects with the fixed mix method for anonymous data forwarding that works over existing ad hoc routing protocol.
Extraction of jet topology using three particle correlations
Creators: name: Ajitanand, N. N.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: Recent theoretical studies have indicated that the topological features of away-side jet fragments can be significantly altered by medium-induced modifications. The leading candidates resulting from such modifications are Mach Cones and deflected jets. We show that three particle correlations are able to distinguish between these different modification scenarios. Initial results from an application of the method to Au+Au collisions at RHIC ($\sqrt{s_{NN}}=200$ GeV) are presented.
description: 4 pages, 3 figs. Proceedings 2nd International Conference on Hard and Electromagnetic Probes of High-Energy Nuclear Collisions, June 9-16, 2006, Asilomar, Pacific Grove, California
Disentanglement of two harmonic oscillators in relativistic motion
Creators: name: Lin, Shih-Yuin
name: Chou, Chung-Hsien
name: Hu, B. L.
Publisher: name: arXiv
Year: 2008
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study the dynamics of quantum entanglement between two Unruh-DeWitt detectors, one stationary (Alice), and another uniformly accelerating (Rob), with no direct interaction but coupled to a common quantum field in (3+1)D Minkowski space. We find that for all cases studied the initial entanglement between the detectors disappears in a finite time ("sudden death"). After the moment of total disentanglement the correlations between the two detectors remain nonzero until late times. The relation between the disentanglement time and Rob's proper acceleration is observer dependent. The larger the acceleration is, the longer the disentanglement time in Alice's coordinate, but the shorter in Rob's coordinate.
description: 16 pages, 8 figures; typos added, minor changes in Secs. I and V
A categorification of the Cartan-Eilenberg formula
Creators: name: Maillard, Jun
Publisher: name: arXiv
Year: 2021
Subjects: subject: Representation Theory (math.RT)
subject: Category Theory (math.CT)
subject: Group Theory (math.GR)
subject: FOS: Mathematics
subject: 18A05, 18A30, 18C15, 18C20, 18D05, 20C05, 20L05

description: We prove a categorification of the stable elements formula of Cartan and Eilenberg. Our formula expresses the derived category and the stable module category of a group as a bilimit of the corresponding categories for the $p$-subgroups.
description: Accepted version, 26 pages
AuGPT: Auxiliary Tasks and Data Augmentation for End-To-End Dialogue with Pre-Trained Language Models
Creators: name: Kulhánek, Jonáš
name: Hudeček, Vojtěch
name: Nekvinda, Tomáš
name: Dušek, Ondřej
Publisher: name: arXiv
Year: 2021
Subjects: subject: Computation and Language (cs.CL)
subject: Artificial Intelligence (cs.AI)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Attention-based pre-trained language models such as GPT-2 brought considerable progress to end-to-end dialogue modelling. However, they also present considerable risks for task-oriented dialogue, such as lack of knowledge grounding or diversity. To address these issues, we introduce modified training objectives for language model finetuning, and we employ massive data augmentation via back-translation to increase the diversity of the training data. We further examine the possibilities of combining data from multiples sources to improve performance on the target dataset. We carefully evaluate our contributions with both human and automatic methods. Our model substantially outperforms the baseline on the MultiWOZ data and shows competitive performance with state of the art in both automatic and human evaluation.
GXB: A tool for expression analysis and data integration
Creators: name: Presnell, Scott
Publisher: name: F1000Research
Year: 2015

description: We present a web-based tool, designed to facilitate the integration and exploration of gene expression data and associated systems level experiments. The Gene Expression Browser (GXB) provides a detailed evaluation of expression levels from both microarray and RNA-seq based transcriptome experiments, supporting the calculation and interactive display of differentially expressed gene lists, while also integrating results from immune-monitoring experiments, clinical, demographic, and other laboratory data. In addition, the application contains communication tools that facilitate the sharing of ideas and discoveries between investigators.
On the Best Uniform Polynomial Approximation to the Checkmark Function
Creators: name: Dragnev, Peter D.
name: Legg, Alan R.
name: Orive, Ramon
Publisher: name: arXiv
Year: 2021
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics
subject: 2020MSC: 41A10, 41A50

