cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Nontrivial spatial behavior of the Gauss-Bonnet curvature invariant of rapidly-rotating Kerr black holes
Creators: name: Hod, Shahar
Publisher: name: arXiv
Year: 2022
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The Gauss-Bonnet curvature invariant has attracted the attention of physicists and mathematicians over the years. In particular, it has recently been proved that black holes can support external matter configurations that are non-minimally coupled to the Gauss-Bonnet invariant of the curved spacetime. Motivated by this physically interesting behavior of black holes in Einstein-Gauss-Bonnet theories, we present a detailed {\it analytical} study of the physical and mathematical properties of the Gauss-Bonnet curvature invariant ${\cal G}_{\text{Kerr}}(r,\cosθ;a/M)$ of spinning Kerr black holes in the spacetime region outside the horizon. Interestingly, we prove that, for all spinning Kerr spacetimes in the physically allowed regime $a/M\in[0,1]$, the spin-dependent maximum curvature of the Gauss-Bonnet invariant is attained at the equator of the black-hole surface. Intriguingly, we reveal that the location of the global minimum of the Gauss-Bonnet invariant has a highly non-trivial functional dependence on the black-hole rotation parameter: (i) For Kerr black holes in the dimensionless slow-rotation $a/M(a/M)^{+}_{\text{crit}}$ are characterized by a non-trivial functional behavior of the Gauss-Bonnet curvature invariant along the black-hole horizon with a spin-dependent polar angle for the global minimum point.
description: 18 pages
Spin-EPR-pair separation by conveyor-mode single electron shuttling in Si/SiGe
Creators: name: Struck, Tom
name: Volmer, Mats
name: Visser, Lino
name: Offermann, Tobias
name: Xue, Ran
name: Tu, Jhih-Sian
name: Trellenkamp, Stefan
name: Cywiński, Łukasz
name: Bluhm, Hendrik
name: Schreiber, Lars R.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Long-ranged coherent qubit coupling is a missing function block for scaling up spin qubit based quantum computing solutions. Spin-coherent conveyor-mode electron-shuttling could enable spin quantum-chips with scalable and sparse qubit-architecture. Its key feature is the operation by only few easily tuneable input terminals and compatibility with industrial gate-fabrication. Single electron shuttling in conveyor-mode in a 420 nm long quantum bus has been demonstrated previously. Here we investigate the spin coherence during conveyor-mode shuttling by separation and rejoining an Einstein-Podolsky-Rosen (EPR) spin-pair. Compared to previous work we boost the shuttle velocity by a factor of 10000. We observe a rising spin-qubit dephasing time with the longer shuttle distances due to motional narrowing and estimate the spin-shuttle infidelity due to dephasing to be 0.7 % for a total shuttle distance of nominal 560 nm. Shuttling several loops up to an accumulated distance of 3.36 $μ$m, spin-entanglement of the EPR pair is still detectable, giving good perspective for our approach of a shuttle-based scalable quantum computing architecture in silicon.
A Fermi Model of Quantum Black Hole
Creators: name: Chu, Chong-Sun
name: Miao, Rong-Xin
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We propose a quantum model of the Schwarzschild black hole as a quantum mechanics of a system of fermionic degrees of freedom. The system has a constant density of states and a Fermi energy that is inversely proportional to the size of the system. Assuming equivalence principle, we show that the degeneracy pressure of the Fermi degrees of freedom is able to withstand the collapse of gravity if the radius of the system is given precisely by the horizon radius of the Schwarzschild black hole. In our model, the fermionic degrees of freedom at each energy level can be entangled in certain different ways, giving rise to a multitude of degenerate ground states of the system. The counting of these microstates reproduces precisely the Bekenstein-Hawking entropy. This simple Fermi model is universal and works also for the Reissner-Nordström charged black hole as well as black hole with a cosmological constant. From the properties of the Fermi variables, we propose that quantum gravity is characterized by a principle of {\it maximal capacity of states} where there can be no more than $V /l_P^3$ quantum states in any volume $V$. It implies a loss of spatial locality below the Planck length and suggests that any singularity predicted by general relativity is resolved and replaced by a quantum space in quantum gravity. In our model, a black hole spacetime is equipped with an uniform distribution of energy levels. This is another reason why black hole can be considered a simple harmonic oscillator of quantum gravity.
description: v3: PRD version
Quantum versus classical nature of a low-temperature magnetic phase transition in TbAl$_3$(BO$_3$)$_4$
Creators: name: Zajarniuk, T.
name: Szewczyk, A.
name: Wisniewski, P.
name: Gutowska, M. U.
name: Puzniak, R.
name: Szymczak, H.
name: Gudim, I.
name: Bedarev, V. A.
name: Pashchenko, M. I.
name: Tomczak, P.
name: Szuszkiewicz, W.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Other Condensed Matter (cond-mat.other)
subject: FOS: Physical sciences

