cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Fabrication and characterization of high quality factor silicon nitride nanobeam cavities
Creators: name: Khan, Mughees
name: Babinec, Thomas
name: McCutcheon, Murray W.
name: Deotare, Parag
name: Lončar, Marko
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: Other Condensed Matter (cond-mat.other)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Si3N4 is an excellent material for applications of nanophotonics at visible wavelengths due to its wide bandgap and moderately large refractive index (n $\approx$ 2.0). We present the fabrication and characterization of Si3N4 photonic crystal nanobeam cavities for coupling to diamond nanocrystals and Nitrogen-Vacancy centers in a cavity QED system. Confocal micro-photoluminescence analysis of the nanobeam cavities demonstrates quality factors up to Q ~ 55,000, which is limited by the resolution of our spectrometer. We also demonstrate coarse tuning of cavity resonances across the 600-700nm range by lithographically scaling the size of fabricated devices. This is an order of magnitude improvement over previous SiNx cavities at this important wavelength range.
Catalytic liquefaction of Kraft lignin in water at subcritical and supercritical conditions.
Creators: name: Da Silva Cardoso, Aderlanio
Publisher: name: Imperial College London
Year: 2019

description: Concerns about the negative environmental impacts caused by the production and consumption of petroleum-based chemicals have made lignocellulosic biomass a promising source of valuable industrial chemicals. Kraft lignin (KL) is a by-product from cellulose production typically treated as a waste or used as a low value fuel in heat and power generation. However, a large amount of this biomass is still not utilized. In principle, a thermo-catalytic process working in subcritical (subCW) or supercritical water (SCW) could be used instead to produce a variety of valuable chemical products from KL. However, the development of such a process remains a challenge. This work aims to obtain oxygenated monoaromatic compounds from KL using SCW as reaction medium. Initially, the effect of temperature, pressure and reaction time on the conversion of KL was investigated. Catalysts were also tested in order to further improve the conversion of KL to bio-oil. These catalysts were prepared by a wet impregnation method and reduced Ni was observed in Ni-CeO2/carbon based catalysts, without using H2. Among these catalysts prepared via wet impregnation, Ni 15MgO/CNF promoted the highest yield of bio-oil (around 62 wt.%), followed by Ni 15CeO2/CNF (around 55 wt.%). In order to increase the stability and activity of Ni-CeO2/CNF, this catalyst was also synthesized via one-pot catalyst synthesis method in subCW and SCW in presence of formic acid as reducing agent. Highly stable and active Ni-CeO2-x/CNF catalysts were successfully obtained in subcritical water and without addition of H2. Ni CeO2-x/CNF promoted the conversion of KL to an extremely high yield of oxygenated monoaromatic-based bio oil (around 79 wt.%), without adding co-solvents and H2. The catalytic liquefaction process developed in this work brings a ground-breaking approach to the synthesis of stable and active catalysts for greener processes in the context of biomass valorisation in water at SCW.
A Fast Approach to Creative Telescoping
Creators: name: Koutschan, Christoph
Publisher: name: arXiv
Year: 2010
Subjects: subject: Symbolic Computation (cs.SC)
subject: Combinatorics (math.CO)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics
subject: 33F10, 68W30

description: In this note we reinvestigate the task of computing creative telescoping relations in differential-difference operator algebras. Our approach is based on an ansatz that explicitly includes the denominators of the delta parts. We contribute several ideas of how to make an implementation of this approach reasonably fast and provide such an implementation. A selection of examples shows that it can be superior to existing methods by a large factor.
description: 9 pages, 1 table, final version as it appeared in the journal
Quantum Heisenberg models and their probabilistic representations
Creators: name: Goldschmidt, Christina
name: Ueltschi, Daniel
name: Windridge, Peter
Publisher: name: arXiv
Year: 2011
Subjects: subject: Mathematical Physics (math-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Probability (math.PR)
subject: FOS: Physical sciences
subject: FOS: Mathematics
subject: 60G55, 60K35, 82B10, 82B20, 82B26

