cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
title: MRI: better than CT in the evaluation of patellar extensor apparatus of the knee
Creators: name: Pires, João
Publisher: name: European Society of Muscoskeletal Radiology
Year: 2016
Subjects: subject: Technical aspects
subject: MR
subject: CT
subject: Musculoskeletal joint
subject: Education and training

description: Learning objectives Background Imaging findings OR Procedure Details Conclusion References Personal Information
description: Learning objectives: To describe the protocol used in our institution to study the extensor apparatus of the knee, and its advantages over computed...
title: Acute Hip Pain and Femoral Neck Fracture Mimics
Creators: name: Ibrahem Adam, Renan
Publisher: name: European Society of Muscoskeletal Radiology
Year: 2016
Subjects: subject: Trauma
subject: Inflammation
subject: Acute
subject: eLearning
subject: MR
subject: CT
subject: Conventional radiography
subject: Musculoskeletal system
subject: Musculoskeletal soft tissue
subject: Musculoskeletal bone

description: Learning objectives Background Imaging findings OR Procedure Details Conclusion References Personal Information
description: Learning objectives: - To provide educational review of causes of acute hip pain other than a fracture neck of femurwith an overview of10 different causes. - To describe the corresponding findings in various imaging...
On the periodic motions of a charged particle in an oscillating magnetic field on the two-torus
Creators: name: Asselle, Luca
name: Benedetti, Gabriele
Publisher: name: arXiv
Year: 2015
Subjects: subject: Dynamical Systems (math.DS)
subject: Symplectic Geometry (math.SG)
subject: FOS: Mathematics
subject: 37J45, 58E05

description: Let $(\mathbb T^2,g)$ be a Riemannian two-torus and let $σ$ be an oscillating $2$-form on $\mathbb T^2$. We show that for almost every small positive number $k$ the magnetic flow of the pair $(g,σ)$ has infinitely many periodic orbits with energy $k$. This result complements the analogous statement for closed surfaces of genus at least $2$ [Asselle and Benedetti, Calc. Var. Partial Differential Equations, 2015] and at the same time extends the main theorem in [Abbondandolo, Macarini, Mazzucchelli, and Paternain, J. Eur. Math. Soc. (JEMS), to appear] to the non-exact oscillating case.
description: 15 pages. Revised version incorporating the precious comments of the referee and the notion of essential family suggested to us by M. Mazzucchelli. Comments are very welcome. To appear in Mathematische Zeitschrift
A Functionally Conserved Gene Regulatory Network Module Governing Olfactory Neuron Diversity
Creators: name: Li, Qingyun
name: Jones, Corbin D.
name: Volkan, Pelin Cayirlioglu
name: Okuwa, Sumie
name: Maciejewski, Abigail
name: Brandt, Alicia T.
name: Reinhold, Dominik
name: Barish, Scott
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Sensory neuron diversity is required for organisms to decipher complex environmental cues. In Drosophila, the olfactory environment is detected by 50 different olfactory receptor neuron (ORN) classes that are clustered in combinations within distinct sensilla subtypes. Each sensilla subtype houses stereotypically clustered 1–4 ORN identities that arise through asymmetric divisions from a single multipotent sensory organ precursor (SOP). How each class of SOPs acquires a unique differentiation potential that accounts for ORN diversity is unknown. Previously, we reported a critical component of SOP diversification program, Rotund (Rn), increases ORN diversity by generating novel developmental trajectories from existing precursors within each independent sensilla type lineages. Here, we show that Rn, along with BarH1/H2 (Bar), Bric-à-brac (Bab), Apterous (Ap) and Dachshund (Dac), constitutes a transcription factor (TF) network that patterns the developing olfactory tissue. This network was previously shown to pattern the segmentation of the leg, which suggests that this network is functionally conserved. In antennal imaginal discs, precursors with diverse ORN differentiation potentials are selected from concentric rings defined by unique combinations of these TFs along the proximodistal axis of the developing antennal disc. The combinatorial code that demarcates each precursor field is set up by cross-regulatory interactions among different factors within the network. Modifications of this network lead to predictable changes in the diversity of sensilla subtypes and ORN pools. In light of our data, we propose a molecular map that defines each unique SOP fate. Our results highlight the importance of the early prepatterning gene regulatory network as a modulator of SOP and terminally differentiated ORN diversity. Finally, our model illustrates how conserved developmental strategies are used to generate neuronal diversity.
FABILUT: The Flexible Agent-Based Integrated Land Use/Transport Model
Creators: name: Ziemke, Dominik
name: Kuehnel, Nico
name: Llorca, Carlos
name: Moeckel, Rolf
name: Nagel, Kai
Publisher: name: Technische Universität Berlin
Year: 2022
Subjects: subject: 380 Handel, Kommunikation, Verkehr
subject: integrated land use/transport model
subject: agent-based model
subject: land use/transport feedback cycle
subject: land use/transport interaction

