cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Compilation of Entangling Gates for High-Dimensional Quantum Systems
Creators: name: Mato, Kevin
name: Ringbauer, Martin
name: Hillmich, Stefan
name: Wille, Robert
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Most quantum computing architectures to date natively support multi-valued logic, albeit being typically operated in a binary fashion. Multi-valued, or qudit, quantum processors have access to much richer forms of quantum entanglement, which promise to significantly boost the performance and usefulness of quantum devices. However, much of the theory as well as corresponding design methods required for exploiting such hardware remain insufficient and generalizations from qubits are not straightforward. A particular challenge is the compilation of quantum circuits into sets of native qudit gates supported by state-of-the-art quantum hardware. In this work, we address this challenge by introducing a complete workflow for compiling any two-qudit unitary into an arbitrary native gate set. Case studies demonstrate the feasibility of both, the proposed approach as well as the corresponding implementation (which is freely available at https://github.com/cda-tum/qudit-entanglement-compilation).
description: 7 pages, 3 figures, 1 table
The smallest planetary drivers of white dwarf pollution
Creators: name: Veras, Dimitri
name: Rosengren, Aaron J.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Many potential mechanisms for delivering planetary debris to within a few Roche radii of white dwarfs rely on gravitational scattering events that feature perturbers which are giant planets or terrestrial planets. However, the population of these planets orbiting white dwarfs is still unknown, and for a substantial fraction of white dwarfs the largest planetary survivors of stellar evolution may be sub-terrestrial mass minor planets. Here, we attempt to identify the smallest mass perturbers that could pollute white dwarfs. Through computationally expensive numerical simulations of both unstable and stable configurations of minor planets, we find that this critical lower bound equals approximately one Luna mass. Further, we find that as this mass limit is approached from above, the typical cooling age at which white dwarf pollution occurs increases. Consequently, there is a two order-of-magnitude range of perturber masses between Earth and its moon that has remained largely unexplored in white dwarf pollution studies, despite the potential formation of thousands of such Luna-sized objects in these systems.
description: Accepted for publication in MNRAS
A long-lasting quiescence phase of the eruptive variable V1118 Ori
Creators: name: Lorenzetti, D.
name: Antoniucci, S.
name: Giannini, T.
name: Harutyunyan, A.
name: Arkharov, A. A.
name: Larionov, V. M.
name: Cusano, F.
name: Di Paola, A.
name: Causi, G. Li
name: Nisini, B.
name: Speziali, R.
name: Vitali, F.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: V1118 Ori is an eruptive variable belonging to the EXor class of Pre-Main Sequence stars whose episodic outbursts are attributed to disk accretion events. Since 2006, V1118 Ori is in the longest quiescence stage ever observed between two subsequent outbursts of its recent history. We present near-infrared photometry of V1118 Ori carried out during the last eight years, along with a complete spectroscopic coverage from 0.35 to 2.5 um. A longterm sampling of V1118 Ori in quiescence has never been done, hence we can benefit from the current circumstance to determine the lowest values (i.e. the zeroes) of the parameters to be used as a reference for evaluating the physical changes typical of more active phases. A quiescence mass accretion rate between 1--3 $\times$ 10$^{-9}$ M$_{\sun}$ yr$^{-1}$ can be derived and the difference with previous determinations is discussed. From line emission and IR colors analysis a visual extinction of 1-2 mag is consistently derived, confirming that V1118 Ori (at least in quiescence) is a low-extinction T Tauri star with a bolometric luminosity of about 2.1 L$_{\sun}$. An anti-correlation exists between the equivalent width of the emission lines and the underlying continuum. We searched the literature for evaluating whether or not such a behaviour is a common feature of the whole class. The anti-correlation is clearly recognizable for all the available EXors in the optical range (H$β$ and H$α$ lines), while it is not as much evident in the infrared (Pa$β$ and Br$γ$ lines). The observed anti-correlation supports the accretion-driven mechanism as the most likely to account for continuum variations.
description: 6 figures, 5 tables, accepted on ApJ
Novel peanut-specific human IgE monoclonal antibodies enable screens for inhibitors of the effector phase in food allergy
Creators: name: Guo, Rishu
name: Burks, A. Wesley
name: Kulis, Michael D.
name: Suber, Jada
name: Zhang, Yugen
name: Iweala, Onyinye I.
name: Smith, Scott A.
