cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Driven-dissipative four-mode squeezing of multilevel atoms in an optical cavity
Creators: name: Sundar, Bhuvanesh
name: Barbarena, Diego
name: Rey, Ana Maria
name: Orioli, Asier Piñeiro
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We utilize multilevel atoms trapped in a driven resonant optical cavity to produce scalable multi-mode squeezed states for quantum sensing and metrology. While superradiance or collective dissipative emission by itself has been typically a detrimental effect for entanglement generation in optical cavities, in the presence of additional drives it can also be used as an entanglement resource. In a recent work [Phys. Rev. Lett. 132, 033601 (2024)], we described a protocol for the dissipative generation of two-mode squeezing in the dark state of a six-level system with only one relevant polarization. There we showed that up to two quadratures can be squeezed. Here, we develop a generalized analytic treatment to calculate the squeezing in any multilevel system where atoms can collectively decay by emitting light into two polarization modes in a cavity. We show that in this more general system up to four spin squeezed quadratures can be obtained. We study how finite-size effects constrain the reachable squeezing, and analytically compute the scaling with $N$. Our findings are readily testable in current optical cavity experiments with alkaline-earth-like atoms.
description: 14 pages, 5 figures + Appendix; References updated; Moved some sections from Appendix to main text
Additional file 1: of Identification of a novel quinoline-based DNA demethylating compound highly potent in cancer cells
Creators: name: Zwergel, Clemens
name: Schnekenburger, Michael
name: Sarno, Federica
name: Battistelli, Cecilia
name: Manara, Maria
name: Stazi, Giulia
name: Mazzone, Roberta
name: Fioravanti, Rossella
name: Gros, Christina
name: FrĂŠdĂŠric Ausseil
name: Florean, Cristina
name: Nebbioso, Angela
name: Strippoli, Raffaele
name: Ushijima, Toshikazu
name: Scotlandi, Katia
name: Tripodi, Marco
name: Arimondo, Paola
name: Altucci, Lucia
name: Diederich, Marc
name: Mai, Antonello
name: Valente, Sergio
Publisher: name: figshare
Year: 2019
Subjects: subject: Space Science
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: Table S1 and Table S2. Supporting information. (DOCX 94 kb)
Spacetime foam as a quantum thermal bath
Creators: name: Garay, Luis J.
Publisher: name: arXiv
Year: 1998
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: An effective model for the spacetime foam is constructed in terms of nonlocal interactions in a classical background. In the weak-coupling approximation, the evolution of the low-energy density matrix is determined by a master equation that predicts loss of quantum coherence. Moreover, spacetime foam can be described by a quantum thermal field that, apart from inducing loss of coherence, gives rise to effects such as gravitational Lamb and Stark shifts as well as quantum damping in the evolution of the low-energy observables.
description: RevTeX 3.01, 4 pages
Hyperbolic Billiards on Surfaces of Constant Curvature
Creators: name: Gutkin, B.
name: Smilansky, U.
name: Gutkin, E.
Publisher: name: arXiv
Year: 1999
Subjects: subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Physical sciences

description: We establish sufficient conditions for the hyperbolicity of the billiard dynamics on surfaces of constant curvature. This extends known results for planar billiards. Using these conditions, we construct large classes of billiard tables with positive Lyapunov exponents on the sphere and on the hyperbolic plane.
description: 28 pages, 14 postscript figures
Leveraging Negative Signals with Self-Attention for Sequential Music Recommendation
Creators: name: Seshadri, Pavan
name: Knees, Peter
Publisher: name: arXiv
Year: 2023
Subjects: subject: Information Retrieval (cs.IR)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Music streaming services heavily rely on their recommendation engines to continuously provide content to their consumers. Sequential recommendation consequently has seen considerable attention in current literature, where state of the art approaches focus on self-attentive models leveraging contextual information such as long and short-term user history and item features; however, most of these studies focus on long-form content domains (retail, movie, etc.) rather than short-form, such as music. Additionally, many do not explore incorporating negative session-level feedback during training. In this study, we investigate the use of transformer-based self-attentive architectures to learn implicit session-level information for sequential music recommendation. We additionally propose a contrastive learning task to incorporate negative feedback (e.g skipped tracks) to promote positive hits and penalize negative hits. This task is formulated as a simple loss term that can be incorporated into a variety of deep learning architectures for sequential recommendation. Our experiments show that this results in consistent performance gains over the baseline architectures ignoring negative user feedback.
description: Accepted to the 1st Workshop on Music Recommender Systems, co-located with the 17th ACM Conference on Recommender Systems (MuRS @ RecSys 2023)
Towards High-resolution Computational Approaches for Structure-based Drug Discovery
Creators: Li, Jianing
Publisher: name: Columbia University
Year: 2011
Subjects: Chemistry
Chemistry, Physical and theoretical
Biochemistry

