cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
title: Antibody-Antigen Binding Affinity Prediction through the use of geometric deep learning
Creators: name: Traxler, Fabian
Publisher: name: TU Wien
Year: 2023
Subjects: subject: binding affinity prediction
subject: machine learning
subject: graph neural networks
subject: geometric deep learning
subject: transfer learning

description: Antibodies are an integral part of our body’s immune system due to their ability to trigger immune responses or render exogenous proteins ineffective. The mechanism of binding of antibodies has been studied thoroughly in order to select promising antibodies or even design new ones. Even though a variety of knowledge-primed methods (e.g. force fields) have been adopted for affinity prediction, the challenge of accurately predicting binding affinity between antibodies and antigens remains. In this thesis, we propose a purely data-driven approach to predict antibody-antigen binding affinity using geometric deep learning methods. Our research aims to evaluate the effectiveness of graph neural networks (GNN) and compare it to a state-of-the-art force field-based method. In order to achieve this, available crystallized antibody-antigen complexes are converted to graph structures and used to train GNN-based learning methods. In addition, given the scarce availability of training data for the antibody-antigen affinity prediction problem, we explore the potential of transfer learning to improve predictive performance (e.g. through the inclusion of general PPI complexes). The implementation of our designed GNN provides a PyTorch framework for generic binding affinity prediction using graph-like structures. The trained GNN outperforms the force field baseline on a diverse set of antibody-antigen complexes by showing robust results across low- and high-quality structures. The implemented transfer-learning techniques did not result in significant performance improvements, although numerous such techniques remain to be explored. The effectiveness of GNNs for affinity prediction and their end-to-end differentiability highlights their potential for studying the mechanisms of antibody binding. These properties further allow applications in the improvement and de novo design of experimental and therapeutic antibodies.
ANOTHER ARCHAEOLOGY IS POSSIBLE: ANARCHIST ARCHAEOLOGY AS DOING AND UNDOING
Creators: name: Schwandt, Zoe
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: Anarchist approaches to archaeological interpretation and practice remain relatively new in the discipline but demonstrate a rich area for further development and engagement. Rather than reflecting chaos, the use of an anarchist framework can disrupt implicit archaeological assumptions; enrich analytical discussions of the material record; and allow for effective collaborative approaches. Such frameworks are especially relevant for their ability to contribute to contemporary theoretical and methodological considerations in archaeology that are working towards the dismantling of harmful narratives and the imagining of alternative futures for archaeology. I argue that future directions in anarchist archaeology should be inspired by practices of mutual aid and direct action and engage in co-processes of dismantling and (re)building through archaeological practice.
MPEC 2023-O113 : 2006 OE10
Creators: name: Minor Planet Center Staff
Publisher: name: The Minor Planet Center
Year: 2023
Subjects: subject: Small Solar System bodies
valueUri: http://astrothesaurus.org/uat/1469

description: The Minor Planet Electronic Circulars contain information on unusual minor planets, routine data on comets and natural satellites, and occasional editorial announcements.  They are published on behalf of Division F of the International Astronomical Union by the Minor Planet Center, Smithsonian Astrophysical Observatory, Cambridge, MA 02138, U.S.A.
title:  Lo sfruttamento delle risorse minerarie e le trasformazioni dell’assetto insediativo nel territorio di Monterano tra tardo medioevo e prima età moderna
Creators: name: Romagnoli, Giuseppe
Publisher: name: Roma Tre University
publisherIdentifier: https://ror.org/05vf0dg29
publisherIdentifierScheme: ROR
Year: 2025

description: La lunghissima storia dell’abitato di Monterano, che si svolge ininterrottamente tra l’età arcaica e la fine del XVIII secolo, è strettamente legata alla presenza dei diversi giacimenti di minerali ferrosi e di zolfo presenti nell’area immediatamente circostante l’abitato. Il contributo prende in considerazione il rapporto tra le modalità di sfruttamento di queste risorse minerarie, le trasformazioni del paesaggio ed l’evoluzione dell’habitat tra il tardo medioevo e la prima età moderna.

The long history of Monterano, which runs continuously between the Archaic age and the end of the 18th century, is closely linked to the presence of the various iron ore and sulfur mines in the area  surrounding the settlement. The paper will examine the relationship between the modes of exploitation of these mineral resources, the transformations of the landscape and the evolution of the habitat between the late Middle Ages and the early modern age.
R symmetries and a heterotic MSSM
Creators: name: Kappl, Rolf
name: Nilles, Hans Peter
name: Schmitz, Matthias
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We employ powerful techniques based on Hilbert- and Groebner bases to analyze particle physics models derived from string theory. Individual models are shown to have a huge landscape of vacua that differ in their phenomenological properties. We explore the (discrete) symmetries of these vacua, the new R symmetry selection rules and their consequences for moduli stabilization.
description: 15 pages
Vision-Based Control of a Handheld Micromanipulator for Robot-Assisted Retinal Surgery
Creators: name: Becker, Brian C.
Publisher: name: Figshare
Year: 2018
Subjects: subject: 80101 Adaptive Agents and Intelligent Robotics
subject: FOS: Computer and information sciences

