cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection
Creators: name: Marsh, Jacob I
name: Johri, Parul
Publisher: name: Oxford University Press (OUP)
Year: 2024

description: Inferring the demographic history of populations provides fundamental insights into species dynamics and is essential for developing a null model to accurately study selective processes. However, background selection and selective sweeps can produce genomic signatures at linked sites that mimic or mask signals associated with historical population size change. While the theoretical biases introduced by the linked effects of selection have been well established, it is unclear whether ancestral recombination graph (ARG)-based approaches to demographic inference in typical empirical analyses are susceptible to misinference due to these effects. To address this, we developed highly realistic forward simulations of human and Drosophila melanogaster populations, including empirically estimated variability of gene density, mutation rates, recombination rates, purifying, and positive selection, across different historical demographic scenarios, to broadly assess the impact of selection on demographic inference using a genealogy-based approach. Our results indicate that the linked effects of selection minimally impact demographic inference for human populations, although it could cause misinference in populations with similar genome architecture and population parameters experiencing more frequent recurrent sweeps. We found that accurate demographic inference of D. melanogaster populations by ARG-based methods is compromised by the presence of pervasive background selection alone, leading to spurious inferences of recent population expansion, which may be further worsened by recurrent sweeps, depending on the proportion and strength of beneficial mutations. Caution and additional testing with species-specific simulations are needed when inferring population history with non-human populations using ARG-based approaches to avoid misinference due to the linked effects of selection.
Soliton-induced Majorana fermions in a one-dimensional atomic topological superfluid
Creators: name: Liu, Xia-Ji
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We theoretically investigate the behavior of dark solitons in a one-dimensional spin-orbit coupled atomic Fermi gas in harmonic traps, by solving self-consistently the Bogoliubov-de Gennes equations. The dark soliton - to be created by phase-imprinting in future experiments - is characterized by a real order parameter, which changes sign at a point node and hosts localized Andreev bound states near the node. By considering both cases of a single soliton and of multiple solitons, we find that the energy of these bound states decreases to zero, when the system is tuned to enter the topological superfluid phase by increasing an external Zeeman field. As a result, two Majorana fermions emerge in the vicinity of each soliton, in addition to the well-known Majorana fermions at the trap edges associated with the nontrivial topology of the superfluid. We propose that the soliton-induced Majorana fermions can be directly observed by using spatially-resolved radio-frequency spectroscopy or indirectly probed by measuring the density profile at the point node. For the latter, the deep minimum in the density profile will disappear due to the occupation of the soliton-induced zero-energy Majorana fermion modes. Our prediction could be tested in a resonantly-interacting spin-orbit coupled $^{40}$K Fermi gas confined in a two-dimensional optical lattice.
description: 9 pages, 8 figures
Fracture investigation of V-notch made of tungsten-copper functionally graded materials
Creators: name: Mohammadi Hosein
name: Salavati Hadi
name: Alizadeh Yoness
name: Filippo, Berto
name: Panin Sergey, V.
Publisher: name: Физическая мезомеханика
Year: 2017
Subjects: FUNCTIONALLY GRADED MATERIALS
TUNGSTEN
COPPER
V-NOTCHES WITH END HOLE
MODE I LOADING
STRAIN ENERGY DENSITY
ФУНКЦИОНАЛЬНЫЕ ГРАДИЕНТНЫЕ МАТЕРИАЛЫ
ВОЛЬФРАМ
МЕДЬ
V-ОБРАЗНЫЙ НАДРЕЗ С ОТВЕРСТИЕМ В ВЕРШИНЕ
НОРМАЛЬНЫЙ ОТРЫВ
ПЛОТНОСТЬ ЭНЕРГИИ ДЕФОРМАЦИИ

description: The fracture of V-notches with end holes made of tungsten-copper functionally graded material under mode I has been studied in this paper. The averaged strain energy density over a well-defined control volume was employed to predict the fracture loads. A numerical approach was used to determine the outer boundary of the control volume. Mechanical properties such as elasticity modulus, Poisson’s ratio, fracture toughness KIc, and ultimate tensile stress have been considered to obey the power law function through the specimen width.
PIVOTING IN NIGERIA’S FISH AND POULTRY VALUE CHAINS IN RESPONSE TO COVID-19 POLICIES AND IMPACTS
Creators: name: Tasie, Saweda
name: Belton, Ben
name: Tasie, Oyinkan
name: Osawe, Wellington
name: Parkhi, Charuta
name: Reardon, Thomas
name: Igbudu, Iveren
name: Muhammed, Aisha
name: Sule, Balaraba
name: Hudu, Muhammad
name: Ibrahim, Aisha
name: Odey, Grace
name: Emmanuel, Adejoh
name: James, Elizabeth
name: Tasie, Saweda
name: Belton, Ben
name: Tasie, Oyinkan
name: Osawe, Wellington
name: Parkhi, Charuta
name: Reardon, Thomas
name: Igbudu, Iveren
name: Muhammed, Aisha
name: Sule, Balaraba
name: Hudu, Muhammad
name: Ibrahim, Aisha
name: Odey, Grace
name: Emmanuel, Adejoh
name: James, Elizabeth
Publisher: name: Unknown
Year: 2021
Subjects: subject: Agricultural and Food Policy
subject: Covid
subject: Policy
subject: Food
subject: Economics
subject: Agriculture