description: The best uniform polynomial approximation of the checkmark function $f(x)=|x-α|$ is considered, as $α$ varies in $(-1,1)$. For each fixed degree $n$, the minimax error $E_n (α)$ is shown to be piecewise analytic in $α$. In addition, $E_n(α)$ is shown to feature $n-1$ piecewise linear decreasing/increasing sections, called V-shapes. The points of the alternation set are proven to be monotone increasing in $α$ and their dynamics are completely characterized. We also prove a conjecture of Shekhtman that for odd $n$, $E_n(α)$ has a local maximum at $α=0$.
description: 23 pages, 6 figures, now accepted for publication in Journal of Approximation Theory
Analysis of Floquet formulation of time-dependent density-functional theory
Creators: name: Samal, Prasanjit
name: Harbola, Manoj K.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Floquet formulation of time-dependent density-functional theory is revisited in light of its recent criticism [Maitra and Burke, Chem. Phys. Lett. 359 (2002), 237]. It is shown that Floquet theory is well founded and its criticism has overlooked important points of both the Runge-Gross formalism and Floquet formulation itself. We substantiate our analysis by examples similar to that considered by Maitra and Burke.
description: 17 pages, 2 figures. accepted for publication in "Chemical Physics Letters"
A Collider Signature of the Supersymmetric Golden Region
Creators: name: Perelstein, Maxim
name: Spethmann, Christian
Publisher: name: arXiv
Year: 2007
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Null results of experimental searches for the Higgs boson and the superpartners imply a certain amount of fine-tuning in the electroweak sector of the Minimal Supersymmetric Standard Model (MSSM). The "golden region" in the MSSM parameter space is the region where the experimental constraints are satisfied and the amount of fine-tuning is minimized. In this region, the stop trilinear soft term is large, leading to a significant mass splitting between the two stop mass eigenstates. As a result, the decay of the heavier stop into the lighter stop and a Z boson is kinematically allowed throughout the golden region. We propose that the experiments at the Large Hadron Collider (LHC) can search for this decay through an inclusive signature, Z+2jb+missing Et+X. We evaluate the Standard Model backgrounds for this channel, and identify a set of cuts that would allow detection of the supersymmetric contribution at the LHC for the MSSM parameters typical of the golden region. We also discuss other possible interpretations of a signal for new physics in the Z+2jb+missing Et+X channel, and suggest further measurements that could be used to distinguish among these interpretations.
description: 23 pages, 5 figures. New in v4: an error fixed in Eq. (13); results unaffected
Mapping the structure of knowledge for teaching nominal categorical data analysis
Creators: name: Groth, Randall E.
name: Bergner, Jennifer A.
Publisher: name: Maryland Shared Open Access Repository
Year: 2013
Subjects: statistics
teacher education
categorical data
statistical knowledge for teaching
partially correct constructs

description: This report describes a model for mapping cognitive structures related to content knowledge for teaching. The model consists of knowledge elements pertinent to teaching a content domain, the nature of the connections among them, and a means for representing the elements and connections visually. The model is illustrated through empirical data generated as prospective teachers were in the process of developing knowledge for teaching nominal categorical data analysis. During a course focused on the development of statistical knowledge for teaching, the prospective teachers analyzed statistical problems, descriptions of children’s statistical thinking, and related classroom scenarios. Their analyses suggested various types of knowledge structures in development. In some cases, they constructed all knowledge elements targeted in the course. In many cases, however, their knowledge structures had missing, incompatible, and/or disconnected elements preventing them from carrying out recommendations for teaching elementary nominal categorical data analysis in an optimal manner. The report contributes to teacher education by drawing attention to prospective teachers’ learning needs, and it contributes to research on teachers’ cognition by providing a method for modeling their cognitive structures.
Mahadata, Industri 4.0 dan Society 5.0: Potensi POGI dalam membangun kesehatan reproduksi Indonesia
Creators: name: Fuad, Anis
Publisher: name: Zenodo
Year: 2021
Subjects: digital health
obstetrics and gynecology
Indonesia