description: This dissertation describes new computational approaches at high resolution for practical structure-based drug discovery. It begins with a brief review of structure-based computational approaches for drug discovery in comparison with ligand-based ones, followed by a discussion of important applications in selecting drug-like compounds and predicting drug metabolites. Since three-dimensional target structures are crucial for structure-based drug discovery, a new methodology based on force fields for protein structure refinement was developed. This methodology employs the VSGB 2.0 energy model in combination with a robust protonation state assignment algorithm and efficient sampling strategies. High accuracy was obtained for predicting 2239 protein side chains and 115 14-20 residue loops. Given the precision and uniform robustness, this methodology is believed for the first time to be suitable to tackle practical problems in structure-based drug discovery. The VSGB 2.0 energy model was then applied in the development of a new accurate approach (IDSite) for predicting P450-mediated drug metabolism, a problem of great practical interest for drug discovery. IDSite is able to efficiently model induced-fit effects using flexible docking and constrained refinements. Sites of metabolism are determined based on the physical interactions between a P450 enzyme and the ligand. Preliminary tests with 56 compounds displayed both low false positive and low false negative rates, which demonstrate the high potential of IDSite to be used in metabolism tests for drug discovery. In conclusion, this dissertation presents new computational approaches at high resolution to problems related to structure-based drug discovery with unprecedented accuracy. Given such high accuracy, these approaches are very promising in addressing practical issues in pharmaceutical research and development, and in enhancing our capability in the search for new safe drugs.
Gravitationally dressed Parke-Taylor amplitudes
Creators: name: Selivanov, K.
Publisher: name: arXiv
Year: 1997
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: A generating function for the Parke-Taylor amplitudes with any number of positive helicity gravitons in addition to the positive helicity gluons is obtained using the recently constructed self-dual classical solution of the type of perturbiner in Yang-Mills theory interacting with gravity.
description: 4 pages, Latex
Additional file 2: of Carboplatin/paclitaxel, E7-vaccination and intravaginal CpG as tri-therapy towards efficient regression of genital HPV16 tumors
Creators: name: Domingos-Pereira, Sonia
name: Galliverti, Gabriele
name: Hanahan, Douglas
name: Nardelli-Haefliger, Denise
Publisher: name: figshare
Year: 2019
Subjects: Medicine
Cancer

description: Effect of C+P on circulating myeloid cell. (PDF 290 kb)
Causal Fermion Systems: Discrete Space-Times, Causation and Finite Propagation Speed
Creators: name: Finster, Felix
Publisher: name: arXiv
Year: 2018
Subjects: subject: Mathematical Physics (math-ph)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The theory of causal fermion systems is a recent approach to fundamental physics. Giving quantum mechanics, general relativity and quantum field theory as limiting cases, it is a candidate for a unified physical theory. The dynamics is described by a novel variational principle, the so-called causal action principle. The causal action principle does not rely on a presupposed space-time structure. Instead, it is a variational principle for space-time itself as well as for all structures in space-time (like particles, fields, etc.). After a general motivation and introduction, we report on mathematical results for two-particle causal fermion systems which state that every minimizer describes a discrete space-time. We explain and make precise that on scales which are much larger than the scale of the microscopic space-time structures, the dynamics of a causal fermion system respects causality with a finite speed of propagation.
description: 16 pages, LaTeX, 9 figures, notes of invited talk given at DICE2018, Castiglioncello, September 2018
Stiphodon multisquamus
Creators: name: Donaldson, James
name: Maeda, Ken
name: Iida, Midori
name: Kobayashi, Hirozumi
name: Ebner, Brendan C.
name: Tran, Hau Duc
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Perciformes
Gobiidae
Stiphodon
Stiphodon multisquamus