description: This report uses a panel dataset from two phone surveys covering February–October 2020 and March– July 2021, with nearly 500 small and medium enterprises (SMEs) in the fish and poultry value chains of eight states in all six of Nigeria’s geopolitical zones. We address three empirical gaps in the knowledge of the impacts of COVID-19 and containment policies on enterprises in these value chains.
X-rays from the episodic dust maker WR 137
Creators: name: Zhekov, Svetozar A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We present an analysis of the XMM-Newton observation of the episodic dust maker WR 137. Global spectral fits show that its X-ray spectrum is well matched by a two-temperature optically-thin plasma emission (kT_1 ~ 0.4 keV and kT_2 ~ 2.2 keV). If we adopt the colliding stellar wind (CSW) picture for this wide WR+O binary, the theoretical CSW spectra match well the shape of the observed X-ray spectrum of WR 137 but they overestimate the observed flux (emission measure) by about two orders of magnitude. To reconcile the model predictions with observations, the mass loss of \WR must be reduced considerably (by about an order of magnitude) with respect to its currently accepted value. In all the spectral fits, the derived X-ray absorption is consistent with the optical extinction to WR 137.
description: Accepted for publication in MNRAS; 9 pages, 4 figures, 2 tables
Rimegepant orally disintegrating tablets in the acute treatment of migraine: a profile of their use
Creators: name: Kim, Esther S.
name: Lyseng-Williamson, Katherine A.
Publisher: name: Adis Journals
Year: 2020
Subjects: Medicine

description: DeclarationsFunding The preparation of this review was not supported by any external funding. Authorship and conflict of interest E. Kim is a contracted employee of Adis International Ltd/Springer Nature, and declares no relevant conflicts of interest. K.A. Lyseng-Williamson is the Editor of Drugs & Therapy Perspectives, was not involved in any publishing decisions for this manuscript, and is a salaried employee of Adis International Limited/Springer Nature. She has no other conflicts of interest to declare. All authors contributed to the review and are responsible for the article content. Ethics approval, consent to participate, consent for publication, availability of data and material, code availability Not applicable.Additional information about this Adis Drug Review can be found here
AbstractRimegepant orally disintegrating tablets (ODT) for sublingual or oral use (Nurtec™ ODT) are a valuable option for the acute treatment of migraine ± aura in adults, especially those with contraindications, treatment failure, or tolerability issues with triptans. Rimegepant is a calcitonin gene-related peptide (CGRP) receptor antagonist, and is the first, and currently only, drug in this class available as an ODT formulation in the USA. A single sublingual dose of rimegepant ODT 75 mg provided freedom from pain, freedom from the most bothersome migraine symptoms (e.g., nausea, phonophobia, photophobia), and freedom from functional disability at 2-h post dose relative to placebo in adults with a migraine attack with pain of moderate or severe intensity ± aura. Beneficial effects on migraine were provided as early as 1-h post dose,) and were sustained for 2–48 h. Rimegepant ODT was well tolerated, with a tolerability profile similar to that of placebo, with no reports of serious, cardiovascular, or hepatic adverse events in patients with migraine.
© Springer Nature Switzerland AG 2020
Longitudinal tracking of perfluorooctanoic acid exposure on mammary epithelial cell spheroids by dynamic optical coherence tomography
Creators: name: Ji, Pan
name: Oldenburg, Amy L.
name: Miranda Buzetta, Abel A.
name: Lockett, Matthew R.
name: Zhou, Haibo
name: Yang, Lin
name: Li, Haolin
Publisher: name: Optica Publishing Group
Year: 2024

description:  We investigated the morphology and intracellular motility of mammary epithelial cell (MCF10DCIS.com) spheroids cultured in 3D artificial extracellular matrix under perfluorooctanoic acid (PFOA) exposure. Dynamic optical coherence tomography (OCT) was employed for real-time, non-invasive imaging of these spheroids longitudinally over 12 days under PFOA exposures up to 500 µM. Despite no significant changes in volume or asphericity of spheroids, morphological alterations were observed in OCT images of spheroids at 100 µM on Day 12 and from Day 4 at 500 µM. Intracellular motility was assessed by the inverse-power-law exponent of the speckle fluctuation spectrum ( α ), and an autocorrelation-based motility amplitude ( M ). Linear regression indicated that both PFOA concentration and culture time are highly significant predictors for both α and M ( p < 0.001 for all). Both PFOA concentration and culture time have positive associations with α and negative association with M , where increased α indicates suppression of higher frequency fluctuations (∼> 2 Hz) relative to those at lower frequencies, and decreased M indicates overall suppression of intracellular motility. This study can lead to the future development of biomarkers for per- and polyfluoroalkyl substances (PFAS) exposure using dynamic OCT and its associated toolkit of quantitative metrics.
$V$-universal Hopf algebras (co)acting on $Ω$-algebras
Creators: name: Agore, Ana
name: Gordienko, Alexey
name: Vercruysse, Joost
Publisher: name: arXiv
Year: 2020
Subjects: subject: Rings and Algebras (math.RA)
subject: Category Theory (math.CT)
subject: Quantum Algebra (math.QA)
subject: Representation Theory (math.RT)
subject: FOS: Mathematics
subject: Primary 16T05, Secondary 16W50, 16T05, 16T25, 16W22