description: Presentasi di Raker POGI (Perkumpulan Obstetri dan Ginekologi Indonesia) pada 26 Februari 2021. Dalam presentasi terdapat 3 topik, meliputi: jargon industri 4.0, teknologi digital untuk kesehatan reproduksi dan peran POGI.
description: {"references": ["https://setkab.go.id/presiden-apresiasi-penggunaan-aplikasi-telemedicine-untuk-kurangi-risiko-tenaga-medis/", "Fukuyama, M. (2018). Society 5.0: Aiming for a new human-centered society.\u00a0Japan Spotlight,\u00a027, 47-50.", "https://www8.cao.go.jp/cstp/english/society5_0/medical_e.html", "Kemenkes (2020). Renstra Kemenkes 2020-2024", "https://www8.cao.go.jp/cstp/english/society5_0/index.html", "https://theprint.in/health/how-covid-is-making-it-tougher-to-tackle-tb-aids-malaria-and-child-health/443658/", "Kaufman, David R., et al. \"Understanding workflow in telehealth video visits: Observations from the IDEATel project.\"\u00a0Journal of Biomedical Informatics\u00a042.4 (2009): 581-592.", "Aziz, Aleha, et al. \"Telehealth for high-risk pregnancies in the setting of the COVID-19 pandemic.\"\u00a0American journal of perinatology\u00a037.8 (2020): 800", "de Mooij, Marnie J. Meylor, et al. \"OB Nest: reimagining low-risk prenatal care.\"\u00a0Mayo Clinic Proceedings. Vol. 93. No. 4. Elsevier, 2018.", "Video Bumilku Kulonprogo (https://www.youtube.com/watch?v=BETPruXhcjk)", "Video TeleCTG (https://www.youtube.com/watch?v=ecYNYZ83jbU)", "Evidence Standards Framework for Digital Health Technologies (March 2019) \u00a9 NICE 2019", "Wenerda, I. (2019). Grup WhatsApp Sebagai Wadah Komunikasi Ibu-Ibu di Era Digital. Jurnal Penelitian Pers Dan Komunikasi Pembangunan, 23(1), 43-53.", "https://www.ama-assn.org/system/files/2020-04/ama-telehealth-playbook.pdf"]}
Semiconductor-metal phase transition and emergent charge density waves in 1T-ZrX$_2$ (X = Se, Te) at the two-dimensional limit
Creators: name: Ren, Ming-Qiang
name: Han, Sha
name: Fan, Jia-Qi
name: Li, Shujing
name: Wang, Shu-Ze
name: Zheng, Fawei
name: Zhang, Ping
name: Ma, Xu-Cun
name: Xue, Qi-Kun
name: Song, Can-Li
Publisher: name: arXiv
Year: 2021
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Charge density wave (CDW) is a collective quantum phenomenon in metals and features a wave-like modulation of the conduction electron density. A microscopic understanding and experimental control of this many-body electronic state in atomically thin materials remain hot topics in materials physics. By means of material engineering, we realized a dimensionality and Zr intercalation induced semiconductor-metal phase transition in 1T-ZrX$_2$ (X = Se, Te) ultra-thin films, accompanied by a commensurate 2 $\times$ 2 CDW order. Furthermore, we observed a CDW energy gap up to 22 meV around the Fermi level. Fourier-transformed scanning tunneling microscopy and angle-resolved photoemission spectroscopy reveal that 1T-ZrX$_2$ films exhibit the simplest Fermi surface among the known CDW materials in TMDCs, consisting only of Zr 4d-derived elliptical electron conduction band at the corners of the Brillouin zone.
description: 29 pages, 4 figures, 4 Supplementary notes
Structural Anomalies at the Magnetic and Ferroelectric Transitions in $RMn_2O_5$ (R=Tb, Dy, Ho)
Creators: name: Cruz, C. R. dela
name: Yen, F.
name: Lorenz, B.
name: Gospodinov, M. M.
name: Chu, C. W.
name: Ratcliff, W.
name: Lynn, J. W.
name: Park, S.
name: Cheong, S-W.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Strong anomalies of the thermal expansion coefficients at the magnetic and ferroelectric transitions have been detected in multiferroic $RMn_2O_5$. Their correlation with anomalies of the specific heat and the dielectric constant is discussed. The results provide evidence for the magnetic origin of the ferroelectricity mediated by strong spin-lattice coupling in the compounds. Neutron scattering data for $HoMn_2O_5$ indicate a spin reorientation at the two low-temperature phase transitions.
Higher Spin Gravities and Presymplectic AKSZ Models
Creators: name: Sharapov, Alexey
name: Skvortsov, Evgeny
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: As a step towards quantization of Higher Spin Gravities we construct the presymplectic AKSZ sigma-model for $4d$ Higher Spin Gravity which is AdS/CFT dual of Chern-Simons vector models. It is shown that the presymplectic structure leads to the correct quantum commutator of higher spin fields and to the correct algebra of the global higher spin symmetry currents. The presymplectic AKSZ model is proved to be unique, it depends on two coupling constants in accordance with the AdS/CFT duality, and it passes some simple checks of interactions.
description: 43+Appendices+biblio=70 pages; comments and refs added, matches the published version
A Surface-Based DNA Algorithm for the Expansion of Symbolic Determinants
Creators: name: Lu, Mi
Publisher: name: figshare
Year: 2021
Subjects: subject: 10399 Numerical and Computational Mathematics not elsewhere classified
subject: FOS: Mathematics