description: Stiphodon multisquamus:
HNUE-F00302, 1 male (40.5 mm SL) and 3 females (32.6-52.2 mm SL), stream 1, 2 Oct. 2018; HNUE-F00303, 2 males (39.3-48.1 mm SL) and 2 females (31.5-33.3 mm SL), stream 4, 29 Oct. 2018.
description: Published as part of Donaldson, James, Maeda, Ken, Iida, Midori, Kobayashi, Hirozumi, Ebner, Brendan C. & Tran, Hau Duc, 2023, New distributional records of four amphidromous gobies (Gobioidei: Sicydiinae) in continental Vietnam, pp. 467-472 in Cybium 47 (4) on page 469, DOI: 10.26028/cybium/2023-019, http://zenodo.org/record/12713800
Geometrically induced spectrum in curved leaky wires
Creators: name: Exner, Pavel
name: Ichinose, Takashi
Publisher: name: arXiv
Year: 2000
Subjects: subject: Mathematical Physics (math-ph)
subject: Condensed Matter (cond-mat)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study measure perturbations of the Laplacian in $L^2(\R^2)$ supported by an infinite curve $Γ$ in the plane which is asymptotically straight in a suitable sense. We show that if $Γ$ is not a straight line, such a ``leaky quantum wire'' has at least one bound state below the threshold of the essential spectrum.
description: LaTeX2e, 16 pages
LLMCarbon: Modeling the end-to-end Carbon Footprint of Large Language Models
Creators: name: Faiz, Ahmad
name: Kaneda, Sotaro
name: Wang, Ruhan
name: Osi, Rita
name: Sharma, Prateek
name: Chen, Fan
name: Jiang, Lei
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computation and Language (cs.CL)
subject: Artificial Intelligence (cs.AI)
subject: Computers and Society (cs.CY)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: The carbon footprint associated with large language models (LLMs) is a significant concern, encompassing emissions from their training, inference, experimentation, and storage processes, including operational and embodied carbon emissions. An essential aspect is accurately estimating the carbon impact of emerging LLMs even before their training, which heavily relies on GPU usage. Existing studies have reported the carbon footprint of LLM training, but only one tool, mlco2, can predict the carbon footprint of new neural networks prior to physical training. However, mlco2 has several serious limitations. It cannot extend its estimation to dense or mixture-of-experts (MoE) LLMs, disregards critical architectural parameters, focuses solely on GPUs, and cannot model embodied carbon footprints. Addressing these gaps, we introduce \textit{\carb}, an end-to-end carbon footprint projection model designed for both dense and MoE LLMs. Compared to mlco2, \carb~significantly enhances the accuracy of carbon footprint estimations for various LLMs. The source code is released at \url{https://github.com/SotaroKaneda/MLCarbon}.
description: 15 pages, 8 figures
Fraction Constraint in Partial Wave Analysis
Creators: name: Dong, Xiang
name: Pan, Chu-Cheng
name: Sun, Yu-Chang
name: Cheng, Ao-Yan
name: Wang, Ao-Bo
name: Cai, Hao
name: Zhu, Kai
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: To resolve the non-convex optimization problem in partial wave analysis, this paper introduces a novel approach that incorporates fraction constraints into the likelihood function. This method offers significant improvements in both the efficiency of pole searching and the reliability of resonance selection within partial wave analysis.
Particle Creation Near the Chronology Horizon
Creators: name: Sushkov, Sergey V.
Publisher: name: arXiv
Year: 1998
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We investigate the phenomenon of particle creation of the massless scalar field in the model of spacetime in which, depending on the model's parameter $\aout$, the chronology horizon could be formed. The model represents a two-dimensional curved spacetime with the topology $R^1 \times S^1$ which is asymptotically flat in the past and in the future. The spacetime is globally hyperbolic and has no causal pathologies if $\aout<1$, and closed timelike curves appear in the spacetime if $\aout\ge 1$. We obtain the spectrum of created particles in the case $\aout<1$. In the limit $\aout \to 1$ this spectrum gives the number of particles created into mode $n$ near the chronology horizon. The main result we have obtained is that the number of scalar particles created into each mode as well as the full number of particles remain finite at the moment of forming of the chronology horizon.
description: 6 pages, RevTeX, one postscript figure. Presented in the GR15, December, 1997, IUCAA, Pune. Submitted to Phys.Rev.D
Bio-Inspired Strategies for Optimizing Radiation Therapy under Uncertainties
Creators: name: K., Keshav Kumar
name: Narasimham, NVSL
Publisher: name: arXiv
Year: 2023
Subjects: subject: Optimization and Control (math.OC)
subject: FOS: Mathematics

description: Radiation therapy is a critical component of cancer treatment. However, the delivery of radiation poses inherent challenges, particularly in minimizing radiation exposure to healthy organs surrounding the tumor site. One significant contributing factor to this challenge is the patient's respiration, which introduces uncertainties in the precise targeting of radiation. Managing these uncertainties during radiotherapy is essential to ensure effective tumor treatment while minimizing the adverse effects on healthy tissues. This research addresses the crucial objective of achieving a balanced dose distribution during radiation therapy under conditions of respiration uncertainty. To tackle this issue, we begin by developing a motion uncertainty model employing probability density functions that characterize breathing motion patterns. This model forms the foundation for our efforts to optimize radiation dose delivery. Next, we employ three bio-inspired optimization techniques: Cuckoo search optimization (CSO), flower pollination algorithm (FPA), and bat search Optimization (BSO). Our research evaluates the dose distribution in Gy on both the tumor and healthy organs by applying these bio-inspired optimization methods to identify the most effective approach. This research ultimately aids in refining the strategies used in radiation therapy planning under the challenging conditions posed by respiration uncertainty. Through the application of bio-inspired optimization techniques and a comprehensive evaluation of dose distribution, we seek to improve the precision and safety of radiation therapy, thereby advancing cancer treatment outcomes.
Towards Real Time Characterization of Grain Growth from the Melt
Creators: Wright, Christopher James
Publisher: name: Columbia University
Year: 2020
Subjects: Materials science
Crystal growth
Grain boundaries
X-rays--Scattering
Microstructure