name: Ye, Ping
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: Background 10% of US residents have food allergies, including 2% with peanut allergy. Mast cell mediators released during the allergy effector phase drive allergic reactions. Therefore, targeting sensitized mast cells may prevent food allergy symptoms. Objective We used novel, human, allergen-specific, IgE monoclonal antibodies (mAbs) created using human hybridoma techniques to design an in vitro system to evaluate potential therapeutics targeting sensitized effector cells. Methods Two human IgE mAbs specific for peanut, generated through human hybridoma techniques, were used to sensitize rat basophilic leukemia (RBL) SX-38 cells expressing the human IgE receptor (FcϵRI). Beta-hexosaminidase release (a marker of degranulation), cytokine production, and phosphorylation of signal transduction proteins downstream of FcϵRI were measured after stimulation with peanut. Degranulation was also measured after engaging inhibitory receptors CD300a and Siglec-8. Results Peanut-specific human IgE mAbs bound FcϵRI, triggering degranulation after stimulation with peanut in RBL SX-38 cells. Sensitized RBL SX-38 cells stimulated with peanut increased levels of phosphorylated SYK and ERK, signal transduction proteins downstream of FcϵRI. Engaging inhibitory cell surface receptors CD300a or Siglec-8 blunted peanut-specific activation. Conclusion Allergen-specific human IgE mAbs, expressed from human hybridomas and specific for a clinically relevant food allergen, passively sensitize allergy effector cells central to the in vitro models of the effector phase of food allergy. Peanut reproducibly activates and induces degranulation of RBL SX-38 cells sensitized with peanut-specific human IgE mAbs. This system provides a unique screening tool to assess the efficacy of therapeutics that target allergy effector cells and inhibit food allergen-induced effector cell activation.
Additional file 7 of Identification of CD8+ T cell subsets that normalize in early-treated people living with HIV receiving antiretroviral therapy
Creators: name: Perdomo-Celis, Federico
name: Arcia-Anaya, David
name: Alzate, Juan Carlos
name: Velilla, Paula A.
name: Díaz, Francisco J.
name: Posada, Maria Paulina
name: Rugeles, María T.
name: Taborda, Natalia A.
Publisher: name: figshare
Year: 2022
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Additional file 7: Table S1. List of flow cytometry antibodies.
Optimal observational scheduling framework for binary and multiple stellar systems
Creators: name: Videla, Miguel
name: Mendez, Rene A.
name: Silva, Jorge F.
name: Orchard, Marcos E.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: FOS: Physical sciences

description: The optimal instant of observation of astrophysical phenomena for objects that vary on human time-sales is an important problem, as it bears on the cost-effective use of usually scarce observational facilities. In this paper we address this problem for the case of tight visual binary systems through a Bayesian framework based on the maximum entropy sampling principle. Our proposed information-driven methodology exploits the periodic structure of binary systems to provide a computationally efficient estimation of the probability distribution of the optimal observation time. We show the optimality of the proposed sampling methodology in the Bayes sense and its effectiveness through direct numerical experiments. We successfully apply our scheme to the study of two visual-spectroscopic binaries, and one purely astrometric triple hierarchical system. We note that our methodology can be applied to any time-evolving phenomena, a particularly interesting application in the era of dedicated surveys, where a definition of the cadence of observations can have a crucial impact on achieving the science goals.
description: Accepted for publication to PASP. 23 pages, 2 Tables, 9 Figures, 2 Appendices
Additional file 1 of New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae)
Creators: name: Ludington, Alastair J.
name: Hammond, Jillian M.
name: Breen, James
name: Deveson, Ira W.
name: Sanders, Kate L.
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology

description: Additional file 1: Fig. S1. Cumulative length of assembled sequences. Fig. S2. Assembly Nx plots. Fig. S3. H. major Hi-C contact map. Fig. S4. H. curtus (West) and H. cyanocinctus Hi-C contact maps. Fig. S5. Genome size estimation. Fig. S6. H. major k-mer spectra and multiplicity. Fig. S7. K-mer spectra for H. elegans, H. curtus (West) and H. cyanocinctus. Fig. S8. Assembly BUSCO completeness. Fig. S9. Length distributions of gene features. Fig. S10. Protein BUSCO completeness. Fig. S11. Hard-mask BUSCO completeness. Fig. S12. H. major sliding window LAI scores. Fig. S13. H. ornatus sliding window LAI scores. Fig. S14. H. curtus (West) sliding window LAI scores. Fig. S15. H. elegans sliding window LAI scores. Fig. S16. PhyloNet networks for varying reticulation values. Fig. S17. Chromosomal synteny before manual curation. Fig. S18. Structural variation between Hydrophis snakes. Fig. S19. Overlap between PAML drop-out and BUSTED-PH methods. Fig. S20. Summary of PAML branch-site (alternate model) results. Fig. S21. Fold enrichment reported by PANTHER.