description: In the past few years since Adelman's pioneering work on solving the HPP (Hamiltonian Path Problem) with a DNA-based computer, many algorithms have been designed on solving NP problems. Most of them are in the solution bases and need some error correction or tolerance technique in order to get good correct results. The advantage of surface-based DNA computing technique with very low error rate, has been shown many times over the solution based DNA computing, but this technique has not been widely used in the DNA computer algorithms design. This is mainly due to the restriction of the surface-based technique comparing with those methods using the DNA strands in solutions. In this paper, we introduce a surface-based DNA computing algorithm for solving a hard computation problem: expansion of symbolic determinants given their patterns of zero entries. The problem is well-known for its exponential difficulty. It is even more difficult than evaluating determinants whose entries are merely numerical. We will show how this problem can be solved with the low error rate surface-based DNA computer using our naïve algorithm.
A Sequential Algorithm for Generating Random Graphs
Creators: name: Bayati, Mohsen
name: Kim, Jeong Han
name: saberi, Amin
Publisher: name: arXiv
Year: 2007
Subjects: subject: Computational Complexity (cs.CC)
subject: Discrete Mathematics (cs.DM)
subject: FOS: Computer and information sciences

description: We present a nearly-linear time algorithm for counting and randomly generating simple graphs with a given degree sequence in a certain range. For degree sequence $(d_i)_{i=1}^n$ with maximum degree $d_{\max}=O(m^{1/4-τ})$, our algorithm generates almost uniform random graphs with that degree sequence in time $O(m\,d_{\max})$ where $m=\f{1}{2}\sum_id_i$ is the number of edges in the graph and $τ$ is any positive constant. The fastest known algorithm for uniform generation of these graphs McKay Wormald (1990) has a running time of $O(m^2d_{\max}^2)$. Our method also gives an independent proof of McKay's estimate McKay (1985) for the number of such graphs. We also use sequential importance sampling to derive fully Polynomial-time Randomized Approximation Schemes (FPRAS) for counting and uniformly generating random graphs for the same range of $d_{\max}=O(m^{1/4-τ})$. Moreover, we show that for $d = O(n^{1/2-τ})$, our algorithm can generate an asymptotically uniform $d$-regular graph. Our results improve the previous bound of $d = O(n^{1/3-τ})$ due to Kim and Vu (2004) for regular graphs.
description: 39 pages
The climate system and the second law of thermodynamics
Creators: name: Singh, Martin S.
name: O'Neill, Morgan E
Publisher: name: arXiv
Year: 2021
Subjects: subject: Atmospheric and Oceanic Physics (physics.ao-ph)
subject: FOS: Physical sciences