description: Specific heat, $C_B$, of a TbAl$_3$(BO$_3$)$_4$ crystal was studied for 50 mK $
description: Preprint submitted to Phys. Rev B. The final version was published (DOI: 10.1103/PhysRevB.105.094418)
Reliability and validity of using the Lokomat to assess lower limb joint position sense in people with incomplete spinal cord injury
Creators: name: Domingo, Antoinette
name: Lam, Tania
Publisher: name: BioMed Central
Year: 2016

description: Background: Proprioceptive sense (knowing where the limbs are in space) is critical for motor control during posture and walking, and is often compromised after spinal cord injury (SCI). The purpose of this study was to assess the reliability and validity of using the Lokomat, a robotic exoskeleton used for gait rehabilitation, to quantitatively measure static position sense of the legs in persons with incomplete SCI. Methods: We used the Lokomat and custom software to assess static position sense in 23 able-bodied (AB) subjects and 23 persons with incomplete SCI (American Spinal Injury Association Impairment Scale level B, C or D). The subject’s leg was placed into a target position (joint angle) at either the hip or knee and asked to memorize that position. The Lokomat then moved the test joint to a “distractor” position. The subject then used a joystick controller to bring the joint back into the memorized target position. The final joint angle was compared to the target angle and the absolute difference was recorded as an error. All movements were passive. Known-groups validity was determined by the ability of the measure to discriminate between able-bodied and SCI subjects. To evaluate test-retest reliability, subjects were tested twice and intra-class correlation coefficients comparing errors from the two sessions were calculated. We also performed a traditional clinical test of proprioception in subjects with SCI and compared these scores to the robotic assessment. Results: The robot-based assessment test was reliable at the hip and knee in persons with SCI (P ≤ 0.001). Hip and knee angle errors in subjects with SCI were significantly greater (P ≤ 0.001) and more variable (P < 0.0001) than in AB subjects. Error scores were significantly correlated to clinical measure of joint position sense (r ≥ 0.507, P ≤ 0.013). Conclusions: This study shows that the Lokomat may be used as a reliable and valid clinical measurement tool for assessing joint position sense in persons with incomplete SCI. Quantitative assessments of proprioceptive deficits after neurological injury will help in understanding its role in the recovery of skilled walking and in the development of interventions to aid in the return to safe community ambulation.
A Directional Vibrotactile Feedback Interface for Ergonomic Postural Adjustment
Creators: name: Kim, Wansoo
name: Garate, Virginia Ruiz
name: Gandarias, Juan M.
name: Lorenzini, Marta
name: Ajoudani, Arash
Publisher: name: arXiv
Year: 2022
Subjects: subject: Human-Computer Interaction (cs.HC)
subject: Robotics (cs.RO)
subject: FOS: Computer and information sciences

description: The objective of this paper is to develop and evaluate a directional vibrotactile feedback interface as a guidance tool for postural adjustments during work. In contrast to the existing active and wearable systems such as exoskeletons, we aim to create a lightweight and intuitive interface, capable of guiding its wearers towards more ergonomic and healthy working conditions. To achieve this, a vibrotactile device called ErgoTac is employed to develop three different feedback modalities that are able to provide a directional guidance at the body segments towards a desired pose. In addition, an evaluation is made to find the most suitable, comfortable, and intuitive feedback modality for the user. Therefore, these modalities are first compared experimentally on fifteen subjects wearing eight ErgoTac devices to achieve targeted arm and torso configurations. The most effective directional feedback modality is then evaluated on five subjects in a set of experiments in which an ergonomic optimisation module provides the optimised body posture while performing heavy lifting or forceful exertion tasks. The results yield strong evidence on the usefulness and the intuitiveness of one of the developed modalities in providing guidance towards ergonomic working conditions, by minimising the effect of an external load on body joints. We believe that the integration of such low-cost devices in workplaces can help address the well-known and complex problem of work-related musculoskeletal disorders.
description: 12 pages. 13 figures. Now published in IEEE Transactions on Haptics DOI: 10.1109/TOH.2021.3112795
Optimal quantum optical control of spin in diamond
Creators: name: Tian, Jiazhao
name: Du, Tianyi
name: Liu, Yu
name: Liu, Haibin
name: Jin, Fangzhou
name: Said, Ressa S.
name: Cai, Jianming
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The nitrogen-vacancy (NV) center spin represents an appealing candidate for quantum information processing. Besides the widely used microwave control, its coherent manipulation may also be achieved using laser as mediated by the excited energy levels. Nevertheless, the multiple levels of the excited state of NV center spin make the coherent transition process become complex and may affect the fidelity of coherent manipulation. Here, we adopt the strategy of optimal quantum control to accelerate coherent state transfer in the ground state manifold of NV center spin using laser. The results demonstrate improved performance in both the speed and the fidelity of coherent state transfer which will be useful for optical control of NV center spin in diamond.
Gilles Pialoux
Creators: name: Leibowitch, Jacques (1942-2020)
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020

