cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
The Fully Convolutional Transformer for Medical Image Segmentation
Creators: name: Tragakis, Athanasios
name: Kaul, Chaitanya
name: Murray-Smith, Roderick
name: Husmeier, Dirk
Publisher: name: arXiv
Year: 2022
Subjects: subject: Image and Video Processing (eess.IV)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences

description: We propose a novel transformer model, capable of segmenting medical images of varying modalities. Challenges posed by the fine grained nature of medical image analysis mean that the adaptation of the transformer for their analysis is still at nascent stages. The overwhelming success of the UNet lay in its ability to appreciate the fine-grained nature of the segmentation task, an ability which existing transformer based models do not currently posses. To address this shortcoming, we propose The Fully Convolutional Transformer (FCT), which builds on the proven ability of Convolutional Neural Networks to learn effective image representations, and combines them with the ability of Transformers to effectively capture long-term dependencies in its inputs. The FCT is the first fully convolutional Transformer model in medical imaging literature. It processes its input in two stages, where first, it learns to extract long range semantic dependencies from the input image, and then learns to capture hierarchical global attributes from the features. FCT is compact, accurate and robust. Our results show that it outperforms all existing transformer architectures by large margins across multiple medical image segmentation datasets of varying data modalities without the need for any pre-training. FCT outperforms its immediate competitor on the ACDC dataset by 1.3%, on the Synapse dataset by 4.4%, on the Spleen dataset by 1.2% and on ISIC 2017 dataset by 1.1% on the dice metric, with up to five times fewer parameters. Our code, environments and models will be available via GitHub.
Scoping review of reviews on single and integrated interventions in controlling and reducing HIV infections among PWID
Creators: name: Moldokmatova, Ainura
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Medicine and Health Sciences
subject: Social and Behavioral Sciences

description: The current review will focus on exploring a broad range of behavioral and pharmaceutical interventions and outcomes in the existing literature from extensive contexts (all geographic settings or service delivery settings, etc.) to answer the following research question: What does the available evidence tell us about the effectiveness of single and integrated interventions to control and reduce HIV infections among PWID?
title: Coronary CT Angiography: efficiency and improvement of the quality care versus invasive coronary angiography.
Creators: name: Martín Díaz, Alfonso
Publisher: name: European Congress of Radiology
Year: 2016
Subjects: subject: Cost-effectiveness
subject: CT-Angiography
subject: Cardiac
subject: Economics

description: Aims and objectives Methods and materials Results Conclusion Personal information References
description: Aims and objectives: In patients who will be undergoing valvular heart surgery, must be preoperatively ruled out associated coronary disease . Currently in our institution it is sistematically applied a protocol designed jointly by Cardiac Surgery, Cardiology and...
Alanine 501 Mutations in Penicillin-Binding Protein 2 from Neisseria gonorrhoeae : Structure, Mechanism, and Effects on Cephalosporin Resistance and Biological Fitness
Creators: name: Jerse, Ann E.
name: Tomberg, Joshua
name: Vincent, Leah R.
name: Fedarovich, Alena
name: Nicholas, Robert A.
name: Unemo, Magnus
name: Davies, Christopher
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Resistance of Neisseria gonorrhoeae to expanded-spectrum cephalosporins such as ceftriaxone and cefixime has increased markedly in the past decade. The primary cephalosporin resistance determinant is a mutated penA gene, which encodes the essential peptidoglycan transpeptidase, penicillin-binding protein 2 (PBP2). Decreased susceptibility and resistance can be conferred by mosaic penA alleles containing upward of 60 amino acid changes relative to wild-type PBP2, or by nonmosaic alleles with relatively few mutations, the most important of which occurs at Ala501 located near the active site of PBP2. Recently, fully cefixime- and ceftriaxone-resistant clinical isolates that harbored a mosaic penA allele with an A501P mutation were identified. To examine the potential of mutations at Ala501 to increase resistance to expanded-spectrum cephalosporins, we randomized codon 501 in a mosaic penA allele and transformed N. gonorrhoeae to increased cefixime resistance. Interestingly, only five substitutions of Ala501 (A501V, A501T, A501P, A501R, and A501S) that increased resistance and preserved essential transpeptidase function were isolated. To understand their structural implications, these mutations were introduced into the nonmosaic PBP2-6140CT, which contains four C-terminal mutations present in PBP2 from the penicillin-resistant strain FA6140. The crystal structure of PBP2-6140CT-A501T was determined and revealed ordering of a loop near the active site and a new hydrogen bond involving Thr501 that connects the loop and the SxxK conserved active site motif. The structure suggests that increased rigidity in the active site region is a mechanism for cephalosporin resistance mediated by Ala501 mutations in PBP2.