description: Integrated land-use transport models are often accused of being too complex, too coarse or too slow. We tightly couple the microscopic land use model SILO (Simple Integrated Land Use Orchestrator) with the agent-based transport simulation model MATSim (Multi-Agent Transport Simulation). The integration of the two models is person-centric. It means, firstly, that travel demand is generated microscopically. Secondly, SILO agents can query individualized travel information to search for housing or jobs (and to choose among available modes). Consequently, travel time matrices (skim matrices) are not needed anymore. Travel time queries can be done for any time of the day (instead of for one or few time periods), any x/y coordinate (instead of a limited number of zones) and take into account properties of the individual. This way, we avoid aggregation issues (e.g., large zones that disguise local differences) and we can account for individual constraints (e.g., nighttime workers who cannot commute by public transport for lack of service). Therefore, the behavior of agents is represented realistically, which allows us to simulate their reaction to novel policies (e.g., emission-class-based vehicle restrictions) and to extract system-wide effects. The model is applied in two study areas: a toy scenario and the metropolitan region of Munich. We simulate various transport and land use policies to test the model capabilities, including public transport extensions, zones restricted for private cars and land use development regulations. The results demonstrate that the increase of the model resolution and model expressiveness facilitates the simulation of such policies and the interpretation of the results.
One-dimensional biological model of synovial joints regenerative rehabilitation in osteoarthritis
Creators: name: Popov, Valentin L.
name: Poliakov, Aleksandr
name: Pakhaliuk, Vladimir
Publisher: name: Technische Universität Berlin
Year: 2022
Subjects: subject: 620 Ingenieurwissenschaften und zugeordnete Tätigkeiten
subject: synovial joint
subject: articular cartilage
subject: osteoarthritis
subject: cell therapy
subject: tissue engineering
subject: regenerative rehabilitation

description: This work is devoted to the study of a one-dimensional phenomenological model of a focal defect regenerative rehabilitation in the articular cartilage. The model is based on six differential equations in partial derivatives of the “Diffusion-Reaction” type, which was previously used by a number of authors to study cellular processes in various tissues under cell therapy conditions. To take into account the influence of moderate mechanical stimulation of immature tissue, an indirect approach was used, as a result of which some model parameters that directly affect cell proliferation and differentiation were varied considering experimental data. The results of the model study show that moderate stimulation of immature tissue in the early stages of repair the focal articular cartilage defect under conditions of cell therapy leads to an intensification of regenerative processes in the tissue and promotes more rapid formation of the extracellular matrix.
title: A Comparison of Two Radiography Scoring Methods Used by Rheumatologist and Radiologist in Patients with Established Rheumatoid Arthritis
Creators: name: Vasilevska Nikodinovska, Violeta
Publisher: name: European Society of Muscoskeletal Radiology
Year: 2016
Subjects: subject: Musculoskeletal joint
subject: Musculoskeletal bone
subject: Extremities
subject: Plain radiographic studies
subject: Staging
subject: Education and training

description: Purpose Methods and Materials Results Conclusion References Personal Information
description: Purpose: There are numerous radiography scoring methods in Rheumatoid Arthritis (RA). The scoring method Sharp van der Heijde (SHS) is considered as a gold standard for the assessment of the disease progression in RA. Simple erosion narrowing score (SENS)...
Arabidopsis AtMORC4 and AtMORC7 Form Nuclear Bodies and Repress a Large Number of Protein-Coding Genes
Creators: name: Pastor, William A.
name: Moissiard, Guillaume
name: Husmann, Dylan
name: Wohlschlegel, James A.
name: Kasmi, Farid El
name: Jacobsen, Steven E.
name: Papikian, Ashot
name: Wang, Haifeng
name: Dangl, Jeffery L.
name: Vashisht, Ajay A.
name: Liu, Wanlu
name: Harris, C. Jake
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: The MORC family of GHKL ATPases are an enigmatic class of proteins with diverse chromatin related functions. In Arabidopsis, AtMORC1, AtMORC2, and AtMORC6 act together in heterodimeric complexes to mediate transcriptional silencing of methylated DNA elements. Here, we studied Arabidopsis AtMORC4 and AtMORC7. We found that, in contrast to AtMORC1,2,6, they act to suppress a wide set of non-methylated protein-coding genes that are enriched for those involved in pathogen response. Furthermore, atmorc4 atmorc7 double mutants show a pathogen response phenotype. We found that AtMORC4 and AtMORC7 form homomeric complexes in vivo and are concentrated in discrete nuclear bodies adjacent to chromocenters. Analysis of an atmorc1,2,4,5,6,7 hextuple mutant demonstrates that transcriptional de-repression is largely uncoupled from changes in DNA methylation in plants devoid of MORC function. However, we also uncover a requirement for MORC in both DNA methylation and silencing at a small but distinct subset of RNA-directed DNA methylation target loci. These regions are characterized by poised transcriptional potential and a low density of sites for symmetric cytosine methylation. These results provide insight into the biological function of MORC proteins in higher eukaryotes.
State of the Art Study of the Safety Argumentation Frameworks for Automated Driving System Safety
Creators: name: Cieslik, Ilona
name: Jiménez, Víctor J. Expósito
name: Martin, Helmut
name: Scharke, Heiko
name: Schneider, Hannes
Publisher: name: arXiv
Year: 2023
Subjects: subject: Software Engineering (cs.SE)
subject: FOS: Computer and information sciences