description: 1 fichier (14 pages)
description: Pièces jointes : Lettre de Jean Pierre Bibard, Président National d’ACTIF Santé à Xavier Bertrand, Ministre de la Santé (1er décembre 2011) ; mail de patient anonymisé à Leibowitch ; présentation du livre de J. Leibowitch issu du blog http://seroposition.canalblog.com/ ; "LE FORÇAGE DU PONT D'ICCARRE ET LA BATAILLE DES TRAITEMENTS DE SUITE RACCOURCIS".
Yu-Shiba-Rusinov bands in a self-assembled kagome lattice of magnetic molecules
Creators: name: Farinacci, Laetitia
name: Reecht, Gael
name: von Oppen, Felix
name: Franke, Katharina J.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Kagome lattices constitute versatile platforms for studying paradigmatic correlated phases. While molecular self-assembly of kagome structures on metallic substrates is promising, it is challenging to realize pristine kagome properties because of hybridization with the bulk degrees of freedom and modified electron-electron interactions. We suggest that a superconducting substrate offers an ideal support for a magnetic kagome lattice. Exchange coupling induces kagome-derived bands at the interface, which are protected from the bulk by the superconducting energy gap. We realize a magnetic kagome lattice on a superconductor by depositing Fe-porphin-chloride molecules on Pb(111) and using temperature-activated de-chlorination and self-assembly. This allows us to control the formation of smaller kagome precursors and long-range ordered kagome islands. Using scanning tunneling microscopy and spectroscopy at 1.6 K, we identify Yu-Shiba-Rusinov states inside the superconducting energy gap and track their hybridization from the precursors to larger islands, where the kagome lattice induces extended YSR bands. These YSR-derived kagome bands are protected inside the superconducting energy gap, motivating further studies to resolve possible spin-liquid or Kondo-lattice-type behavior.
Transport properties of a $3$-dimensional holographic effective theory with gauge-axion coupling
Creators: name: Li, Yi-Lin
name: Wang, Xi-Jing
name: Fu, Guoyang
name: Wu, Jian-Pin
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: In this paper, we implement a $3$-dimensional holographic effective theory with gauge-axion coupling. The analytical black hole solution is worked out. We investigate the Direct current (DC) thermoelectric conductivities. A novel property is that DC electric conductivity for vanishing gauge-axion coupling is temperature dependent. It is different from that of $4$-dimensional axion model whose DC electric conductivity is temperature independent. In addition, the gauge-axion coupling induces a metal insulator transition (MIT) at zero temperature. The properties of other DC thermoelectric conductivities are also discussed. Moreover we find that the Wiedemann-Franz (WF) law is violated in our model.
description: 19 pages, 8 figures, accepted by Physics Letters B
The landscape of transposable elements in the finished genome of the fungal wheat pathogen Mycosphaerella graminicola
Creators: name: Dhillon, Braham
name: Gill, Navdeep
name: Hamelin, Richard C.
name: Goodwin, Stephen B.
Publisher: name: BioMed Central
Year: 2015

description: Background: In addition to gene identification and annotation, repetitive sequence analysis has become an integral part of genome sequencing projects. Identification of repeats is important not only because it improves gene prediction, but also because of the role that repetitive sequences play in determining the structure and evolution of genes and genomes. Several methods using different repeat-finding strategies are available for whole-genome repeat sequence analysis. Four independent approaches were used to identify and characterize the repetitive fraction of the Mycosphaerella graminicola (synonym Zymoseptoria tritici) genome. This ascomycete fungus is a wheat pathogen and its finished genome comprises 21 chromosomes, eight of which can be lost with no obvious effects on fitness so are dispensable. Results Using a combination of four repeat-finding methods, at least 17% of the M. graminicola genome was estimated to be repetitive. Class I transposable elements, that amplify via an RNA intermediate, account for about 70% of the total repetitive content in the M. graminicola genome. The dispensable chromosomes had a higher percentage of repetitive elements as compared to the core chromosomes. Distribution of repeats across the chromosomes also varied, with at least six chromosomes showing a non-random distribution of repetitive elements. Repeat families showed transition mutations and a CpA → TpA dinucleotide bias, indicating the presence of a repeat-induced point mutation (RIP)-like mechanism in M. graminicola. One gene family and two repeat families specific to subtelomeres also were identified in the M. graminicola genome. A total of 78 putative clusters of nested elements was found in the M. graminicola genome. Several genes with putative roles in pathogenicity were found associated with these nested repeat clusters. This analysis of the transposable element content in the finished M. graminicola genome resulted in a thorough and highly curated database of repetitive sequences. Conclusions This comprehensive analysis will serve as a scaffold to address additional biological questions regarding the origin and fate of transposable elements in fungi. Future analyses of the distribution of repetitive sequences in M. graminicola also will be able to provide insights into the association of repeats with genes and their potential role in gene and genome evolution.
Generalized Reference Kernel for One-class Classification
Creators: name: Raitoharju, Jenni
name: Iosifidis, Alexandros
Publisher: name: arXiv
Year: 2022
Subjects: subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: In this paper, we formulate a new generalized reference kernel hoping to improve the original base kernel using a set of reference vectors. Depending on the selected reference vectors, our formulation shows similarities to approximate kernels, random mappings, and Non-linear Projection Trick. Focusing on small-scale one-class classification, our analysis and experimental results show that the new formulation provides approaches to regularize, adjust the rank, and incorporate additional information into the kernel itself, leading to improved one-class classification accuracy.
What a Publication Tells You -- Benefits of Narrative Information Access in Digital Libraries
Creators: name: Kroll, Hermann
name: Plötzky, Florian
name: Pirklbauer, Jan
name: Balke, Wolf-Tilo
Publisher: name: arXiv
Year: 2022
Subjects: subject: Digital Libraries (cs.DL)
subject: FOS: Computer and information sciences
subject: H.4

