cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Clonality in Kaposi's sarcoma
Creators: name: Diaz-Cano, Salvador J.
name: H J Wolfe
Publisher: name: figshare
Year: 2012
Subjects: Molecular Biology
Medicine
Cancer

description: The paper addresses the topic of the clonal origin of neoplasms that frequently present as multiple lesions, such as Kaposi's sarcoma in patients with human immunodeficiency virus infection. The authors used a statistical analysis that showed the low likelihood that their findings would occur by chance. We suggest caution in the interpretation of these calculations because of the skewing of X-chromosome methylation in different tissues. Synchronic or metachronic tumors can be shown to be truly monoclonal (derived from the same clone) only if several molecular markers are concordant. An analysis of X-chromosome inactivation cannot distinguish metastatic tumors (arising from a single clone) from synchronic tumors arising from different clones but expressing the same inactivated X chromosome. The results obtained by analyzing a single molecular marker prove clonal expansion of a subgroup of tumor cells with proliferative advantages, but they do not prove actual clonality, especially when the assay is based on patterns of methylation that may be influenced by the functional status of the cell, tumor progression, or both.
Thomas Psota: Waldgeister und Reisseelen. Die Revitalisierung von Ritualen zur Erhaltung der komplementaren Produktion in Südwest- Sumatra
Creators: name: Graf, Arndt
Publisher: name: ASIEN: The German Journal on Contemporary Asia
Year: 2021

description: ASIEN: The German Journal on Contemporary Asia, Nr. 73 (1999): ASIEN (Oktober)
Unidirectional spin wave emission by travelling pair of magnetic field profiles
Creators: name: Philippe, Gauthier
name: Moalic, Mathieu
name: Kłos, Jarosław W.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We demonstrate that the spin wave Cherenkov effect can be used to design the unidirectional spin wave emitter with tunable frequency and switchable direction of emission. In our numerical studies, we propose to use a pair of traveling profiles of the magnetic field which generate the spin waves, for sufficiently large velocity of their motion. In the considered system, the spin waves of shorter (longer) wavelengths are induced at the front (back) of the moving profiles and interfere constructively or destructively, depending on the velocity of the profiles. Moreover, we showed that the spin waves can be confined between the pair of traveling profiles of the magnetic field. This work opens the perspectives for the experimental studies in hybrid magnonic-superconducting systems where the magnetic vortices in a superconductor can be used as moving sources of the magnetic field driving the spin waves in the ferromagnetic subsystem.
description: 4 pages, 3 figures
Increased beta-catenin protein and somatic APC mutations in sporadic aggressive fibromatoses (desmoid tumors)
Creators: name: Diaz-Cano, Salvador J.
name: B A Alman
name: C Li
name: H J Wolfe
name: M E Pajerski
Publisher: name: figshare
Year: 2012
Subjects: subject: Molecular Biology
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Cell Biology
subject: Cancer

description: Sporadic aggressive fibromatosis (also called desmoid tumor) is a monoclonal proliferation of spindle (fibrocyte-like) cells that is locally invasive but does not metastasize. A similarity to abdominal fibromatoses (desmoids) in familial adenomatous polyposis and a cytogenetic study showing partial deletion of 5q in a subset of aggressive fibromatoses suggests that the adenomatous polyposis coli (APC) gene plays a role in its pathogenesis. APC helps regulate the cellular level of beta-catenin, which is a downstream mediator in Wnt (Wingless) signaling. beta-Catenin has a nuclear function (binds transcription factors) and a cell membrane function (is a component of epithelial cell adherens junctions). Six cases of aggressive fibromatosis of the extremities from patients without familial adenomatous polyposis, or a family history of colon cancer, were studied. Immunohistochemistry, using carboxy and amino terminus antibodies to APC, and DNA sequencing showed that three of the six contained an APC-truncating mutation, whereas normal tissues did not contain a mutation. Western blot and Northern dot blot showed that all six tumors had a higher level of beta-catenin protein than surrounding normal tissues, despite containing similar levels of beta-catenin mRNA. Immunohistochemistry localized beta-catenin throughout the cell in tumor tissues, although it localized more to the periphery in cells from normal tissues. Reverse transcription polymerase chain reaction showed that the tumors expressed N-cadherin but not E-cadherin (a pattern of expression of proteins making up adherens junctions similar to fibrocytes), suggesting that the specific adherens junctions present in epithelial cells are not necessary for beta-catenin function. Increased beta-catenin may cause the growth advantage of cells in this tumor through a nuclear mechanism. The increased protein level, relative to the RNA level, suggests that beta-catenin is degraded at a lower rate compared with normal tissues. In some cases, this is caused by a somatic mutation resulting in a truncated APC protein.
Investigating and Improving Latent Density Segmentation Models for Aleatoric Uncertainty Quantification in Medical Imaging
Creators: name: Valiuddin, M. M. Amaan
name: Viviers, Christiaan G. A.
name: van Sloun, Ruud J. G.
name: de With, Peter H. N.
name: van der Sommen, Fons
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Data uncertainties, such as sensor noise, occlusions or limitations in the acquisition method can introduce irreducible ambiguities in images, which result in varying, yet plausible, semantic hypotheses. In Machine Learning, this ambiguity is commonly referred to as aleatoric uncertainty. In image segmentation, latent density models can be utilized to address this problem. The most popular approach is the Probabilistic U-Net (PU-Net), which uses latent Normal densities to optimize the conditional data log-likelihood Evidence Lower Bound. In this work, we demonstrate that the PU-Net latent space is severely sparse and heavily under-utilized. To address this, we introduce mutual information maximization and entropy-regularized Sinkhorn Divergence in the latent space to promote homogeneity across all latent dimensions, effectively improving gradient-descent updates and latent space informativeness. Our results show that by applying this on public datasets of various clinical segmentation problems, our proposed methodology receives up to 11% performance gains compared against preceding latent variable models for probabilistic segmentation on the Hungarian-Matched Intersection over Union. The results indicate that encouraging a homogeneous latent space significantly improves latent density modeling for medical image segmentation.
Application-Oriented Benchmarking of Quantum Generative Learning Using QUARK
Creators: name: Kiwit, Florian J.
name: Marso, Marwa
name: Ross, Philipp
name: Riofrío, Carlos A.
name: Klepsch, Johannes
name: Luckow, Andre
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: Machine Learning (cs.LG)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences
subject: C.4
subject: 81-04