description: The second law of thermodynamics implies a relationship between the net entropy export by the Earth and its internal irreversible entropy production. The application of this constraint for the purpose of understanding Earth's climate is reviewed. Both radiative processes and material processes are responsible for irreversible entropy production in the climate system. Focusing on material processes, an entropy budget for the climate system is derived which accounts for the multi-phase nature of the hydrological cycle. The entropy budget facilitates a heat-engine perspective of atmospheric circulations that has been used to propose theories for convective updraft velocities, tropical cyclone intensity, and the atmospheric meridional heat transport. Such theories can only be successful, however, if they properly account for the irreversible entropy production associated with water in all its phases in the atmosphere. Irreversibility associated with such moist processes is particularly important in the context of global climate change, for which the concentration of water vapor in the atmosphere is expected to increase, and recent developments toward understanding the response of the atmospheric heat engine to climate change are discussed. Finally, the application of variational approaches to the climate and geophysical flows is briefly reviewed, including the use of equilibrium statistical mechanics to predict behavior of long-lived coherent structures, and the controversial maximum entropy production principle.
description: 70 pages, 14 figures, 2 tables
A new approach to advance the DNA computing
Creators: name: Lu, Mi
Publisher: name: figshare
Year: 2021
Subjects: subject: 10399 Numerical and Computational Mathematics not elsewhere classified
subject: FOS: Mathematics

description: It has been evidenced that DNA computing can solve those problems which are currently intractable on even the fastestelectronic computers. The algorithm design for DNA computing, however, is not straightforward. Both a significant knowledge of the DNA molecule and a strong background in computer engineering are required to develop efficient DNA computing algorithms. The existing models based on which a few DNA computing algorithms were developed are not sufficiently powerful and robust to attract potential users. In this paper, a new DNA computing model is introduced based on which new algorithms are developed to solve the 3-Coloring problem. These new algorithms are presented as vehicles for demonstrating the advantages of the new model, and they can be expanded to solve other NP-complete problems. Our new algorithms can significantly speed up computation and therefore achieve a better time performance. Furthermore, with the given resource, our algorithms can solve problems of much greater size as compared to existing DNA computing algorithms. In addition, the error rate can be greatly reduced by applying our new algorithms. All of the advantages provided by the new model make DNA computing very efficient and attractive in solving computational intense problems.
Projection Filtering with Observed State Increments with Applications in Continuous-Time Circular Filtering
Creators: name: Kutschireiter, Anna
name: Rast, Luke
name: Drugowitsch, Jan
Publisher: name: arXiv
Year: 2021
Subjects: subject: Robotics (cs.RO)
subject: Methodology (stat.ME)
subject: FOS: Computer and information sciences