description: These notes give a mathematical introduction to two seemingly unrelated topics: (i) quantum spin systems and their cycle and loop representations, due to Tóth and Aizenman-Nachtergaele; (ii) coagulation-fragmentation stochastic processes. These topics are nonetheless related, as we argue that the lengths of cycles and loops satisfy an effective coagulation-fragmentation process. This suggests that their joint distribution is Poisson-Dirichlet. These ideas are far from being proved, but they are backed by several rigorous results, notably of Dyson-Lieb-Simon and Schramm.
description: 48 pages, 9 figures
Ultrafast Demagnetization of Iron Induced by Optical versus Terahertz Pulses
Creators: name: Chekhov, Alexander L.
name: Behovits, Yannic
name: Heitz, Julius J. F.
name: Denker, C.
name: Reiss, David A.
name: Wolf, M.
name: Weinelt, Martin
name: Brouwer, Piet W.
name: Münzenberg, M.
name: Kampfrath, Tobias
Publisher: name: Freie Universität Berlin
Year: 2021
Subjects: subject: Demagnetization
subject: Electron relaxation
subject: Spin dynamics
subject: 500 Naturwissenschaften und Mathematik::530 Physik::530 Physik

description: We study ultrafast magnetization quenching of ferromagnetic iron following excitation by an optical versus a terahertz pump pulse. While the optical pump (photon energy of 3.1 eV) induces a strongly nonthermal electron distribution, terahertz excitation (4.1 meV) results in a quasithermal perturbation of the electron population. The pump-induced spin and electron dynamics are interrogated by the magneto-optic Kerr effect (MOKE). A deconvolution procedure allows us to push the time resolution down to 130 fs, even though the driving terahertz pulse is about 500 fs long. Remarkably, the MOKE signals exhibit an almost identical time evolution for both optical and terahertz pump pulses, despite the 3 orders of magnitude different number of excited electrons. We are able to quantitatively explain our results using a nonthermal model based on quasielastic spin-flip scattering. It shows that, in the small-perturbation limit, the rate of demagnetization of a metallic ferromagnet is proportional to the excess energy of the electrons, independent of the precise shape of their distribution. Our results reveal that, for simple metallic ferromagnets, the dynamics of ultrafast demagnetization and of the closely related terahertz spin transport do not depend on the pump photon energy.
How higher-spin gravity surpasses the spin two barrier: no-go theorems versus yes-go examples
Creators: name: Bekaert, Xavier
name: Boulanger, Nicolas
name: Sundell, Per
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Aiming at non-experts, we explain the key mechanisms of higher-spin extensions of ordinary gravity. We first overview various no-go theorems for low-energy scattering of massless particles in flat spacetime. In doing so we dress a dictionary between the S-matrix and the Lagrangian approaches, exhibiting their relative advantages and weaknesses, after which we high-light potential loop-holes for non-trivial massless dynamics. We then review positive yes-go results for non-abelian cubic higher-derivative vertices in constantly curved backgrounds. Finally we outline how higher-spin symmetry can be reconciled with the equivalence principle in the presence of a cosmological constant leading to the Fradkin--Vasiliev vertices and Vasiliev's higher-spin gravity with its double perturbative expansion (in terms of numbers of fields and derivatives).
description: LaTeX, 50 pages, minor changes, many refs added; version accepted for publication in Reviews of Modern Physics
Additional file 1 of Mechanical power during extracorporeal membrane oxygenation and hospital mortality in patients with acute respiratory distress syndrome
Creators: name: Chiu, Li-Chung
name: Shih-Wei Lin
name: Li-Pang Chuang
name: Hsin-Hsien Li
name: Liu, Pi-Hua
name: Tsai, Feng-Chun
name: Chih-Hao Chang
name: Chen-Yiu Hung
name: Chung-Shu Lee
name: Shaw-Woei Leu
name: Han-Chung Hu
name: Huang, Chung-Chi
name: Huang-Pin Wu
name: Kao, Kuo-Chin
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Computational Biology