description: Benchmarking of quantum machine learning (QML) algorithms is challenging due to the complexity and variability of QML systems, e.g., regarding model ansatzes, data sets, training techniques, and hyper-parameters selection. The QUantum computing Application benchmaRK (QUARK) framework simplifies and standardizes benchmarking studies for quantum computing applications. Here, we propose several extensions of QUARK to include the ability to evaluate the training and deployment of quantum generative models. We describe the updated software architecture and illustrate its flexibility through several example applications: (1) We trained different quantum generative models using several circuit ansatzes, data sets, and data transformations. (2) We evaluated our models on GPU and real quantum hardware. (3) We assessed the generalization capabilities of our generative models using a broad set of metrics that capture, e.g., the novelty and validity of the generated data.
description: 10 pages, 10 figures
Herbert und Mariana Röttgen (Pseudonyme: Victor und Victoria Trimondi): Der Schatten des Dalai Lama: Sexualität, Magie und Politik im tibetischen Buddhismus
Creators: name: Bayer, Achim
Publisher: name: ASIEN: The German Journal on Contemporary Asia
Year: 2021

description: ASIEN: The German Journal on Contemporary Asia, Nr. 73 (1999): ASIEN (Oktober)
Interactive Multi Interest Process Pattern Discovery
Creators: name: Vazifehdoostirani, Mozhgan
name: Genga, Laura
name: Lu, Xixi
name: Verhoeven, Rob
name: van Laarhoven, Hanneke
name: Dijkman, Remco
Publisher: name: arXiv
Year: 2023
Subjects: subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: Process pattern discovery methods (PPDMs) aim at identifying patterns of interest to users. Existing PPDMs typically are unsupervised and focus on a single dimension of interest, such as discovering frequent patterns. We present an interactive multi interest driven framework for process pattern discovery aimed at identifying patterns that are optimal according to a multi-dimensional analysis goal. The proposed approach is iterative and interactive, thus taking experts knowledge into account during the discovery process. The paper focuses on a concrete analysis goal, i.e., deriving process patterns that affect the process outcome. We evaluate the approach on real world event logs in both interactive and fully automated settings. The approach extracted meaningful patterns validated by expert knowledge in the interactive setting. Patterns extracted in the automated settings consistently led to prediction performance comparable to or better than patterns derived considering single interest dimensions without requiring user defined thresholds.
description: 16 pages, 5 figures, To appear in the preceedings of 21st International Conference on Business Process Management (BPM), 11-15 September 2023, Utrecht, the Netherlands
Excavations at North Elmham, 1967-8: an interim report
Creators: name: Wade-Martins, Peter
Publisher: name: Archaeology Data Service
Year: 2020

description: Norfolk Archaeology, 34 (4), 352-397
description: Of all the sites of Anglo-Saxon sees, North Elmham may offer one of the best opportunities for excavation of preconquest structures. An outline of the history of the East Anglian diocese is followed by discussion of some of the problems, caused by the ambiguity of the documentary evidence, which archaeology may help to solve. A summary of recent discoveries in the North Elmham area (eg RB, pagan, and mid-Saxon material) which have shed new light on the origins and early development of North Elmham, forms an introduction to a discussion of the village itself. The plan of medieval Elmham, which differs somewhat from the modern one, is considered and the structures so far found in the park excavations near the cathedral are described. The buildings recovered (provisionally dated to mid- and Late Saxon periods) are notably varied in plan and construction. Plans for future work are outlined. Au(adp)
Von virtuellen Bibliotheken und Datenbanken - weitere einführende Bemerkungen zum Nutzen des Internets für Südostasienstudien
Creators: name: Wischermann, Jörg
name: Sander, Ingvar
Publisher: name: ASIEN: The German Journal on Contemporary Asia
Year: 2021

description: --
description: ASIEN: The German Journal on Contemporary Asia, Nr. 73 (1999): ASIEN (Oktober)
The importance of forest floor connectivity on saproxylic arthropod succession in a lowland tropical rainforest.
Creators: name: Sharpe, Izzy
Publisher: name: Lancaster University
Year: 2024