description: Angular path integration is the ability of a system to estimate its own heading direction from potentially noisy angular velocity (or increment) observations. Non-probabilistic algorithms for angular path integration, which rely on a summation of these noisy increments, do not appropriately take into account the reliability of such observations, which is essential for appropriately weighing one's current heading direction estimate against incoming information. In a probabilistic setting, angular path integration can be formulated as a continuous-time nonlinear filtering problem (circular filtering) with observed state increments. The circular symmetry of heading direction makes this inference task inherently nonlinear, thereby precluding the use of popular inference algorithms such as Kalman filters, rendering the problem analytically inaccessible. Here, we derive an approximate solution to circular continuous-time filtering, which integrates state increment observations while maintaining a fixed representation through both state propagation and observational updates. Specifically, we extend the established projection-filtering method to account for observed state increments and apply this framework to the circular filtering problem. We further propose a generative model for continuous-time angular-valued direct observations of the hidden state, which we integrate seamlessly into the projection filter. Applying the resulting scheme to a model of probabilistic angular path integration, we derive an algorithm for circular filtering, which we term the circular Kalman filter. Importantly, this algorithm is analytically accessible, interpretable, and outperforms an alternative filter based on a Gaussian approximation.
description: 15 pages, 3 figures, accepted at IEEE Transactions on Signal Processing
Performance of AAOmega: the AAT multi-purpose fibre-fed spectrograph
Creators: name: Sharp, R.
name: Saunder, W.
name: Smith, G.
name: Churilov, V.
name: Correll, D.
name: Dawson, J.
name: Farrel, T.
name: Frost, G.
name: Haynes, R.
name: Heald, R.
name: Lankshear, A.
name: Mayfield, D.
name: Waller, L.
name: Whittard, D.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: AAOmega is the new spectrograph for the 2dF fibre-positioning system on the Anglo-Australian Telescope. It is a bench-mounted, double-beamed design, using volume phase holographic (VPH) gratings and articulating cameras. It is fed by 392 fibres from either of the two 2dF field plates, or by the 512 fibre SPIRAL integral field unit (IFU) at Cassegrain focus. Wavelength coverage is 370 to 950nm and spectral resolution 1,000-8,000 in multi-Object mode, or 1,500-10,000 in IFU mode. Multi-object mode was commissioned in January 2006 and the IFU system will be commissioned in June 2006. The spectrograph is located off the telescope in a thermally isolated room and the 2dF fibres have been replaced by new 38m broadband fibres. Despite the increased fibre length, we have achieved a large increase in throughput by use of VPH gratings, more efficient coatings and new detectors - amounting to a factor of at least 2 in the red. The number of spectral resolution elements and the maximum resolution are both more than doubled, and the stability is an order of magnitude better. The spectrograph comprises: an f/3.15 Schmidt collimator, incorporating a dichroic beam-splitter; interchangeable VPH gratings; and articulating red and blue f/1.3 Schmidt cameras. Pupil size is 190mm, determined by the competing demands of cost, obstruction losses, and maximum resolution. A full suite of VPH gratings has been provided to cover resolutions 1,000 to 7,500, and up to 10,000 at particular wavelengths.
description: 13 pages, 4 figures; presented at SPIE, Astronomical Telescopes and Instrumentation, 24 - 31 May 2006, Orlando, Florida USA
A Characterization of the Convexity of Cyclic Polygons in Terms of the Central Angles
Creators: name: Pinelis, Iosif
Publisher: name: arXiv
Year: 2006
Subjects: subject: General Mathematics (math.GM)
subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 51M04, 52A25, 52A10

description: Let P be a cyclic n-gon with n\ge3, the central angles þ_0,...,þ_{n-1} in (-π,π], and the winding number w:=(þ_0+...+þ_{n-1})/(2π). The vertices of P are assumed to be all distinct from one another. It is then proved that P is convex if and only if one of the following four conditions holds: (I) w=1 and þ_0,...,þ_{n-1}>0; (II) w=-1 and þ_0,...,þ_{n-1}<0; (III) w=0 and exactly one of the angles þ_0,...,þ_{n-1} is negative; (IV) w=0 and exactly one of the angles þ_0,...,þ_{n-1} is positive.
description: 13 pages
Twisted tori and fluxes: a no go theorem for Lie groups of weak G_2 holonomy
Creators: name: Fre', P.
name: Trigiante, M.
Publisher: name: arXiv
Year: 2006
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this paper we prove the theorem that there exists no 7--dimensional Lie group manifold G of weak G2 holonomy. We actually prove a stronger statement, namely that there exists no 7--dimensional Lie group with negative definite Ricci tensor Ric_{IJ}. This result rules out (supersymmetric and non--supersymmetric) Freund--Rubin solutions of M--theory of the form AdS_4\times G and compactifications with non--trivial 4--form fluxes of Englert type on an internal group manifold G. A particular class of such backgrounds which, by our arguments are excluded as bulk supergravity compactifications corresponds to the so called compactifications on twisted--tori, for which G has structure constants $τ^K{}_{IJ}$ with vanishing trace $τ^J{}_{IJ}=0$. On the other hand our result does not have bearing on warped compactifications of M--theory to four dimensions and/or to compactifications in the presence of localized sources (D--branes, orientifold planes and so forth). Henceforth our result singles out the latter compactifications as the preferred hunting grounds that need to be more systematically explored in relation with all compactification features involving twisted tori.
description: 38 pages, tar file containing LaTeX source and youngtab.sty
Randomized Broadcast Channel Access Algorithms for Ad Hoc Networks
Creators: name: Lu, Mi
Publisher: name: figshare
Year: 2021
Subjects: subject: 100503 Computer Communications Networks
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: The problem of broadcast channel access in single-hopand multihop ad hoc networks is considered. Two novelrandomized and distributed channel access algorithms aredeveloped and analyzed for single-hop and multihop networks, respectively. These algorithms are designed based on maximizing the worst-case channel efficiency, by optimizing some key parameters, including the backoff probability distribution and the slot length. The proposed algorithm for single-hop networks offers significantly higher throughput than the CSMA methods when the traffic load is heavy, while still achieving good performance when the load is light or medium. The proposed algorithm for multihop networks can flexibly adapt to the traffic load, and offers much better throughput performance than the existing broadcast scheduling algorithms in light or medium load.
Valence Instability and Superconductivity in Heavy Fermion Systems
Creators: name: Holmes, Alexander T.
name: Jaccard, Didier
name: Miyake, Kazumasa
Publisher: name: arXiv
Year: 2006
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Many cerium-based heavy fermion (HF) compounds have pressure-temperature phase diagrams in which a superconducting region extends far from a magnetic quantum critical point. In at least two compounds, CeCu2Si2 and CeCu2Ge2, an enhancement of the superconducting transition temperature was found to coincide with an abrupt valence change, with strong circumstantial evidence for pairing mediated by critical valence, or charge transfer, fluctuations. This pairing mechanism, and the valence instability, is a consequence of a f-c Coulomb repulsion term U_fc in the hamiltonian. While some non-superconducting Ce compounds show a clear first order valence instability, analogous to the Ce alpha-gamma transition, we argue that a weakly first order valence transition may be a general feature of Ce-based HF systems, and both magnetic and critical valence fluctuations may be responsible for the superconductivity in these systems.
description: 11 pages, 16 figures
Hydrocarbon pollution from urban runoff in the Brunette watershed
Creators: name: Larkin, Gillian Alexandra.
Publisher: name: University of British Columbia
Year: 2009