First semi-empirical test of the white dwarf mass-radius relationship using a single white dwarf via astrometric microlensing
Creators: name: McGill, Peter
name: Anderson, Jay
name: Casertano, Stefano
name: Sahu, Kailash C.
name: Bergeron, Pierre
name: Blouin, Simon
name: Dufour, Patrick
name: Smith, Leigh C.
name: Evans, N. Wyn
name: Belokurov, Vasily
name: Smart, Richard L.
name: Bellini, Andrea
name: Calamida, Annalisa
name: Dominik, Martin
name: Kains, Noé
name: Klüter, Jonas
name: Nielsen, Martin Bo
name: Wambsganss, Joachim
Publisher: name: arXiv
Year: 2022
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: In November 2019, the nearby single, isolated DQ-type white dwarf LAWD 37 (WD 1142-645) aligned closely with a distant background source and caused an astrometric microlensing event. Leveraging astrometry from \Gaia{} and followup data from the \textit{Hubble Space Telescope} we measure the astrometric deflection of the background source and obtain a gravitational mass for LAWD~37. The main challenge of this analysis is in extracting the lensing signal of the faint background source whilst it is buried in the wings of LAWD~37's point spread function. Removal of LAWD 37's point spread function induces a significant amount of correlated noise which we find can mimic the astrometric lensing signal. We find a deflection model including correlated noise caused by the removal of LAWD~37's point spread function best explains the data and yields a mass for LAWD 37 of $0.56\pm0.08 M_{\odot}$. This mass is in agreement with the theoretical mass-radius relationship and cooling tracks expected for CO core white dwarfs. Furthermore, the mass is consistent with no or trace amounts of hydrogen that is expected for objects with helium-rich atmospheres like LAWD 37. We conclude that further astrometric followup data on the source is likely to improve the inference on LAWD 37's mass at the $\approx3$ percent level and definitively rule out purely correlated noise explanations of the data. This work provides the first semi-empirical test of the white dwarf mass-radius relationship using a single, isolated white dwarf and supports current model atmospheres of DQ white dwarfs and white dwarf evolutionary theory.
description: 23 pages, 18 figures, accepted to MNRAS
Magneto-transport phenomena related to the chiral anomaly in Weyl semimetals
Creators: name: Spivak, B. Z.
name: Andreev, A. V.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We present a theory of magnetotransport phenomena related to the chiral anomaly in Weyl semimetals. We show that conductivity, thermal conductivity, thermoelectric and the sound absorption coefficients exhibit strong and anisotropic magnetic field dependences. We also discuss properties of magneto-plasmons and magneto-polaritons, whose existence is entirely determined by the chiral anomaly. Finally, we discuss the conditions of applicability of the quasi-classical description of electron transport phenomena related to the chiral anomaly.
description: 7 pages, 1 figure
Packaged and Free Satellite Tobacco Mosaic Virus (STMV) RNA Genomes Adopt Distinct Conformational States
Creators: name: Weeks, Kevin M.
name: Dethoff, Elizabeth A.
name: Larman, Bridget C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: The RNA genomes of viruses likely undergo multiple functionally important conformational changes during their replication cycles, changes that are poorly understood at present. We used two complementary in-solution RNA structure probing strategies (SHAPE-MaP and RING-MaP) to examine the structure of the RNA genome of satellite tobacco mosaic virus inside authentic virions and in a capsid-free state. Both RNA states feature similar three-domain architectures in which each major replicative function-translation, capsid coding, and genome synthesis-fall into distinct domains. There are, however, large conformational differences between the in-virion and capsid-free states, primarily in one arm of the central T domain. These data support a model in which the packaged capsid-bound RNA is constrained in a local high-energy conformation by the native capsid shell. The removal of the viral capsid then allows the RNA genome to relax into a more thermodynamically stable conformation. The RNA architecture of the central T domain thus likely changes during capsid assembly and disassembly and may play a role in genome packaging.
title: Urogenital complications and incidental urogenital findings in Crohn's disease
Creators: name: Haliloglu, Nuray
Publisher: name: European Congress of Radiology
Year: 2016
Subjects: subject: Obstruction / Occlusion
subject: Inflammation
subject: Complications
subject: MR
subject: Genital / Reproductive system male
subject: Genital / Reproductive system female
subject: Abdomen

description: Aims and objectives Methods and materials Results Conclusion Personal information References
description: Aims and objectives: Crohn’s disease is a chronic granulomatous inﬂammatory disease of the gastrointestinal tract with a tendency toward remission and relapse. Abscesses, fistulas, strictures or adhesions of intestinal segments are among well-known complications of...
The effect of night shifts on physicians’ empathy for patients’ pain and prescription of analgesics
Creators: name: Gordon-Hecker, Tom
name: Hillel, Shoham
name: Israel, Salomon
name: Perry, Anat
name: Caruso, Eugene
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Medicine and Health Sciences
subject: Social and Behavioral Sciences

description: Pre-registration of planned analyses of additional data from Hadassa medical centers
Non-local order parameters for fermion chains via the partial transpose
Creators: name: Mayer, Lorenz P.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: In the last two decades, a vast variety of topological phases have been described, predicted, classified, proposed, and measured. While there is a certain unity in method and philosophy, the phenomenology differs wildly. This work deals with the simplest such case: fermions in one spatial dimension, in the presence of a symmetry group $G$ which contains anti-unitary symmetries. A complete classification of topological phases, in this case, is available. Nevertheless, these methods are to some extent lacking as they generally do not allow to determine the class of a given system easily. This paper will take up proposals for non-local order parameters defined through anti-unitary symmetries. They are shown to be homotopy invariants on a suitable set of ground states. For matrix product states, an interpretation of these invariants is provided: in particular, for a particle-hole symmetry, the invariant determines a real division super algebra $\mathbb{D}$ such that the bond algebra is a matrix algebra over $\mathbb{D}$.