description: Tropical saproxylic arthropods form a high proportion of diversity on
 earth yet are significantly understudied compared to their temperate
 counterparts. Litter provides habitat space, a stable microclimate and
 nutrients for arthropods. However, the influence of the forest floor on
 saproxylic arthropods remains relatively unknown. This study investigates
 the effects of longterm litter removal and its interactions with tree-size
 (diameter at breast height (DBH), wood

 density and deadwood age on saproxylic arthropods in a neotropical forest.
 Complementary sampling methods, namely emergence traps and wood samples
 were used to collect arthropods from deadwood. In wood samples, arthropod
 abundance and richness increased with deadwood age in control plots and
 declined in litter removal plots. Furthermore, community composition
 showed a clear trajectory in the control plots that was disrupted by

 litter removal. This suggests that forest floor connectivity is important
 for saproxylic succession with isolated deadwood fragments acting as
 refuges between the hostile bare soil. Wood density and DBH did not
 influence arthropod succession. Non-significant findings for emergence
 traps are attributed to the collection of flying taxa, which are less
 susceptible to

 the challenges posed by the bare soil in the litter removal plots.
 Comparison with the results of a previous studies on soil and litter fauna
 in the same litter manipulation experiment found distinct communities
 between habitats: a high proportion of fauna were forest floor
 generalists, some were specialists of a particular habitat, and others
 appeared to migrate between. I conclude that forest floor connectivity
 plays a vital role in the succession of arthropods in deadwood.
Performance of Rotation-Symmetric Bosonic Codes in a Quantum Repeater Network
Creators: name: Li, Pei-Zhe
name: Dias, Josephine
name: Munro, William J.
name: van Loock, Peter
name: Nemoto, Kae
name: Piparo, Nicoló Lo
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum error correction codes based on continuous variables play an important role for the implementation of quantum communication systems. A natural application of such codes occurs within quantum repeater systems which are used to combat severe channel losses and local gate errors. In particular, channel loss drastically reduces the distance of communication between remote users. Here we consider a cavity-QED based repeater scheme to address the losses in the quantum channel. This repeater scheme relies on the transmission of a specific class of rotationally invariant error-correcting codes. We compare several rotation-symmetric bosonic codes (RSBCs) being used to encode the initial states of two remote users connected by a quantum repeater network against the convention of the cat codes and we quantify the performance of the system using the secret key rate. In particular, we determine the number of stations required to exchange a secret key over a fixed distance and establish the resource overhead.
description: 10 pages, 7 figures
Model weights (RoBERTa-eval) for ACL 2020 paper "Designing Precise and Robust Dialogue Evaluators"
Creators: name: Zhao, Tianyu
Publisher: name: Zenodo
Year: 2020
Subjects: dialogue, evaluation, natural language processing

description: Model weights (RoBERTa-eval) for ACL 2020 paper "Designing Precise and Robust Dialogue Evaluators"
Use of Benzodiazepines in BC : Is it consistent with recommendations?
Creators: name: Therapeutics Initiative (University Of British Columbia)
Publisher: name: The University of British Columbia
Year: 2023

description: Therapeutics Letter 54 considers whether the use of benzodiazepines in British Columbia (BC), Canada is consistent with recommendations. Conclusions: The pattern of utilization of benzos in BC appears inconsistent with the recommendations of educational groups, regulators and manufacturers: Approximately 170,000 people are receiving amounts incompatible with short-term or intermittent use. The two groups most vulnerable to adverse effects, women and the elderly, are the highest users. Use of long half-life drugs (>10 hours) predominates. The overall benefits and harms from this drug exposure in BC is unknown.
Characterization of Gonadal Differentiation and Isolation of Factors Involved in Reproductive Development in Marine Bivalves
Creators: name: Roberts, Steven
Publisher: name: figshare
Year: 2012
Subjects: subject: Physiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Marine Biology
subject: Developmental Biology

description: Research Proposal (non-funded) submitted to USDA. Includes reviewer comments. Summary The long term goal of the research proposed by the PD is to characterize the reproductive biology in marine bivalves, concentrating particularly on aspects that could be used to develop novel approaches to induce sterility. The specific objectives of the research proposed here are to: 1) characterize gonad differentiation in juvenile bivalves and 2) isolate factors involved in gametogenesis in adult bivalves. To complete the first objective two approaches will be taken. First, a histological and in situ analysis approach will be used to characterize migration of germ cells and development of early gametes. Specifically, conventional histological techniques will be combined with cellular localization of vasa, a germ cell specific marker, in juvenile oysters and scallops. The second approach will be to use Expressed Sequence Tag (EST) analysis to identify transcripts expressed during early gonad differentiation. In order to isolate factors involved in gametogenesis, two approaches will be taken. A reverse transcription polymerase chain reaction (RT-PCR) approach to isolate candidate genes based on sequence homology will be used. Targeted genes for RT-PCR include Gonadotropin Releasing Hormone (GnRH) neuropeptide and aromatase, a key enzyme in sex steroid metabolism. In addition, EST analysis will be used to identify transcripts expressed in the ganglia of clams and gonads of oysters during gametogenesis. Upon completion of these objectives, 1) information will be provided on appropriate times to manipulate sex in bivalves and 2) reproductive factors will be elucidated that could eventually be used at targets to induce sterility in bivalves.
Case Study: Center for Sustainable and Circular Bioeconomy and Energy
Creators: name: LOBA - Customer Experience Design
name: Avans University of Applied Sciences
name: Q PLAN International (Greece)
name: University of Bologna
name: FVA New Media Research (Italy)
Publisher: name: Zenodo
Year: 2024