A short guide to topological terms in the effective theories of condensed matter
Creators: name: Tanaka, Akihiro
name: Takayoshi, Shintaro
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: This article is meant as a gentle introduction to the "topological terms" that often play a decisive role in effective theories describing topological quantum effects in condensed matter systems. We first take up several prominent examples, mainly from the area of quantum magnetism and superfluids/superconductors. We then briefly discuss how these ideas are now finding incarnations in the studies of symmetry-protected topological phases, which are in a sense the generalization of the concept of topological insulators to a wider range of materials, including magnets and cold atoms.
description: 18 pages, 6 figures, Pedagogical review article written for the focus issue "Materials Science of Topological Insulators and Superconductors" of the journal, Science and Technology of Advanced Materials (STAM)
A Wide-Field View on Multiple Stellar Populations in 28 Milky Way Globular Clusters
Creators: name: Leitinger, E.
name: Baumgardt, H.
name: Cabrera-Ziri, I.
name: Hilker, M.
name: Pancino, E.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The majority of Galactic globular clusters (GCs) contain multiple stellar populations displaying specific chemical abundance variations. In particular, GCs generally contain a `primordial' population with abundances similar to field stars, along with an `enriched' population exhibiting light element anomalies. In this paper we present a homogeneous and wide-view analysis of multiple stellar populations in 28 Galactic GCs. By using a combination of HST photometry together with wide-field, ground-based photometry we are able to analyse between 84% and 99% of all stars in each cluster. For each GC, we classify stars into separate sub-populations using the well-established $C_{\rm{UBI}}$ colour index, and investigate the spatial distributions of these populations. Our results show that dynamically young GCs can contain either centrally concentrated enriched or primordial populations, or no centrally concentrated population. Dynamically old GCs show fully mixed populations as expected. The existence of clusters born with centrally concentrated primordial (and homogeneously mixed) populations exacerbates the mass-budget problem facing many cluster formation scenarios. The diversity in these results also highlights the need for additional theories that can account for the wide variety of initial conditions that we find. We finally investigate the enriched star fraction as a function of different global parameters in our GC sample, using also data for young and low-mass clusters from the Small- and Large Magellanic Clouds and confirm earlier results that the enriched star fraction strongly correlates with the initial mass of a cluster.
description: 26 pages, 29 figures. Accepted by MNRAS
Computational materials for "Negative Membrane potential accelerates sugar uptake by stabilizing the outward-facing conformation of the Na+/glucose symporter vSGLT"
Creators: name: Naughton, Fiona
name: Grabe, Michael
name: Marcoline, Frank
Publisher: name: Zenodo
Year: 2023

description: Materials used for running of MD simulations and computational model calculations described in the article:
Farha Khan, Matthias Elgeti, Samuel Grandfield, Aviv Paz, Fiona B. Naughton, Frank V. Marcoline, Thorsten Althoff, Natalia Ermolova, Ernest M. Wright, Wayne L. Hubbell, Michael Grabe, Jeff Abramson "Negative Membrane potential accelerates sugar uptake by stabilizing the outward-facing conformation of the Na+/glucose symporter vSGLT". 2023.

init_vSGLT[+/-]na.gro: Initial coordinate files for production molecular dynamics simulation runs of vSGLT with (+na) and without (-na) sodium bound
md_vSGLT[+/-]na_[01/02/03].tpr: Simulation input files in Gromacs 2020.6 format for production MD runs of vSGLT starting with (+na) or without (-na) sodium in the binding site; three repeats (01,02,03) with different initial velocities
md_vSGLT[+/-]na_[01/02/03].gro: Final snapshots at 100ns for each MD run above
KhanMathModel08.20.2023.mmd: Berkeley Madonna (Version 10) code for 5 state model of transport; will reproduce Figure 6 panels b, c and d.
vSGLT_gatingcharge.solv.in: code for calculating gating charges
vSGLT_[inward/outward]-facing3.orient1.pqr: structures used in gating charge calculation
 
Associated experimental data can be found at 10.5281/zenodo.8431613.
The magnetic field driven superconductor-metal transition in disordered hole-overdoped cuprates
Creators: name: Johnsen, Lina G.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: By solving the Bogoliubov-de Gennes equations for a $d$-wave superconductor, we explore how the interplay between disorder and the orbital depairing of an external magnetic field influences the superconductor-metal transition of the hole-overdoped cuprates. For highly disordered systems, we find granular Cooper paring to persist above the critical field where the superfluid stiffness goes to zero. We also show that because the vortices are attracted to regions where the superconducting pairing is already weak, the Caroli-de Gennes-Matricon zero-bias peak in the local density of states at the vortex cores disappears already at moderate disorder.
description: 10 pages (+ 4 pages of appendix), 3 figures
Mechanisms of mutant β-catenin in endometrial cancer progression
Creators: name: Gladden, Andrew B.
name: Parrish, Molly L.
name: Broaddus, Russell R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: Endometrial carcinoma (EC) is the most diagnosed gynecological malignancy in Western countries. Both incidence and mortality rates of EC have steadily risen in recent years. Despite generally favorable prognoses for patients with the endometrioid type of EC, a subset of patients has been identified with decreased progression-free survival. Patients in this group are distinguished from other endometrioid EC patients by the presence of exon 3 hotspot mutations in CTNNB1, the gene encoding for the β-catenin protein. β-catenin is an evolutionarily conserved protein with critical functions in both adherens junctions and Wnt-signaling. The exact mechanism by which exon 3 CTNNB1 mutations drive EC progression is not well understood. Further, the potential contribution of mutant β-catenin to adherens junctions’ integrity is not known. Additionally, the magnitude of worsened progression-free survival in patients with CTNNB1 mutations is context dependent, and therefore the importance of this subset of patients can be obscured by improper categorization. This review will examine the history and functions of β-catenin, how these functions may change and drive EC progression in CTNNB1 mutant patients, and the importance of this patient group in the broader context of the disease.