description: Single crystal materials have unique properties which are endowed by their long ranging atomic order. Growing these crystalline materials can be difficult, as entropy favors disordered grains. The optical floating zone furnace provides an efficient way to make novel single crystal materials, enabling the study of crystals with complex chemical makeup which other techniques would not be able to provide. However, the growth mechanisms of these crystals is poorly understood, leaving the process of making them prone to trial and error and limiting its application in the broader research community. This work aims to understand the microstructural dynamics of floating zone growth using x-ray scattering techniques. These techniques include x-ray diffraction tomography and two dimensional crystal mapping. One focus of this work is building the computational infrastructure to process the large stream of heterogeneous data which results from these techniques. Additionally, this work includes computational and experimental commissioning of the x-ray diffraction tomography technique, helping to understand the advantages and limitations of the current approaches. These pieces of infrastructure are then used to characterize the growth of Rutile crystals via a float zone furnace. Particular attention is paid to the competition amongst the grains, and how certain grains are selected from the plethora which are created at the beginning of the growth.
Large deviations for trajectory observables of diffusion processes in dimension $d>1$ in the double limit of large time and small diffusion coefficient
Creators: name: Monthus, Cecile
Publisher: name: arXiv
Year: 2023
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Probability (math.PR)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: For diffusion processes in dimension $d>1$, the statistics of trajectory observables over the time-window $[0,T]$ can be studied via the Feynman-Kac deformations of the Fokker-Planck generator, that can be interpreted as euclidean non-hermitian electromagnetic quantum Hamiltonians. It is then interesting to compare the four regimes corresponding to the time $T$ either finite or large and to the diffusion coefficient $D$ either finite or small. (1) For finite $T$ and finite $D$, one needs to consider the full time-dependent quantum problem that involves the full spectrum of the Hamiltonian. (2) For large time $T \to + \infty$ and finite $D$, one only needs to consider the ground-state properties of the quantum Hamiltonian to obtain the generating function of rescaled cumulants and to construct the corresponding canonical conditioned processes. (3) For finite $T$ and $D \to 0$, one only needs to consider the dominant classical trajectory and its action satisfying the Hamilton-Jacobi equation, as in the semi-classical WKB approximation of quantum mechanics. (4) In the double limit $T \to + \infty$ and $D \to 0$, the simplifications in the large deviations in $\frac{T}{D}$ of trajectory observables can be analyzed via the two orders of limits, i.e. either from the limit $D \to 0$ of the ground-state properties of the quantum Hamiltonians of (2), or from the limit of long classical trajectories $T \to +\infty$ in the semi-classical WKB approximation of (3). This general framework is illustrated in dimension $d=2$ with rotational invariance.
description: v2=revised version (41 pages)
Towards Spiritual Dignity, Opting Out of Neoliberalism’s Cultural Imperialism
Creators: Sieber, Alexander
Publisher: name: Columbia University
Year: 2018
Subjects: Human rights
Dignity
Neoliberalism
Spirituality

description: From the recent literature, one observes a growing discontent with neoliberalism among scholars of human dignity. New nomenclature such as “the new chronic,”1 “wounded attachments,” 2 and “third-order suffering” 3 have become part of the conversation in how dignity is defined. Most notably, they identify the human spirit as a dimension of political action – such as human rights protection – opening the door for fresh discourse on how the human spirit could be protected via law. I explore how the law is used to protect the human spirit and how law may adapt to someday explicitly protect all souls from the ills of postmodernity. My objective is to build a concrete understanding of how the human spirit features in human rights law. How can one fix the problem of neoliberalism’s cultural imperialism using a cultural rights approach? I ask: Why not address cultural imperialism of non-indigenous souls much like the United Nations Declaration on the Rights of Indigenous Peoples (UNDRIP) has done for indigenous souls? That is, why not protect the whole of humanity with adequate cultural rights to spirit, and how would that look? I determine that there are clauses in UNDRIP and the Universal Declaration of Human Rights (UDHR) that would promote such a measure.
Towards Trouble-Free Networks for End Users
Creators: Kim, Kyung Hwa
Publisher: name: Columbia University
Year: 2018
Subjects: Computer science
Computer network resources
Internet users
Computer network protocols