description: The automotive industry is experiencing a transition from assisted to highly automated driving. New concepts for validation of Automated Driving System (ADS) include amongst other a shift from a "technology based" approach to a "scenario based" assessment. The safety validation and type approval process of ADS are seen as the biggest challenges for the automotive industry today. Having in mind a variety of existing white papers, standardization activities and regulatory approaches, manufactures still struggle with selecting the best practices that keep aligned with their Safety Management System and Safety Culture. A step forward would be to implement a harmonized global safety assurance scheme that is compliant with relevant regulations, laws, standards, and reflects local rules. Today many communities (regulatory bodies, local authorities, industrial stake-holders) work on proof-of-concept framework for the Safety Argumentation as an answer to this problem. Unfortunately, there is still no consensus on one definitive methodology and a set of safety metrics to measure ADS safety. An objective of this summary report is to facilitate a comprehensive review and analysis of the literature concerning available methods and approaches for vehicle safety, engineering frameworks, processes of scenario-based evaluation and a vendor- and technology-neutral Safety Argumentation approaches and tools.
title: Ankle MRI in assessment of the "subtle cavus foot”
Creators: name: Costa, Carla
Publisher: name: European Society of Muscoskeletal Radiology
Year: 2016
Subjects: subject: Education and training
subject: Perception image
subject: MR
subject: Musculoskeletal system

description: Learning objectives Background Imaging findings OR Procedure Details Conclusion References Personal Information
description: Learning objectives: To detect image findings in ankle MRI that can help suspect of a "subtle cavus foot"...
Dynamic and stochastic systems as a framework for metaphysics and the philosophy of science
Creators: name: List, Christian
name: Pivato, Marcus
Publisher: name: arXiv
Year: 2015
Subjects: subject: History and Philosophy of Physics (physics.hist-ph)
subject: FOS: Physical sciences

description: Scientists often think of the world (or some part of it) as a dynamical system, a stochastic process, or a generalization of such a system. Prominent examples of systems are (i) the system of planets orbiting the sun or any other classical mechanical system, (ii) a hydrogen atom or any other quantum-mechanical system, and (iii) the earth's atmosphere or any other statistical mechanical system. We introduce a simple and general framework for describing such systems and show how it can be used to examine some familiar philosophical questions, including the following: how can we define nomological possibility, necessity, determinism, and indeterminism; what are symmetries and laws; what regularities must a system display to make scientific inference possible; is there any metaphysical basis for invoking principles of parsimony such as Occam's Razor when we make such inferences; and what is the role of space and time in a system? Our framework is intended to serve as a toolbox for the formal analysis of systems that is applicable in several areas of philosophy.
description: 57 pages, including three appendices; five figures
A newly-designed femtosecond KBe$_2$BO$_3$F$_2$ device with pulse duration down to 55 fs for time- and angle-resolved photoemission spectroscopy
Creators: name: Zhong, Haoyuan
name: Bao, Changhua
name: Lin, Tianyun
name: Zhou, Shaohua
name: Zhou, Shuyun
Publisher: name: arXiv
Year: 2023
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Developing a widely tunable vacuum ultraviolet (VUV) source with sub-100 femtoseconds (fs) pulse duration is critical for ultrafast pump-probe techniques such as time- and angle-resolved photoemission spectroscopy (TrARPES). While a tunable probe source with photon energy of 5.3 - 7.0 eV has been recently implemented for TrARPES by using a KBe$_2$BO$_3$F$_2$ (KBBF) device, the time resolution of 280 - 320 fs is still not ideal, which is mainly limited by the duration of the VUV probe pulse generated by the KBBF device. Here, by designing a new KBBF device which is specially optimized for fs applications, an optimum pulse duration of 55 fs is obtained after systematic diagnostics and optimization. More importantly, a high time resolution of 81 - 95 fs is achieved for TrARPES measurements covering the probe photon energy range of 5.3 - 7.0 eV, making it particularly useful for investigating the ultrafast dynamics of quantum materials. Our work extends the application of KBBF device to ultrafast pump-probe techniques with the advantages of both widely tunable VUV source and ultimate time resolution.
description: 8 pages, 4 figures
Fast Adversarial Training with Smooth Convergence
Creators: name: Zhao, Mengnan
name: Zhang, Lihe
name: Kong, Yuqiu
name: Yin, Baocai
Publisher: name: arXiv
Year: 2023
Subjects: subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Fast adversarial training (FAT) is beneficial for improving the adversarial robustness of neural networks. However, previous FAT work has encountered a significant issue known as catastrophic overfitting when dealing with large perturbation budgets, \ie the adversarial robustness of models declines to near zero during training. To address this, we analyze the training process of prior FAT work and observe that catastrophic overfitting is accompanied by the appearance of loss convergence outliers. Therefore, we argue a moderately smooth loss convergence process will be a stable FAT process that solves catastrophic overfitting. To obtain a smooth loss convergence process, we propose a novel oscillatory constraint (dubbed ConvergeSmooth) to limit the loss difference between adjacent epochs. The convergence stride of ConvergeSmooth is introduced to balance convergence and smoothing. Likewise, we design weight centralization without introducing additional hyperparameters other than the loss balance coefficient. Our proposed methods are attack-agnostic and thus can improve the training stability of various FAT techniques. Extensive experiments on popular datasets show that the proposed methods efficiently avoid catastrophic overfitting and outperform all previous FAT methods. Code is available at \url{https://github.com/FAT-CS/ConvergeSmooth}.
Science Gateway for Distributed Multiscale Course Management in e-Science and e-Learning - Use Case for Study and Investigation of Functionalized Nanomaterials
Creators: name: Gordienko, Yuri
name: Stirenko, Serhii
name: Gatsenko, Olexandr
name: Bekenov, Lev
Publisher: name: arXiv
Year: 2015
Subjects: subject: Computers and Society (cs.CY)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences

description: The current tendency of human learning and teaching is targeted to development and integration of digital technologies (like cloud solutions, mobile technology, learning analytics, big data, augmented reality, natural interaction technologies, etc.). Our Science Gateway (http://scigate.imp.kiev.ua) in collaboration with High Performance Computing Center (http://hpcc.kpi.ua) is aimed on the close cooperation among the main actors in learning and researching world (teachers, students, scientists, supporting personnel, volunteers, etc.) with industry and academia to propose the new frameworks and interoperability requirements for the building blocks of a digital ecosystem for learning (including informal learning) that develops and integrates the current and new tools and systems. It is the portal for management of distributed courses (workflows), tools, resources, and users, which is constructed on the basis of the Liferay framework and gUSE/WS-PGRADE technology. It is based on development of multi-level approach (as to methods/algorithms) for effective study and research through flexible selection and combination of unified modules ("gaming" with modules as with LEGO-bricks). It allows us to provide the flexible and adjustable framework with direct involvement in real-world and scientific use cases motivated by the educational aims of students and real scientific aims in labs.
description: 6 pages, 4 figures, 2 tables. 38th International Convention on Information and Communication Technology, Electronics and Microelectronics (MIPRO 2015); Distributed Computing, Visualization and Biomedical Engineering (DC VIS) May 25-29, 2015 (Opatija, Croatia)
SPME-DART Interface and Multi-slot Syringe for Arrow Fiber
Creators: name: Newsome, G. Asher
Publisher: name: Museum Conservation Institute
Year: 2023
Subjects: Analytical chemistry not elsewhere classified
Analytical spectrometry

description: 1. eMachineShop CAD files for four components of a desorption and sampling system for joining a DART probe, Vapur interface, and SPME Arrow fiber syringe in a Restek injection guide 2. Assembly instructions in a readme document 3. eMachineShop CAD file for a replacement Arrow syringe with: multiple slots on one side for discrete DART desorption; multiple slots on the opposite side for manual sampling to the same positions on the fiber; and a channel to rotate the plunger set screw between sides
title: Enchondroma vs (low-grade) chondrosarcoma: where are we at, right now?
Creators: name: Abreu, Natacha
Publisher: name: European Society of Muscoskeletal Radiology
Year: 2016
Subjects: subject: Diagnostic procedure
subject: MR
subject: CT
subject: Conventional radiography
subject: Musculoskeletal system
subject: Cancer

description: Learning objectives Background Imaging findings OR Procedure Details Conclusion References Personal Information
description: Learning objectives: - to extensive review the literature and to attempt to identify most helpful imaging features to differentiate a benign from a malignant cartilage tumor, according to recent literature. - to define “borderline”...
Light-induced emergent phenomena in 2D materials and topological materials
Creators: name: Bao, Changhua
name: Tang, Peizhe
name: Sun, Dong
name: Zhou, Shuyun
Publisher: name: arXiv
Year: 2023
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Light-matter interaction in 2D and topological materials provides a fascinating control knob for inducing emergent, non-equilibrium properties and achieving new functionalities in the ultrafast time scale (from fs to ps). Over the past decade, intriguing light-induced phenomena, e.g., Bloch-Floquet states and photo-induced phase transitions, have been reported experimentally, but many still await experimental realization. In this Review, we discuss recent progress on the light-induced phenomena, in which the light field could act as a time-periodic field to drive Floquet states, induce structural and topological phase transitions in quantum materials, couple with spin and various pseudospins, and induce nonlinear optical responses that are affected by the geometric phase. Perspectives on the opportunities of proposed light-induced phenomena as well as open experimental challenges are also discussed.
title: Musculoskeletal complications in AIDS
Creators: name: Cardenal Urdampilleta, Jaime
Publisher: name: European Society of Muscoskeletal Radiology
Year: 2016
Subjects: subject: Cancer
subject: AIDS
subject: Abscess
subject: Puncture
subject: Education
subject: Diagnostic procedure
subject: MR
subject: CT
subject: Conventional radiography
subject: Musculoskeletal soft tissue
subject: Musculoskeletal joint
subject: Musculoskeletal bone

description: Learning objectives Background Imaging findings OR Procedure Details Conclusion References Personal Information
description: Learning objectives: Musculoskeletal manifestations of Acquired Immunodeficiency Syndrome are not as common as CNS or pulmonary complications. Nonetheless, their prevalence is high. Depending on the condition, aetiology may be related to the HIV infection itself, the...
Homological stability for automorphism groups of RAAGs
Creators: name: Gandini, Giovanni
name: Wahl, Nathalie
Publisher: name: arXiv
Year: 2015
Subjects: subject: Algebraic Topology (math.AT)
subject: Geometric Topology (math.GT)
subject: FOS: Mathematics
subject: 20F65, 20F28

description: We show that the homology of the automorphism group of a right-angled Artin group stabilizes under taking products with any right-angled Artin group.
description: final version
title: Direct MR arthrography using axial traction maneuvers: techniques and applications
Creators: name: Nueffer, Jean-Philippe
Publisher: name: European Society of Muscoskeletal Radiology
Year: 2016
Subjects: subject: Education and training
subject: Arthrography
subject: MR
subject: Musculoskeletal joint