Additional file 8 of Identification of CD8+ T cell subsets that normalize in early-treated people living with HIV receiving antiretroviral therapy
Creators: name: Perdomo-Celis, Federico
name: Arcia-Anaya, David
name: Alzate, Juan Carlos
name: Velilla, Paula A.
name: Díaz, Francisco J.
name: Posada, Maria Paulina
name: Rugeles, María T.
name: Taborda, Natalia A.
Publisher: name: figshare
Year: 2022
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Additional file 8: Table S2. Therapeutic schemes in the study cohort.
Perceptions and experiences of Congolese midwives implementing a low-cost battery-operated heart rate meter during newborn resuscitation
Creators: name: Iyer, Pooja
name: Myklebust, Helge
name: Eilevstjønn, Joar
name: Patterson, Janna
name: Kamath-Rayne, Beena D.
name: Lokangaka, Adrien
name: Berkelhamer, Sara
name: Tshefu, Antoinette
name: Thornton, Madeline
name: Bauserman, Melissa
name: Bose, Carl
name: Ishoso, Daniel
name: Patterson, Jackie K.
name: Mafuta, Eric
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: Background 900,000 newborns die from respiratory depression each year; nearly all of these deaths occur in low- and middle-income countries. Deaths from respiratory depression are reduced by evidence-based resuscitation. Electronic heart rate monitoring provides a sensitive indicator of the neonate's status to inform resuscitation care, but is infrequently used in low-resource settings. In a recent trial in the Democratic Republic of the Congo, midwives used a low-cost, battery-operated heart rate meter (NeoBeat) to continuously monitor heart rate during resuscitations. We explored midwives' perceptions of NeoBeat including its utility and barriers and facilitators to use. Methods After a 20-month intervention in which midwives from three facilities used NeoBeat during resuscitations, we surveyed midwives and conducted focus group discussions (FGDs) regarding the incorporation of NeoBeat into clinical care. FGDs were conducted in Lingala, the native language, then transcribed and translated from Lingala to French to English. We analyzed data by: (1) coding of transcripts using Nvivo, (2) comparison of codes to identify patterns in the data, and (3) grouping of codes into categories by two independent reviewers, with final categories determined by consensus. Results Each midwife from Facility A used NeoBeat on an estimated 373 newborns, while each midwife at facilities B and C used NeoBeat an average 24 and 47 times, respectively. From FGDs with 30 midwives, we identified five main categories of perceptions and experiences regarding the use of NeoBeat: (1) Providers' initial skepticism evolved into pride and a belief that NeoBeat was essential to resuscitation care, (2) Providers viewed NeoBeat as enabling their resuscitation and increasing their capacity, (3) NeoBeat helped providers identify flaccid newborns as liveborn, leading to hope and the perception of saving of lives, (4) Challenges of use of NeoBeat included cleaning, charging, and insufficient quantity of devices, and (5) Providers desired to continue using the device and to expand its use beyond resuscitation and their own facilities. Conclusion Midwives perceived that NeoBeat enabled their resuscitation practices, including assisting them in identifying non-breathing newborns as liveborn. Increasing the quantity of devices per facility and developing systems to facilitate cleaning and charging may be critical for scale-up.
An expanded population of CD8dim T cells with features of mitochondrial dysfunction and senescence is associated with persistent HIV-associated Kaposi’s sarcoma under ART
Creators: name: Weideman, Ann Marie K.
name: Maurer, Toby
name: Clutton, Genevieve T.
name: Goonetilleke, Nilu P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: HIV-associated Kaposi’s sarcoma (KS), which is caused by Kaposi’s sarcoma-associated herpesvirus, usually arises in the context of uncontrolled HIV replication and immunosuppression. However, disease occasionally occurs in individuals with durable HIV viral suppression and CD4 T cell recovery under antiretroviral therapy (ART). The underlying mechanisms associated with this phenomenon are unclear. Suppression of viral infections can be mediated by CD8 T cells, which detect infected cells via their T cell receptor and the CD8 coreceptor. However, CD8 T cells exhibit signs of functional exhaustion in untreated HIV infection that may not be fully reversed under ART. To investigate whether KS under ART was associated with phenotypic and functional perturbations of CD8 T cells, we performed a cross-sectional study comparing HIV-infected individuals with persistent KS under effective ART (HIV+ KS+) to HIV-infected individuals receiving effective ART with no documented history of KS (HIV+ KSneg). A subset of T cells with low cell surface expression of CD8 (“CD8dim T cells”) was expanded in HIV+ KS+ compared with HIV+ KSneg participants. Relative to CD8bright T cells, CD8dim T cells exhibited signs of senescence (CD57) and mitochondrial alterations (PGC-1α, MitoTracker) ex vivo. Mitochondrial activity (MitoTracker) was also reduced in proliferating CD8dim T cells. These findings indicate that an expanded CD8dim T cell population displaying features of senescence and mitochondrial dysfunction is associated with KS disease under ART. CD8 coreceptor down-modulation may be symptomatic of ongoing disease.