description: We develop a theory which unifies the universal (co)acting bi/Hopf algebras as studied by Sweedler, Manin and Tambara with the recently introduced \cite{AGV1} bi/Hopf-algebras that are universal among all support equivalent (co)acting bi/Hopf algebras. Our approach uses vector spaces endowed with a family of linear maps between tensor powers of $A$, called $Ω$-algebras. This allows us to treat algebras, coalgebras, braided vector spaces and many other structures in a unified way. We study $V$-universal measuring coalgebras and $V$-universal comeasuring algebras between $Ω$-algebras $A$ and $B$, relative to a fixed subspace $V$ of $\Vect(A,B)$. By considering the case $A=B$, we derive the notion of a $V$-universal (co)acting bialgebra (and Hopf algebra) for a given algebra $A$. In particular, this leads to a refinement of the existence conditions for the Manin--Tambara universal coacting bi/Hopf algebras. We establish an isomorphism between the $V$-universal acting bi/Hopf algebra and the finite dual of the $V$-universal coacting bi/Hopf algebra under certain conditions on $V$ in terms of the finite topology on $\End_F(A)$.
description: 31 pages; the formulation of Theorem 4.7 was clarified and minor misprints were corrected
Should antenatal corticosteroids be used in the late preterm period in pregnant patients with pregestational or gestational diabetes?
Creators: name: Cornwell, Neil S.
name: Boggiano, Victoria L.
name: Wright, Sarah T.
name: Farahi, Narges
Publisher: name: Wolters Kluwer
Year: 2024

description: This clinical question was developed as an HDA
through a standardized, systemic methodology (HDA
Methods, Supplemental Digital Content).
Poor prognosis among radiation associated bladder cancer is defined by clinicogenomic features
Creators: name: Jin, Dexter X.
name: Frampton, Garrett M
name: Moore, Jay A
name: Wijetunga, N. Ari
name: Gessner, Kathryn H.
name: Damrauer, Jeffrey S
name: Corcoran, David L.
name: Milowsky, Matthew I.
name: Galsky, Matthew D
name: Wobker, Sara E
name: Kim, William Y
name: Repka, Michael
name: Kanchi, Krishna
name: Rose, Tracy L
name: Sud, Shivani
name: Fleischmann, Zoe
name: Sturdivant, Michael
Publisher: name: American Association for Cancer Research (AACR)
Year: 2024

description: Radiation therapy (RT) for prostate cancer has been associated with an increased risk for the development of bladder cancer. We aimed to integrate clinical and genomic data to better understand the development of RT-associated bladder cancer. A retrospective analysis was performed to identify control (CTRL; n= 41) and RT-associated (n=41) bladder cancer patients. RT and CTRL specific features were then identified through integration and analysis of the genomic sequencing data and clinical variables. RT-associated bladder tumors were significantly enriched for alterations in KDM6A and ATM, while CTRL tumors were enriched for CDKN2A mutation. Globally, there was an increased number of variants within RT tumors, albeit at a lower variant allele frequency. Mutational signature analysis revealed three predominate motif patterns, with similarity to SBS2/13 (APOBEC3A), SBS5 (ERCC2/Smoking) and SBS6/15 (MMR). Poor prognostic factors in the RT cohort include, a short tumor latency, smoking status, the presence of the smoking and XRT mutational signatures, and CDKN2A copy number loss. Based on the clinical and genomic findings, we suggest, at least two potential pathways leading to RT-associated bladder cancer; the first, occurs in the setting of field cancerization, related to smoking or pre-existing genetic alterations and leads to the development of more aggressive bladder tumors, and the second, in which RT initiates the oncogenic process in otherwise healthy urothelium, leading to a longer latency and less aggressive disease.
Auxiliary Features-Guided Super Resolution for Monte Carlo Rendering
Creators: name: Hou, Qiqi
name: Liu, Feng
Publisher: name: arXiv
Year: 2023
Subjects: subject: Graphics (cs.GR)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: This paper investigates super resolution to reduce the number of pixels to render and thus speed up Monte Carlo rendering algorithms. While great progress has been made to super resolution technologies, it is essentially an ill-posed problem and cannot recover high-frequency details in renderings. To address this problem, we exploit high-resolution auxiliary features to guide super resolution of low-resolution renderings. These high-resolution auxiliary features can be quickly rendered by a rendering engine and at the same time provide valuable high-frequency details to assist super resolution. To this end, we develop a cross-modality Transformer network that consists of an auxiliary feature branch and a low-resolution rendering branch. These two branches are designed to fuse high-resolution auxiliary features with the corresponding low-resolution rendering. Furthermore, we design residual densely-connected Swin Transformer groups to learn to extract representative features to enable high-quality super-resolution. Our experiments show that our auxiliary features-guided super-resolution method outperforms both super-resolution methods and Monte Carlo denoising methods in producing high-quality renderings.
description: Accepted by CGF
The Calderón Projector for Fibred Cusp Operators
Creators: name: Fritzsch, Karsten
name: Grieser, Daniel
name: Schrohe, Elmar
Publisher: name: arXiv
Year: 2020
Subjects: subject: Analysis of PDEs (math.AP)
subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 58J40 (Primary) 35J75, 58J32, 35J58 (Secondary)