description: During the first half of the twentieth century, the Brunette watershed underwent rapid urbanization with water resources largely forsaken in the name of development. Urban runoff has been recognized as the major continuing source of contaminants to the urban streams. This study examines hydrocarbon pollution in the Brunette watershed. Total petroleum hydrocarbon (TPH) concentrations were determined in lake core sediments, streambed sediments, stormwater and street surface sediments from throughout the watershed. The lake core sediments provided a record for change ; TPH concentrations increased tenfold over the last 200 years, due to regional development and anthropogenic inputs. TPH concentrations found in streambed sediments were generally higher than those cited in the literature (up to 4800 ug/g), indicating some highly contaminated areas. Streambed sediments from industrialized regions had the highest TPH concentrations, implicating highly developed areas as sources. Hydrocarbons found in stormwater were predominantly aliphatic (66.8 - 92.1%) and particulate associated (75.3 - 96.7%) ; mean concentrations (0.96 - 5.79 mg/L) were similar to those reported in the literature. Suspended solids and hydrocarbon loadings were greatest during the first flush ; TPH concentrations were measured as high as 8.6 mg/L. The influence of catchment land use, dilution of street runoff by the stream volume, and traffic intensity on mean hydrocarbon concentration in stormwater runoff is evident. Relationships between hydrocarbon concentration and Microtox® EC50 values suggest that hydrocarbon content is a consequential contributor to stormwater toxicity. TPH concentrations were remarkably uniform in street sediments from throughout the watershed (average 5812 ug/g). The exception was parking lots where concentrations were considerably higher (6629 - 12111 ug/g). Suspended solids in stormwater are considerably enriched in hydrocarbons compared to their source street surface sediments. Oil stains in traffic lanes and parking stalls implicate road washoff as the source. This study found that hydrocarbon pollution is prevalent in the Brunette watershed. The watershed lacks responsible, sustainable resource management. Actions such as restructuring institutions to form an effective framework, creation of economic incentives, installation of management technologies, use of source control measures, reclamation projects and expansion of public education programs are needed to generate results.
Witnessing Wigner Negativity
Creators: name: Chabaud, Ulysse
name: Emeriau, Pierre-Emmanuel
name: Grosshans, Frédéric
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Physics (quant-ph)
subject: Optimization and Control (math.OC)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: Negativity of the Wigner function is arguably one of the most striking non-classical features of quantum states. Beyond its fundamental relevance, it is also a necessary resource for quantum speedup with continuous variables. As quantum technologies emerge, the need to identify and characterize the resources which provide an advantage over existing classical technologies becomes more pressing. Here we derive witnesses for Wigner negativity of single-mode and multimode quantum states, based on fidelities with Fock states, which can be reliably measured using standard detection setups. They possess a threshold expectation value indicating whether the measured state has a negative Wigner function. Moreover, the amount of violation provides an operational quantification of Wigner negativity. We phrase the problem of finding the threshold values for our witnesses as an infinite-dimensional linear optimisation problem. By relaxing and restricting the corresponding linear programs, we derive two converging hierarchies of semidefinite programs, which provide numerical sequences of increasingly tighter upper and lower bounds for the threshold values. We further show that our witnesses form a complete family - each Wigner negative state is detected by at least one witness - thus providing a reliable method for experimentally witnessing Wigner negativity of quantum states from few measurements. From a foundational perspective, our findings provide insights on the set of positive Wigner functions which still lacks a proper characterisation.
description: 29 pages + 40 pages of appendices, 6 figures, 4 tables. v2: Added link to the set of Wigner positive states. v3: Extension to the multimode setting. v4: Accepted to Quantum; fixed typos. v5: Mistake in Eq.(57) in v4 and revision accordingly. v6: more details on programs p.6
Evaluating and optimizing variant calling: a comparison of Roche 454, Ion Torrent PGM and Illumina NextSeq sequencing data
Creators: name: Sandmann, Sarah
name: Graaf, Aniek De
name: Reijden, Bert Van Der
name: Jansen, Joop
name: Dugas, Martin
Publisher: name: F1000Research
Year: 2015