Asteroseismic measurement of slow, nearly-uniform surface-to-core rotation in the main sequence F star KIC 9244992
Creators: name: Saio, Hideyuki
name: Kurtz, Donald W.
name: Takata, Masao
name: Shibahashi, Hiromoto
name: Murphy, Simon J.
name: Sekii, Takashi
name: Bedding, Timothy R.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We have found a rotationally split series of core g-mode triplets and surface p-mode multiplets in a main sequence F star, KIC 9244992. Comparison with models shows that the star has a mass of about 1.45 M$_\odot$, and is at an advanced stage of main sequence evolution in which the central hydrogen abundance mass fraction is reduced to about 0.1. This is the second case, following KIC 11145123, of an asteroseismic determination of the rotation of the deep core and surface of an A-F main-sequence star. We have found, essentially model-independently, that the rotation near the surface, obtained from p-mode splittings, is 66 d, slightly slower than the rotation of 64 d in the core, measured by g-mode splittings. KIC 9244992 is similar to KIC 11145123 in that both are near the end of main-sequence stage with very slow and nearly uniform rotation. This indicates the angular momentum transport in the interior of an A-F star during the main sequence stage is much stronger than that expected from standard theoretical formulations.
description: 15 pages, 17 figures, accepted for publication in MNRAS
Additional file 1 of A systematic quality evaluation and review of nanomaterial genotoxicity studies: a regulatory perspective
Creators: name: Siivola, Kirsi K.
name: Burgum, Michael J.
name: Suárez-Merino, Blanca
name: Clift, Martin J. D.
name: Doak, Shareen H.
name: Catalán, Julia
Publisher: name: figshare
Year: 2022
Subjects: subject: Information Systems
subject: FOS: Computer and information sciences

description: Additional file 1. Reproduction of the scores and criteria used in the GUIDEnano quality approach.
Additional file 1 of Neuromuscular diseases associated with COVID-19 vaccines: a systematic review and pooled analysis of 258 patients
Creators: name: Tayebi, Amirhossein
name: Samimisedeh, Parham
name: Jafari Afshar, Elmira
name: Mahmoudnia, Saeideh
name: Milan, Nesa
name: Ayati, Aryan
name: Madady, Aryan
name: Rastad, Hadith
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Science Policy
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: Additional file 1: Supplementary Table 1. Quality assessment of the included case series based on the JBI checklist for case series. Supplementary Table 2. Guillain barre syndrome studies and patients’ characteristics by case. Supplementary Table 3. Guillain Barre patients’ findings, treatments, and outcomes by case. Supplementary Table 4. Parsonage turner studies and patients’ characteristics by case. Supplementary Table 5. Parsonage turner patients’ findings, treatments, and outcomes by case. Supplementary table 6. Facial nerve palsy patients’ findings, treatments, and clinical outcomes by case. Supplementary table 7.  Small fiber neuropathy and tolosa-hunt patients’ findings, treatments, and clinical outcomes by case. Supplementary Table 8. Myasthenia gravis studies and patients’ characteristics by case. Supplementary Table 9. Myasthenia gravis patients’ findings, treatments, and clinical outcomes by case.
Explaining Deep Models through Forgettable Learning Dynamics
Creators: name: Benkert, Ryan
name: Aribido, Oluwaseun Joseph
name: AlRegib, Ghassan
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Even though deep neural networks have shown tremendous success in countless applications, explaining model behaviour or predictions is an open research problem. In this paper, we address this issue by employing a simple yet effective method by analysing the learning dynamics of deep neural networks in semantic segmentation tasks. Specifically, we visualize the learning behaviour during training by tracking how often samples are learned and forgotten in subsequent training epochs. This further allows us to derive important information about the proximity to the class decision boundary and identify regions that pose a particular challenge to the model. Inspired by this phenomenon, we present a novel segmentation method that actively uses this information to alter the data representation within the model by increasing the variety of difficult regions. Finally, we show that our method consistently reduces the amount of regions that are forgotten frequently. We further evaluate our method in light of the segmentation performance.