description: Knowledge bases allow effective access paths in digital libraries. Here users can specify their information need as graph patterns for precise searches and structured overviews (by allowing variables in queries). But especially when considering textual sources that contain narrative information, i.e., short stories of interest, harvesting statements from them to construct knowledge bases may be a serious threat to the statements' validity. A piece of information, originally stated in a coherent line of arguments, could be used in a knowledge base query processing without considering its vital context conditions. And this can lead to invalid results. That is why we argue to move towards narrative information access by considering contexts in the query processing step. In this way digital libraries can allow users to query for narrative information and supply them with valid answers. In this paper we define narrative information access, demonstrate its benefits for Covid 19 related questions, and argue on the generalizability for other domains such as political sciences.
description: Accepted at JCDL2022, 8 pages, 1 figure
Second-Order Coherence Across the Brillouin Lasing Threshold
Creators: name: Cryer-Jenkins, E. A.
name: Enzian, G.
name: Freisem, L.
name: Moroney, N.
name: Price, J. J.
name: Svela, A. Ø.
name: Major, K. D.
name: Vanner, M. R.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Optics (physics.optics)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Brillouin-Mandelstam scattering is one of the most accessible nonlinear optical phenomena and has been widely studied since its theoretical discovery one hundred years ago. The scattering mechanism is a three-wave mixing process between two optical fields and one acoustic field and has found a broad range of applications spanning microscopy to ultra-narrow-linewidth lasers. Building on the success of utilizing this nonlinearity at a classical level, a rich avenue is now being opened to explore Brillouin scattering within the paradigm of quantum optics. Here, we take a key step in this direction by employing quantum optical techniques yet to be utilized for Brillouin scattering to characterize the second-order coherence of Stokes scattering across the Brillouin lasing threshold. We use a silica microsphere resonator and single-photon counters to observe the expected transition from bunched statistics of thermal light below the lasing threshold to Poissonian statistics of coherent light above the threshold. Notably, at powers approaching the lasing threshold, we also observe super-thermal statistics, which arise due to instability and a ``flickering'' in and out of lasing as the pump field is transiently depleted. The statistics observed across the transition, including the ``flickering'', are a result of the full nonlinear three-wave mixing process and cannot be captured by a linearized model. These measurements are in good agreement with numerical solutions of the three-wave Langevin equations and are well demarcated by analytical expressions for the instability and the lasing thresholds. These results demonstrate that applying second-order-coherence and photon-counting measurements to Brillouin scattering provides new methods to advance our understanding of Brillouin scattering itself and progress toward quantum-state preparation and characterization of acoustic modes.
description: Main (8 pages, 2 figures) + Supplementary (6 pages, 1 figures), Submitted
VSA: Reconfigurable Vectorwise Spiking Neural Network Accelerator
Creators: name: Lien, Hong-Han
name: Hsu, Chung-Wei
name: Chang, Tian-Sheuan
Publisher: name: arXiv
Year: 2022
Subjects: subject: Hardware Architecture (cs.AR)
subject: FOS: Computer and information sciences
subject: B.5.m

description: Spiking neural networks (SNNs) that enable low-power design on edge devices have recently attracted significant research. However, the temporal characteristic of SNNs causes high latency, high bandwidth and high energy consumption for the hardware. In this work, we propose a binary weight spiking model with IF-based Batch Normalization for small time steps and low hardware cost when direct training with input encoding layer and spatio-temporal back propagation (STBP). In addition, we propose a vectorwise hardware accelerator that is reconfigurable for different models, inference time steps and even supports the encoding layer to receive multi-bit input. The required memory bandwidth is further reduced by two-layer fusion mechanism. The implementation result shows competitive accuracy on the MNIST and CIFAR-10 datasets with only 8 time steps, and achieves power efficiency of 25.9 TOPS/W.
description: 5 pages, 8 figures, published in IEEE ISCAS 2021
title: Psychological Outcomes of Religiosity in the Elderly
Creators: name: Hogge, Deanna R.
Publisher: name: Old Dominion University
publisherIdentifier: https://ror.org/04zjtrb98
publisherIdentifierScheme: ROR
Year: 1996