description: Additional file 1: Table S1. Ventilator settings before and during the first 3 days of ECMO between the earlier years and later years.
Simplicial cohomology of band semigroup algebras
Creators: name: Choi, Yemon
name: Gourdeau, Frédéric
name: White, Michael C.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Functional Analysis (math.FA)
subject: FOS: Mathematics
subject: Primary 16E40, 43A20

description: We establish simplicial triviality of the convolution algebra $\ell^1(S)$, where $S$ is a band semigroup. This generalizes results of the first author [Glasgow Math. J. 2005, Houston J. Math. 2010]. To do so, we show that the cyclic cohomology of this algebra vanishes in all odd degrees, and is isomorphic in even degrees to the space of continuous traces on $\ell^1(S)$. Crucial to our approach is the use of the structure semilattice of $S$, and the associated grading of $S$, together with an inductive normalization procedure in cyclic cohomology; the latter technique appears to be new, and its underlying strategy may be applicable to other convolution algebras of interest.
description: v1: AMS-LaTeX, 24 pages, 1 figure. v2: some typos corrected; a few minor adjustments made for clarity; references updated. Accepted June 2011 by Proc. Royal Soc. Edinburgh Sect. A
The effects of diversion terraces, grassed waterways, and tile drainage on selected soil properties and greenhouse gas emissions
Creators: name: Driscoll, Bryan Andrew
Publisher: name: University of British Columbia
Year: 2022

description: New Brunswick is one of the largest potato producing regions in Canada, which has experienced soil erosion and a decline in soil health due to intensive tillage from potato production. To address these concerns and the uncertainties of temperature and precipitation pattern changes from climate change, a new system has been proposed for soil and water conservation in Atlantic Canada. The landscape integrated soil and water conservation (LISWC) system combines diversion terraces, grassed waterways, tile drainage, water retention structures, supplemental irrigation, conservation tillage, and soil-landscape restoration. The objective was to evaluate the effects of diversion terraces, grassed waterways, and tile drainage relative to contour tillage on selected soil properties and greenhouse gas emissions over the initial three seasons of management implementation. The study site consisted of three land management practices (LMPs): contour tillage (CT), diversion terraces and grassed waterways (DTGW), and diversion terraces, grassed waterways, and tile drainage (DTGW+TD). Aggregate stability decreased in all LMPs, and LMP had a significant effect on labile carbon (POXC). CT led to a decrease of 11.2% POXC over the study period, while DTGW increased 19.8% and DTGW+TD increased 50.6%. Mineral associated organic matter (MAOM) carbon was affected by LMP: CT carbon concentrations decreased 3.75%, while DTGW+TD rose 9.7% and DTGW rose 15.8%. I also conducted a short-term incubation experiment in February of 2021 to quantify greenhouse gas fluxes in response to volumetric water content (20%, 27%, 35%, and 40%), nitrogen fertilizer application rates (0 and 170 kg N ha-1), and temperature (10°C and 25°C). Overall, both DTGW and DTGW+TD offer potential for improvement of soil health, relative to CT, in the second and third years of implementation, with increases in the labile C fraction POXC, a fraction significantly related to SOC, and increases in MAOM. This is the first study in the area measuring GHG emissions from erosion control structures. This study demonstrated that DTGW+TD significantly reduced the loss of CO₂ relative to DTGW, while also not emitting significantly more than CT, in the three years after implementation. Results were similar with respect to loss of nitrogen as N₂O.
Rydberg state mediated quantum gates and entanglement of pairs of neutral atoms
Creators: name: Saffman, M
name: Zhang, X L
name: Gill, A T
name: Isenhower, L
name: Walker, T G
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: Experiments performed within the last year have demonstrated Rydberg state mediated quantum gates and deterministic entanglement between pairs of trapped neutral atoms. These experiments validate ten year old proposals for Rydberg mediated quantum logic, but are only the beginning of ongoing efforts to improve the fidelity of the results obtained and scale the experiments to larger numbers of qubits. We present here a summary of the results to date, along with a critical evaluation of the prospects for higher fidelity Rydberg gates.
description: submitted to ICAP 2010 proceedings
The impact of the light exposure on the morphological properties of selected photoresists
Creators: name: Sikora, Andrzej
name: Janus, Paweł
name: Sierakowski, Andrzej
Publisher: name: The Faculty of Fundamental Problems of Technology, Wrocław University of Science and Technology, Poland
Year: 2019
Subjects: photolitography, polymer degradation, atomic force microscopy