Writing and erasing of temporal cavity solitons by direct phase modulation of the cavity driving field
Creators: name: Jang, Jae K.
name: Erkintalo, Miro
name: Murdoch, Stuart G.
name: Coen, Stephane
Publisher: name: arXiv
Year: 2015
Subjects: subject: Optics (physics.optics)
subject: Pattern Formation and Solitons (nlin.PS)
subject: FOS: Physical sciences

description: Temporal cavity solitons (CSs) are persisting pulses of light that can manifest themselves in continuously driven passive resonators, such as macroscopic fiber ring cavities and monolithic microresonators. Experiments so far have demonstrated two techniques for their excitation, yet both possess drawbacks in the form of system complexity or lack of control over soliton positioning. Here we experimentally demonstrate a new CS writing scheme that alleviates these deficiencies. Specifically, we show that temporal CSs can be excited at arbitrary positions through direct phase modulation of the cavity driving field, and that this technique also allows existing CSs to be selectively erased. Our results constitute the first experimental demonstration of temporal cavity soliton excitation via direct phase modulation, as well as their selective erasure (by any means). These advances reduce the complexity of CS excitation and could lead to controlled pulse generation in monolithic microresonators.
description: 5 pages, 5 figures
Early ACEI/ARB use and in-hospital outcomes of acute myocardial infarction patients with systolic blood pressure <100 mmHg and undergoing percutaneous coronary intervention: Findings from the CCC-ACS project
Creators: name: Zhao, Xuedong
name: Fonarow, Gregg C.
name: Nie, Shaoping
name: Ma, Changsheng
name: Morgan, Louise
name: Zhao, Dong
name: Zhao, Guanqi
name: Que, Bin
name: Liu, Jing
name: Zhou, Mengge
name: Ai, Hui
name: Wang, Ge
name: Smith, Sidney C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: BackgroundFew studies have evaluated whether acute myocardial infarction (AMI) patients with relatively low blood pressure benefit from early ACEI/ARB use in the era of percutaneous coronary intervention (PCI).ObjectivesThis study evaluated the associations of ACEI/ARB use within 24 h of admission with in-hospital outcomes among AMI patients with SBP < 100 mmHg and undergoing PCI.MethodsThis study was based on the Improving Care for Cardiovascular Disease in China-ACS project, a collaborative registry and quality improvement project of the American Heart Association and the Chinese Society of Cardiology. Between November 2014 and December 2019, a total of 94,623 patients with AMI were enrolled. Of them, 4,478 AMI patients with SBP < 100 mmHg and undergoing PCI but without clinically diagnosed cardiogenic shock at admission were included. Multivariable logistic regression and propensity score-matching analysis were used to evaluate the association between early ACEI/ARB use and in-hospital major adverse cardiac events (MACEs), a combination of all-cause death, cardiogenic shock, and cardiac arrest.ResultsOf AMI patients, 24.41% (n = 1,093) were prescribed ACEIs/ARBs within 24 h of admission. Patients with early ACEI/ARB use had a significantly lower rate of MACEs than those without ACEI/ARB use (1.67% vs. 3.66%, p = 0.001). In the logistic regression analysis, early ACEI/ARB use was associated with a 45% lower risk of MACEs (odds ratio: 0.55, 95% CI: 0.33–0.93; p = 0.027). Further propensity score-matching analysis still showed that patients with early ACEI/ARB use had a lower rate of MACEs (1.96% vs. 3.93%, p = 0.009).ConclusionThis study found that among AMI patients with an admission SBP < 100 mmHg undergoing PCI, early ACEI/ARB use was associated with better in-hospital outcomes. Additional studies of the early use of ACEIs/ARBs in AMI patients with relatively low blood pressure are warranted.
Additional file 1 of The role of patients’ stories in medicine: a systematic scoping review
Creators: name: Quah, Elaine Li Ying
name: Chua, Keith Zi Yuan
name: Lin, Casper Keegan Ronggui
name: Vijayan, Andrew Vimal
name: Abdul Hamid, Nur Amira Binte
name: Owyong, Jasmine Lerk Juan
name: Satku, Neeta
name: Woong, Natalie
name: Lim, Crystal
name: Phua, Gillian Li Gek
name: Ong, Eng Koon
name: Fong, Warren
name: Krishna, Lalit Kumar Radha
Publisher: name: figshare
Year: 2024
Subjects: Medicine
Biological Sciences not elsewhere classified
Science Policy

description: Additional file 1. Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) Checklist.
Additional file 2 of A systematic quality evaluation and review of nanomaterial genotoxicity studies: a regulatory perspective
Creators: name: Siivola, Kirsi K.
name: Burgum, Michael J.
name: Suárez-Merino, Blanca
name: Clift, Martin J. D.
name: Doak, Shareen H.
name: Catalán, Julia
Publisher: name: figshare
Year: 2022
Subjects: subject: Information Systems
subject: FOS: Computer and information sciences

description: Additional file 2. Outcomes of the qualified publication and evaluation of the NanoInformaTIX database instance.
The human right to a healthy environment—time for the public health community to take urgent action
Creators: name: Hesselman, Marlies
name: Meier, Benjamin Mason
name: Buse, Kent
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: The public health community should urgently leverage the human right to a healthy environment to protect planetary health, argue Kent Buse and colleagues.