description: Network applications and Internet services fail all too frequently. However, end users cannot effectively identify the root cause using traditional troubleshooting techniques due to the limited capability to distinguish failures caused by local network elements from failures caused by elements located outside the local area network.
      To overcome these limitations, we propose a new approach, one that leverages collaboration of user machines to assist end users in diagnosing various failures related to Internet connectivity and poor network performance.
      First, we present DYSWIS ("Do You See What I See?"), an automatic network fault detection and diagnosis system for end users. DYSWIS identifies the root cause(s) of network faults using diagnostic rules that consider diverse information from multiple nodes. In addition, the DYSWIS rule system is specially designed to support crowdsourced and distributed probes. We also describe the architecture of DYSWIS and compare its performance with other tools. Finally, we demonstrate that the system successfully detects and diagnoses network failures which are difficult to diagnose using a single-user probe.
      Failures in lower layers of the protocol stack also have the potential to disrupt Internet access; for example, slow Internet connectivity is often caused by poor Wi-Fi performance. Channel contention and non-Wi-Fi interference are the primary reasons for this performance degradation. We investigate the characteristics of non-Wi-Fi interference that can severely degrade Wi-Fi performance and present WiSlow ("Why is my Wi-Fi slow?"), a software tool that diagnoses the root causes of poor Wi-Fi performance. WiSlow employs user-level network probes and leverages peer collaboration to identify the physical location of these causes. The software includes two principal methods: packet loss analysis and 802.11 ACK number analysis. When the issue is located near Wi-Fi devices, the accuracy of WiSlow exceeds 90%.
      Finally, we expand our collaborative approach to the Internet of Things (IoT) and propose a platform for network-troubleshooting on home devices. This platform takes advantage of built-in technology common to modern devices --- multiple communication interfaces. For example, when a home device has a problem with an interface it sends a probe request to other devices using an alternative interface. The system then exploits cooperation of both internal devices and remote machines. We show that this approach is useful in home networks by demonstrating an application that contains actual diagnostic algorithms.
Additional file 3: of Carboplatin/paclitaxel, E7-vaccination and intravaginal CpG as tri-therapy towards efficient regression of genital HPV16 tumors
Creators: name: Domingos-Pereira, Sonia
name: Galliverti, Gabriele
name: Hanahan, Douglas
name: Nardelli-Haefliger, Denise
Publisher: name: figshare
Year: 2019
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Immunology
subject: FOS: Clinical medicine
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Ivag CpG after E7LP or C+P +E7LP vaccination increased E7-specific IFN-Îł secreting cells in Cervix-Vagina (CV). (PDF 203 kb)
GW190521: tracing imprints of spin-precession on the most massive black hole binary
Creators: name: Miller, Simona J.
name: Isi, Maximiliano
name: Chatziioannou, Katerina
name: Varma, Vijay
name: Mandel, Ilya
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: GW190521 is a remarkable gravitational-wave signal on multiple fronts: its source is the most massive black hole binary identified to date and could have spins misaligned with its orbit, leading to spin-induced precession -- an astrophysically consequential property linked to the binary's origin. However, due to its large mass, GW190521 was only observed during its final 3-4 cycles, making precession constraints puzzling and giving rise to alternative interpretations, such as eccentricity. Motivated by these complications, we trace the observational imprints of precession on GW190521 by dissecting the data with a novel time domain technique, allowing us to explore the morphology and interplay of the few observed cycles. We find that precession inference hinges on a quiet portion of the pre-merger data that is suppressed relative to the merger-ringdown. Neither pre-merger nor post-merger data alone are the sole driver of inference, but rather their combination: in the quasi-circular scenario, precession emerges as a mechanism to accommodate the lack of a stronger pre-merger signal in light of the observed post-merger. In terms of source dynamics, the pre-merger suppression arises from a tilting of the binary with respect to the observer. Establishing such a consistent picture between the source dynamics and the observed data is crucial for characterizing the growing number of massive binary observations and bolstering the robustness of ensuing astrophysical claims.
description: 11 pages (excluding references), 9 figures
Additional file 1: of BacTag - a pipeline for fast and accurate gene and allele typing in bacterial sequencing data based on database preprocessing
Creators: name: Khachatryan, Lusine
name: Kraakman, Margriet
name: Bernards, Alexandra
name: Laros, Jeroen
Publisher: name: figshare
Year: 2019
Subjects: subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: BacTag dependencies. Programming languages and software packages used to build the BacTag pipeline. (PDF 23 kb)
Intelligent architectures for robotics: The merging of cognition and emotion
Creators: name: Pessoa, Luiz
Publisher: name: arXiv
Year: 2019
Subjects: subject: Robotics (cs.RO)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: What is the place of emotion in intelligent robots? In the past two decades, researchers have advocated for the inclusion of some emotion-related components in the general information processing architecture of autonomous agents, say, for better communication with humans, or to instill a sense of urgency to action. The framework advanced here goes beyond these approaches and proposes that emotion and motivation need to be integrated with all aspects of the architecture. Thus, cognitive-emotional integration is a key design principle. Emotion is not an "add on" that endows a robot with "feelings" (for instance, reporting or expressing its internal state). It allows the significance of percepts, plans, and actions to be an integral part of all its computations. It is hypothesized that a sophisticated artificial intelligence cannot be built from separate cognitive and emotional modules. A hypothetical test inspired by the Turing test, called the Dolores test, is proposed to test this assertion.
description: 7 figures
What do Topologists want from Seiberg--Witten theory? (A review of four-dimensional topology for physicists)
Creators: name: Iga, Kevin
Publisher: name: arXiv
Year: 2002
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In 1983, Donaldson shocked the topology world by using instantons from physics to prove new theorems about four-dimensional manifolds, and he developed new topological invariants. In 1988, Witten showed how these invariants could be obtained by correlation functions for a twisted N=2 SUSY gauge theory. In 1994, Seiberg and Witten discovered dualities for such theories, and in particular, developed a new way of looking at four-dimensional manifolds that turns out to be easier, and is conjectured to be equivalent to, Donaldson theory. This review describes the development of this mathematical subject, and shows how the physics played a pivotal role in the current understanding of this area of topology.
description: 51 pages, 10 figures, 8 postscript files. Submitted to International Journal of Modern Physics A, July 2002 Uses Latex 2e with class file ws-ijmpa.cls (included in tar file)
Complex-valued universal linear transformations and image encryption using spatially incoherent diffractive networks
Creators: name: Yang, Xilin
name: Rahman, Md Sadman Sakib
name: Bai, Bijie
name: Li, Jingxi
name: Ozcan, Aydogan
Publisher: name: arXiv
Year: 2023
Subjects: subject: Optics (physics.optics)
subject: Neural and Evolutionary Computing (cs.NE)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: As an optical processor, a Diffractive Deep Neural Network (D2NN) utilizes engineered diffractive surfaces designed through machine learning to perform all-optical information processing, completing its tasks at the speed of light propagation through thin optical layers. With sufficient degrees-of-freedom, D2NNs can perform arbitrary complex-valued linear transformations using spatially coherent light. Similarly, D2NNs can also perform arbitrary linear intensity transformations with spatially incoherent illumination; however, under spatially incoherent light, these transformations are non-negative, acting on diffraction-limited optical intensity patterns at the input field-of-view (FOV). Here, we expand the use of spatially incoherent D2NNs to complex-valued information processing for executing arbitrary complex-valued linear transformations using spatially incoherent light. Through simulations, we show that as the number of optimized diffractive features increases beyond a threshold dictated by the multiplication of the input and output space-bandwidth products, a spatially incoherent diffractive visual processor can approximate any complex-valued linear transformation and be used for all-optical image encryption using incoherent illumination. The findings are important for the all-optical processing of information under natural light using various forms of diffractive surface-based optical processors.
description: 16 Pages, 3 Figures
Platforms and Tools for Data Management in Large-Scale Facilities
Creators: name: Gonzalez-Beltran, Alejandra
Publisher: name: Zenodo
Year: 2021
Subjects: data management, large-scale facilities, FAIR data, common APIs, common standards, common vocabularies