Three Pyrimidine Decarboxylations in the Absence of a Catalyst
Creators: name: Wolfenden, Richard
name: Shen, Lin
name: Yang, Weitao
name: Lewis, Charles A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: The epigenetic modification of DNA by 5-methylation of cytosine residues can be reversed by the action of the TET family of dioxygenases that oxidize the methyl group to produce 5-carboxycytosine (5caC), which can be converted to cytosine in a final decarboxylation step. Likewise, 5-carboxyuracil (5caU) is decarboxylated to uracil in the last step in pyrimidine salvage. In view of the extreme difficulty of decarboxylating derivatives of orotic acid (6caU), it seemed desirable to establish the rates of decarboxylation of 5caC and 5caU in the absence of a catalyst. Arrhenius analysis of experiments performed at elevated temperatures indicates that 5caU decomposes with a rate constant of 1.1 × 10-9 s-1 (ΔH⧧ = 25 kcal/mol) in a neutral solution at 25 °C. The decomposition of 5caC is somewhat slower (k25 = 5.0 × 10-11 s-1; ΔH⧧ = 27 kcal/mol) and leads to the initial accumulation of cytosine as an intermediate, followed by the relatively rapid deamination of cytosine (k25 = 1.9 × 10-10 s-1; ΔH⧧ = 23.4 kcal/mol). Both 5caC and 5caU are decarboxylated many orders of magnitude more rapidly than 6caU is (k25 = 1.3 × 10-17 s-1). Ab initio simulations indicate that in all three cases, the favored route of spontaneous decarboxylation in water involves direct elimination of CO2 with the assistance of an explicit water molecule.
Phonon-limited resistivity of multilayer graphene systems
Creators: name: Davis, Seth M.
name: Chou, Yang-Zhi
name: Wu, Fengcheng
name: Sarma, Sankar Das
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: We calculate the theoretical contribution to the doping and temperature ($T$) dependence of electrical resistivity due to scattering by acoustic phonons in Bernal bilayer graphene (BBG) and rhombohedral trilayer graphene (RTG). We focus on the role of nontrivial geometric features of the detailed, anisotropic $k\cdot p$ band structures of these systems - e.g. Van Hove singularities, Lifshitz transitions, Fermi surface anisotropy, and band curvature near the gap - whose effects on transport have not yet been systematically studied. We find that these geometric features strongly influence the temperature and doping dependencies of the resistivity. In particular, the band geometry leads to a nonlinear $T$-dependence in the high-$T$ equipartition regime, complicating the usual $T^4$ to $T$ Bloch-Grüneisen crossover. Our focus on BBG and RTG is motivated by recent experiments in these systems that have discovered several exotic low-$T$ superconductivity proximate to complicated hierarchies of isospin-polarized phases. These interaction-driven phases are intimately related to the geometric features of the band structures, highlighting the importance of understanding the influence of band geometry on transport. While resolving the effects of the anisotropic band geometry on the scattering times requires nontrivial numerical solution, our approach is rooted in intuitive Boltzmann theory. We compare our results with recent experiment and discuss how our predictions can be used to elucidate the relative importance of various scattering mechanisms in these systems.
On fundamental groups of plane curve complements
Creators: name: Bartolo, Enrique Artal
name: Dimca, Alexandru
Publisher: name: arXiv
Year: 2015
Subjects: subject: Algebraic Geometry (math.AG)
subject: Algebraic Topology (math.AT)
subject: FOS: Mathematics

description: In this paper we discuss some properties of fundamental groups and Alexander polynomials of plane curves. We discuss the relationship of the non-triviality of Alexander polynomials and the notion of (nearly) freeness for irreducible plane curves. We reprove and restate in modern terms a somewhat forgotten result of Zariski. Finally, we describe some topological properties of curves with abelian fundamental group.