description: A Calderón projector for an elliptic operator $P$ on a manifold with boundary $X$ is a projection from general boundary data to the set of boundary data of solutions $u$ of $Pu=0$. Seeley proved in 1966 that for compact $X$ and for $P$ uniformly elliptic up to the boundary there is a Calderón projector which is a pseudodifferential operator on $\partial X$. We generalize this result to the setting of fibred cusp operators, a class of elliptic operators on certain non-compact manifolds having a special fibred structure at infinity. This applies, for example, to the Laplacian on certain locally symmetric spaces or on particular singular spaces, such as a domain with cusp singularity or the complement of two touching smooth strictly convex domains in Euclidean space. Our main technical tool is the $ϕ$-pseudodifferential calculus introduced by Mazzeo and Melrose. In our presentation we provide a setting that may be useful for doing analogous constructions for other types of singularities.
description: 47 pages, 2 figures, 2 appendices, v2: minor corrections, added sec'n 5.1
Niger State Business Environment, Sustainable Development, and the Implications for Agri-Food (Micro, Small and Medium Enterprises) Value Chain Actors: Stakeholder Perception and Evidence Report
Creators: name: Obekpa, Hephzibah
name: Tasie, Oyinkan
name: Obekpa, Hephzibah
name: Tasie, Oyinkan
Publisher: name: Unknown
Year: 2022
Subjects: subject: Agricultural and Food Policy
subject: Policy
subject: Agriculture
subject: Food
subject: Nigeria
subject: Economics

description: This report is a product of in-depth consultation during a workshop and focus group discussion from relevant stakeholders, including Small and Medium Enterprises Development Agency of Nigeria (SMEDAN), Nigerian Association of Small and Medium Enterprises (NASME), Policymakers (Ministry of Agriculture, Ministry of Commerce, and Ministry of Justice) and different associations from Niger State.
Solar neutrino physics with low-threshold dark matter detectors
Creators: name: Billard, J.
name: Strigari, L.
name: Figueroa-Feliciano, E.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Experiment (hep-ex)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Dark matter detectors will soon be sensitive to Solar neutrinos via two distinct channels: coherent neutrino-nucleus scattering and neutrino electron elastic scattering. We establish an analysis method for extracting Solar model properties and neutrino properties from these measurements, including the possible effects of sterile neutrinos which have been hinted at by some reactor experiments and cosmological measurements. Even including sterile neutrinos, through the coherent scattering channel a 1 ton-year exposure with a low-threshold Germanium detector could improve on the current measurement of the normalization of the $^8$B Solar neutrino flux down to 3% or less. Combining with the elastic scattering data will provide constraints on both the high and low energy survival probability, and will improve on the uncertainty on the active-to-sterile mixing angle by a factor of two. This sensitivity to active-to-sterile transitions is competitive and complementary to forthcoming dedicated short baseline sterile neutrino searches with nuclear decays.
description: 12 pages, 4 figures, 3 tables
Mechanism Design for Perturbation Stable Combinatorial Auctions
Creators: name: Fikioris, Giannis
name: Fotakis, Dimitris
Publisher: name: arXiv
Year: 2020
Subjects: subject: Computer Science and Game Theory (cs.GT)
subject: FOS: Computer and information sciences

description: Motivated by recent research on combinatorial markets with endowed valuations by (Babaioff et al., EC 2018) and (Ezra et al., EC 2020), we introduce a notion of perturbation stability in Combinatorial Auctions (CAs) and study the extend to which stability helps in social welfare maximization and mechanism design. A CA is $γ\textit{-stable}$ if the optimal solution is resilient to inflation, by a factor of $γ\geq 1$, of any bidder's valuation for any single item. On the positive side, we show how to compute efficiently an optimal allocation for 2-stable subadditive valuations and that a Walrasian equilibrium exists for 2-stable submodular valuations. Moreover, we show that a Parallel 2nd Price Auction (P2A) followed by a demand query for each bidder is truthful for general subadditive valuations and results in the optimal allocation for 2-stable submodular valuations. To highlight the challenges behind optimization and mechanism design for stable CAs, we show that a Walrasian equilibrium may not exist for $γ$-stable XOS valuations for any $γ$, that a polynomial-time approximation scheme does not exist for $(2-ε)$-stable submodular valuations, and that any DSIC mechanism that computes the optimal allocation for stable CAs and does not use demand queries must use exponentially many value queries. We conclude with analyzing the Price of Anarchy of P2A and Parallel 1st Price Auctions (P1A) for CAs with stable submodular and XOS valuations. Our results indicate that the quality of equilibria of simple non-truthful auctions improves only for $γ$-stable instances with $γ\geq 3$.
Higher Spin Currents in Orthogonal Wolf Space
Creators: name: Ahn, Changhyun
name: Paeng, Jinsub
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: For the N=4 superconformal coset theory by [SO(N+4)/SO(N) x SU(2)] x U(1) (that contains an orthogonal Wolf space) with N=4, the N=2 WZW affine current algebra is obtained. The 16 generators (or 11 generators) of the large N=4 linear (or nonlinear) superconformal algebra are described by these WZW affine currents explicitly. Along the line of large N=4 holography, the extra 16 currents with spins (2,5/2,5/2, 3), (5/2, 3, 3, 7/2), (5/2, 3, 3, 7/2), and (3, 7/2, 7/2, 4) are obtained in terms of the WZW affine currents. The lowest spin of this N=4 multiplet is two rather than one which is for an unitary Wolf space. The operator product expansions (OPEs) between the above 11 currents and these extra 16 higher spin currents are found explicitly.
description: 76 pages. arXiv admin note: text overlap with arXiv:1311.6205
The Effect of Statin Treatment on Synaptogenesis in the Hippocampus.
Creators: name: Taylor, Sara
name: Adhikari, Rabin
Publisher: name: SAGE Publications
Year: 2024