description: Presentation delivered at the UK Catalysis Hub virtual workshop on data management. https://ukcatalysishub.co.uk/save-the-date-uk-catalysis-hub-data-management-virtual-workshop/
BOSHLANG'ICH TA'LIMDA AXBOROT TEXNOLOGIYALARIDAN FOYDALANISH USULLARI VA AFZALLIKLARI
Creators: name: Shamsiddinov, G'iyosjon
name: Ro'ziqulova, Barchin
name: Inatillayeva, Laziza
Publisher: name: Zenodo
Year: 2024

description: Ushbu maqolada axborot kommunikatsion texnologiyalari, ya’ni zamonaviy kompyuter texnologiyalari imkoniyatlaridan umumta’lim maktablarining boshlang‘ich sinf darslarida foydalanishning usullari va afzalliklari yoritilgan.
Additional file 1 of Different information needs in subgroups of people with diabetes mellitus: a latent class analysis
Creators: name: Borgmann, Sandra O.
name: Gontscharuk, Veronika
name: Sommer, Jana
name: Laxy, Michael
name: Ernstmann, Nicole
name: Karl, Florian M.
name: Rückert-Eheberg, Ina-Maria
name: Schwettmann, Lars
name: Ladwig, Karl-Heinz
name: Peters, Annette
name: Icks, Andrea
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Science Policy
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1: Appendix 1. Information Needs in Diabetes Questionnaire
Towards a Gravitational Analog to S-duality in Non-abelian Gauge Theories
Creators: name: Garcia-Compean, H.
name: Obregon, O.
name: Plebanski, J. F.
name: Ramirez, C.
Publisher: name: arXiv
Year: 1997
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: For non-abelian non-supersymmetric gauge theories, generic dual theories have been constructed. In these theories the couplings appear inverted. However, they do not possess a Yang-Mills structure but rather are a kind of non-linear sigma model. It is shown that for a topological gravitational model an analog to this duality exists.
description: LaTeX, 14 pages, no figures, minor corrections
Collective infrared excitation in rare-earth Gd$_x$La$_{1-x}$B$_6$ hexaborides
Creators: name: Zhukova, E. S.
name: Gorshunov, B. P.
name: Komandin, G. A.
name: Alyabyeva, L. N.
name: Muratov, A. V.
name: Aleshchenko, Yu. A.
name: Anisimov, M. A.
name: Shitsevalova, N. Yu.
name: Polovets, S. E.
name: Filipov, V. B.
name: Sluchanko, N. E.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Other Condensed Matter (cond-mat.other)
subject: FOS: Physical sciences