Fractional Edgeworth Expansion: Corrections to the Gaussian-Lévy Central Limit Theorem
Creators: name: Hazut, Netanel
name: Medalion, Shlomi
name: Kessler, David A.
name: Barkai, Eli
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: In this article we generalize the classical Edgeworth expansion for the probability density function (PDF) of sums of a finite number of symmetric independent identically distributed random variables with a finite variance to sums of variables with an infinite variance which converge by the generalized central limit theorem to a Lévy $α$-stable density function. Our correction may be written by means of a series of fractional derivatives of the Lévy and the conjugate Lévy PDFs. This series expansion is general and applies also to the Gaussian regime. To describe the terms in the series expansion, we introduce a new family of special functions and briefly discuss their properties. We implement our generalization to the distribution of the momentum for atoms undergoing Sisyphus cooling, and show the improvement of our leading order approximation compared to previous approximations. In vicinity of the transition between Lévy and Gauss behaviors, convergence to asymptotic results slows down.
Identifying Coupling Structure in Complex Systems through the Optimal Causation Entropy Principle
Creators: name: Sun, Jie
name: Cafaro, Carlo
name: Bollt, Erik M.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: Information Theory (cs.IT)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Inferring the coupling structure of complex systems from time series data in general by means of statistical and information-theoretic techniques is a challenging problem in applied science. The reliability of statistical inferences requires the construction of suitable information-theoretic measures that take into account both direct and indirect influences, manifest in the form of information flows, between the components within the system. In this work, we present an application of the optimal causation entropy (oCSE) principle to identify the coupling structure of a synthetic biological system, the repressilator. Specifically, when the system reaches an equilibrium state, we use a stochastic perturbation approach to extract time series data that approximate a linear stochastic process. Then, we present and jointly apply the aggregative discovery and progressive removal algorithms based on the oCSE principle to infer the coupling structure of the system from the measured data. Finally, we show that the success rate of our coupling inferences not only improves with the amount of available data, but it also increases with a higher frequency of sampling and is especially immune to false positives.
Additional file 2 of The role of patients’ stories in medicine: a systematic scoping review
Creators: name: Quah, Elaine Li Ying
name: Chua, Keith Zi Yuan
name: Lin, Casper Keegan Ronggui
name: Vijayan, Andrew Vimal
name: Abdul Hamid, Nur Amira Binte
name: Owyong, Jasmine Lerk Juan
name: Satku, Neeta
name: Woong, Natalie
name: Lim, Crystal
name: Phua, Gillian Li Gek
name: Ong, Eng Koon
name: Fong, Warren
name: Krishna, Lalit Kumar Radha
Publisher: name: figshare
Year: 2024
Subjects: Medicine
Biological Sciences not elsewhere classified
Science Policy

description: Additional file 2. Search Strategies.
Robust Human Identity Anonymization using Pose Estimation
Creators: name: Zhang, Hengyuan
name: Liao, Jing-Yan
name: Paz, David
name: Christensen, Henrik I.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Many outdoor autonomous mobile platforms require more human identity anonymized data to power their data-driven algorithms. The human identity anonymization should be robust so that less manual intervention is needed, which remains a challenge for current face detection and anonymization systems. In this paper, we propose to use the skeleton generated from the state-of-the-art human pose estimation model to help localize human heads. We develop criteria to evaluate the performance and compare it with the face detection approach. We demonstrate that the proposed algorithm can reduce missed faces and thus better protect the identity information for the pedestrians. We also develop a confidence-based fusion method to further improve the performance.
description: Source code will be available at https://github.com/AutonomousVehicleLaboratory/anonymization
Explaining Deep Neural Networks for Bearing Fault Detection with Vibration Concepts
Creators: name: Decker, Thomas
name: Lebacher, Michael
name: Tresp, Volker
Publisher: name: arXiv
Year: 2023
Subjects: subject: Machine Learning (cs.LG)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: Concept-based explanation methods, such as Concept Activation Vectors, are potent means to quantify how abstract or high-level characteristics of input data influence the predictions of complex deep neural networks. However, applying them to industrial prediction problems is challenging as it is not immediately clear how to define and access appropriate concepts for individual use cases and specific data types. In this work, we investigate how to leverage established concept-based explanation techniques in the context of bearing fault detection with deep neural networks trained on vibration signals. Since bearings are prevalent in almost every rotating equipment, ensuring the reliability of intransparent fault detection models is crucial to prevent costly repairs and downtimes of industrial machinery. Our evaluations demonstrate that explaining opaque models in terms of vibration concepts enables human-comprehensible and intuitive insights about their inner workings, but the underlying assumptions need to be carefully validated first.
description: 2023 IEEE 21st International Conference on Industrial Informatics (INDIN)
IgG-like bispecific antibodies with potent and synergistic neutralization against circulating SARS-CoV-2 variants of concern
Creators: name: Hou, Yixuan J.
name: Ke, Hanzhong
name: Kuzmina, Natalia A.
name: Ronk, Adam J.
name: Leist, Sarah R.
name: Nguyen, Katrina
name: Honko, Anna
name: Tomasovic, Luke
name: Byrne, Patrick O.