description: Explore this case study collected by BioGov.net partners in Greece! This valuable resource provides a quick understanding of the Center for Sustainable and Circular Bioeconomy and Energy case study.
Enabling the Deployment of Any-Scale Robotic Applications in Microservice Architectures through Automated Containerization
Creators: name: Busch, Jean-Pierre
name: Reiher, Lennart
name: Eckstein, Lutz
Publisher: name: arXiv
Year: 2023
Subjects: subject: Robotics (cs.RO)
subject: FOS: Computer and information sciences

description: In an increasingly automated world -- from warehouse robots to self-driving cars -- streamlining the development and deployment process and operations of robotic applications becomes ever more important. Automated DevOps processes and microservice architectures have already proven successful in other domains such as large-scale customer-oriented web services (e.g., Netflix). We recommend to employ similar microservice architectures for the deployment of small- to large-scale robotic applications in order to accelerate development cycles, loosen functional dependence, and improve resiliency and elasticity. In order to facilitate involved DevOps processes, we present and release a tooling suite for automating the development of microservices for robotic applications based on the Robot Operating System (ROS). Our tooling suite covers the automated minimal containerization of ROS applications, a collection of useful machine learning-enabled base container images, as well as a CLI tool for simplified interaction with container images during the development phase. Within the scope of this paper, we embed our tooling suite into the overall context of streamlined robotics deployment and compare it to alternative solutions. We release our tools as open-source software at https://github.com/ika-rwth-aachen/dorotos.
description: 6 pages; Submitted to IEEE International Conference on Robotics and Automation (ICRA) 2024
Optical and Raman spectroscopies of 171Yb3+:Y2SiO5 hyperfine structure for application toward microwave-to-optical transducer
Creators: name: Lim, Hee-Jin
name: Choi, Ga-Hyun
name: Hong, Ki Suk
Publisher: name: arXiv
Year: 2023
Subjects: subject: Optics (physics.optics)
subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: This study analyzed the optical techniques for high resolution, low-noise spectroscopy of a hyperfine structure (HFS) made of ytterbium-isotope 171 ions ($^{171}\mathrm{Yb}^{3+}$:$\mathrm{Y}_2\mathrm{SiO}_5$). Large energy spacings in $^{171}\mathrm{Yb}^{3+}$ are advantageous for spin-state preparations of quantum memory and construction of a transducer, thereby promoting the simultaneous stable control of the optical frequencies of lasers over a wide range of 3 GHz. We also built our own 2.7-K cryogenic system for optical, radio-wave-assisted spectroscopy. We attained to high resolution and sensitivity both in pump-probe saturation spectroscopy (PPS) and Raman heterodyne spectroscopy (RHS). Our frequency-stabilized PPS achieved a high-resolution spectrum of the HFS, whereas our setup of RHS enabled the efficient detection of paramagnetic spin resonance efficiently for a wide range of radio frequencies. As the underlying Raman process is an up-converting transduction, we present the optimization of the sensitivity of Raman heterodyne detections by selecting the best crystal orientation and efficient radio-wave coupling in future applications toward photon transducers.
Voc4Cat: Vocabulary guidelines for NFDI4Cat
Creators: name: Moustakas, Nikolaos
name: Behr, Alexander
name: Borgelt, Hendrik
name: Huskova, Nadiia
name: Khare, Rachit
name: Talab, Manal
name: Köbl, Julia
name: Chandrashekhar, Vishwas
name: Petrenko, Taras
name: Dörr, Mark
name: Linke, David
Publisher: name: Zenodo
Year: 2024
Subjects: Vocabularies
Guidelines
NFDI4Cat

description: The Voc4Cat guidelines have been developed as a blueprint towards suggesting, adding, and editing content to the vocabularies developed throughout NFDI4Cat. The aim of Voc4Cat is to provide guidelines to guarantee consistency and coherence on selection of concepts and terms between all catalysis-related vocabularies in NFDI4Cat. Voc4Cat evolved over the course of Task Area 1 (TA1): Ontology Development and Metadata Standards of NFDI4Cat
Online Supervised Training of Spaceborne Vision during Proximity Operations using Adaptive Kalman Filtering
Creators: name: Park, Tae Ha
name: D'Amico, Simone
Publisher: name: arXiv
Year: 2023
Subjects: subject: Robotics (cs.RO)
subject: FOS: Computer and information sciences