description: OPTICA APPLICATA; 01/2019; ISSN 1429-7507
Determination of Boundary Scattering, Intermagnon Scattering, and the Haldane Gap in Heisenberg Chains
Creators: name: Ueda, Hiroshi
name: Kusakabe, Koichi
Publisher: name: arXiv
Year: 2011
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Low-lying magnon dispersion in a S=1 Heisenberg antiferromagnetic (AF) chain is analyzed using the non-Abelian DMRG method. The scattering length $a_{\rm b}$ of the boundary coupling and the inter-magnon scattering length $a$ are determined. The scattering length $a_{\rm b}$ is found to exhibit a characteristic diverging behavior at the crossover point. In contrast, the Haldane gap $Δ$, the magnon velocity $v$, and $a$ remain constant at the crossover. Our method allowed estimation of the gap of the S=2 AF chain to be $Δ= 0.0891623(9)$ using a chain length longer than the correlation length $ξ$.
description: 6 pages, 3 figures, 1 table, accepted in Phys. Rev. B
An analogue of the Kac-Weisfeiler conjecture
Creators: name: Tikaradze, Akaki
Publisher: name: arXiv
Year: 2010
Subjects: subject: Representation Theory (math.RT)
subject: Quantum Algebra (math.QA)
subject: FOS: Mathematics

description: In this paper we discuss an analogue of the Kac-Weisfeiler conjecture for a certain class of almost commutative algebras. In particular, we prove the Kac-Weisfeiler type statement for rational Cherednik algebras.
description: A significantly revised version, 13 pages, submitted
Staphylococcus aureus isolates from Eurasian Beavers (Castor fiber) carry a novel phage-borne bicomponent leukocidin related to the Panton-Valentine leukocidin
Creators: name: Monecke, Stefan
name: Feßler, Andrea T.
name: Burgold-Voigt, Sindy
name: Krüger, Henrike
name: Mühldorfer, Kristin
name: Wibbelt, Gudrun
name: Liebler-Tenorio, Elisabeth M.
name: Reinicke, Martin
name: Hanke, Dennis
name: Schwarz, Stefan
Publisher: name: Freie Universität Berlin
Year: 2021
Subjects: subject: Ecology
subject: FOS: Biological sciences
subject: Microbiology
subject: Molecular biology
subject: Zoology
subject: 600 Technik, Medizin, angewandte Wissenschaften::630 Landwirtschaft::630 Landwirtschaft und verwandte Bereiche