description: Surgeons increasingly need to perform complex operations on extremely small anatomy. Many existing and promising new surgeries are effective, but difficult or impossible to perform because humans lack the extraordinary control required at sub-millimeter scales. Using micromanipulators, surgeons gain higher positioning accuracy and additional dexterity as the instrument removes tremor and scales hand motions. While these aids are advantageous, they do not actively consider the goals or intentions of the operator and thus cannot provide context-specific behaviors, such as motion scaling around anatomical targets, prevention of unwanted contact with pre-defined tissue areas, compensation for moving anatomy, and other helpful task-dependent actions.
This thesis explores the fusion of visual information with micromanipulator control and enforces task-specific behaviors that respond in synergy with the surgeon’s intentions and motions throughout surgical procedures. By exploiting real-time microscope view observations, a-priori knowledge of surgical operations, and pre-operative data prepared before the surgery, we hypothesize that micromanipulators can employ individualized and targeted aids to further help the surgeon. Specifically, we propose a vision-based control framework of virtual fixtures for handheld micromanipulator robots that naturally incorporates tremor suppression and motion scaling. We develop real-time vision systems to track the surgeon and anatomy and design fast, new algorithms for analysis of the retina. Virtual fixtures constructed from visually tracked anatomy allows for complex task-specific behaviors that monitor the surgeon’s actions and react appropriately to cooperatively accomplish the procedure.
Particular focus is given to vitreoretinal surgery as a good choice for vision-based control because several new and promising surgical techniques in the eye depend on fine manipulations of tiny and delicate retinal structures. Experiments with Micron, the fully handheld micromanipulator developed in our lab, show that vision-based virtual fixtures significantly increase pointing precision by reducing positioning error during synthetic, but medically relevant hold-still and tracing tasks. To evaluate the proposed framework in realistic environments, we consider three demanding retinal procedures: membrane peeling, laser photocoagulation, and vessel cannulation. Preclinical trials on artificial phantoms, ex vivo, and in vivo animal models demonstrate that vision-based control of a micromanipulator significantly improves surgeon performance (p < 0.05).
Vision-Based Navigation for a Small Fixed-Wing Airplane in Urban Environment
Creators: name: Hwangbo, Myung
Publisher: name: Figshare
Year: 2018
Subjects: subject: 80101 Adaptive Agents and Intelligent Robotics
subject: FOS: Computer and information sciences

description: An urban operation of unmanned aerial vehicles (UAVs) demands a high level of autonomy for tasks presented in a cluttered environment. While fixed-wing UAVs are well suited for long-endurance missions at a high altitude, enabling them to navigate inside an urban area brings another level of challenges. Their inability to hover and low agility in motion cause more difficulties on finding a feasible path to move safely in a compact region, and the limited payload allows only low-grade sensors for state estimation and control.
We address the problem of achieving vision-based autonomous navigation for a small fixed-wing in an urban area with contributions to the following several key topics. Firstly, for robust attitude estimation during dynamic maneuvering, we take advantage of the line regularity in an urban scene, which features vertical and horizontal edges of man-made structures. The sensor fusion with gravity-related line segments and gyroscopes in a Kalman filter can provide driftless and realtime attitude for ight stabilization. Secondly, as a prerequisite to sensor fusion, we present a convenient self-calibration scheme based on the factorization method. Natural references such as gravity, vertical edges, and distant scene points, available in urban fields, are sufficient to find intrinsic and extrinsic parameters of inertial and vision sensors. Lastly, to generate a dynamically feasible motion plan, we propose a discrete planning method that encodes a path into interconnections of finite trim states, which allow a significant dimension reduction of a search space and result in naturally implementable paths integrated with ight controllers. The most probable path to reach a target is computed by the Markov Decision Process with motion uncertainty due to wind, and a minimum target observation time is imposed on the final motion plan to consider a camera's limited field-of-view.
In this thesis, the effectiveness of our vision-based navigation system is demonstrated by what we call an "air slalom" task in which the UAV must autonomously search and localize multiple gates, and pass through them sequentially. Experiment results with a 1m wing-span airplane show essential navigation capabilities demanded in urban operations such as maneuvering passageways between buildings.
Differences between semi-quantitative and quantitative approaches for probabilistic assessment of technological risks
Creators: name: Rosner, Elsa
name: Brissaud, Florent
name: Declerck, Bruno
name: Flauw, Yann
name: De Dianous, Valérie
Publisher: name: arXiv
Year: 2015
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics

description: The aim of this paper is to compare the probabilistic approach based on fault trees and event trees, to an approach called "semi-quantitative" as presented by the guide Omega 10 (INERIS, 2008), for the industrial risk management. A brief presentation of the ''classical'' probabilistic risk assessment as well as the ''semi-quantitative'' approach is proposed. Then, a case study is detailed to illustrate and compare their use. This case study focuses on a low pressure separator (water/gas/condensate) for which scenarios have been identified around the undesired event "gas leak due to overpressure in the separator.'' The system includes a control loop and the following safety barriers: an alarm with operator actions, a safety instrumented system, two safety relief valves, and a blast-proof partition. This case study therefore represents a relatively conventional system in the industry. Regarding to the implementation of the two approaches, the assessment according to the Omega 10 guide is easier and faster. In terms of results, differences can be observed, up to a factor 10.
description: in French
A New Model of Nonlocal Modified Gravity
Creators: name: Dimitrijevic, Ivan
name: Dragovich, Branko
name: Grujic, Jelena
name: Rakic, Zoran
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We consider a new modified gravity model with nonlocal term of the form $R^{-1} \mathcal{F}(\Box) R. $ This kind of nonlocality is motivated by investigation of applicability of a few unusual ansätze to obtain some exact cosmological solutions. In particular, we find attractive and useful quadratic ansatz $\Box R = q R^{2}.$
description: 11 pages
The Fundamental Signature of Star Formation Quenching from AGN Feedback: A Critical Dependence of Quiescence on Supermassive Black Hole Mass, Not Accretion Rate
Creators: name: Bluck, Asa FL
name: Piotrowska, Joanna M
name: Maiolino, Roberto
Publisher: name: Apollo - University of Cambridge Repository
Year: 2023
Subjects: 310
Galaxies and Cosmology

description: Abstract We identify the intrinsic dependence of star formation quenching on a variety of galactic and environmental parameters, utilizing a machine-learning approach with Random Forest classification. We have previously demonstrated the power of this technique to isolate causality, not mere correlation, in complex astronomical data. First, we analyze three cosmological hydrodynamical simulations (Eagle, Illustris, and IllustrisTNG), selecting snapshots spanning the bulk of cosmic history from comic noon (z ∼ 2) to the present epoch, with stellar masses in the range 9 < log ( M * / M ⊙ ) < 12 . In the simulations, black hole mass is unanimously found to be the most predictive parameter of central galaxy quenching at all epochs. Perhaps surprisingly, black hole accretion rate (and hence the bolometric luminosity of active galactic nuclei, AGN) is found to be of little predictive power over quenching. This theoretical result is important for observational studies of galaxy quenching, as it cautions against using the current AGN state of a galaxy as a useful proxy for the cumulative impact of AGN feedback on a galactic system. The latter is traced by black hole mass, not AGN luminosity. Additionally, we explore a subset of “observable” parameters, which can be readily measured in extant wide-field galaxy surveys targeting z = 0–2, at 9 < log ( M * / M ⊙ ) < 12 . All three simulations predict that, in lieu of black hole mass, the stellar gravitational potential will outperform the other parameters in predicting quenching. We confirm this theoretical prediction observationally in the SDSS (at low redshifts) and in CANDELS (at intermediate and high redshifts).
VPLACEMENT: Contention Aware Virtual Machine Placement System
Creators: name: Ankur Kumar Sharma
Publisher: name: Figshare
Year: 2018
Subjects: subject: 89999 Information and Computing Sciences not elsewhere classified
subject: FOS: Computer and information sciences

description: Maximizing the number of cohosted virtual machines (VMs) while still maintaining the desired performance level is a critical goal in cloud. As we pack more virtual machines on a physical machine (PM), the resource contention increases, thereby affecting the response time. This virtual machine placement problem has been vastly studied and most of effort has been in either allocating more resources to virtual machines (resizing) or migrating them to a higher capacity PM based on the resource demand estimation. Studies have also shown that in the presence of resource contention the resource demand estimation mechanisms could predict more resource requirement than actually needed. Hence deciding virtual machine placement and allocated resources based on utilization estimation could lead to inefficient usage of PM resources. We propose a novel approach to solve this problem which focuses on overall application response time rather than individual virtual machines. Large scale applications are deployed as multi-tier components. These components interact with each other so that application can perform its task. Our placement algorithm uses the dependency relationship between these components to understand application response time behavior. Our solution focuses on reducing the performance degradation because of resource contention. We propose a VM placement system termed as Vplacement. This system uses the traffic analysis to understand the dependency relationship between application components. This dependency relationship and traffic analysis provides some vital iii data like impact of component processing time on application response time, the probability of resource contention between a pair of component nodes (coArrival Probability) etc. The impact and coarrival probability is used by the placement engine of Vplacement to minimize the degradation of application performance because of resource contention by cohosting the low impact component nodes together.
Functional safety: matching the complexity of methods with the complexity of systems
Creators: name: Brissaud, F
name: Declerck, B
Publisher: name: arXiv
Year: 2015
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics

description: In line with the IEC 61508 functional safety standard, it is required to assess the safety integrity of a system due to random hardware failures. For a rarely used function (operating in a low demand mode), the measurement used is average probability of a dangerous failure on demand (PFDavg). In this paper, four methods have been applied to different configurations of a case study: failure tree analysis with the software GRIF/Tree, multi-phase Markov graphs with the software GRIF/Markov, stochastic Petri nets with predicates with the software GRIF/Petri, and approximate equations (developed by DNV and different from those given in the IEC 61508 standard) using the software OrbitSIL. It is shown that all these methods can lead to similar results for the estimating of the PFDavg, taking into account the required characteristics of the standard. The choice of method must be made without bias, based on an agreement between the modelling efforts, goals, and the system properties. To assist the analyst in this task, a discussion of the benefits and limitations of each of these methods is presented.
description: in French
Constructing homonationalist identities in relation to religious and LGBTQ+ outgroups: a case study of r/RightWingLGBT
Creators: name: Dickey, Briar
name: Spierings, Niels
name: van Klingeren, Marijn
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Science Policy

description: Recent research on homonationalism addresses the ideological and electoral combination of LGBTQ+ politics and radical-right populism. However, right-wing LGBTQ+ identities remain seemingly paradoxical, as right-wing Christianity-rooted conservatism is generally hostile to LGBTQ+ empowerment. Grounded in literature on populist radical right and its relationship with religion and sexuality, as well as social identity theory, we argue that right-wing LGBTQ+ people resolve identity tension by creating a positive group image. Analysing over 2,500 posts on a prominent (new/alt/populist) right-wing LGBTQ+ Reddit community, r/RightWingLGBT, we found right-wing LGBTQ+ users maintain a positive self-identity by positioning themselves against ‘degenerate, liberal, non-binary queers’, thus limiting themselves to narrow iterations of acceptable queerness which are congruent with hetero- and cis-normativity. Islam replaces Christianity as the primary anti-LGBTQ+ outgroup, which, alongside a normalisation and naturalisation of religious-rooted moral selves, helps to reconcile LGBTQ+ identities and right-wing populism and establish homonationalism as a bottom-up phenomenon.
Additional file 1 of A synthesis of recent tools and perspectives in migratory connectivity studies
Creators: name: Gregory, Killian A.
name: Francesiaz, Charlotte
name: Jiguet, Frédéric
name: Besnard, Aurélien
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer

description: Additional file 1. Filtering of publications from the Web of Science: methodology for searching and analysing the Web of Science database for what concerns migratory connectivity studies.
Additional file 1 of Multi-tissue epigenetic analysis identifies distinct associations underlying insulin resistance and Alzheimer’s disease at CPT1A locus
Creators: name: Sarnowski, Chloé
name: Huan, Tianxiao
name: Ma, Yiyi
name: Joehanes, Roby
name: Beiser, Alexa
name: DeCarli, Charles S.
name: Heard-Costa, Nancy L.
name: Levy, Daniel
name: Lin, Honghuang
name: Liu, Ching-Ti
name: Liu, Chunyu
name: Meigs, James B.
name: Satizabal, Claudia L.
name: Florez, Jose C.
name: Hivert, Marie-France
name: Dupuis, Josée
name: De Jager, Philip L.
name: Bennett, David A.
name: Seshadri, Sudha
name: Morrison, Alanna C.
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1. Supplementary Materials including additional Text, Figures and Tables.
Mid-Infrared spectroscopy of impactites from the Noerdlinger Ries impact crater
Creators: name: Morlok, A.
name: Stojic, A. N.
name: Dittmar, I.
name: Hiesinger, H.
name: Tiedeken, M.
name: Sohn, M.
name: Weber, I.
name: Helbert, J.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Geophysics (physics.geo-ph)
subject: FOS: Physical sciences