description: This work presents an Online Supervised Training (OST) method to enable robust vision-based navigation about a non-cooperative spacecraft. Spaceborne Neural Networks (NN) are susceptible to domain gap as they are primarily trained with synthetic images due to the inaccessibility of space. OST aims to close this gap by training a pose estimation NN online using incoming flight images during Rendezvous and Proximity Operations (RPO). The pseudo-labels are provided by adaptive unscented Kalman filter where the NN is used in the loop as a measurement module. Specifically, the filter tracks the target's relative orbital and attitude motion, and its accuracy is ensured by robust on-ground training of the NN using only synthetic data. The experiments on real hardware-in-the-loop trajectory images show that OST can improve the NN performance on the target image domain given that OST is performed on images of the target viewed from a diverse set of directions during RPO.
description: Accepted to ICRA'2024. Final revised version
Voc4cat: Vocabulary guidelines for NFDI4Cat
Creators: name: Moustakas, Nikolaos
name: Behr, Alexander
name: Borgelt, Hendrik
name: Huskova, Nadiia
name: Khare, Rachit
name: Talab, Manal
name: Köbl, Julia
name: Chandrashekhar, Vishwas
name: Petrenko, Taras
name: Dörr, Mark
name: Linke, David
Publisher: name: Zenodo
Year: 2023
Subjects: Vocabularies
Guidelines
NFDI4Cat

description: The Voc4Cat guidelines have been developed as a blueprint towards suggesting, adding, and editing content to the vocabularies developed throughout NFDI4Cat. The aim of Voc4Cat is to provide guidelines to guarantee consistency and coherence on selection of concepts and terms between all catalysis-related vocabularies in NFDI4Cat. Voc4Cat, initially inspired by the AGROVOC editorial guidelines of FAO, evolved over the course of Task Area 1 (TA1): Ontology Development and Metadata Standards of NFDI4Cat
Physics-informed State-space Neural Networks for Transport Phenomena
Creators: name: Dave, Akshay J.
name: Vilim, Richard B.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Machine Learning (cs.LG)
subject: Systems and Control (eess.SY)
subject: Computational Physics (physics.comp-ph)
subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Physical sciences

description: This work introduces Physics-informed State-space neural network Models (PSMs), a novel solution to achieving real-time optimization, flexibility, and fault tolerance in autonomous systems, particularly in transport-dominated systems such as chemical, biomedical, and power plants. Traditional data-driven methods fall short due to a lack of physical constraints like mass conservation; PSMs address this issue by training deep neural networks with sensor data and physics-informing using components' Partial Differential Equations (PDEs), resulting in a physics-constrained, end-to-end differentiable forward dynamics model. Through two in silico experiments -- a heated channel and a cooling system loop -- we demonstrate that PSMs offer a more accurate approach than a purely data-driven model. In the former experiment, PSMs demonstrated significantly lower average root-mean-square errors across test datasets compared to a purely data-driven neural network, with reductions of 44 %, 48 %, and 94 % in predicting pressure, velocity, and temperature, respectively.
 Beyond accuracy, PSMs demonstrate a compelling multitask capability, making them highly versatile. In this work, we showcase two: supervisory control of a nonlinear system through a sequentially updated state-space representation and the proposal of a diagnostic algorithm using residuals from each of the PDEs. The former demonstrates PSMs' ability to handle constant and time-dependent constraints, while the latter illustrates their value in system diagnostics and fault detection. We further posit that PSMs could serve as a foundation for Digital Twins, constantly updated digital representations of physical systems.
description: 19 pages, 13 figures
Pockets of Open Cells and Drizzle in Marine Stratocumulus
Creators: name: Stevens, Bjorn
name: Vali, Gabor
name: Comstock, Kimberly
name: Woods, Robert
name: Van Zanten, Margreet C.
name: Austin, Philip H.
name: Bretherton, Christopher S.
name: Lenschow, Donald H.
Publisher: name: American Meteorological Society
Year: 2016

description: Data from recent field studies in the northeast and southeast Pacific are used to investigate pockets of open cells (POCs) that are embedded in otherwise uniform stratocumulus. The cellular structure within a POC resembles broader regions of open cellular convection typically found further offshore. In both regions, cells are composed of precipitating cell walls and cell interiors with depleted cloud water and even clearing. POCs are long lived and embedded in broader regions of stratocumulus where average droplet sizes are relatively large. In contrast, stratiform, or unbroken, cloud formations tend to be accompanied by less, or no, drizzle, suggesting that precipitation is necessary for the sustenance of the open cellular structure. Because, by definition, open cells are associated with a reduction in cloud cover these observations provide direct evidence of a connection between cloudiness and precipitation—a linchpin of hypotheses that posit a connection between changes in the atmospheric aerosol and climate. Copyright 2005 American Meteorological Society (AMS). Permission to use figures, tables, and brief excerpts from this work in scientific and educational works is hereby granted provided that the source is acknowledged. Any use of material in this work that is determined to be “fair use” under Section 107 of the U.S. Copyright Act or that satisfies the conditions specified in Section 108 of the U.S. Copyright Act (17 USC §108, as revised by P.L. 94-553) does not require the AMS’s permission. Republication, systematic reproduction, posting in electronic form, such as on a web site or in a searchable database, or other uses of this material, except as exempted by the above statement, requires written permission or a license from the AMS. Additional details are provided in the AMS Copyright Policy, available on the AMS Web site located at (http://www.ametsoc.org/) or from the AMS at 617-227-2425 or copyright@ametsoc.org.
A decade of data citations - from principles to action
Creators: name: Puebla, Iratxe
Publisher: name: Zenodo
Year: 2024
Subjects: data citations
open data
metadata

description: 2024 marks ten years of the FORCE11 Data Citation principles. At this session of the FORCE2024 conference, we discussed with three panelists the achievements in data citations over the past decade, the challenges we've faced, and explored steps to meet the growing demand for insights into the use and impact of open data.