description: Using Fourier-transform infrared spectroscopy and optical ellipsometry, room temperature spectra of complex conductivity of single crystals of hexaborides Gd$_x$La$_{1-x}$B$_6$, $x$(Gd)$=0$, 0.01, 0.1, 0.78, 1 are determined in the frequency range 30$-$35000$~cm^{-1}$. In all compounds, in addition to the Drude free-carrier spectral component, a broad excitation is discovered with the unusually large dielectric contribution $Δ$$\varepsilon$=5000 -- 15000 and non-Lorentzian lineshape. It is suggested that the origin of the excitation is connected with the dynamic cooperative Jahn-Teller effect of B$_6$ clusters. Analysis of the spectra together with the results of DC and Hall resistivity measurements shows that only 30$-$50$\%$ of the conduction band electrons are contributing to the free carrier conductivity with the rest being involved in the formation of an overdamped excitation, thus providing possible explanation of remarkably low work function of thermoemission of Gd$_x$La$_{1-x}$B$_6$ and non-Fermi-liquid behavior in GdB$_6$ crystals.
description: 7 pages, 5 figures, 1 table
Additional file 1 of Uncertainty-aware approach for multiple imputation using conventional and machine learning models: a real-world data study
Creators: name: Wabina, Romen Samuel
name: Looareesuwan, Panu
name: Sonsilphong, Suphachoke
name: Teza, Htun
name: Ponthongmak, Wanchana
name: McKay, Gareth
name: Attia, John
name: Pattanateepapon, Anuchate
name: Panitchote, Anupol
name: Thakkinstian, Ammarin
Publisher: name: figshare
Year: 2025
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Chemical Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer
subject: Mental Health

description: Supplementary Material 1.
Additional file 1 of Nano delivery of simvastatin targets liver sinusoidal endothelial cells to remodel tumor microenvironment for hepatocellular carcinoma
Creators: name: Yu, Zhuo
name: Guo, Jianfeng
name: Liu, Yun
name: Wang, Menglin
name: Liu, Zhengsheng
name: Gao, Yueqiu
name: Huang, Leaf
Publisher: name: figshare
Year: 2022
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Additional file 1: Figure S1. Simvastatin shows no obvious cytotoxicity. Cytotoxicity study of SK-Hep1, LX2 and Huh7 cells treated with simvastatin at different concentrations (n = 3). Figure S2. Simvastatin inhibits the activity of HSC via LSEC. (A) The expression of KLF2 and eNOS was quantified in SK-Hep1 cells treated with indicated concentration of simvastatin for 24 h (n = 3). (B) The expression of α-SMA and collagen1 was quantified in LPS-activated LX2 treated with the supernatant of SK-Hep1 upon different doses of simvastatin treatment with or without L-NAME (n = 3). (C) The expression of CXCL16 was quantified in SK-Hep1 cells treated with the indicated concentrations of simvastatin for 24 h (n = 3). **p < 0.01, ***p < 0.001. Figure S3. Synthesis of the LSEC-targeting PLGA-PEG. (A) The synthesis process of PLGA-PEG-mannan. (B) 1H-NMR spectra of the synthesized particles PLGA-PEG-mannan. Comparing the integrated area of peak g (mannan protons) and peak a (protons in PEG), the ratio of mannose to PEG is approximately 4.5. Figure S4. Simvastatin NPs show no obvious toxicity in mice. (A) HE staining of major organs from mice with various treatments. Scale bar stands for 50 μm. (B) Body weight changes during treatment. (C) Mice blood routine test and (D) Hepatorenal function test after treatment (n = 5). n.s. = not significant. Table S1. Antibody list. Table S2. Gene Primer list for real-time PCR. Table S3. Cytokine Primer list for real-time PCR.
Towards a definition of Shimura curves in positive characteristics
Creators: Xia, Jie
Publisher: name: Columbia University
Year: 2014
Subjects: subject: Mathematics
subject: FOS: Mathematics

description: In the thesis, we present some answers to the question
      What is an appropriate definition of Shimura curves in positive characteristics ?
      The answer is obvious for Shimura curves of PEL type due to the moduli interpretation. Thus what is more interesting is the answer on Shimura curves of Hodge type.
      Inspired by an example constructed by David Mumford, we find conditions on a proper smooth curve over a field of positive characteristic which guarantee that it lifts to a Shimura curve of Hodge type over the complex numbers. These conditions are in terms of geometry mod p, such as Barsotti-Tate groups, Dieudonne isocrystals, crystalline Hodge cycles and l-adic monodromy. Thus one can take them as definitions of Shimura curves in positive characteristics. More generally, We define ``weak" Shimura curves in characteristic p.
      Along the way, we prove if a Barsotti-Tate group is versally deformed over a proper curve over an algebraically closed field of positive characteristic, then it admits a unique deformation to the corresponding Witt ring. This deformation result serves as one of the key ingredients in the proofs.
Additional file 1: of Challenging dominant breast cancer research agendas: perspectives on the outcomes of the interagency breast cancer and environment research coordinating committee
Creators: name: Richter, Lauren
Publisher: name: figshare
Year: 2019
Subjects: subject: Sociology
subject: FOS: Sociology
subject: Cancer
subject: Science Policy