description: Staphylococcus aureus can be a harmless coloniser, but it can also cause severe infections in humans, livestock and wildlife. Regarding the latter, only few studies have been performed and knowledge on virulence factors is insufficient. The aim of the present study was to study S. aureus isolates from deceased wild beavers (Castor fiber). Seventeen isolates from eleven beavers, found in Germany and Austria, were investigated. Antimicrobial and biocide susceptibility tests were performed. Isolates were characterised using S. aureus-specific DNA microarrays, spa typing and whole-genome sequencing. From two isolates, prophages were induced by mitomycin C and studied by transmission electron microscopy. Four isolates belonged to clonal complex (CC) 8, CC12, and CC398. Twelve isolates belonged to CC1956 and one isolate was CC49. The CC49 and CC1956 isolates carried distinct lukF/S genes related to the Panton-Valentine leukocidin (PVL) from human isolates of S. aureus. These genes were located on related, but not identical, Siphovirus prophages. The beavers, from which those isolates originated, suffered from abscesses, purulent organ lesions and necrotising pneumonia, i.e., clinical manifestations resembling symptoms of severe PVL-associated disease in humans. It might thus be assumed that the “Beaver Leukocidin (BVL, lukF/S-BV)”-positive strains are beaver-specific pathogens, and further studies on their clinical role as well as on a possible transmissibility to other species, including humans, are warranted.
Additional file 2 of Activation of NLRP3 inflammasome in lung epithelial cells triggers radiation-induced lung injury
Creators: name: Rao, Xinrui
name: Zhou, Dong
name: Deng, Huilin
name: Chen, Yunshang
name: Wang, Jian
name: Zhou, Xiaoshu
name: Jie, Xiaohua
name: Xu, Yingzhuo
name: Wu, Zilong
name: Wang, Geng
name: Dong, Xiaorong
name: Zhang, Sheng
name: Meng, Rui
name: Wu, Chuangyan
name: Xing, Shijie
name: Fan, Kai
name: Wu, Gang
name: Zhou, Rui
Publisher: name: figshare
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Pharmacology
subject: Science Policy
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Additional file 2: Table S1. The primer sequences used in qRT-PCR. Table S2. Primer sequence of IL1R mutant and wild type.
Construction and evaluation of classifiers for forensic document analysis
Creators: name: Saunders, Christopher P.
name: Davis, Linda J.
name: Lamas, Andrea C.
name: Miller, John J.
name: Gantz, Donald T.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Applications (stat.AP)
subject: Methodology (stat.ME)
subject: FOS: Computer and information sciences

description: In this study we illustrate a statistical approach to questioned document examination. Specifically, we consider the construction of three classifiers that predict the writer of a sample document based on categorical data. To evaluate these classifiers, we use a data set with a large number of writers and a small number of writing samples per writer. Since the resulting classifiers were found to have near perfect accuracy using leave-one-out cross-validation, we propose a novel Bayesian-based cross-validation method for evaluating the classifiers.
description: Published in at http://dx.doi.org/10.1214/10-AOAS379 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org)
MOESM4 of Engineered global regulator H-NS improves the acid tolerance of E. coli
Creators: name: Gao, Xianxing
name: Yang, Xiaofeng
name: Li, Jiahui
name: Zhang, Yan
name: Chen, Ping
name: Lin, Zhanglin
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Computational Biology

description: Additional file 4: Figure S2. Fold change of the expression of H-NS at transcriptional level obtained by qRT-PCR.
Additional file 2 of Mechanical power during extracorporeal membrane oxygenation and hospital mortality in patients with acute respiratory distress syndrome
Creators: name: Chiu, Li-Chung
name: Shih-Wei Lin
name: Li-Pang Chuang
name: Hsin-Hsien Li
name: Liu, Pi-Hua
name: Tsai, Feng-Chun
name: Chih-Hao Chang
name: Chen-Yiu Hung
name: Chung-Shu Lee
name: Shaw-Woei Leu
name: Han-Chung Hu
name: Huang, Chung-Chi
name: Huang-Pin Wu
name: Kao, Kuo-Chin
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Computational Biology

description: Additional file 2: Table S2. Ventilator settings parameters during the first 3 days of ECMO.
Cosmic ray spectral hardening due to dispersion in the source injection spectra
Creators: name: Yuan, Qiang
name: Zhang, Bing
name: Bi, Xiao-Jun
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Recent cosmic ray (CR) experiments discovered that the CR spectra experience a remarkable hardening for rigidity above several hundred GV. We propose that this is caused by the superposition of the CR energy spectra of many sources that have a dispersion in the injection spectral indices. Adopting similar parameters as those of supernova remnants derived from the Fermi $γ$-ray observations, we can reproduce the observational CR spectra of different species well. This may be interpreted as evidence to support the supernova remnant origin of CRs below the knee. We further propose that the same mechanism may explain the "ankle" of the ultra high energy CR spectrum.
description: 5 pages, 3 figures and 1 table. Updated with the diffusion propagation model, accepted by Phys. Rev. D
Marek’s Disease Virus Modulates T Cell Proliferation via Activation of Cyclooxygenase 2-Dependent Prostaglandin E2
Creators: name: Kamble, Nitin
name: Gurung, Angila
name: Kaufer, Benedikt B.
name: Pathan, Ansar Ahmed
name: Behboudi, Shahriar
Publisher: name: Freie Universität Berlin
Year: 2021
Subjects: subject: Marek’s disease virus
subject: T cell proliferation
subject: COX2 = cyclooxygenase 2
subject: PGE2
subject: immunosuppression
subject: 600 Technik, Medizin, angewandte Wissenschaften::630 Landwirtschaft::630 Landwirtschaft und verwandte Bereiche