Speakers:

Scott Edmunds, Gigascience Press 

Ricardo Hartley Belmar, Universidad Central de Chile & Data Observatory Foundation

Kristi Holmes, Northwestern University
Eigenstate correlations, the eigenstate thermalization hypothesis, and quantum information dynamics in chaotic many-body quantum systems
Creators: name: Hahn, Dominik
name: Luitz, David J.
name: Chalker, J. T.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We consider the statistical properties of eigenstates of the time-evolution operator in chaotic many-body quantum systems. Our focus is on correlations between eigenstates that are specific to spatially extended systems and that characterise entanglement dynamics and operator spreading. In order to isolate these aspects of dynamics from those arising as a result of local conservation laws, we consider Floquet systems in which there are no conserved densities. The correlations associated with scrambling of quantum information lie outside the standard framework established by the eigenstate thermalisation hypothesis (ETH). In particular, ETH provides a statistical description of matrix elements of local operators between pairs of eigenstates, whereas the aspects of dynamics we are concerned with arise from correlations amongst sets of four or more eigenstates. We establish the simplest correlation function that captures these correlations and discuss features of its behaviour that are expected to be universal at long distances and low energies. We also propose a maximum-entropy Ansatz for the joint distribution of a small number $n$ of eigenstates. In the case $n = 2$ this Ansatz reproduces ETH. For $n = 4$ it captures both the growth with time of entanglement between subsystems, as characterised by the purity of the time-evolution operator, and also operator spreading, as characterised by the behaviour of the out-of-time-order correlator. We test these ideas by comparing results from Monte Carlo sampling of our Ansatz with exact diagonalisation studies of Floquet quantum circuits.
description: 25 pages, 24 figures
To Give or Not To Give: Pandemic Vaccine Donation Policy
Creators: name: Holleran, Abraham
name: Martonosi, Susan E.
name: Veatch, Michael
Publisher: name: arXiv
Year: 2023
Subjects: subject: Populations and Evolution (q-bio.PE)
subject: Optimization and Control (math.OC)
subject: Physics and Society (physics.soc-ph)
subject: FOS: Biological sciences
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 90B50

description: The global SARS-CoV-2 (COVID-19) pandemic highlighted the challenge of equitable vaccine distribution between high- and low-income countries. Many high-income countries were reluctant or slow to distribute extra doses of the vaccine to lower-income countries via the COVID-19 Vaccines Global Access (COVAX) collaboration. In addition to moral objections to such vaccine nationalism, vaccine inequity during a pandemic could contribute to the evolution of new variants of the virus and possibly increase total deaths, including in the high-income countries. Using the COVID-19 pandemic as a case study, we use the epidemiological model of Holleran et al. that incorporates virus mutation. We identify realistic scenarios under which a donor country prefers to donate vaccines before distributing them locally in order to minimize local deaths during a pandemic. We demonstrate that a nondonor-first vaccination policy can delay, sometimes dramatically, the emergence of more-contagious variants. Even more surprising, donating all vaccines is sometimes better for the donor country than a sharing policy in which half of the vaccines are donated and half are retained because of the impact donation can have on delaying the emergence of a more contagious virus. Nondonor-first vaccine allocation is optimal in scenarios in which the local health impact of the vaccine is limited or when delaying emergence of a variant is especially valuable. In all cases, we find that vaccine distribution is not a zero-sum game between donor and nondonor countries. Thus, in addition to moral reasons to avoid vaccine nationalism, donor nations can also realize local health benefits from donating vaccines. The insights yielded by this framework can be used to guide equitable vaccine distribution in future pandemics.
description: 21 pages, 4 figures. arXiv admin note: substantial text overlap with arXiv:2303.05917
DNA extraction from formalin-fixed, paraffin-embedded tissues: protein digestion as a limiting step for retrieval of high-quality DNA
Creators: name: Diaz-Cano, Salvador J.
name: S P Brady
Publisher: name: figshare
Year: 2012
Subjects: Molecular Biology
Medicine
Cancer