description: This study is part of an effort to build a mid-infrared database (7-14micron) of spectra for MERTIS (Mercury Radiometer and Thermal Infrared Spectrometer), an instrument onboard of the ESA/JAXA BepiColombo space probe to be launched to Mercury in 2017. Mercury was exposed to abundant impacts throughout its history. This study of terrestrial impactites can provide estimates of the effects of shock metamorphism on the mid-infrared spectral properties of planetary materials. In this study, we focus on the Noerdlinger Ries crater in Southern Germany, a well preserved and easily accessible impact crater with abundant suevite impactites. Suevite and melt glass bulk samples from Otting and Aumuehle, as well as red suevite from Polsingen were characterized and their reflectance spectra in mid-infrared range obtained. In addition, in-situ mid-infrared spectra were made from glasses and matrix areas in thin sections. The results show similar, but distinguishable spectra for both bulk suevite and melt glass samples, as well as in-situ measurements. Impact melt glass from Aumuehle and Otting have spectra dominated by a Reststrahlen band at 9.3-9.6 micron. Bulk melt rock from Polsingen and bulk suevite and fine-grained matrix have their strongest band between 9.4 to 9.6 micron. There are also features between 8.5 and 9 micron, and 12.5 - 12.8 micron associated with crystalline phases. There is evidence of weathering products in the fine-grained matrix, such as smectites. Mercury endured many impacts with impactors of all sizes over its history. So spectral characteristics observed for impactites formed only in a single impact like in the Ries impact event can be expected to be very common on planetary bodies exposed to many more impacts in their past. We conclude that in mid-infrared remote sensing data the surface of Mercury can be expected to be dominated by features of amorphous materials.
Variability in the phytoplankton response to upwelling across the iron limitation mosaic within the California Current System
Creators: name: Lin, YuanYu
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: Coastal upwelling currents such as the California Current System (CCS) provide for some of the most productive biological systems in the world. The seasonality and topography of these regions dictate the intensity of upwelling and entrainment of nutrients, providing for photosynthetic growth by autotrophic plankton that not only cascades up the marine food chain, but also initiates carbon export and sequestration. Diatoms, a distinct taxon of the very phytoplankton functional groups that lie at the base of this food chain, dominate these upwelling events using a “shift-up” response to nitrate entrainment, where they constitutively maintain an elevated pool of nitrogen transport and assimilation genes even before upwelling events occur. And despite the abundance of macronutrients found within the CCS, phytoplankton are often limited by the micronutrient iron, an important trace element involved in photosynthesis and nitrogen assimilation. The mechanisms behind how these phytoplankton – the basis of the marine food web – acclimate to the different stages of the upwelling conveyor belt cycle (UCBC) with respect to iron limitation remains largely uncharacterized. Adding to this complexity is the knowledge that iron bioavailability heavily influences phytoplankton growth dynamics and elemental stoichiometry in this region, and climate change is projected to alter the availability of iron in many parts of the CCS. This project explores the phytoplankton response to the iron limitation mosaic within the CCS, where varying degrees of iron limitation along the California coast may have significant influences on phytoplankton community structure with respect to the UCBC. Samples were collected in situ during a 2019 field incubation experiment conducted on the research vessel R/V Oceanus off the coasts of Oregon and California. Physiological measurements and meta-transcriptomic analysis indicate that iron limitation was not initially evident at either incubation site, but induced iron limitation during the incubations caused noticeable physiological and differential gene expression changes within the phytoplankton taxa, especially in diatoms. This may have significant implications for upwelling events in future oceans, where ocean acidification is projected to decrease the bioavailability of iron in coastal upwelling regions. The onset of climate change and its many complexities could drastically alter phytoplankton community composition in future coastal oceans, and likewise play a significant role in shaping the seed populations that are so vital to the marine ecosystem processes in the CCS.
Additional file 2 of Meningioma animal models: a systematic review and meta-analysis
Creators: name: Andersen, Mikkel Schou
name: Kofoed, Mikkel Seremet
name: Paludan-Müller, Asger Sand
name: Pedersen, Christian Bonde
name: Mathiesen, Tiit
name: Mawrin, Christian
name: Wirenfeldt, Martin
name: Kristensen, Bjarne Winther
name: Olsen, Birgitte Brinkmann
name: Halle, Bo
name: Poulsen, Frantz Rom
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: Additional file 2: The PRISMA abstract checklist.
How the Higgs potential got its shape
Creators: name: Mund, Jens
name: Karl-Henning, Rehren
name: Schroer, Bert
Publisher: name: Freie Universität Berlin
Year: 2023
Subjects: subject: quantum field theory
subject: massive vector boson
subject: scalar field
subject: 500 Naturwissenschaften und Mathematik::530 Physik::530 Physik

description: String-localized quantum field theory allows renormalizable couplings involving massive vector bosons, without invoking negative-norm states and compensating ghosts. We analyze the most general coupling of a massive vector boson to a scalar field, and find that the scalar field necessarily comes with a quartic potential which has the precise shape of the shifted Higgs potential. In other words: the shape of the Higgs potential has not to be assumed, but arises as a consistency condition among fundamental principles of QFT: Hilbert space, causality, and covariance. The consistency can be achieved by relaxing the localization properties of auxiliary quantities, including interacting charged fields, while observable fields and the S-matrix are not affected. This is an instance of the “L-V formalism” – a novel model-independent scheme that can be used as a tool to “renormalize the non-renormalizable” by adding a total derivative to the interaction.
Handheld Micromanipulator for Robot - Assisted Microsurgery
Creators: name: Sungwook  Yang
Publisher: name: Figshare
Year: 2018
Subjects: subject: 80101 Adaptive Agents and Intelligent Robotics
subject: FOS: Computer and information sciences