Acetylation of lysine 109 modulates pregnane X receptor DNA binding and transcriptional activity
Creators: name: Walton, William G.
name: Li, Hao
name: Biswas, Arunima
name: Mani, Sridhar
name: Pasquel, Danielle
name: Krasowski, Matthew D.
name: Redinbo, Matthew R.
name: Kortagere, Sandhya
name: Doricakova, Aneta
name: Dvorak, Zdenek
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Pregnane X receptor (PXR) is a major transcriptional regulator of xenobiotic metabolism and transport pathways in the liver and intestines, which are critical for protecting organisms against potentially harmful xenobiotic and endobiotic compounds. Inadvertent activation of drug metabolism pathways through PXR is known to contribute to drug resistance, adverse drug–drug interactions, and drug toxicity in humans. In both humans and rodents, PXR has been implicated in non-alcoholic fatty liver disease, diabetes, obesity, inflammatory bowel disease, and cancer. Because of PXR's important functions, it has been a therapeutic target of interest for a long time. More recent mechanistic studies have shown that PXR is modulated by multiple PTMs. Herein we provide the first investigation of the role of acetylation in modulating PXR activity. Through LC–MS/MS analysis, we identified lysine 109 (K109) in the hinge as PXR's major acetylation site. Using various biochemical and cell-based assays, we show that PXR's acetylation status and transcriptional activity are modulated by E1A binding protein (p300) and sirtuin 1 (SIRT1). Based on analysis of acetylation site mutants, we found that acetylation at K109 represses PXR transcriptional activity. The mechanism involves loss of RXRα dimerization and reduced binding to cognate DNA response elements. This mechanism may represent a promising therapeutic target using modulators of PXR acetylation levels.
How do men process divorce؟ A protocol for a scoping review
Creators: name: Farahani, Hanieh
name: Sadeghi, Mansoureh
name: Mootabi, Fereshteh
name: Ahmadi, Fazlollah
name: Bigham, Zahra
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Social and Behavioral Sciences
subject: dissolution
subject: men
subject: postdivorce
subject: post-separation

description: Divorce is one of the most major stressors in life. the focus of studies is more concentrated on the effects of divorce on children and women, while the consequences of this phenomenon on men are regrettably neglected.divorced men are at highly significant risk for early death based on the cumulative number of years that men lived as divorcees. hypertension is mainly known as a consequence of distress among divorced men (McEwen, 1998). Similarly, the negative outcomes of depression in divorced men are much worse than such consequences in women. a limited number of heterogeneous researches have concentrated on the experience of divorce in men. However, they are heading for more negative consequences (Helgeson, 1994). to eliminate these shortcomings, we intend to use a Scoping review method to run an exploratory study of the current heterogeneous literature.
title: Ultrasound-guided drainage of soft tissue haematomas
Creators: name: Almazán, Eva
Publisher: name: European Congress of Radiology
Year: 2016
Subjects: subject: Haemorrhage
subject: Blood
subject: Puncture
subject: Drainage
subject: Ultrasound
subject: Soft tissues / Skin
subject: Musculoskeletal system

description: Aims and objectives Methods and materials Results Conclusion Personal information References
description: Aims and objectives: - To present our experience and results about percutaneous drainage of soft tissue haematomas treated by multiple puncture and injecting...
Dimensional crossover in self-organised super-radiant phases of ultra cold atoms inside a cavity
Creators: name: Shakya, Poornima
name: Ratnakar, Amulya
name: Ghosh, Sankalpa
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We consider a condensate of ultra cold bosonic atoms in a linear optical cavity illuminated by a two-pump configuration where each pump is making different angles with the direction of the cavity axis. We show such configuration allows a smooth transition from a one-dimensional quantum optical lattice configuration to a two-dimensional quantum optical lattice configuration induced by the cavity-atom interaction. Using a Holstein-Primakoff transformation, we find out the atomic density profile of such self-organised ground state in the super-radiant phase as a function of the angular orientations of the pump in such dynamical quantum optical lattice, and, also provide an analysis of their structures in coordinate and momentum space. In the later part of the paper, we show how the corresponding results can also be qualitatively understood in terms of an Extended Bose-Hubbard model in such quantum optical lattice potential.
description: Latex file and ten figures (Accepted for Publication in Journal of Physics B: At. Mol. Opt.)
Covert connection of filaments
Creators: name: Filippov, Boris
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We analyse the relationship between two near filaments, which do not show any connection in H-alpha images but reveal close magnetic connectivity during filament activations in Extreme Ultraviolet (EUV) observations. A twisted flux rope, which connects a half of one filament with another filament, becomes visible during several activations but seems to exist all the time of the filaments presence on the disc. Solar Dynamic Observatory} (SDO) and Solar Terrestrial Relations Observatory (STEREO) observed the region with the filaments from two points of view separated by the angle of about 120 deg. On 2012 July 27, SDO observed the filament activation on disc, while for the STEREO B position the filaments were visible at the limb. Nearly identical interaction episode was observed on 2012 August 04 by STEREO A on disc and by SDO at the limb. This good opportunity allows us to disentangle the 3-D shape of the connecting flux rope and in particular to determine with high reliability the helicity sign of the flux rope, which looks ambiguous in preliminary inspections of on-disc EUV images only.} The complex magnetic structure of the region consists of three braided flux ropes in the vicinity of the coronal null point. Using observations of the flux rope fine structure and plasma motions within it from two points of view, we determine the negative sign of helicity of the flux rope, which corresponds to dextral chirality of the filaments. The observations, despite the tangled fine structure in some EUV images, support flux rope filament models. They give more evidence for the one-to-one relationship between the filament chirality and the flux rope helicity.
description: 13 pages, 12 figures, to appear in MNRAS
title: Perianal infections in neutropenic patients with hematological malignancy: magnetic resonance imaging findings
Creators: name: Haliloglu, Nuray
Publisher: name: European Congress of Radiology
Year: 2016
Subjects: subject: Gastrointestinal tract
subject: Abdomen
subject: MR
subject: Treatment effects
subject: Abscess
subject: Fistula
subject: Infection

description: Aims and objectives Methods and materials Results Conclusion Personal information References
description: Aims and objectives: Infection is a common problem in patients with hematological malignancies receiving chemotherapy. The disease spectrum of perianal infection might range from mild local cellulitis to life-threatening sepsis. Besides anal pain and discomfort which...