description: Marek’s disease virus (MDV), an avian alphaherpesvirus, infects chickens, transforms CD4+ T cells, and induces immunosuppression early during infection. However, the exact mechanisms involved in MDV-induced immunosuppression are yet to be identified. Here, our results demonstrate that MDV infection in vitro and in vivo induces activation of cyclooxygenase-2 (COX-2) and production of prostaglandin E2 (PGE2). This exerts its inhibitory effects on T cell proliferation at day 21 post infection via PGE2 receptor 2 (EP2) and receptor 4 (EP4). Impairment of the MDV-induced T cell proliferation was associated with downregulation of IL-2 and transferrin uptake in a COX-2/PGE2 dependent manner in vitro. Interestingly, oral administration of a COX-2 inhibitor, meloxicam, during MDV infection inhibited COX-2 activation and rescued T cell proliferation at day 21 post infection. Taken together, our results reveal a novel mechanism that contributes to immunosuppression in the MDV-infected chickens.
Finding the best clearing approach - Towards 3D wide-scale multimodal imaging of aged human brain tissue
Creators: name: Rusch, Henriette
name: Brammerloh, Malte
name: Stieler, Jens
name: Sonntag, Mandy
name: Mohammadi, Siawoosh
name: Weiskopf, Nikolaus
name: Arendt, Thomas
name: Kirilina, Evgeniya
name: Morawski, Markus
Publisher: name: Freie Universität Berlin
Year: 2022
Subjects: subject: Tissue clearing
subject: CLARITY
subject: IDISCO
subject: Light sheet microscopy
subject: Immunohistochemistry
subject: 100 Philosophie und Psychologie::150 Psychologie::150 Psychologie

description: The accessibility of new wide-scale multimodal imaging techniques led to numerous clearing techniques emerging over the last decade. However, clearing mesoscopic-sized blocks of aged human brain tissue remains an extremely challenging task. Homogenizing refractive indices and reducing light absorption and scattering are the foundation of tissue clearing. Due to its dense and highly myelinated nature, especially in white matter, the human brain poses particular challenges to clearing techniques. Here, we present a comparative study of seven tissue clearing approaches and their impact on aged human brain tissue blocks (> 5 mm). The goal was to identify the most practical and efficient method in regards to macroscopic transparency, brief clearing time, compatibility with immunohistochemical processing and wide-scale multimodal microscopic imaging. We successfully cleared 26 × 26 × 5 mm3-sized human brain samples with two hydrophilic and two hydrophobic clearing techniques. Optical properties as well as light and antibody penetration depths highly vary between these methods. In addition to finding the best clearing approach, we compared three microscopic imaging setups (the Zeiss Laser Scanning Microscope (LSM) 880 , the Miltenyi Biotec Ultramicroscope ll (UM ll) and the 3i Marianas LightSheet microscope) regarding optimal imaging of large-scale tissue samples. We demonstrate that combining the CLARITY technique (Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging compatible Tissue hYdrogel) with the Zeiss LSM 880 and combining the iDISCO technique (immunolabeling-enabled three-dimensional imaging of solvent-cleared organs) with the Miltenyi Biotec UM ll are the most practical and efficient approaches to sufficiently clear aged human brain tissue and generate 3D microscopic images. Our results point out challenges that arise from seven clearing and three imaging techniques applied to non-standardized tissue samples such as aged human brain tissue.
Nuancing the 2:3 ratio : microtiming analyses of dance music from the transnational Macedonian region
Creators: name: Bernacki, Nathan Sparhawk
Publisher: name: University of British Columbia
Year: 2022