description: Interview Questions for IBCERCC Research Project. (DOCX 60 kb)
title: Die Vorträge der Hauptversammlung der Internationalen Gesellschaft für Geschichte der Pharmazie e.V. während des Internationalen Pharmaziegeschichtlichen Kongresses in Dubrovnik vom 26. - 31. August 1959
Creators: name: :None
Publisher: name: Internationale Gesellschaft für Geschichte der Pharmazie
Year: 1960
Subjects: subject: 615

description: Veröffentlichungen der Internationalen Gesellschaft für Geschichte der Pharmazie e.V., vol. 16
Effective average action and nonperturbative renormalization group equation in higher derivative quantum gravity
Creators: name: Granda, L. N.
name: Odintsov, S. D.
Publisher: name: arXiv
Year: 1998
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We study the exact renormalization group (RG) in $R^2$-gravity in the effective average action formalism using the background field method. The truncated evolution equation (where truncation is made to low-derivatives functionals space) for such a theory in a de Sitter background leads to a set of nonperturbative RG equations for cosmological and gravitational coupling constants. The gauge dependence problem is solved by working in the physical Landau-De Witt gauge corresponding to gauge-fixing independent effective action. Approximate solution of nonperturbative RG equations reveals the appearence of antiscreening or screening behaviour of Newtonian coupling, depending on the higher-derivatives coupling constants. The existence of unstable UV fixed points is also mentioned.
description: Latex file, 10 pages, to appear in Grav.and Cosm.,v.4,1998
Precise predictions for multi-${\rm TeV}$ and ${\rm PeV}$ energy neutrino scattering rates
Creators: name: Gauld, Rhorry
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: The scattering rate of multi-${\rm TeV}$ and ${\rm PeV}$ energy neutrinos is fast becoming an interesting topic in (astro)particle-physics. This is due to experimental progress at Neutrino Telescopes such as IceCube which have begun to gain sensitivity to the flux of neutrinos in this energy range. In view of this, a precise calculation of the scattering rate of neutrinos upon atoms is presented. The two main components of the calculation are the differential cross-section predictions for neutrino scattering upon an atomic nucleus (such as that which make up water), as well as upon atomic electrons. In the first case, the predictions for neutrino-nucleon cross-sections in charged- and neutral-current scattering are refined by including resonant contributions generated within the photon field of the nucleus, which alter the considered distributions by up to $\approx 4\%$. In the latter case, radiative corrections are provided for all $2\to2$ scattering processes of the form $\barν_e e^-\to f\bar{f}^{\prime}$. For antineutrino energies of $E_{\barν_e}\approx6{\rm~PeV}$, where these processes become resonantly enhanced (the Glashow resonance) and dominate the total cross-section, these corrections amount to $\approx-10\%$.
description: 7 pages, 5 figures. v2: Matches published version. Additionally includes coherent scattering results. All numerical results available from zeondo record: https://zenodo.org/record/3766134
Clouds and Clarity: Revisiting Atmospheric Feature Trends in Neptune-size Exoplanets
Creators: name: Brande, Jonathan
name: Crossfield, Ian J. M.
name: Kreidberg, Laura
name: Morley, Caroline V.
name: Barman, Travis
name: Benneke, Björn
name: Christiansen, Jessie L.
name: Dragomir, Diana
name: Fortney, Jonathan J.
name: Greene, Thomas P.
name: Hardegree-Ullman, Kevin K.
name: Howard, Andrew W.
name: Knutson, Heather A.
name: Lothringer, Joshua D.
name: Mikal-Evans, Thomas
Publisher: name: arXiv
Year: 2023
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: Over the last decade, precise exoplanet transmission spectroscopy has revealed the atmospheres of dozens of exoplanets, driven largely by observatories like the Hubble Space Telescope. One major discovery has been the ubiquity of atmospheric aerosols, often blocking access to exoplanet chemical inventories. Tentative trends have been identified, showing that the clarity of planetary atmospheres may depend on equilibrium temperature. Previous work has often grouped dissimilar planets together in order to increase the statistical power of any trends, but it remains unclear from observed transmission spectra whether these planets exhibit the same atmospheric physics and chemistry. We present a re-analysis of a smaller, more physically similar sample of 15 exo-Neptune transmission spectra across a wide range of temperatures (200-1000 K). Using condensation cloud and hydrocarbon haze models, we find that the exo-Neptune population is best described by low cloud sedimentation efficiency ($\mathrm{f_{sed}}\sim0.1$) and high metallicity ($100\times$ Solar). There is an intrinsic scatter of $\sim0.5$ scale height, perhaps evidence of stochasticity in these planets' formation processes. Observers should expect significant attenuation in transmission spectra of Neptune-size exoplanets, up to 6 scale heights for equilibrium temperatures between 500 and 800 K. With JWST's greater wavelength sensitivity, colder (<500 K) planets should be high-priority targets given their clearer atmospheres, and the need to distinguish between the "super-puffs" and more typical gas-dominated planets.
description: Published in ApJL. 11 pages, 3 figures, 4 tables