description: Three components of religiosity- organizational religious involvement, nonorganizational religious involvement, and subjective religiosity- were examined for effects on wellbeing, depression, and coping in an elderly sample. A multiple regression analysis, in which demographic variables were controlled for, did not result in any significant findings. The lack of statistically significant findings conflict with a large body of research on religion and psychosocial and health outcomes. The current findings suggest that while traditional religious involvement may be beneficial to those who participate, this involvement does not account for significantly increased well-being, better coping, and less depression for the individuals of this elderly sample. One possibility for the lack of significant results with this sample may be due to the large number of this sample, eighty eight percent, who considered themselves to be fairly to very religious. This lack of diversity within the sample may have hindered significant results from surfacing. The lack of significant findings may highlight a need for two improvements in this research area: the development of measures designed to tap into a more "spiritual" component of individuals (as distinguished from religious practices) and the study of effects of more unconventional forms of religious involvement such as among individuals who seek spiritual direction from less traditional perspectives.
Brain white matter integrity and association with age at onset in pediatric obsessive-compulsive disorder
Creators: name: Rosso, Isabelle M
name: Olson, Elizabeth A
name: Britton, Jennifer C
name: Stewart, S E
name: Papadimitriou, George
name: Killgore, William D
name: Makris, Nikos
name: Wilhelm, Sabine
name: Jenike, Michael A
name: Rauch, Scott L
Publisher: name: BioMed Central
Year: 2015

description: Background: Obsessive-compulsive disorder (OCD) is a common and debilitating neuropsychiatric illness thought to involve abnormal connectivity of widespread brain networks, including frontal-striatal-thalamic circuits. At least half of OCD cases arise in childhood and their underlying neuropathology may differ at least in part from that of adult-onset OCD. Yet, only a few studies have examined brain white matter (WM) integrity in childhood-onset OCD using diffusion tensor imaging (DTI), and none have examined potential associations with age at onset. Results In this study, 17 youth with OCD and 19 healthy control subjects, ages 10 to 19 years, underwent DTI on a 3T Siemens scanner. DSM-IV diagnoses were established with standardized interviews, and OCD symptom severity was evaluated using the Children’s Yale-Brown Obsessive-Compulsive Scale (CY-BOCS). Voxel-wise analyses were conducted on data processed with tract-based spatial statistics (TBSS) to derive measures of fractional anisotropy (FA), axial diffusivity (AD), radial diffusivity (RD), and mean diffusivity (MD). OCD patients had significantly lower FA in seven WM clusters, with over 80% of significant voxels in bilateral frontal cortex and corpus callosum (CC). There were no regions of significantly higher FA in patients compared with controls. Patients also had significantly higher RD in right frontal cortex and right body of the CC. Earlier age at onset of OCD correlated significantly with lower FA in the right thalamus and with higher RD in the right CC. FA and RD were not significantly associated with symptom severity. Conclusions These findings point to compromised WM integrity and reduced myelination in some brain regions of children with OCD, particularly the CC and fiber tracts that connect the frontal lobes to widespread cortical and subcortical targets. They also suggest that age at onset may be a moderator of some of the WM changes in pediatric OCD.
Intratumoral heterogeneity in a minority of ovarian low-grade serous carcinomas
Creators: name: Tone, Alicia A.
name: McConechy, Melissa K.
name: Yang, Winnie
name: Ding, Jiarui
name: Yip, Stephen
name: Kong, Esther
name: Wong, Kwong-Kwok
name: Gershenson, David M.
name: Mackay, Helen
name: Shah, Sohrab
name: Gilks, C. Blake
name: Tinker, Anna V.
name: Clarke, Blaise
name: McAlpine, Jessica N.
name: Huntsman, David G.
Publisher: name: BioMed Central
Year: 2016