name: Olmedillas, Eduardo
name: Zhu, Quan
name: Storm, Nadia
name: Coherd, Christian
name: Johnson, Rebecca
name: Chang, Matthew R.
name: Saphire, Erica Ollmann
name: Tse, Longping V.
name: Schäfer, Alexandra
name: Alter, Galit
name: Baric, Ralph S.
name: McLellan, Jason S.
name: Griffiths, Anthony
name: Kamkaew, Maliwan
name: Bukreyev, Alexander
name: Marasco, Wayne A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2022

description: Monoclonal antibodies are a promising approach to treat COVID-19, however the emergence of SARS-CoV-2 variants has challenged the efficacy and future of these therapies. Antibody cocktails are being employed to mitigate these challenges, but neutralization escape remains a major challenge and alternative strategies are needed. Here we present two anti-SARS-CoV-2 spike binding antibodies, one Class 1 and one Class 4, selected from our non-immune human single-chain variable fragment (scFv) phage library, that are engineered into four, fully-human IgG-like bispecific antibodies (BsAb). Prophylaxis of hACE2 mice and post-infection treatment of golden hamsters demonstrates the efficacy of the monospecific antibodies against the original Wuhan strain, while promising in vitro results with the BsAbs demonstrate enhanced binding and distinct synergistic effects on neutralizing activity against circulating variants of concern. In particular, one BsAb engineered in a tandem scFv-Fc configuration shows synergistic neutralization activity against several variants of concern including B.1.617.2. This work provides evidence that synergistic neutralization can be achieved using a BsAb scaffold, and serves as a foundation for the future development of broadly reactive BsAbs against emerging variants of concern.
Modification of electronic structure and thermoelectric properties of hole-doped tungsten dichalcogenides
Creators: name: Kriener, M.
name: Kikkawa, A.
name: Suzuki, T.
name: Akashi, R.
name: Arita, R.
name: Tokura, Y.
name: Taguchi, Y.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We present a study on the modification of the electronic structure and hole-doping effect for the layered dichalcogenide WSe_2 with a multi-valley band structure, where Ta is doped on the W site along with a partial substitution of Te for its lighter counterpart Se. By means of band-structure calculations and specific-heat measurements, the introduction of Te is theoretically and experimentally found to change the electronic states in WSe_2. While in WSe_2 the valence-band maximum is located at the Gamma point, the introduction of Te raises the bands at the K point with respect to the Gamma point. In addition, thermal-transport measurements reveal a smaller thermal conductivity at room temperature of W_1-xTa_xSe_1.6Te_0.4 than reported for W_1-xTa_xSe_2. However, when approaching 900 K, the thermal conductivities of both systems converge while the resistivity in W_1-xTa_xSe_1.6Te_0.4 is larger than in W_1-xTa_xSe_2, leading to comparable but slightly smaller values of the figure of merit in W_1-xTa_xSe_1.6Te_0.4.
description: 11 pages, 8 figures
Capacity analysis of a multi-cell multi-antenna cooperative cellular network with co-channel interference
Creators: name: Ge, Xiaohu
name: Huang, Kun
name: Wang, Cheng-Xiang
name: Hong, Xuemin
name: Yang, Xi
Publisher: name: arXiv
Year: 2014
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: Information Theory (cs.IT)
subject: FOS: Computer and information sciences

description: Characterization and modeling of co-channel interference is critical for the design and performance evaluation of realistic multi-cell cellular networks. In this paper, based on alpha stable processes, an analytical co-channel interference model is proposed for multi-cell multiple-input multi-output (MIMO) cellular networks. The impact of different channel parameters on the new interference model is analyzed numerically. Furthermore, the exact normalized downlink average capacity is derived for a multi-cell MIMO cellular network with co-channel interference. Moreover, the closed-form normalized downlink average capacity is derived for cell-edge users in the multi-cell multiple-input single-output (MISO) cooperative cellular network with co-channel interference. From the new co-channel interference model and capacity, the impact of cooperative antennas and base stations on cell-edge user performance in the multi-cell multi-antenna cellular network is investigated by numerical methods. Numerical results show that cooperative transmission can improve the capacity performance of multi-cell multi-antenna cooperative cellular networks, especially in a scenario with a high density of interfering base stations. The capacity performance gain is degraded with the increased number of cooperative antennas or base stations.
A Thompson group for the basilica
Creators: name: Belk, James
name: Forrest, Bradley
Publisher: name: arXiv
Year: 2012
Subjects: subject: Group Theory (math.GR)
subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics
subject: 20F65 (Primary) 20F38, 37F10 (Secondary)

description: We describe a Thompson-like group of homeomorphisms of the basilica Julia set. Each element of this group acts as a piecewise-linear homeomorphism of the unit circle that preserves the invariant lamination for the basilica. We develop an analogue of tree pair diagrams for this group which we call arc pair diagrams, and we use these diagrams to prove that the group is finitely generated. We also prove that the group is virtually simple.
description: Published version