description: Learning objectives Background Imaging findings OR Procedure Details Conclusion References Personal Information
description: Learning objectives: The objectives of this educational poster presentation are: To present the various techniques and practical tips and tricks for direct MR arthrography with axial traction. To review the different applications and highlight the benefits of using...
Phase transition of two-dimensional Ising models on the honeycomb and related lattices with striped random impurities
Creators: name: Morita, Satoshi
name: Suzuki, Sei
Publisher: name: arXiv
Year: 2015
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: Two-dimensional Ising models on the honeycomb lattice and the square lattice with striped random impurities are studied to obtain their phase diagrams. Assuming bimodal distributions of the random impurities where all the non-zero couplings have the same magnitude, exact critical values for the fraction p of ferromagnetic bonds at the zero-temperature (T=0) are obtained. The critical lines in the p-T plane are drawn by numerically evaluating the Lyapunov exponent of random matrix products.
description: 16 pages, 7 figures, references added, to appear in J. Stat. Phys
title: Turning back the clock: Beliefs about gender roles during lockdown (LIEPP Working Paper, n°133)
Creators: name: Boring, Anne
name: Moroni, Gloria
Publisher: name: Sciences Po - LIEPP
Year: 2022
Subjects: subject: FOS: Social sciences
valueUri: http://www.oecd.org/science/inno/38235147.pdf

description: We study the impact of lockdown measures on beliefs about gender roles. We collect data from a representative sample of 1,000 individuals in France during the first COVID-19 lockdown in 2020. To measure beliefs about gender roles, we use questions from the 2018 wave of the European Values Study, and match respondents from the two surveys to compare beliefs before and during lockdown. We find evidence that the lockdown period was associated with a shift towards more traditional beliefs about gender roles. The effects are concentrated among men from the most time-constrained households and from households where bargaining with a partner over sharing responsibility for household production was likely to be an issue. Finally, we find evidence that beliefs about gender equality may be a luxury good: beliefs in equal gender roles increase with household income. Overall, our results suggest that men are more likely to hold egalitarian beliefs about gender roles when these beliefs are not costly for them.
title: Differential diagnosis of anterior knee pain in Magnetic Resonance Imaging (MRI): a literature review
Creators: name: Augustinavicius, Vytautas
Publisher: name: European Society of Muscoskeletal Radiology
Year: 2016
Subjects: subject: Musculoskeletal joint
subject: MR
subject: Diagnostic procedure
subject: Education
subject: Education and training

description: Learning objectives Background Imaging findings OR Procedure Details Conclusion References Personal Information
description: Learning objectives: To understand the most frequent etiological factors and radiological features of anterior knee pain, its differential diagnosis in...
Genome-Wide Interaction Analyses between Genetic Variants and Alcohol Consumption and Smoking for Risk of Colorectal Cancer
Creators: name: Hopper, John L.
name: Seminara, Daniela
name: Toth, Reka
name: Campbell, Peter T.
name: Hoffmeister, Michael
name: Harrison, Tabitha A.
name: Potter, John D.
name: Thibodeau, Stephen N.
name: Küry, Sébastien
name: Hsu, Li
name: Giovannucci, Edward L.
name: Berndt, Sonja I.
name: Bien, Stephanie A.
name: Newcomb, Polly A.
name: Thornquist, Mark
name: Haile, Robert W.
name: Jiao, Shuo
name: Lemire, Mathieu
name: Bezieau, Stephane
name: Gallinger, Steven
name: Jenkins, Mark A.
name: White, Emily
name: Rudolph, Anja
name: Gong, Jian
name: Du, Mengmeng
name: Baron, John A.
name: Peters, Ulrike
name: Schrotz-King, Petra
name: Jeon, Jihyoun
name: Hutter, Carolyn M.
name: Schoen, Robert E.
name: Ulrich, Cornelia M.
name: Slattery, Martha L.
name: Nishihara, Reiko
name: Ogino, Shuji
name: Duggan, David
name: Casey, Graham
name: Brenner, Hermann
name: Wallace, Robert
name: Lindor, Noralane M.
name: Hayes, Richard B.
name: Le Marchand, Loic
name: Lin, Yi
name: Figueiredo, Jane C.
name: Chang-Claude, Jenny
name: Chan, Andrew T.
name: Kocarnik, Jonathan
name: Hudson, Thomas J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Genome-wide association studies (GWAS) have identified many genetic susceptibility loci for colorectal cancer (CRC). However, variants in these loci explain only a small proportion of familial aggregation, and there are likely additional variants that are associated with CRC susceptibility. Genome-wide studies of gene-environment interactions may identify variants that are not detected in GWAS of marginal gene effects. To study this, we conducted a genome-wide analysis for interaction between genetic variants and alcohol consumption and cigarette smoking using data from the Colon Cancer Family Registry (CCFR) and the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO). Interactions were tested using logistic regression. We identified interaction between CRC risk and alcohol consumption and variants in the 9q22.32/HIATL1 (Pinteraction = 1.76×10−8; permuted p-value 3.51x10-8) region. Compared to non-/occasional drinking light to moderate alcohol consumption was associated with a lower risk of colorectal cancer among individuals with rs9409565 CT genotype (OR, 0.82 [95% CI, 0.74–0.91]; P = 2.1×10−4) and TT genotypes (OR,0.62 [95% CI, 0.51–0.75]; P = 1.3×10−6) but not associated among those with the CC genotype (p = 0.059). No genome-wide statistically significant interactions were observed for smoking. If replicated our suggestive finding of a genome-wide significant interaction between genetic variants and alcohol consumption might contribute to understanding colorectal cancer etiology and identifying subpopulations with differential susceptibility to the effect of alcohol on CRC risk.
A comparative study of divisive hierarchical clustering algorithms
Creators: name: Roux, Maurice
Publisher: name: arXiv
Year: 2015
Subjects: subject: Data Structures and Algorithms (cs.DS)
subject: Quantitative Methods (q-bio.QM)
subject: FOS: Computer and information sciences
subject: FOS: Biological sciences
subject: 62-07