description: Background: Ovarian low-grade serous carcinoma (LGSC) has fewer mutations than ovarian high-grade serous carcinoma (HGSC) and a less aggressive clinical course. However, an overwhelming majority of LGSC patients do not respond to conventional chemotherapy resulting in a poor long-term prognosis comparable to women diagnosed with HGSC. KRAS and BRAF mutations are common in LGSC, leading to clinical trials targeting the MAPK pathway. We assessed the stability of targetable somatic mutations over space and/or time in LGSC, with a view to inform stratified treatment strategies and clinical trial design. Methods: Eleven LGSC cases with primary and recurrent paired samples were identified (stage IIB-IV). Tumor DNA was isolated from 1–4 formalin-fixed paraffin-embedded tumor blocks from both the primary and recurrence (n = 37 tumor and n = 7 normal samples). Mutational analysis was performed using the Ion Torrent AmpliSeqTM Cancer Panel, with targeted validation using Fluidigm-MiSeq, Sanger sequencing and/or Raindance Raindrop digital PCR. Results: KRAS (3/11), BRAF (2/11) and/or NRAS (1/11) mutations were identified in five unique cases. A novel, non-synonymous mutation in SMAD4 was observed in one case. No somatic mutations were detected in the remaining six cases. In two cases with a single matched primary and recurrent sample, two KRAS hotspot mutations (G12V, G12R) were both stable over time. In three cases with multiple samplings from both the primary and recurrent surgery some mutations (NRAS Q61R, BRAF V600E, SMAD4 R361G) were stable across all samples, while others (KRAS G12V, BRAF G469V) were unstable. Conclusions: Overall, the majority of cases with detectable somatic mutations showed mutational stability over space and time while one of five cases showed both temporal and spatial mutational instability in presumed drivers of disease. Investigation of additional cases is required to confirm whether mutational heterogeneity in a minority of LGSC is a general phenomenon that should be factored into the design of clinical trials and stratified treatment for this patient population.
Can protein expression be "solved"?
Creators: name: Baranowski, Catherine
name: Martin, Hector Garcia
name: Oyarzún, Diego
name: Petzold, Christopher
name: Nikolados, Evangelos-Marios
name: Jaaks-Kraatz, Sebastian
name: Gaber, Aljaž
name: Chalkley, Robert
name: Scannell, Devin
name: Sevey, Rachel
name: Jewett, Michael
name: Kelly, Peter
name: DeBenedictis, Erika
name: Align to Innovate
Publisher: name: Zenodo
Year: 2024

description: Recombinant protein expression is central to biotechnology’s application in academic exploration as well as human health, climate applications and the bioeconomy in general. However, not all proteins can be expressed in all organisms, and the field lacks a predictive model of soluble protein overexpression that could replace laborious experimental trial-and-error. Here, we discuss the state of the field and identify the lack of large, high-fidelity datasets as the primary bottleneck to progress. We review possible assays that could be used for data collection to identify a path toward an extensible experimental platform for collecting soluble recombinant protein overexpression data across organisms. We suggest that the resulting dataset should be used to train increasingly generalizable predictive models of protein expression to answer the question: “How can predictive protein expression be solved?”.
Extended Abstract: Productive Parallel Programming with Parsl
Creators: name: Chard, Kyle
name: Babuji, Yadu
name: Woodard, Anna
name: Clifford, Ben
name: Li, Zhuozhao
name: Hategan, Mihael
name: Foster, Ian
name: Wilde, Mike
name: Katz, Daniel S.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Computer and information sciences

description: Parsl is a parallel programming library for Python that aims to make it easy to specify parallelism in programs and to realize that parallelism on arbitrary parallel and distributed computing systems. Parsl relies on developers annotating Python functions-wrapping either Python or external applications-to indicate that these functions may be executed concurrently. Developers can then link together functions via the exchange of data. Parsl establishes a dynamic dependency graph and sends tasks for execution on connected resources when dependencies are resolved. Parsl's runtime system enables different compute resources to be used, from laptops to supercomputers, without modification to the Parsl program.
Can protein expression be "solved"?
Creators: name: Baranowski, Catherine
name: Martin, Hector Garcia
name: Oyarzún, Diego A.
name: Petzold, Christopher
name: Nikolados, Evangelos-Marios
name: Jaaks-Kraatz, Sebastian
name: Gaber, Aljaž
name: Chalkley, Robert J.
name: Scannell, Devin
name: Sevey, Rachel
name: Jewett, Michael C.
name: Kelly, Peter
name: DeBenedictis, Erika
name: Align to Innovate
Publisher: name: Zenodo
Year: 2024