Zero Hausdorff dimension spectrum for the almost Mathieu operator
Creators: name: Last, Yoram
name: Shamis, Mira
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mathematical Physics (math-ph)
subject: Spectral Theory (math.SP)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We study the almost Mathieu operator at critical coupling. We prove that there exists a dense $G_δ$ set of frequencies for which the spectrum is of zero Hausdorff dimension.
description: v1: 24 pp. v2: 25 pp, corrected the statement of Theorem 3 and added explanations in the proof of Theorem 2
Cardiac ubiquitin ligases: Their role in cardiac metabolism, autophagy, cardioprotection and therapeutic potential
Creators: name: Willis, Monte S.
name: Parry, Traci L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Both the ubiquitin-proteasome system (UPS) and the lysosomal autophagy system have emerged as complementary key players responsible for the turnover of cellular proteins. The regulation of protein turnover is critical to cardiomyocytes as post-mitotic cells with very limited regenerative capacity. In this focused review, we describe the emerging interface between the UPS and autophagy, with E3’s regulating autophagy at two critical points through multiple mechanisms. Moreover, we discuss recent insights in how both the UPS and autophagy can alter metabolism at various levels, to present new ways to think about therapeutically regulating autophagy in a focused manner to optimize disease-specific cardioprotection, without harming the overall homeostasis of protein quality control.
Failure prediction in a non-crimp basalt fibre reinforced epoxy composite
Creators: name: Chowdhury, Indraneel R.
name: O'Dowd, Noel
name: COMER, ANTHONY
Publisher: name: University of Limerick
Year: 2023
Subjects: classificationCode: 40
subject: Engineering

description: Failure analysis in non-crimp fabric (NCF) based fibre reinforced composite materials is challenging due to the complexity associated with multiaxial fabric architectures and the interaction of different failure modes. In this study an in-situ 3-point bend test under scanning electron microscopy (SEM) has been performed to analyse the failure behaviour of a NCF basalt epoxy composite manufactured by vacuum assisted resin transfer moulding (VaRTM) technique. The failure mechanisms observed during the in-situ 3-point bend test are compared to those from standard (ex-situ) flexure and interlaminar shear strength (ILSS) tests on the same material. Finite element analysis of each test configuration is also conducted to analyse the in-ply stress distributions and to predict the damage initiating stresses. The study reveals that fibre/matrix debonding leading to matrix cracking in the 90◦ sub-ply is the damage initiating failure mode, with final failure occurring due to fibre buckling in neighbouring 0◦ sub-plies. The finite element analysis reveals that matrix cracking in the 90◦ sub-ply is controlled by shear stresses ranging between 35 and 45 MPa
Alpha-lipoic acid supplementation protects enzymes from damage by nitrosative and oxidative stress
Creators: name: Osorio, Cristina
name: Hamlett, Eric D.
name: Yi, Xianwen
name: Simington, Stephen
name: Maeda, Nobuyo
name: Xu, Longquan
name: Winnik, Witold
name: Robinette, Jennifer
name: Hiller, Sylvia
name: Alzate, Oscar
name: DeKroon, Robert
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: S-nitrosylation of mitochondrial enzymes involved in energy transfer under nitrosative stress may result in ATP deficiency. We investigated whether α-lipoic acid, a powerful antioxidant, could alleviate nitrosative stress by regulating S-nitrosylation, which could result in retaining the mitochondrial enzyme activity.
Neural networks with excitatory and inhibitory components: direct and inverse problems by a mean-field approach
Creators: name: di Volo, M.
name: Burioni, R.
name: Casartelli, M.
name: Livi, R.
name: Vezzani, A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Neurons and Cognition (q-bio.NC)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: We study the dynamics of networks with inhibitory and excitatory leaky-integrate-and-fire neurons with short-term synaptic plasticity in the presence of depressive and facilitating mechanisms. The dynamics is analyzed by a Heterogeneous Mean-Field approximation, that allows to keep track of the effects of structural disorder in the network. We describe the complex behavior of different classes of excitatory and inhibitory components, that give rise to a rich dynamical phase-diagram as a function of the fraction of inhibitory neurons. By the same mean field approach, we study and solve a global inverse problem: reconstructing the degree probability distributions of the inhibitory and excitatory components and the fraction of inhibitory neurons from the knowledge of the average synaptic activity field. This approach unveils new perspectives in the numerical study of neural network dynamics and in the possibility of using these models as testbed for the analysis of experimental data.