description: A general scheme for divisive hierarchical clustering algorithms is proposed. It is made of three main steps : first a splitting procedure for the subdivision of clusters into two subclusters, second a local evaluation of the bipartitions resulting from the tentative splits and, third, a formula for determining the nodes levels of the resulting dendrogram. A number of such algorithms is given. These algorithms are compared using the Goodman-Kruskal correlation coefficient. As a global criterion it is an internal goodness-of-fit measure based on the set order induced by the hierarchy compared to the order associated to the given dissimilarities. Applied to a hundred of random data tables, these comparisons are in favor of two methods based on unusual ratio-type formulas for the splitting procedures, namely the Silhouette criterion and Dunn's criterion. These two criteria take into account both the within cluster and the between cluster mean dissimilarity. In general the results of these two algorithms are better than the classical Agglomerative Average Link method.
description: 11 pages, 1 figure
Genomic Characterization of Metformin Hepatic Response
Creators: name: Eckalbar, Walter L.
name: Giacomini, Kathleen M.
name: Etheridge, Amy S.
name: Wright, Fred
name: Laurance, Megan
name: Yee, Sook Wah
name: Smith, Robin P.
name: Lin, Lawrence
name: Luizon, Marcelo R.
name: Ahituv, Nadav
name: Innocenti, Federico
name: Gallins, Paul J.
name: Jones, Stacy L.
name: Wang, Yao
name: Molony, Cliona
name: Zhou, Yihui
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Metformin is used as a first-line therapy for type 2 diabetes (T2D) and prescribed for numerous other diseases. However, its mechanism of action in the liver has yet to be characterized in a systematic manner. To comprehensively identify genes and regulatory elements associated with metformin treatment, we carried out RNA-seq and ChIP-seq (H3K27ac, H3K27me3) on primary human hepatocytes from the same donor treated with vehicle control, metformin or metformin and compound C, an AMP-activated protein kinase (AMPK) inhibitor (allowing to identify AMPK-independent pathways). We identified thousands of metformin responsive AMPK-dependent and AMPK-independent differentially expressed genes and regulatory elements. We functionally validated several elements for metformin-induced promoter and enhancer activity. These include an enhancer in an ataxia telangiectasia mutated (ATM) intron that has SNPs in linkage disequilibrium with a metformin treatment response GWAS lead SNP (rs11212617) that showed increased enhancer activity for the associated haplotype. Expression quantitative trait locus (eQTL) liver analysis and CRISPR activation suggest that this enhancer could be regulating ATM, which has a known role in AMPK activation, and potentially also EXPH5 and DDX10, its neighboring genes. Using ChIP-seq and siRNA knockdown, we further show that activating transcription factor 3 (ATF3), our top metformin upregulated AMPK-dependent gene, could have an important role in gluconeogenesis repression. Our findings provide a genome-wide representation of metformin hepatic response, highlight important sequences that could be associated with interindividual variability in glycemic response to metformin and identify novel T2D treatment candidates.
title: “The Forgotten Rotator Cuff Tendon” – Subscapularis under the spotlight!
Creators: name: Al-Ani, Zeid
Publisher: name: European Society of Muscoskeletal Radiology
Year: 2016
Subjects: subject: Musculoskeletal system
subject: Anatomy
subject: MR
subject: Education
subject: Trauma

description: Purpose Methods and Materials Results Conclusion References Personal Information
description: Purpose: Define the normal anatomy of subscapularis tendon and its appearance on imaging. Describe the function of subscapularis in glenohumeral joint stabilisation and the effect of subscapularis tendon tear on shoulder biomechanics. Highlight the imaging...
Inverse boundary value problem for the Helmholtz equation: quantitative conditional Lipschitz stability estimates
Creators: name: Beretta, Elena
name: de Hoop, Maarten V.
name: Faucher, Florian
name: Scherzer, Otmar
Publisher: name: arXiv
Year: 2015
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: We study the inverse boundary value problem for the Helmholtz equation using the Dirichlet-to-Neumann map at selected frequencies as the data. A conditional Lipschitz stability estimate for the inverse problem holds in the case of wavespeeds that are a linear combination of piecewise constant functions (following a domain partition) and gives a framework in which the scheme converges. The stability constant grows exponentially as the number of subdomains in the domain partition increases. We establish an order optimal upper bound for the stability constant. We eventually realize computational experiments to demonstrate the stability constant evolution for three dimensional wavespeed reconstruction.
description: 21 pages, 7 figures. arXiv admin note: text overlap with arXiv:1406.2391
Photon correlation spectroscopy with heterodyne mixing based on soft x-ray magnetic circular dichroism
Creators: name: Klose, Christopher
name: Büttner, Felix
name: Hu, Wen
name: Mazzoli, Claudio
name: Beach, Geoffrey S. D.
name: Eisebitt, Stefan
name: Pfau, Bastian
Publisher: name: Technische Universität Berlin
Year: 2022
Subjects: subject: 530 Physik
subject: magnetic domains
subject: coherent X-ray scattering
subject: X-ray magnetic circular dichroism