description: Recombinant protein expression is central to biotechnology’s application in academic exploration as well as human health, climate applications and the bioeconomy in general. However, not all proteins can be expressed in all organisms, and the field lacks a predictive model of soluble protein overexpression that could replace laborious experimental trial-and-error. Here, we discuss the state of the field and identify the lack of large, high-fidelity datasets as the primary bottleneck to progress. We review possible assays that could be used for data collection to identify a path toward an extensible experimental platform for collecting soluble recombinant protein overexpression data across organisms. We suggest that the resulting dataset should be used to train increasingly generalizable predictive models of protein expression to answer the question: “How can predictive protein expression be solved?”.
The logic of causally closed spacetime subsets
Creators: name: Casini, H.
Publisher: name: arXiv
Year: 2002
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The causal structure of space-time offers a natural notion of an opposite or orthogonal in the logical sense, where the opposite of a set is formed by all points non time-like related with it. We show that for a general space-time the algebra of subsets that arises from this negation operation is a complete orthomodular lattice, and thus has several of the properties characterizing the algebra physical propositions in quantum mechanics. We think this fact could be used to investigate causal structure in an algebraic context. As a first step in this direction we show that the causal lattice is in addition atomic, find its atoms, and give necesary and sufficient conditions for ireducibility.
description: 17 pages, 8 figures
Stochastic backgrounds of gravitational waves and spherical detectors
Creators: name: Lobo, J. Alberto
name: Montero, Alvaro
Publisher: name: arXiv
Year: 2002
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The analysis of how a stochastic background of gravitational radiation interacts with a spherical detector is given in detail, which leads to explicit expressions for the system response functions, as well as for the cross-correlation matrix of different readout channels. It is shown that distinctive features of GW induced random detector excitations, relative to locally generated noise, are in practice insufficient to separate the signal from the noise by means of a single sphere, if prior knowledge on the GW spectral density is nil. The situation significantly improves when such previous knowledge is available, due to the omnidirectionality and multimode capacities of a spherical GW antenna.
description: 19 pages
Black-hole threshold solutions in stiff fluid collapse
Creators: name: Brady, Patrick R.
name: Choptuik, Matthew W.
name: Gundlach, Carsten
name: Neilsen, David W.
Publisher: name: arXiv
Year: 2002
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Numerical studies of the gravitational collapse of a stiff (P=rho) fluid have found the now familiar critical phenomena, namely scaling of the black hole mass with a critical exponent and continuous self-similarity at the threshold of black hole formation. Using the equivalence of an irrotational stiff fluid to a massless scalar field, we construct the critical solution as a scalar field solution by making a self-similarity ansatz. We find evidence that this solution has exactly one growing perturbation mode; both the mode and the critical exponent, gamma ~ 0.94, derived from its eigenvalue agree with those measured in perfect fluid collapse simulations. We explain why this solution is seen as a critical solution in stiff fluid collapse but not in scalar field collapse, and conversely why the scalar field critical solution is not seen in stiff fluid collapse, even though the two systems are locally equivalent.
description: RevTex, 14 pages, 5 ps figures
On the existence of global solutions for $T^{3}$-Gowdy spacetimes with stringy matter
Creators: name: Narita, Makoto
Publisher: name: arXiv
Year: 2002
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Mathematical Physics (math-ph)
subject: Analysis of PDEs (math.AP)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We show a global existence theorem for Einstein-matter equations of $T^{3}$-Gowdy symmetric spacetimes with stringy matter. The areal time coordinate is used. It is shown that this spacetime has a crushing singularity into the past. From these results we can show that the spacetime is foliated by compact hypersurfaces of constant mean curvature.
description: 10 pages, to appear in Classical and Quantum Gravity
Rising Tides: Analytic Modeling of Tidal Effects in Binary Neutron Star Mergers
Creators: name: O'Dell, Alexander
name: Hamilton, Maria C. Babiuc
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The gravitational waves produced by binary neutron star mergers offer a unique window into matter behavior under extreme conditions. In this context, we model analytically the effect of matter on the gravitational waves from binary neutron star mergers. We start with a binary black hole system, leveraging the post-Newtonian formalism for the inspiral and the Backwards-one-Body model for the merger. We combine the two methods to generate a baseline waveform and we validate our results against numerical relativity simulations. Next, we integrate tidal effects in phase and amplitude to account for matter and spacetime interaction, by using the NRTidal model, and test its accuracy against numerical relativity predictions, for two equations of state, finding a mismatch around the merger. Subsequently, we lift the restriction on the coefficients to be independent of the tidal deformability, and recalibrate them using the numerical relativity predictions. We obtain better fits for phase and amplitude around the merger, and are able to extend the phase modeling beyond the merger. We implement our method in a new open-source Python code, steered by a Jupyter Notebook. Our research offers new perspectives on analytically modeling the effect of tides on the gravitational waves from binary neutron star mergers.
description: 28 pages, 8 figures
WKB metastable quantum states of a de Sitter--Reissner-Nordstroem dust shell
Creators: name: Ansoldi, Stefano
Publisher: name: arXiv
Year: 2003
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We study the dynamics of a spherically symmetric dust shell separating two spacetime domains, the 'interior' one being a part of the de Sitter spacetime and the exterior one having the 'extremal' Reissner-Nordstroem geometry. Extending the ideas of previous works on the subject, we show that the it is possible to determine the (metastable) WKB quantum states of this gravitational system.
description: IOPart class, 16 figures
Potential impact of subsequent entry biologics in nephrology practice in Canada
Creators: name: Martinusen, Daniel J
name: Lo, Clifford
name: Marin, Judith G
name: Tsao, Nicole W
name: Leung, Marianna
Publisher: name: BioMed Central
Year: 2015