Infrared Divergences in $e^{+}e^{-}\rightarrow 2\; jets$ in the Light Front Coherent State Formalism
Creators: name: Bhamre, Deepesh
name: Misra, Anuradha
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We study infrared (IR) divergences in light front quantum chromodynamics using a coherent state basis in light front time-ordered Hamiltonian perturbation theory. In computation of the S-matrix elements in Hamiltonian formalism, the IR divergences appear in the form of vanishing energy denominators. We consider the process $e^{+}e^{-}\rightarrow 2\; jets$ at $\mathcal{O}(g^{2})$ in strong coupling, construct the coherent state representing the outgoing particles, and explicitly show that the `true' IR divergences cancel to this order when the matrix elements are calculated between coherent states instead of Fock states.
description: 23 pages, 5 figures. Published version. Minor additions and changes compared to v2
title: Lymphomatosis Cerebri: MRI findings of a rare form of primary central nervous system lymphoma.
Creators: name: Farras Roca, Lara
Publisher: name: European Congress of Radiology
Year: 2016
Subjects: subject: Neuroradiology brain
subject: MR
subject: MR-Diffusion/Perfusion
subject: MR-Spectroscopy
subject: Diagnostic procedure
subject: Lymphoma
subject: Dementia

description: Learning objectives Background Findings and procedure details Conclusion Personal information References
description: Learning objectives: To describe the radiologic characteristics of this rare variant of primary central nervous system lymphoma. To provide the radiologist the main diagnostic clues for the diagnosis of lymphomatosis cerebri with MRI in order to include this entity in...
The algebra of observables in Gaußian normal spacetime coordinates
Creators: name: Bodendorfer, Norbert
name: Duch, Paweł
name: Lewandowski, Jerzy
name: Świeżewski, Jędrzej
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We discuss the canonical structure of a spacetime version of the radial gauge, i.e. Gaußian normal spacetime coordinates. While it was found for the spatial version of the radial gauge that a "local" algebra of observables can be constructed, it turns out that this is not possible for the spacetime version. The technical reason for this observation is that the new gauge condition needed to upgrade the spatial to a spacetime radial gauge does not Poisson-commute with the previous gauge conditions. It follows that the involved Dirac bracket is inherently non-local in the sense that no complete set of observables can be found which is constructed locally and at the same time has local Dirac brackets. A locally constructed observable here is defined as a finite polynomial of the canonical variables at a given physical point specified by the Gaußian normal spacetime coordinates.
description: 16 pages; discussion of the cosmological constant added; matches published version
Live-cell imaging approaches for the investigation of xenobiotic-induced oxidant stress
Creators: name: Gibbs-Flournoy, Eugene
name: Wages, Phillip A.
name: Cheng, Wan-Yun
name: Samet, James M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Oxidant stress is arguably a universal feature in toxicology. Research studies on the role of oxidant stress induced by xenobiotic exposures have typically relied on the identification of damaged biomolecules using a variety of conventional biochemical and molecular techniques. However, there is increasing evidence that low-level exposure to a variety of toxicants dysregulates cellular physiology by interfering with redox-dependent processes.
Is Draco II one of the faintest dwarf galaxies? First study from Keck/DEIMOS spectroscopy
Creators: name: Martin, Nicolas F.
name: Geha, Marla
name: Ibata, Rodrigo A.
name: Collins, Michelle L. M.
name: Laevens, Benjamin P. M.
name: Bell, Eric F.
name: Rix, Hans-Walter
name: Ferguson, Annette M. N.
name: Chambers, Kenneth C.
name: Wainscoat, Richard J.
name: Waters, Christopher
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present the first spectroscopic analysis of the faint and compact stellar system Draco II (Dra II, M_V=-2.9+/-0.8, r_h=19^{+8}_{-6} pc), recently discovered in the Pan-STARRS1 3π survey. The observations, conducted with DEIMOS on the Keck II telescope, establish some of its basic characteristics: the velocity data reveal a narrow peak with 9 member stars at a systemic heliocentric velocity =-347.6^{+1.7}_{-1.8} km/s, thereby confirming Dra II is a satellite of the Milky Way; we infer a velocity dispersion with σ_{vr}=2.9+/-2.1 km/s (<8.4 km/s at the 95% confidence level), which implies log_{10}(M_{1/2})=5.5^{+0.4}_{-0.6} and log_{10}((M/L)_{1/2})=2.7^{+0.5}_{-0.8}, in Solar units; furthermore, very weak Calcium triplet lines in the spectra of the high signal-to-noise member stars imply [Fe/H]
description: 5 pages, 4 figures, 1 table. Excepted for publication in MNRAS. Full table 1 available upon request. v2: moderate revisions of the text, conclusion unchanged
Applications of Generative Adversarial Networks in Neuroimaging and Clinical Neuroscience
Creators: name: Wang, Rongguang
name: Bashyam, Vishnu
name: Yang, Zhijian
name: Yu, Fanyang
name: Tassopoulou, Vasiliki
name: Chintapalli, Sai Spandana
name: Skampardoni, Ioanna
name: Sreepada, Lasya P.