description: Deranged lipid homeostasis has been implicated in neurodegenerative diseases. Cholesterol reducing compounds such as statins have received special attention for the possibility that they may be able to ameliorate or prevent cognitive loss associated with neurodegeneration. However, there is much dissension concerning the actual effect of statins on cognitive function. The aim of this study is to investigate the effects of pitavastatin on hippocampal synaptogenesis because the hippocampus is crucial for memory formation. We also evaluated the effects of pitavastatin on local hippocampal estrogen synthesized in the hippocampus itself and its effect on Brain-Derived Neurotrophic Factor (BDNF). Using a hippocampal cell line, H19-7, we found that hippocampal neurons exposed to pitavastatin demonstrate a significant reduction in the synaptic marker postsynaptic density protein 95 (psd-95). The pitavastatin treated neurons also exhibited decreased production of local estrogen and their expression of BDNF mRNA was decreased. These results suggest that statins reduce the ability of hippocampal neurons to form synapses by restricting the production of local estrogen. Because neural connections in the hippocampus are crucial for memory formation, our findings implicate statins as medications that may compromise cognitive function.
Sepsis Diagnostics: Intensive Care Scoring Systems Superior to MicroRNA Biomarker Testing
Creators: name: Schumann, Julia
name: Link, Fabian
name: Krohn, Knut
name: Burgdorff, Anna-Maria
name: Christel, Annett
Publisher: name: Universitäts- und Landesbibliothek Sachsen-Anhalt
Year: 2020
Subjects: subject: sepsis
subject: inflammation
subject: biomarker
subject: sequential organ failure assessment (SOFA) score
subject: miRNA
subject: cytokines
subject: 600

description: Sepsis represents a serious medical problem accounting for numerous deaths of critically ill patients in intensive care units (ICUs). An early, sensitive, and specific diagnosis is considered a key element for improving the outcome of sepsis patients. In addition to classical laboratory markers, ICU scoring systems and serum miRNAs are discussed as potential sepsis biomarkers. In the present prospective observational study, the suitability of miRNAs in sepsis diagnosis was tested based on proper validated and normalized data (i.e., absolute quantification by means of Droplet Digital PCR (ddPCR)) in direct comparison to classical sepsis markers and ICU scores within the same patient cohort. Therefore, blood samples of septic intensive care patients (n = 12) taken at day of admission at ICU were compared to non-septic intensive care patients (n = 12) and a healthy control group (n = 12). Our analysis indicates that all tested biomarkers have only a moderate informative power and do not allow an unequivocal differentiation between septic and non-septic ICU patients. In conclusion, there is no standalone laboratory parameter that enables a reliable diagnosis of sepsis. miRNAs are not superior to classical parameters in this respect. It seems recommendable to measure multiple parameters and scores and to interpret them with regard to the clinical presentation.
A Finite Time Combinatorial Algorithm for Instantaneous Dynamic Equilibrium Flows
Creators: name: Graf, Lukas
name: Harks, Tobias
Publisher: name: arXiv
Year: 2020
Subjects: subject: Computer Science and Game Theory (cs.GT)
subject: Computational Complexity (cs.CC)
subject: Optimization and Control (math.OC)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: Instantaneous dynamic equilibrium (IDE) is a standard game-theoretic concept in dynamic traffic assignment in which individual flow particles myopically select en route currently shortest paths towards their destination. We analyze IDE within the Vickrey bottleneck model, where current travel times along a path consist of the physical travel times plus the sum of waiting times in all the queues along a path. Although IDE have been studied for decades, several fundamental questions regarding equilibrium computation and complexity are not well understood. In particular, all existence results and computational methods are based on fixed-point theorems and numerical discretization schemes and no exact finite time algorithm for equilibrium computation is known to date. As our main result we show that a natural extension algorithm needs only finitely many phases to converge leading to the first finite time combinatorial algorithm computing an IDE. We complement this result by several hardness results showing that computing IDE with natural properties is NP-hard.
description: 32 pages, 10 figures
Coherent heteronuclear spin dynamics in an ultracold spin-1 mixture
Creators: name: Li, Xiaoke
name: Zhu, Bing
name: He, Xiaodong
name: Wang, Fudong
name: Guo, Mingyang
name: Xu, Zhi-Fang
name: Zhang, Shizhong
name: Wang, Dajun
Publisher: name: arXiv
Year: 2015
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We report the observation of coherent heteronuclear spin dynamics driven by inter-species spin-spin interaction in an ultracold spinor mixture, which manifests as periodical and well correlated spin oscillations between two atomic species. In particular, we investigate the magnetic field dependence of the oscillations and find a resonance behavior which depends on {\em both} the linear and quadratic Zeeman effects and the spin-dependent interaction. We also demonstrate a unique knob for controlling the spin dynamics in the spinor mixture with species-dependent vector light shifts. Our finds are in agreement with theoretical simulations without any fitting parameters.
description: 13 pages including the supplementary material
Artificial Golgi reactions for targeted glycosylation
Creators: name: Makrydaki, Elli
Publisher: name: Imperial College London
Year: 2020