description: Purpose of review: Subsequent entry biologics may soon be a reality in Canadian nephrology practice. Along with opportunities to reduce health care costs, these agents pose unique challenges that must be met for successful implementation. Understanding the experiences around the globe in both regulatory affairs and implementation will be a valuable guide for Canadian clinicians. This report provides an executive summary of the information required to guide decisions to use or implement subsequent entry biologics by comparing Canadian regulations to other developed nations, discussing their clinical issues and predicting their impact on the Canadian market and nephrology practice. We hope that this review will assist clinicians and policy makers to navigate this complex subject and to make informed decisions in the best interest of their patients. Sources of information Sources of information include published literature and reports available in the public domain including guidelines obtained from regulatory agencies and information shared by Pharmaceutical companies. Lastly, we generated information from our own focus group consisting of nephrologists, a regulatory body representative, a hospital formulary representative, a patient representative, a hospital administrator, and a health economist. Findings There exists a common and robust approach in the G20 countries for approval and regulation of subsequent entry biologics. Although by definition these agents do not have advantages (other than costs) or disadvantages compared to the original biologic, there are potential concerns and economic uncertainties regarding their implementation. Where SEBs are on the market, their market share is variable and modest. Limitations We did not purchase third party reports for up to the minute marketing data. Since there are no subsequent entry biologics currently on the Canadian market, the information is only predictive. Implications The nephrology community will have to work with patients, payers, and regulatory bodies to ensure safe and effective use of subsequent entry biologics. Cost savings can be achieved but these agents should only be used after fully understanding their unique challenges. At this time, they should not be automatically substitutable and only used for Health Canada-approved indications. Only through good pharmacovigilence will health care providers and patients become better informed.
Additional file 1 of Developmental regulation of canonical and small ORF translation from mRNAs
Creators: name: Patraquim, Pedro
name: Mumtaz, Muhammad Ali Shahzad
name: Pueyo, José Ignacio
name: Aspden, Julie Louise
name: Juan-Pablo Couso
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1. Patraquim_Supplemental_Information_Additional File 1.pdf: Supplementary Figures and Tables.
Boyer-Finley equation and systems of hydrodynamic type
Creators: name: Ferapontov, E.
name: Korotkin, D.
name: Shramchenko, V.
Publisher: name: arXiv
Year: 2004
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We reduce Boyer-Finley equation to a family of compatible systems of hydrodynamic type, with characteristic speeds expressed in terms of spaces of rational functions. The systems of hydrodynamic type are then solved by the generalized hodograph method, providing solutions of the Boyer-Finley equation including functional parameters.
Kappa-symmetric non-abelian Born-Infeld actions in three dimensions
Creators: name: Drummond, J. M.
name: Howe, P. S.
name: Lindstrom, U.
Publisher: name: arXiv
Year: 2002
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: A superembedding construction of general non-abelian Born-Infeld actions in three dimensions is described. These actions have rigid target space and local worldvolume supersymmetry(i.e. kappa symmetry). The standard abelian Born-Infeld gauge multiplet is augmented with an additional worldvolume SU(N) gauge supermultiplet. It is shown how to construct single-trace actions and in particular a kappa-supersymmetric extension of the symmetrised trace action.
description: 14 pages
Covariant and quasi-covariant quantum dynamics in Robertson-Walker space-times
Creators: name: Buchholz, Detlev
name: Mund, Jens
name: Summers, Stephen J.
Publisher: name: arXiv
Year: 2002
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We propose a canonical description of the dynamics of quantum systems on a class of Robertson-Walker space-times. We show that the worldline of an observer in such space-times determines a unique orbit in the local conformal group SO(4,1) of the space-time and that this orbit determines a unique transport on the space-time. For a quantum system on the space-time modeled by a net of local algebras, the associated dynamics is expressed via a suitable family of ``propagators''. In the best of situations, this dynamics is covariant, but more typically the dynamics will be ``quasi-covariant'' in a sense we make precise. We then show by using our technique of ``transplanting'' states and nets of local algebras from de Sitter space to Robertson-Walker space that there exist quantum systems on Robertson-Walker spaces with quasi-covariant dynamics. The transplanted state is locally passive, in an appropriate sense, with respect to this dynamics.
description: 21 pages, 1 figure
Estimating uncertainty in calculated ambient RF field levels for hazard assessments
Creators: name: Anderson, Vitas
Publisher: name: Swinburne
Year: 2024

description: Just as for measured evaluations, the calculation of ambient levels of radiofrequency (RF) electric and magnetic fields for hazard assessments can entail random uncertainty, the extent of which depends on: how well the method of analysis approximates the governing electromagnetic equations (i.e. Maxwell's equations); how closely the modeled object represents its real counterpart in form and composition, and; computational round off error. While uncertainty estimates are commonly required for RF measurements, they are rarely provided for calculated assessments. In this paper, a process for calculating uncertainty for calculated assessments is proposed. It incorporates a series of validation tests which are used to gauge the uncertainty in the computational technique and round off error. The comparator in the validation tests must be independent of the technique (e.g. measurement of antenna gain) and may vary for different types of analyses (e.g. full wave solutions vs ray tracing methods). Variational targets are set for the validation tests, and the uncertainty estimate for computational uncertainty diminishes as more tests are passed. Once determined in this way, the standard uncertainty for computational technique is then combined in a multiplicative model with standard uncertainties for other influence quantities such as forward power to the antenna and field scattering effects of nearby objects. By using the proposed approach, it will be possible to provide systematic corrections and uncertainty estimates for calculated assessments as they are for RF measurements, thereby allowing meaningful comparisons between them.