name: Sahoo, Dushyant
name: Nikita, Konstantina
name: Abdulkadir, Ahmed
name: Wen, Junhao
name: Davatzikos, Christos
Publisher: name: arXiv
Year: 2022
Subjects: subject: Machine Learning (cs.LG)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Image and Video Processing (eess.IV)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Generative adversarial networks (GANs) are one powerful type of deep learning models that have been successfully utilized in numerous fields. They belong to a broader family called generative methods, which generate new data with a probabilistic model by learning sample distribution from real examples. In the clinical context, GANs have shown enhanced capabilities in capturing spatially complex, nonlinear, and potentially subtle disease effects compared to traditional generative methods. This review appraises the existing literature on the applications of GANs in imaging studies of various neurological conditions, including Alzheimer's disease, brain tumors, brain aging, and multiple sclerosis. We provide an intuitive explanation of various GAN methods for each application and further discuss the main challenges, open questions, and promising future directions of leveraging GANs in neuroimaging. We aim to bridge the gap between advanced deep learning methods and neurology research by highlighting how GANs can be leveraged to support clinical decision making and contribute to a better understanding of the structural and functional patterns of brain diseases.
Milky Way's eccentric constituents with $Gaia$, APOGEE $\&$ GALAH
Creators: name: Myeong, G. C.
name: Belokurov, Vasily
name: Aguado, David S.
name: Evans, N. Wyn
name: Caldwell, Nelson
name: Bradley, James
Publisher: name: arXiv
Year: 2022
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We report the results of an unsupervised decomposition of the local stellar halo in the chemo-dynamical space spanned by the abundance measurements from APOGEE DR17 and GALAH DR3. In our Gaussian Mixture Model, only four independent components dominate the halo in the Solar neighborhood, three previously known $Aurora$, $Splash$ and Gaia-Sausage/Enceladus (GS/E) and one new, $Eos$. Only one of these four is of accreted origin, namely the GS/E, thus supporting the earlier claims that the GS/E is the main progenitor of the Galactic stellar halo. We show that $Aurora$ is entirely consistent with the chemical properties of the so-called Heracles merger. In our analysis in which no predefined chemical selection cuts are applied, $Aurora$ spans a wide range of [Al/Fe] with a metallicity correlation indicative of a fast chemical enrichment in a massive galaxy, the young Milky Way. The new halo component dubbed $Eos$ is classified as $in situ$ given its high mean [Al/Fe]. $Eos$ shows strong evolution as a function of [Fe/H], where it changes from being the closest to GS/E at its lowest [Fe/H] to being indistinguishable from the Galactic low-$α$ population at its highest [Fe/H]. We surmise that at least some of the outer thin disk of the Galaxy started its evolution in the gas polluted by the GS/E, and $Eos$ is an evidence of this process.
description: 16 pages, 5 figures, 2 tables. Published at the ApJ and the published version is also available (open access) -- e.g., from NASA ADS page
title: Transarterial chemoembolization (TACE) for unresectable intrahepatic cholangiocarcinoma (ICC)
Creators: name: Kartsouni, Victoria
Publisher: name: European Congress of Radiology
Year: 2016
Subjects: subject: Cancer
subject: Chemoembolisation
subject: Catheters
subject: Arterial access
subject: CT
subject: Catheter arteriography
subject: Liver
subject: Interventional vascular

description: Aims and objectives Methods and materials Results Conclusion Personal information References
description: Aims and objectives: Intrahepatic cholangiocarcinoma is an uncommon malignancy with poor prognosis with 5-year survival rate <5%, including patients that undergoing surgery. Resection is the only curative treatment but only 30% of patients present at a resectable...
Group field theories generating polyhedral complexes
Creators: name: Thürigen, Johannes
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Group field theories are a generalization of matrix models which provide both a second quantized reformulation of loop quantum gravity as well as generating functions for spin foam models. While states in canonical loop quantum gravity, in the traditional continuum setting, are based on graphs with vertices of arbitrary valence, group field theories have been defined so far in a simplicial setting such that states have support only on graphs of fixed valency. This has led to the question whether group field theory can indeed cover the whole state space of loop quantum gravity. In this contribution based on [1] I present two new classes of group field theories which satisfy this objective: i) a straightforward, but rather formal generalization to multiple fields, one for each valency and ii) a simplicial group field theory which effectively covers the larger state space through a dual weighting, a technique common in matrix and tensor models. To this end I will further discuss in some detail the combinatorial structure of the complexes generated by the group field theory partition function. The new group field theories do not only strengthen the links between the mentioned quantum gravity approaches but, broadening the theory space of group field theories, they might also prove useful in the investigation of renormalizability.