description: Many magnetic equilibrium states and phase transitions are characterized by fluctuations. Such magnetic fluctuation can, in principle, be detected with scattering-based x-ray photon correlation spectroscopy (XPCS). However, in the established approach of XPCS, the magnetic scattering signal is quadratic in the magnetic scattering cross section, which results not only in often prohibitively small signals but also in a fundamental inability to detect negative correlations (anticorrelations). Here, we propose to exploit the possibility of heterodyne mixing of the magnetic signal with static charge scattering to reconstruct the first-order (linear) magnetic correlation function. We show that the first-order magnetic scattering signal reconstructed from heterodyne scattering now directly represents the underlying magnetization texture. Moreover, we suggest a practical implementation based on an absorption mask rigidly connected to the sample, which not only produces a static charge scattering signal but also eliminates the problem of drift-induced artificial decay of the correlation functions. Our method thereby significantly broadens the range of scientific questions accessible by magnetic x-ray photon correlation spectroscopy.
Gone but not forgotten
Creators: name: Henderson, D.
Publisher: name: arXiv
Year: 2015
Subjects: subject: History and Philosophy of Physics (physics.hist-ph)
subject: FOS: Physical sciences

description: In this reminiscence I discuss the influence of Henry Eyring and John Barker upon my life and work. Others, especially my family, have been of even greater personal influence. However, these two great and grand men were of tremendous scientific influence. Of course, others who came before Eyring and Barker, especially Boltzmann and van der Waals and later Onsager and Eyring's contemporary, Kirkwood, have been influential, but only indirectly as I never met them. Eyring and Barker are not the only scientists who have inspired me. Many who influenced me have contributed articles to this special issue or have worked with me. I single out Eyring and Barker because I met them early in my career and because they have passed away and are now present only in spirit. They are gone but should not be forgotten; I take this occasion to remind the readers about these two outstanding scientists and fine men and offer this reminiscence as thanks to them.
description: 7 pages, 2 figures
Haploinsufficiency for Core Exon Junction Complex Components Disrupts Embryonic Neurogenesis and Causes p53-Mediated Microcephaly
Creators: name: Tsai, Yi-Hsuan
name: McMahon, John J.
name: Mao, Hanqian
name: Wang, Zefeng
name: Silver, Debra L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: The exon junction complex (EJC) is an RNA binding complex comprised of the core components Magoh, Rbm8a, and Eif4a3. Human mutations in EJC components cause neurodevelopmental pathologies. Further, mice heterozygous for either Magoh or Rbm8a exhibit aberrant neurogenesis and microcephaly. Yet despite the requirement of these genes for neurodevelopment, the pathogenic mechanisms linking EJC dysfunction to microcephaly remain poorly understood. Here we employ mouse genetics, transcriptomic and proteomic analyses to demonstrate that haploinsufficiency for each of the 3 core EJC components causes microcephaly via converging regulation of p53 signaling. Using a new conditional allele, we first show that Eif4a3 haploinsufficiency phenocopies aberrant neurogenesis and microcephaly of Magoh and Rbm8a mutant mice. Transcriptomic and proteomic analyses of embryonic brains at the onset of neurogenesis identifies common pathways altered in each of the 3 EJC mutants, including ribosome, proteasome, and p53 signaling components. We further demonstrate all 3 mutants exhibit defective splicing of RNA regulatory proteins, implying an EJC dependent RNA regulatory network that fine-tunes gene expression. Finally, we show that genetic ablation of one downstream pathway, p53, significantly rescues microcephaly of all 3 EJC mutants. This implicates p53 activation as a major node of neurodevelopmental pathogenesis following EJC impairment. Altogether our study reveals new mechanisms to help explain how EJC mutations influence neurogenesis and underlie neurodevelopmental disease.
The Evolution of the Far-UV Luminosity Function and Star Formation Rate Density of the Chandra Deep Field South from z=0.2-1.2 with Swift/UVOT
Creators: name: Hagen, Lea M. Z.
name: Hoversten, Erik A.
name: Gronwall, Caryl
name: Wolf, Christopher
name: Siegel, Michael H.
name: Page, Mathew
name: Hagen, Alex
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We use deep Swift UV/Optical Telescope (UVOT) near-ultraviolet (1600A to 4000A) imaging of the Chandra Deep Field South to measure the rest-frame far-UV (FUV; 1500A) luminosity function (LF) in four redshift bins between z=0.2 and 1.2. Our sample includes 730 galaxies with u < 24.1 mag. We use two methods to construct and fit the LFs: the traditional V_max method with bootstrap errors and a maximum likelihood estimator. We observe luminosity evolution such that M* fades by ~2 magnitudes from z~1 to z~0.3 implying that star formation activity was substantially higher at z~1 than today. We integrate our LFs to determine the FUV luminosity densities and star formation rate densities from z=0.2 to 1.2. We find evolution consistent with an increase proportional to (1+z)^1.9 out to z~1. Our luminosity densities and star formation rates are consistent with those found in the literature, but are, on average, a factor of ~2 higher than previous FUV measurements. In addition, we combine our UVOT data with the MUSYC survey to model the galaxies' ultraviolet-to-infrared spectral energy distributions and estimate the rest-frame FUV attenuation. We find that accounting for the attenuation increases the star formation rate densities by ~1 dex across all four redshift bins.
description: 20 pages, 8 figures, 6 tables; accepted for publication in ApJ
title: Bone Marrow oedema patterns in Spine pathology
Creators: name: Isaac, Amanda
Publisher: name: European Society of Muscoskeletal Radiology
Year: 2016
Subjects: subject: Musculoskeletal spine
subject: Oncology
subject: Management
subject: MR-Diffusion/Perfusion
subject: MR-Functional imaging
subject: MR
subject: Imaging sequences
subject: Physiological studies
subject: Decision analysis
subject: Trauma
subject: Acute
subject: Biological effects