description: Robot-assisted surgery has been increasingly adopted in a wide variety of surgical applications because it offers fine manipulation with high precision and dexterity. Despite the commercial success of robotic platforms, practical use in microsurgery is still challenging due to a considerable level of accuracy required at sub-millimeter scales. Limited visualization and constrained accessibility also hinder operation under operating microscopes. Furthermore, lack of tactile feedback may lead to substantial and even irrecoverable injury. To address these issues in microsurgery, a handheld micromanipulator, Micron, has been introduced as an alternative to conventional robotic platforms. It allows surgeons to directly maneuver surgical tools, while selectively filtering out erroneous motion such as hand tremor. Thus, surgeons can attain the natural feel of manual operation and also direct tactile feedback from the tool attached to Micron. However, the existing Micron still entails several drawbacks in terms of the lack of degrees of freedom, limited range of motion, and ergonomically undesirable design. This thesis presents a new design of the handheld micromanipulator and also explores automated microsurgery in conjunction with image-guidance. For the design of a miniature 6-DOF manipulator, a new optimization framework is introduced, resulting in the optimal dimension of the manipulator given the limited force capability of the miniature actuators used. Given the 6-DOF manipulation, the new platform allows the possibility of imposing a remote center of motion (RCM) for controlling an end-effector, which is generally required in most of minimally invasive surgery. Moreover, the new manipulator attains an order-of-magnitude increase in the range of motion so that it enables automated operations for intraocular OCT scanning and laser photocoagulation. We experimentally verify the design of the 6-DOF Micron and also evaluate its handheld performance under various conditions, which shows significant reduction of hand tremor. In addition, the 6-DOF Micron is utilized to improve the quality of handheld OCT imaging and obtain multi-dimensional structures from single-fiber OCT scanning. The goal of this thesis is to accomplish automated subtasks in microsurgery using the newly developed handheld micromanipulator and image-guidance in realistic environments. Initial work demonstrates the feasibility of automated intraocular laser photocoagulation using position-based visual servoing, while compensating the eye movement. To realize automated surgery in an intact eye, we propose a monocular hybrid visual servoing scheme, incorporating cone beam reconstruction for surface estimation, partitioned visual servoing control, and adaptive frameworks in control. These approaches are validated through experiments with the eye phantom in vitro and porcine eyes ex vivo.
Understanding the competing pathways leading to hydropyrene and isoelisabethatriene
Creators: name: Zev, Shani
name: Ringel, Marion
name: Driller, Ronja
name: Loll, Bernhard
name: Bruck, Thomas
name: Major, Dan T.
Publisher: name: Freie Universität Berlin
Year: 2023
Subjects: subject: diterpenes
subject: enzyme mechanism
subject: quantum mechanics
subject: terpene synthases
subject: thermodynamic and kinetic control
subject: 500 Naturwissenschaften und Mathematik::540 Chemie::540 Chemie und zugeordnete Wissenschaften

description: Terpene synthases are responsible for the biosynthesis of terpenes, the largest family of natural products. Hydropyrene synthase generates hydropyrene and hydropyrenol as its main products along with two byproducts, isoelisabethatrienes A and B. Fascinatingly, a single active site mutation (M75L) diverts the product distribution towards isoelisabethatrienes A and B. In the current work, we study the competing pathways leading to these products using quantum chemical calculations in the gas phase. We show that there is a great thermodynamic preference for hydropyrene and hydropyrenol formation, and hence most likely in the synthesis of the isoelisabethatriene products kinetic control is at play.
String Field Theory -- A Modern Introduction
Creators: name: Erbin, Harold
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: This book provides an introduction to string field theory (SFT). String theory is usually formulated in the worldsheet formalism, which describes a single string (first-quantization). While this approach is intuitive and could be pushed far due to the exceptional properties of two-dimensional theories, it becomes cumbersome for some questions or even fails at a more fundamental level. These motivations have led to the development of SFT, a description of string theory using the field theory formalism (second-quantization). As a field theory, SFT provides a rigorous and constructive formulation of string theory. The main objective is to construct the closed bosonic SFT and to explain how to assess the consistency of string theory with it. The accent is put on providing the reader with the foundations, conceptual understanding and intuition of what SFT is. After reading this book, they should be able to study the applications from the literature. The book is organized in two parts. The first part reviews the topics of the worldsheet theory that are necessary to build SFT (worldsheet path integral, CFT and BRST quantization). The second part starts by introducing general concepts of SFT from the BRST quantization. Then, it introduces off-shell string amplitudes before providing a Feynman diagrams interpretation from which the building blocks of SFT are extracted. After constructing the closed SFT, it is used to outline the proofs of several important consistency properties, such as background independence, unitarity and crossing symmetry. Finally, the generalization to the superstring is also discussed. This book grew up from lecture notes for a course given at the Ludwig-Maximilians-Universität LMU (winter semesters 2017-2018 and 2018-2019). The current document is the draft of the manuscript published by Springer.
description: This is a preprint of the following textbook: String Field Theory: A Modern Introduction, authored by Dr. Harold Erbin, 2021, Springer reproduced with permission of Springer. The final authenticated version is available online at: https://doi.org/10.1007/978-3-030-65321-7. 318 pages
Evidence for an Anhydrous Carbonaceous Extrasolar Minor Planet
Creators: name: Jura, M.
name: Dufour, P.
name: Xu, S.
name: Zuckerman, B.
name: Klein, B.
name: Young, E. D.
name: Melis, C.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: Using Keck/HIRES, we report abundances of 11 different elements heavier than helium in the spectrum of Ton 345, a white dwarf that has accreted one of its own minor planets. This particular extrasolar planetesimal which was at least 60% as massive as Vesta appears to have been carbon-rich and water-poor; we suggest it was compositionally similar to those Kuiper Belt Objects with relatively little ice.
description: ApJ, accepted
Balance training to reduce visual reliance: A pilot study
Creators: name: Heckard, Grace
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: 16 participants participated in a 4 week (12 session) balance training protocol. Pre and post-testing used a gait assessment to examine margin of stability and center of pressure. Senaptec sensory station was used to examine the relationship between variables of interest and visual skills. 4 groups were distinguished by stable and unstable surfaces and eyes open and eyes closed. There was no relationship between variables of interest and surface type or visual condition.
Honey bees infer source location from the dances of returning foragers
Creators: name: Wang, Zhengwei
name: Chen, Xiuxian
name: Becker, Frank
name: Greggers, Uwe
name: Walter, Stefan
name: Werner, Marleen
name: Gallistel, Charles R.
name: Menzel, Randolf
Publisher: name: Freie Universität Berlin
Year: 2023
Subjects: subject: Apis mellifera
subject: waggle dance
subject: landmark guidance
subject: cognitive map
subject: vector communication
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie

description: Honeybees (Apis mellifera carnica) communicate the direction and distance to a food source by means of a waggle dance. We ask whether bees recruited by the dance use it only as a flying instruction, with the technical form of a polar vector, or also translate it into a location vector that enables them to set courses directed toward the food source from arbitrary locations within their familiar territory. The flights of recruits captured on exiting the hive and released at distant sites were tracked by radar. The recruits performed first a straight flight in approximately the compass direction indicated by the dance. However, this “vector” portion of their flights and the ensuing tortuous “search” portion were strongly and differentially affected by the release site. Searches were biased toward the true location of the food and away from the location specified by translating the origin for the danced polar vector to the release site. We conclude that by following the dance recruits get two messages, a polar flying instruction (bearing and range from the hive) and a location vector that enables them to approach the source from anywhere in their familiar territory. The dance communication is much richer than thought so far.
Additional file 5 of Meningioma animal models: a systematic review and meta-analysis
Creators: name: Andersen, Mikkel Schou
name: Kofoed, Mikkel Seremet
name: Paludan-Müller, Asger Sand
name: Pedersen, Christian Bonde
name: Mathiesen, Tiit
name: Mawrin, Christian
name: Wirenfeldt, Martin
name: Kristensen, Bjarne Winther
name: Olsen, Birgitte Brinkmann
name: Halle, Bo
name: Poulsen, Frantz Rom
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: Additional file 5: Full original search strategy.
Numerical studies of various Neel-VBS transitions in SU(N) anti-ferromagnets
Creators: name: Kaul, Ribhu K.
name: Block, Matthew
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: In this manuscript we review recent developments in the numerical simulations of bipartite SU(N) spin models by quantum Monte Carlo (QMC) methods. We provide an account of a large family of newly discovered sign-problem free spin models which can be simulated in their ground states on large lattices, containing O(10^5) spins, using the stochastic series expansion method with efficient loop algorithms. One of the most important applications so far of these Hamiltonians are to unbiased studies of quantum criticality between Neel and valence bond phases in two dimensions -- a summary of this body of work is provided. The article concludes with an overview of the current status of and outlook for future studies of the "designer" Hamiltonians.
description: Mini-review article for the proceedings of CCP 2014 (Boston)
Re-evaluation of Apollo 17 Lunar Seismic Profiling Experiment data
Creators: name: Heffels, Alexandra
name: Knapmeyer, Martin
name: Oberst, Jürgen
name: Haase, Isabel
Publisher: name: Technische Universität Berlin
Year: 2016
Subjects: subject: 620 Ingenieurwissenschaften und zugeordnete Tätigkeiten
subject: Apollo 17
subject: seismic data
subject: velocity-depth profile
subject: Lunar Reconnaissance Orbiter
subject: 3-D positions
subject: lunar module