description: N-linked glycosylation constitutes a Critical Quality Attribute for biotherapeutics. It is known to affect drug efficiency, efficacy and half-life. Glycosylation is a non-templated and complex process owning firstly to the promiscuity of the enzymes involved and secondly to enzyme and nucleotide sugar donor availability. This leads to heterogeneity amongst cell-derived glycoproteins, limiting therapeutic efficacy. Production of biotherapeutics focuses on controlling the glycosylation profile to enhance their activity and produce tailored drugs. Despite the intense efforts to control glycosylation, current methods face important limitations including simplicity, cost and lack of homogeneity. The work presented here addresses the current limitations by developing an Artificial Golgi Reactor (AGR) that allows bespoke N-linked glycosylation of glycoproteins in an artificial environment. Specifically, this novel proof-of-concept system comprises immobilised glycosyltransferase (GnTI, GalT) and glycosidase enzymes (ManII). These enzymes comprise a glycosylation pathway where promiscuity naturally exists. A method to express, in vivo biotinylate and immobilise GnTI and GalT was developed enabling “one-step immobilisation/purification”. ManII was biotinylated using an alternative chemical approach and similarly immobilised. The immobilised enzymes were used in a sequential fashion to reconstruct the N-linked glycosylation pathway on artificial glycans and on a monomeric Fc expressed in glycoengineered Pichia pastoris. The spatiotemporal separation tackled enzyme promiscuity, resulting in increased glycoform homogeneity (>95% conversion). Finally, immobilised GalT was used to enhance the galactosylation profile of three IgGs, yielding 80.2 – 96.3 % terminal galactosylation. Enzyme recycling was further demonstrated for 7 cycles, with a combined reaction time greater than 140-hours. The methods and results outlined in this work demonstrate the application of the AGR as an in vitro glycosylation strategy applied post-expression that is easy to implement, modular and reusable. Furthermore, it has the potential to be expanded and applied for the large-scale manufacture of bespoke biotherapeutics.
FLEE-GNN: A Federated Learning System for Edge-Enhanced Graph Neural Network in Analyzing Geospatial Resilience of Multicommodity Food Flows
Creators: name: Qu, Yuxiao
name: Rao, Jinmeng
name: Gao, Song
name: Zhang, Qianheng
name: Chao, Wei-Lun
name: Su, Yu
name: Miller, Michelle
name: Morales, Alfonso
name: Huber, Patrick
Publisher: name: arXiv
Year: 2023
Subjects: subject: Machine Learning (cs.LG)
subject: Artificial Intelligence (cs.AI)
subject: Computers and Society (cs.CY)
subject: Social and Information Networks (cs.SI)
subject: FOS: Computer and information sciences
subject: I.2

description: Understanding and measuring the resilience of food supply networks is a global imperative to tackle increasing food insecurity. However, the complexity of these networks, with their multidimensional interactions and decisions, presents significant challenges. This paper proposes FLEE-GNN, a novel Federated Learning System for Edge-Enhanced Graph Neural Network, designed to overcome these challenges and enhance the analysis of geospatial resilience of multicommodity food flow network, which is one type of spatial networks. FLEE-GNN addresses the limitations of current methodologies, such as entropy-based methods, in terms of generalizability, scalability, and data privacy. It combines the robustness and adaptability of graph neural networks with the privacy-conscious and decentralized aspects of federated learning on food supply network resilience analysis across geographical regions. This paper also discusses FLEE-GNN's innovative data generation techniques, experimental designs, and future directions for improvement. The results show the advancements of this approach to quantifying the resilience of multicommodity food flow networks, contributing to efforts towards ensuring global food security using AI methods. The developed FLEE-GNN has the potential to be applied in other spatial networks with spatially heterogeneous sub-network distributions.
description: 10 pages, 5 figures
Classical $n$-body system in geometrical and volume variables. I. Three-body case
Creators: name: Escobar-Ruiz, A. M.
name: Linares, R.
name: Turbiner, Alexander V
name: Miller, Willard
Publisher: name: arXiv
Year: 2020
Subjects: subject: Mathematical Physics (math-ph)
subject: Dynamical Systems (math.DS)
subject: Chaotic Dynamics (nlin.CD)
subject: Classical Physics (physics.class-ph)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We consider the classical 3-body system with $d$ degrees of freedom $(d>1)$ at zero total angular momentum. The study is restricted to potentials $V$ that depend solely on relative (mutual) distances $r_{ij}=\mid {\bf r}_i - {\bf r}_j\mid$ between bodies. Following the proposal by J. L. Lagrange, in the center-of-mass frame we introduce the relative distances (complemented by angles) as generalized coordinates and show that the kinetic energy does not depend on $d$, confirming results by Murnaghan (1936) at $d=2$ and van Kampen-Wintner (1937) at $d=3$, where it corresponds to a 3D solid body. Realizing $\mathbb{Z}_2$-symmetry $(r_{ij} \rightarrow -r_{ij})$ we introduce new variables $ρ_{ij}=r_{ij}^2$, which allows us to make the tensor of inertia non-singular for binary collisions. In these variables the kinetic energy is a polynomial function in the $ρ$-phase space. The 3 body positions form a triangle (of interaction) and the kinetic energy is $\mathcal{S}_3$-permutationally invariant wrt interchange of body positions and masses (as well as wrt interchange of edges of the triangle and masses). For equal masses, we use lowest order symmetric polynomial invariants of $\mathbb{Z}_2^{\otimes3} \oplus \mathcal{S}_3$ to define new generalized coordinates, they are called the {\it geometrical variables}. Two of them of the lowest order (sum of squares of sides of triangle and square of the area) are called {\it volume variables}. We study three examples in some detail: (I) 3-body Newton gravity in $d=3$, (II) 3-body choreography in $d=2$ on the algebraic lemniscate by Fujiwara et al where the problem becomes one-dimensional in the geometrical variables, and (III) the (an)harmonic oscillator.
description: 32 pages, 2 figures
Formation of Ultracold NaRb Feshbach Molecules
Creators: name: Wang, Fudong
name: He, Xiaodong
name: Li, Xiaoke
name: Zhu, Bing
name: Chen, Jun
name: Wang, Dajun
Publisher: name: arXiv
Year: 2015
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We report the creation of ultracold bosonic $^{23}$Na$^{87}$Rb Feshbach molecules via magneto-association. By ramping the magnetic field across an interspecies Feshbach resonance, at least 4000 molecules can be produced out of the near degenerate ultracold mixture. Fast loss due to inelastic atom-molecule collisions is observed, which limits the pure molecule number, after residual atoms removal, to 1700. The pure molecule sample can live for 21.8(8) ms in the optical trap, long enough for future molecular spectroscopy studies toward coherently transferring to the singlet ro-vibrational ground state, where these molecules are stable against chemical reaction and have a permanent electric dipole moment of 3.3 Debye. We have also measured the Feshbach molecule's binding energy near the Feshbach resonance by the oscillating magnetic field method and found these molecules have a large closed-channel fraction.
description: 5 figures
Improving Family Medicine Residents' Provision of Gender-Affirming Care.
Creators: name: Smith, Riley
name: Kaplan, Benjamin
Publisher: name: Society of Teachers of Family Medicine
Year: 2024