description: Several DNA extraction methods have been used for formalin-fixed, paraffin-embedded tissues, with variable results being reported regarding the suitability of DNA obtained from such sources to serve as template in polymerase chain reaction (PCR)-based genetic analyses. We present a method routinely used for archival material in our laboratory that reliably yields DNA of sufficient quality for PCR studies. This method is based on extended proteinase K digestion (250 micrograms/ml in an EDTA-free calcium-containing buffer supplemented with mussel glycogen) followed by phenol-chloroform extraction. Agarose gel electrophoresis of both digestion buffer aliquots and PCR amplification of the beta-globin gene tested the suitability of the retrieved DNA for PCR amplification.
Topological Density Correlations in a Fermi Gas
Creators: name: Tam, Pok Man
name: Kane, Charles L.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: A Fermi gas of non-interacting electrons, or ultra-cold fermionic atoms, has a quantum ground state defined by a region of occupancy in momentum space known as the Fermi sea. The Euler characteristic $χ_F$ of the Fermi sea serves to topologically classify these gapless fermionic states. The topology of a $D$ dimensional Fermi sea is physically encoded in the $D+1$ point equal time density correlation function. In this work, we first present a simple proof of this fact by showing that the evaluation of the correlation function can be formulated in terms of a triangulation of the Fermi sea with a collection of points, links and triangles and their higher dimensional analogs. We then make use of the topological $D+1$ point density correlation to reveal universal structures of the more general $M$ point density correlation functions in a $D$ dimensional Fermi gas. Two experimental methods are proposed for observing these correlations in $D=2$. In cold atomic gases imaged by quantum gas microscopy, our analysis supports the feasibility of measuring the third order density correlation, from which $χ_F$ can be reliably extracted in systems with as few as around 100 atoms. For solid-state electron gases, we propose measuring correlations in the speckle pattern of intensity fluctuations in nonlinear X-ray scattering experiments.
description: 9+5 pages, 7 figures. Comments are welcome
Planning for renewal : mapping primary health care in British Columbia
Creators: name: Watson, Diane E. (Diane Elizabeth), 1963-
name: Krueger, Hans
name: Mooney, Dawn
name: Black, Charlyn, 1954-
Publisher: name: Centre for Health Services and Policy Research (CHSPR)
Year: 2014

description: The goal of this project was to quickly compile a snapshot of the PHC system in British Columbia- and the health of its users- to inform policy and planning for the renewal of this sector. We created a set of profiles to reflect different facets of the PHC system, drawing primarily on information from readily available sources, but also conducting some important new analytic work. Each indicator, or profile, was mapped to advance our understanding of geographic variation and distribution across the province’s six health authorities, 16 health service delivery areas, and 89 local health areas, and presented in a way to illustrate the relationship between health status and PHC services use.
Analysis of clonality of atypical cutaneous lymphoid infiltrates associated with drug therapy by PCR/DGGE
Creators: name: Diaz-Cano, Salvador J.
name: H J Wolfe
name: S P Brady
name: C M Magro
Publisher: name: figshare
Year: 2012
Subjects: Molecular Biology
Medicine
Hematology
Cancer

description: Atypical lymphocytic infiltrates that mimic cutaneous lymphoma (ie, pseudolymphoma) are often observed in skin biopsy specimens from patients with altered immune function. The latter may reflect systemic immune dysregulatory states such as collagen vascular disease or human immunodeficiency virus infection. Among the iatrogenic causes are drug therapy with agents that abrogate lymphocyte function. These drugs encompass the anticonvulsants, antidepressants, phenothiazines, calcium channel blockers, and angiotensin-converting enzyme inhibitors. The appellation of lymphomatoid hypersensitivity reaction has been applied to cases of drug-associated pseudolymphoma. Pathologically and clinically, the distinction of such cases from cutaneous lymphoma is difficult. We employed the polymerase chain reaction (PCR) on archival material of proven drug-associated lymphomatoid hypersensitivity reactions both to explore its utility as an adjunct in diagnosis and to investigate the genotypic aberrations induced by drug therapy. Formalin-fixed, paraffin-embedded biopsy specimens from seven cutaneous T-cell lymphomas (CTCL), one nodal T-cell lymphoma, two cutaneous B-cell lymphomas, three typical hypersensitivity reactions, one tonsil, and 14 lymphomatoid hypersensitivity reactions were studied. Control cases for which DNA derived from fresh tissue was used include the Jurkat T-cell tumor line, placenta, one nodal B-cell lymphoma, and one case of reactive lymph node hyperplasia. DNA was obtained and purified by standard methods, then amplified with oligonucleotide primers specific for the T-cell receptor gamma locus and the immunoglobulin heavy chain genes. T-cell amplicons were analyzed by denaturing gradient gel electrophoresis (DGGE) and B-cell amplicons by either nondenaturing polyacrylamide or agarose gel electrophoresis. The nodal and Jurkat T-cell lymphomas, six of seven CTCL, one cutaneous B-cell lymphoma, and 2 of 14 lymphomatoid hypersensitivity reactions showed dominant ("monoclonal") T-cell gene rearrangement patterns, and the remainder of cases were polyclonal. A causal relationship between drug therapy and skin eruption was ascertained in the two patients showing T-cell rearrangements, and both experienced complete and sustained lesional resolution on discontinuation of the implicated drug. The only immunoglobulin heavy chain gene rearrangements detected by PCR were in two of the three B-cell lymphomas. We conclude that PCR/DGGE is a powerful method for assaying T-cell clonality in archival tissue and can aid in the discrimination of reactive from malignant cutaneous infiltrates with appropriate clinicopathologic correlation. Recognition that a monoclonal TCRgamma rearrangement can be observed in cases of drug-associated lymphomatoid hypersensitivity may help in avoiding a misdiagnosis of malignant lymphoma.
Intervalley coherence and intrinsic spin-orbit coupling in rhombohedral trilayer graphene
Creators: name: Arp, Trevor
name: Sheekey, Owen
name: Zhou, Haoxin
name: Tschirhart, C. L.
name: Patterson, Caitlin L.
name: Yoo, H. M.
name: Holleis, Ludwig
name: Redekop, Evgeny
name: Babikyan, Grigory
name: Xie, Tian
name: Xiao, Jiewen
name: Vituri, Yaar
name: Holder, Tobias
name: Taniguchi, Takashi
name: Watanabe, Kenji
name: Huber, Martin E.
name: Berg, Erez
name: Young, Andrea F.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Rhombohedral graphene multilayers provide a clean and highly reproducible platform to explore the emergence of superconductivity and magnetism in a strongly interacting electron system. Here, we use electronic compressibility and local magnetometry to explore the phase diagram of this material class in unprecedented detail. We focus on rhombohedral trilayer in the quarter metal regime, where the electronic ground state is characterized by the occupation of a single spin and valley isospin flavor. Our measurements reveal a subtle competition between valley imbalanced (VI) orbital ferromagnets and intervalley coherent (IVC) states in which electron wave functions in the two momentum space valleys develop a macroscopically coherent relative phase. Contrasting the in-plane spin susceptibility of the IVC and VI phases reveals the influence of graphene's intrinsic spin-orbit coupling, which drives the emergence of a distinct correlated phase with hybrid VI and IVC character. Spin-orbit also suppresses the in-plane magnetic susceptibility of the VI phase, which allows us to extract the spin-orbit coupling strength of $λ\approx 50μ$eV for our hexagonal boron nitride-encapsulated graphene system. We discuss the implications of finite spin-orbit coupling on the spin-triplet superconductors observed in both rhombohedral and twisted graphene multilayers.
Implicit-explicit schemes for incompressible flow problems with variable viscosity
Creators: name: Barrenechea, Gabriel R.
name: Castillo, Ernesto
name: Pacheco, Douglas R. Q.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics

description: In this work we study different Implicit-Explicit (IMEX) schemes for incompressible flow problems with variable viscosity. Unlike most previous work on IMEX schemes, which focuses on the convective part, we here focus on treating parts of the diffusive term explicitly to reduce the coupling between the velocity components. We present different, both monolithic and fractional-step, IMEX alternatives for the variable-viscosity Navier--Stokes system, analysing their theoretical and algorithmic properties. Stability results are proven for all the methods presented, with all these results being unconditional, except for one of the discretisations using a fractional-step scheme, where a CFL condition (in terms of the problem data) is required for showing stability. Our analysis is supported by a series of numerical experiments.
Influence of intratumour heterogeneity in the interpretation of marker results in phaeochromocytomas
Creators: name: Diaz-Cano, Salvador J.
name: Blanes, Alfredo
Publisher: name: figshare
Year: 2012
Subjects: Molecular Biology
Medicine
Cell Biology
Cancer

description: Krijger et al.1 try to predict the clinical behaviour of a phaeochromocytomas (PCCs) on the basis of the immunoreactivity of three markers (p53, bcl-2, and c-erbB-2). They conclude that the co-expression of p53 and bcl-2 proteins may assist that prediction. Our own preliminary results2,3 mainly agree with theirs and point towards two interrelated biological issues: firstly, the clonal evolution of neo- plasms and intratumour heterogeneity of markers; and secondly, the importance of apoptosis in tumour initiation and progression. Krijger et al. clearly indicate the importance of p53 and bcl-2 in the pathogenesis of a subgroup of PCCs. However, the variability of marker expression and the potential relationship with kinetic features are also helpful in understanding the pathogenesis of PCC.
Cross-Field Diffusion Effects on Particle Transport in a Solar Coronal Flux Rope
Creators: name: Husidic, Edin
name: Wijsen, Nicolas
name: Linan, Luis
name: Brchnelova, Michaela
name: Vainio, Rami
name: Poedts, Stefaan
Publisher: name: arXiv
Year: 2024
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: Solar energetic particles (SEPs) associated with solar flares and coronal mass ejections (CMEs) are key agents of space weather phenomena, posing severe threats to spacecraft and astronauts. Recent observations by Parker Solar Probe (PSP) indicate that the magnetic flux ropes of a CME can trap energetic particles and act as barriers, preventing other particles from crossing. In this paper, we introduce the novel COCONUT+PARADISE model to investigate the confinement of energetic particles within a flux rope and the effects of cross-field diffusion (CFD) on particle transport in the solar corona, particularly in the presence of a CME. Using the global magnetohydrodynamic coronal model COCONUT, we generate background configurations containing a CME modeled as a Titov-Démoulin flux rope (TDFR). We then utilize the particle transport code PARADISE to inject monoenergetic 100 keV protons inside one of the TDFR legs near its footpoint and evolve the particles through the COCONUT backgrounds. To study CFD, we employ two different approaches regarding the perpendicular proton mean free path (MFP): a constant MFP and a Larmor radius-dependent MFP. We contrast these results with those obtained without CFD. While particles remain fully trapped within the TDFR without CFD, we find that even relatively small perpendicular MFP values allow particles on the outer layers to escape. In contrast, the initially interior trapped particles stay largely confined. Finally, we highlight how our model and this paper's results are relevant for future research on particle acceleration and transport in an extended domain encompassing both the corona and inner heliosphere.
description: 16 pages, 8 figures, accepted for publication by ApJ Letters