description: We re-analyzed Apollo 17 Lunar Seismic Profiling Experiment (LSPE) data to improve our knowledge of the subsurface structure of this landing site. We use new geometrically accurate 3-D positions of the seismic equipment deployed by the astronauts, which were previously derived using high-resolution images by Lunar Reconnaissance Orbiter (LRO) in combination with Apollo astronaut photography. These include coordinates of six Explosive Packages (EPs) and four geophone stations. Re-identified P-wave arrival times are used to calculate two- and three-layer seismic velocity models. A strong increase of seismic velocity with depth can be confirmed, in particular, we suggest a more drastic increase than previously thought. For the three-layer model the P-wave velocities were calculated to 285, 580, and 1825 m/s for the uppermost, second, and third layer, respectively, with the boundaries between the layers being at 96 and 773 m depth. When compared with results obtained with previously published coordinates, we find (1) a slightly higher velocity (+4%) for the uppermost layer, and (2) lower P-wave velocities for the second and third layers, representing a decrease of 34% and 12% for second and third layer, respectively. Using P-wave arrival time readings of previous studies, we confirm that velocities increase when changing over from old to new coordinates. In the three-layer case, this means using new coordinates alone leads to thinned layers, velocities rise slightly for the uppermost layer and decrease significantly for the layers below.
Minimizing execution time of artificial neural networks on resource-restricted devices
Creators: name: Rockschies, Marius
Publisher: name: TUHH Universitätsbibliothek
Year: 2019
Subjects: classificationCode: 004
subject: Computer Sciences
classificationCode: 620
subject: Engineering and Applied Operations

description: Artificial Neural Networks are a key technology in today’s area of machine learning. They impact various parts in our lives and are therefore important in many ways. Compressing Artificial Neural Networks, in particular the weight matrices, by slightly manipulating them, while maintaining accuracy has been studied in recent research. One of the most promising methods called Deep Compression achieved remarkable compression rates. The reduction in size by Deep Compression should also be beneficial for the execution time. In this work, the benefit was studied with the objective of reducing the execution time on resource-restricted hardware. Furthermore, the benefit of simpler fixed-point arithmetic was investigated in this context. Based on deeper insights and practical evaluations of Deep Compression, this work gives an assessment and guidance towards a minimum execution time of Artificial Neural Networks.
Implementation of hyperbolic complex numbers in Julia language
Creators: name: Korolkova, Anna V.
name: Gevorkyan, Migran N.
name: Kulyabov, Dmitry S.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Mathematical Software (cs.MS)
subject: FOS: Computer and information sciences

description: Background: Hyperbolic complex numbers are used in the description of hyperbolic spaces. One of the well-known examples of such spaces is the Minkowski space, which plays a leading role in the problems of the special theory of relativity and electrodynamics. However, such numbers are not very common in different programming languages. Purpose: Of interest is the implementation of hyperbolic complex in scientific programming languages, in particular, in the Julia language. Methods: The Julia language is based on the concept of multiple dispatch. This concept is an extension of the concept of polymorphism for object-oriented programming languages. To implement hyperbolic complex numbers, the multiple dispatching approach of the Julia language was used. Results: The result is a library that implements hyperbolic numbers. Conclusions: Based on the results of the study, we can conclude that the concept of multiple dispatching in scientific programming languages is convenient and natural.
description: in English; in Russian
An Unfolding Method for X-ray Spectro-Polarimetry
Creators: name: Kislat, Fabian
name: Beilicke, Matthias
name: Guo, Qingzhen
name: Zajczyk, Anna
name: Krawczynski, Henric
Publisher: name: arXiv
Year: 2014
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: X-ray polarimetry has great scientific potential and new experiments, such as X-Calibur, PoGOLite, XIPE, and GEMS, will not only be orders of magnitude more sensitive than previous missions, but also provide the capability to measure polarization over a wide energy range. However, the measured spectra depend on the collection area, detector responses, and, in case of balloon-borne experiments, the absorption of X-rays in the atmosphere, all of which are energy dependent. Combined with the typically steep source spectra, this leads to significant biases that need to be taken into account to correctly reconstruct energy-resolved polarization properties. In this paper, we present a method based on an iterative unfolding algorithm that makes it possible to simultaneously reconstruct the energy spectrum and the polarization properties as a function of true photon energy. We apply the method to a simulated X-Calibur data set and show that it is able to recover both the energy spectrum and the energy-dependent polarization fraction.
description: 12 pages, 7 figures, accepted for publication in Astropart. Phys
A complete survey of texture zeros in general and symmetric quark mass matrices
Creators: name: Ludl, Patrick Otto
name: Grimus, Walter
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We perform a systematic analysis of all possible texture zeros in general and symmetric quark mass matrices. Using the values of masses and mixing parameters at the electroweak scale, we identify for both cases the maximally restrictive viable textures. Furthermore, we investigate the predictive power of these textures by applying a numerical predictivity measure recently defined by us. With this measure we find no predictive textures among the viable general quark mass matrices, while in the case of symmetric quark mass matrices most of the 15 maximally restrictive textures are predictive with respect to one or more light quark masses.
description: 11 pages, no figures