description: BACKGROUND AND OBJECTIVES: Family physicians are uniquely poised to provide gender-affirming care (GAC) to transgender and nonbinary patients, but current undergraduate and graduate medical education in this field is lacking. Little is known about the impact of various GAC curricula on the clinical care provided by resident physicians. We aimed to assess the efficacy of a multimodal educational framework on the quality of GAC provided by residents at a large academic family medicine program.
METHODS: This pilot study used chart review to assess the impact of a multifaceted educational intervention around GAC in an academic family medicine practice. Components included faculty-specific didactics, resident feedback and didactics, standardized note templates, and compiled resources. We completed pre- and postintervention analysis of resident-led GAC encounters using a novel rubric based on standards of care and compared these results using descriptive statistics.
RESULTS: Following a multimodal educational intervention, residents demonstrated improvement in multiple domains of gender-affirming care, including documenting informed consent, counseling on pregnancy and contraception, and laboratory monitoring for patients initiating gender-affirming hormone therapy.
CONCLUSIONS: This widespread improvement suggested that a multimodal approach to resident and faculty education may help enhance the quality of GAC provided by family medicine residents. Chart review offers a feasible and effective method for identifying gaps in resident knowledge and documentation in GAC. Further research should specifically explore faculty development in this area and expanded patient-centered quality metrics and outcomes that encompass GAC.
Collective properties of defects, multiscale plasticity, and shock induced phenomena in solids
Creators: name: Naimark, O.B.
name: Bayandin Yu.V.
name: Zocher Marvin, A.
Publisher: name: Физическая мезомеханика
Year: 2017
Subjects: STRUCTURAL RELAXATION
COLLECTIVE MODES OF DEFECTS
MULTISCALE PLASTICITY
SHOCK WAVES
СТРУКТУРНАЯ РЕЛАКСАЦИЯ
КОЛЛЕКТИВНЫЕ МОДЫ ДЕФЕКТОВ
МНОГОУРОВНЕВАЯ ПЛАСТИЧНОСТЬ
УДАРНЫЕ ВОЛНЫ

description: A statistically based approach is developed for the construction of constitutive equations that provides linkages between defect-induced mechanisms of structural relaxation, thermally activated plastic flow, and material response to extreme loading conditions. The collective properties of defects have been studied to establish the interaction of multiscale defect dynamics and plastic flow, and to explain the mechanisms leading to the universal self-similar structure of shock wave fronts. An explanation for structural universality of the steady-state plastic shock front (the four power law) and the self-similarity of shock wave profiles under reloading (unloading) is proposed. Structural characterization under transition from thermally activated dislocation glide to nonlinear dislocation drag effects is developed in terms of scaling invariants (effective temperatures) related to mesodefect induced morphology formed during the different stages of plastic deformation.
Acute Kidney Injury in Inflammatory Bowel Disease Patients: A Nationwide Comparative Analysis
Creators: name: Thorpe, Carolyn T.
name: Hu, Yichun
name: Kshirsagar, Abhijit V.
name: Saha, Manish K.
name: Falk, Ronald J.
name: Barnes, Edward L.
name: Hogan, Susan L.
Publisher: name: Elsevier
Year: 2024