description: Learning objectives Background Imaging findings OR Procedure Details Conclusion References Personal Information
description: Learning objectives: To correlate the appearances of marrow oedema patterns with underlying physiological and pathological processes affecting the spine To understand the value of utilising various MRI sequences to characterise lesions. To categorise the imaging...
Phyllosilicates as earth-abundant layered materials for electronics and optoelectronics: Prospects and challenges in their ultrathin limit
Creators: name: Barcelos, Ingrid D.
name: de Oliveira, Raphaela
name: Schleder, Gabriel R.
name: Matos, Matheus J. S.
name: Longuinhos, Raphael
name: Ribeiro-Soares, Jenaina
name: Barboza, Ana Paula M.
name: Prado, Mariana C.
name: Pinto, Elisângela S.
name: Gobato, Yara Galvão
name: Chacham, Hélio
name: Neves, Bernardo R. A.
name: Cadore, Alisson R.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences

description: Phyllosilicate minerals are an emerging class of naturally occurring layered insulators with large bandgap energy that have gained attention from the scientific community. This class of lamellar materials has been recently explored at the ultrathin two-dimensional level due to their specific mechanical, electrical, magnetic, and optoelectronic properties, which are crucial for engineering novel devices (including heterostructures). Due to these properties, phyllosilicates minerals can be considered promising low-cost nanomaterials for future applications. In this Perspective article, we will present relevant features of these materials for their use in potential 2D-based electronic and optoelectronic applications, also discussing some of the major challenges in working with them.
description: 29 pages, 4 figures
The COMIX polarimeter: a compact device for XUV polarization analysis
Creators: name: Pancaldi, Matteo
name: Strüber, Christian
name: Friedrich, Bertram
name: Pedersoli, Emanuele
name: Angelis, Dario De
name: Nikolov, Ivaylo
name: Manfredda, Michele
name: Foglia, Laura
name: Yulin, Sergiy
name: Spezzani, Carlo
name: Sacchi, Maurizio
name: Eisebitt, Stefan
name: Korff Schmising, Clemens Von
name: Capotondi, Flavio
Publisher: name: Technische Universität Berlin
Year: 2022
Subjects: subject: 530 Physik
subject: extreme-ultraviolet polarimetry
subject: free-electron laser
subject: pump–probe experiments
subject: magnetic materials

description: We report on the characterization of a novel extreme-ultraviolet polarimeter based on conical mirrors to simultaneously detect all the components of the electric field vector for extreme-ultraviolet radiation in the 45–90 eV energy range. The device has been characterized using a variable polarization source at the Elettra synchrotron, showing good performance in the ability to determine the radiation polarization. Furthermore, as a possible application of the device, Faraday spectroscopy and time-resolved experiments have been performed at the Fe M2,3-edge on an FeGd ferrimagnetic thin film using the FERMI free-electron laser source. The instrument is shown to be able to detect the small angular variation induced by an optical external stimulus on the polarization state of the light after interaction with magnetic thin film, making the device an appealing tool for magnetization dynamics research.
Tracking People in Highly Dynamic Industrial Environments
Creators: name: Papaioannou, Savvas
name: Markham, Andrew
name: Trigoni, Niki
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: To date, the majority of positioning systems have been designed to operate within environments that have long-term stable macro-structure with potential small-scale dynamics. These assumptions allow the existing positioning systems to produce and utilize stable maps. However, in highly dynamic industrial settings these assumptions are no longer valid and the task of tracking people is more challenging due to the rapid large-scale changes in structure. In this paper we propose a novel positioning system for tracking people in highly dynamic industrial environments, such as construction sites. The proposed system leverages the existing CCTV camera infrastructure found in many industrial settings along with radio and inertial sensors within each worker's mobile phone to accurately track multiple people. This multi-target multi-sensor tracking framework also allows our system to use cross-modality training in order to deal with the environment dynamics. In particular, we show how our system uses cross-modality training in order to automatically keep track environmental changes (i.e. new walls) by utilizing occlusion maps. In addition, we show how these maps can be used in conjunction with social forces to accurately predict human motion and increase the tracking accuracy. We have conducted extensive real-world experiments in a construction site showing significant accuracy improvement via cross-modality training and the use of social forces.