description: accepted for publication in PoS, Frontiers of Fundamental Physics 14 (AMU Marseille)
Geometrical Scaling in Inelastic Inclusive Particle Production at the LHC
Creators: name: Praszalowicz, Michal
name: Francuz, Anna
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Analyzing recent ALICE data on inelastic pp scattering at the LHC energies we show that charged particle distributions exhibit geometrical scaling (GS). We show also that the inelastic cross-section is scaling as well and that in this case the quality of GS is better than for multiplicities. Moreover, exponent $λ$ characterizing the saturation scale is for the cross-section scaling compatible with the one found in deep inelastic ep scattering at HERA. Next, by parametrizing charged particles distributions by the Tsallis-like formula, we find a somewhat unexpected solution that still exhibits GS, but differs from the "standard" one where the Tsallis temperature is proportional to the saturation scale.
description: 9 pages, 7 figures
Fuel availability and fate in cardiac metabolism: A tale of two substrates
Creators: name: Pascual, Florencia
name: Coleman, Rosalind A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: The heart’s extraordinary metabolic flexibility allows it to adapt to normal changes in physiology in order to preserve its function. Alterations in the metabolic profile of the heart have also been attributed to pathological conditions such as ischemia and hypertrophy; however, research during the past decade has established that cardiac metabolic adaptations can precede the onset of pathologies. It is therefore critical to understand how changes in cardiac substrate availability and use trigger events that ultimately result in heart dysfunction. This review examines the mechanisms by which the heart obtains fuels from the circulation or from mobilization of intracellular stores. We next describe experimental models that exhibit either an increase in glucose use or a decrease in FA oxidation, and how these aberrant conditions affect cardiac metabolism and function. Finally, we highlight the importance of alternative, and relatively under investigated, strategies for the treatment of heart failure.
A meta-analysis of the effects of peer observation on risky decision-making in adolescence
Creators: name: Schäfer, Lena
name: Figner, Bernd
name: Somerville, Leah
name: Powers, Katherine
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Social and Behavioral Sciences

description: This project aims to quantify the magnitude of the effect of direct peer observation on adolescent risky decisions relative to risky decisions made alone. We also aim to investigate key methodological and theoretical moderators that may act as possible sources of influence to amplify or reduce the effect of direct peer observation.
New Insights into Protein Hydroxylation and Its Important Role in Human Diseases
Creators: name: Takada, Mamoru
name: Wei, Wenyi
name: Zurlo, Giada
name: Guo, Jianping
name: Zhang, Qing
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Protein hydroxylation is a post-translational modification catalyzed by 2-oxoglutarate-dependent dioxygenases. The hydroxylation modification can take place on various amino acids, including but not limited to proline, lysine, asparagine, aspartate and histidine. A classical example of this modification is hypoxia inducible factor alpha (HIF-α) prolyl hydroxylation, which affects HIF-α protein stability via the Von-Hippel Lindau (VHL) tumor suppressor pathway, a Cullin 2-based E3 ligase adaptor protein frequently mutated in kidney cancer. In addition to protein stability regulation, protein hydroxylation may influence other post-translational modifications or the kinase activity of the modified protein (such as Akt and DYRK1A/B). In other cases, protein hydroxylation may alter protein-protein interaction and its downstream signaling events in vivo (such as OTUB1, MAPK6 and eEF2K). In this review, we highlight the recently identified protein hydroxylation targets and their pathophysiological roles, especially in cancer settings. Better understanding of protein hydroxylation will help identify novel therapeutic targets and their regulation mechanisms to foster development of more effective treatment strategies for various human cancers.
Novel effects of the $W$-boson mass shift in the 3-3-1 model
Creators: name: Van Loi, Duong
name: Van Dong, Phung
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The recent precision measurement of the $W$-boson mass reveals an exciting hint for the new physics as of the 3-3-1 model. We indicate that the 3-3-1 model contains distinct sources by itself that may cause the $W$-mass deviation, as measured, such as the tree-level $Z$-$Z'$ mixing, the tree-level $W$-$Y$ and $Z$-$Z'$-$X$ mixings, as well as the non-degenerate gauge vector $(X,Y)$ and new Higgs doublets. We point out that the gauge vector doublet negligibly contributes to this mass shift, whereas the rest of the effects with tree-level mixings governed by $Z$-$Z'$ and new Higgs doublets are significant. A discussion of scalar sextet contributions is also given.
description: 38 pages, 4 figures; Matches published version
Quantum electron transport controlled by cavity vacuum fields
Creators: name: Arwas, Geva
name: Ciuti, Cristiano
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We explore theoretically how the coupling to cavity vacuum fields affects the electron transport in quantum conductors due to the counter-rotating-wave terms of light-matter interaction. We determine the quantum conductance in terms of the transmission coefficients predicted by an effective electron Hamiltonian. The coupling between bare electronic states is mediated by virtual processes involving intermediate states with one electron (or one hole) on top of the Fermi sea and one virtual cavity photon. We study the behavior of the quantum conductance in the presence of artificial or disordered single-particle potentials, as well as a spatially varying cavity mode. As illustrative examples, we apply our theory to 1D conductors and to disordered 2D quantum Hall systems. We show how the cavity vacuum fields can lead to both large enhancement or suppression of electron conductance in the ballistic regime, as well as modification of the conductance quantization and fluctuations.
description: Final version published in PRB