description: Rationale & Objective: About 25%-40% of patients with inflammatory bowel disease (IBD) may have extraintestinal manifestations, mainly involving the liver, skin, and joints. Kidney involvement in patients with IBD has been reported, but there are no estimates of its prevalence in population-based studies in the United States. We compared the frequency of acute kidney injury (AKI) among hospitalizations with IBD with that among hospitalizations with collagen vascular diseases and hospitalizations with neither condition.
Study Design: Retrospective, population-based cohort study.Setting & Participants: Healthcare Cost and Utilization Project-Nationwide Inpatient Sample database.
Outcomes: AKI and AKI requiring dialysis.
Analytical Approach: Regression models were used to compare the occurrence of AKI among groups. Inverse probability of treatment weighting was applied to balance groups on covariates.
Results: The final sample comprised 5,735,804 hospitalizations, including 57,121 with IBD, 159,930 with collagen vascular diseases, and 5,518,753 with neither IBD nor collagen vascular diseases. AKI was observed in 13%, 15%, and 12.2% of hospitalizations with IBD, collagen vascular diseases, and the general population, respectively. When adjusting for demographic, hospital, and clinical characteristics using inverse probability of treatment weighting, hospitalizations with IBD had higher odds of being diagnosed with AKI than both those with collagen vascular diseases (odds ratio [OR], 1.32; 95% confidence interval [CI], 1.27-1.38) and the general population (OR, 1.27; 95% CI, 1.23-1.31) and also had higher odds of being diagnosed with AKI requiring dialysis than those with collagen vascular diseases (OR, 1.59; 95% CI, 1.31-1.94) or than the general population (OR, 1.45; 95% CI, 1.25-1.68).
Limitations: Cross-sectional analysis, underreporting of International Classification of Diseases codes, and analyses relevant to in-hospital stays only.
Conclusions: The prevalence and risk of AKI among hospitalizations with IBD is greater than that of hospitalizations with collagen vascular diseases and the general population. Coexisting kidney disease should be considered among patients with a known diagnosis of IBD.
Periodic Points and Smooth Rays
Creators: name: Petersen, Carsten L.
name: Zakeri, Saeed
Publisher: name: arXiv
Year: 2020
Subjects: subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics
subject: 37F10, 37F20, 37F25

description: Let $P: {\mathbb C} \to {\mathbb C}$ be a polynomial map with disconnected filled Julia set $K_P$ and let $z_0$ be a repelling or parabolic periodic point of $P$. We show that if the connected component of $K_P$ containing $z_0$ is non-degenerate, then $z_0$ is the landing point of at least one {\it smooth} external ray. The statement is optimal in the sense that all but one ray landing at $z_0$ may be broken.
description: 10 pages, 3 figures
Near fatal case of mirvetuximab soravtansine-gynx induced interstitial lung disease and a review of the primary literature
Creators: name: Clark, Joshua
name: Boucher, Richard C.
name: Choi, Hee Jae
name: Jones, Alexis R.
name: Albright, Benjamin B.
name: Blake, Andrew
name: Vasher, Scott
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2024

description: Folate receptor alpha (FRα) is a novel target for therapeutics that is
over-expressed in solid tumor malignancies including ovarian, endometrial,
and breast cancer and is expressed in non-malignant tissue such
as alveolar cells (Scaranti et al., 2020; Parker et al., 2005). Antibodydrug
conjugates (ADCs) are targeted therapies that utilize monoclonal
antibodies to exploit the expression of certain antigens or receptors
overexpressed on malignant cells, such as FRα. These antibodies are
conjugated to a cytotoxic agent, known as the “payload.” Mirvetuximab
soravtansine-gynx (henceforth referred to as “mirvetuximab”) is an ADC
that targets FRα, linked to a cytotoxic agent, maytansinoid DM4. Maytansinoid
DM4 exhibits its cytotoxic effects through microtubule inhibition,
with additional bystander effect against adjacent cells not
expressing FRα (Scaranti et al., 2020; Elahere, 2024; Moore et al., 2023).
The collision of two-kinks defects
Creators: name: Mendonça, T. S.
name: de Oliveira, H. P.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We have investigated the head-on collision of a two-kink and a two-antikink pair that arises as a generalization of the $ϕ^4$ model. We have evolved numerically the Klein-Gordon equation with a new spectral algorithm whose accuracy and convergence were attested by the numerical tests. As a general result, the two-kink pair is annihilated radiating away most of the scalar field. It is possible the production of oscillons-like configurations after the collision that bounce and coalesce to form a small amplitude oscillon at the origin. The new feature is the formation of a sequence of quasi-stationary structures that we have identified as lump-like solutions of non-topological nature. The amount of time these structures survives depends on the fine-tuning of the impact velocity.
description: 14 pages, 9 figures
Double Chooz: Latest results
Creators: name: Crespo-Anadón, J. I.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: The latest results from the Double Chooz experiment on the neutrino mixing angle $θ_{13}$ are presented. A detector located at an average distance of 1050 m from the two reactor cores of the Chooz nuclear power plant has accumulated a live time of 467.90 days, corresponding to an exposure of 66.5 GW-ton-year (reactor power $\times$ detector mass $\times$ live time). A revised analysis has boosted the signal efficiency and reduced the backgrounds and systematic uncertainties compared to previous publications, paving the way for the two detector phase. The measured $\sin^2 2θ_{13} = 0.090^{+0.032}_{-0.029}$ is extracted from a fit to the energy spectrum. A deviation from the prediction above a visible energy of 4 MeV is found, being consistent with an unaccounted reactor flux effect, which does not affect the $θ_{13}$ result. A consistent value of $θ_{13}$ is measured in a rate-only fit to the number of observed candidates as a function of the reactor power, confirming the robustness of the result.
description: 6 pages, 5 figures, Proceedings of the Neutrino Oscillation Workshop (NOW 2014), Otranto (Italy), September 7-14 2014