description: There are various next-generation sequencing (NGS) techniques, all of them striving to replace Sanger sequencing as the gold standard. The ongoing development of NGS methods has greatly reduced turnaround time and cost of sequencing. However, false positive calls of SNVs and specially indels are a widely known problem of basically all NGS sequencers.

We developed optimized variant calling pipelines for three common NGS sequencers considering both SNVs and short indels. Amplicon-based targeted sequencing of 20 genes known to be recurrently mutated in myeloid dysplastic syndromes (MDS) was performed in parallel on Roche 454, Ion Torrent PGM and Illumina NextSeq500 platforms. Diagnostic material of MDS patients — partially sequenced twice on each sequencing platform — formed the basis of the optimization, representing the learning cohort. If required, called variants were confirmed by Sanger sequencing of the original patient material.

We calculated various parameters to characterize both SNVs and indels. Yet, instead of setting arbitrary thresholds for each parameter, we combined them to estimate generalized linear models returning a probability for each variant to be a true positive. A single threshold for each model was chosen to provide maximum sensitivity as well as a maximum positive predictive value.

Subsequently, we performed a comparison of the three NGS platforms and their previously optimized variant calling pipelines. Sequencing data from additional MDS patients with lab validated SNVs and indels formed the basis of the comparison, representing the validation cohort.
CONFOLD: residue-residue contact-guided ab initio protein folding
Creators: name: Jianlin Cheng
name: Adhikari, Badri
Publisher: name: F1000Research
Year: 2015

description: We present an ab initio protein folding method to build three-dimensional models from scratch using predicted contacts and secondary structures. Our method first translates contacts and secondary structures into distance, dihedral angle and hydrogen bond restraints according to a set of new conversion rules, and then provides these restraints as input for a distance geometry algorithm to build tertiary structure models. The initially reconstructed models are used to regenerate a set of physically realistic contact restraints and detect secondary structure patterns, which are then used to reconstruct final structural models. This unique two-stage modeling approach of integrating contacts and secondary structures improves the quality and accuracy of structural models. We validate our method on two standard benchmark datasets using true contacts and secondary structures. Our method improves TM-score of reconstructed protein models by 45% and 42% over existing method on the two datasets. On the dataset for benchmarking reconstruction methods with predicted contacts and secondary structures, average TM-score of best models reconstructed by our method is 0.59, 5.5% higher than an existing method. CONFOLD web server is available at http://protein.rnet.missouri.edu/confold/