description: Balkan meters are traditionally perceived in the ethnomusicological literature through a 2:3 ratio underlain by a series of isochronous subdivisions. Through beat inter-onset-interval (IOI) analysis I show how this conception obscures and neglects timing nuances, using examples of dance music from the transnational Macedonian region. Chapter 1 analyzes two songs from the Pirin-Macedonia region of Bulgaria featuring a 3-beat “long-short-short” meter. IOI analysis demonstrates that the beat proportions of these songs do not align with that governed by a 2:3 beat ratio underlain by a series of isochronous subdivisions. Chapter 2 analyzes the song “Daoulari Tsalar” of the Zurla/Tapan tradition in Greek-Macedonia. This tradition features a characteristic metric progression from a slow and loose treatment to a fast and strict treatment of a beat cycle. This analysis articulates how sections featuring slow and loose cycling, when beats are coordinated by the steps of the lead dancer, are non-isochronous, yet do not conform to any isochronous subdivision layer nor a 2:3 beat ratio. In addition to quantitative timing discussions, this thesis also addresses emic musical conceptions and the political contextualization of such dance musics, demonstrating how analysis and ethnography can act as mutually informative methodologies.
Additional file 3 of Mechanical power during extracorporeal membrane oxygenation and hospital mortality in patients with acute respiratory distress syndrome
Creators: name: Chiu, Li-Chung
name: Shih-Wei Lin
name: Li-Pang Chuang
name: Hsin-Hsien Li
name: Liu, Pi-Hua
name: Tsai, Feng-Chun
name: Chih-Hao Chang
name: Chen-Yiu Hung
name: Chung-Shu Lee
name: Shaw-Woei Leu
name: Han-Chung Hu
name: Huang, Chung-Chi
name: Huang-Pin Wu
name: Kao, Kuo-Chin
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Computational Biology

description: Additional file 3: Table S3. Cox proportional hazard regression analysis of factors associated with 90-day hospital mortality.
Photon echo quantum memories in inhomogeneously broadened two level atoms
Creators: name: McAuslan, D. L.
name: Ledingham, P. M.
name: Naylor, W. R.
name: Beavan, S. E.
name: Hedges, M. P.
name: Sellars, M. J.
name: Longdell, J. J.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Here we propose a solid-state quantum memory that does not require spectral holeburning, instead using strong rephasing pulses like traditional photon echo techniques. The memory uses external broadening fields to reduce the optical depth and so switch off the collective atom-light interaction when desired. The proposed memory should allow operation with reasonable efficiency in a much broader range of material systems, for instance Er3+ doped crystals which have a transition at 1.5 um. We present analytic theory supported by numerical calculations and initial experiments.
description: 7 pages, 8 figures
Early volumetric changes of hippocampus and medial prefrontal cortex following medial temporal lobe resection
Creators: name: Pajkert, Anna
name: Ploner, Christoph J.
name: Lehmann, Thomas‐Nicolas
name: Witte, Veronica A.
name: Oltmanns, Frank
name: Sommer, Werner
name: Holtkamp, Martin
name: Heekeren, Hauke R.
name: Finke, Carsten
Publisher: name: Charité - Universitätsmedizin Berlin
Year: 2020
Subjects: subject: default mode network
subject: hippocampus
subject: medial prefrontal cortex
subject: medial temporal lobe resection
subject: plasticity
subject: 600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit::610 Medizin und Gesundheit

description: Previous studies have shown that cognitive demands and physical exercise stimulate adult neurogenesis in the dentate gyrus and hippocampus. Recent observations in healthy humans and patients with mild cognitive impairment moreover suggest that training-induced increases in hippocampal volume may be associated with improved memory performance. The corresponding plasticity processes in hippocampal volume may occur on timescales of months to years. For patients with focal lesions in this region, previous functional imaging studies suggest that increased recruitment of the contralateral hippocampus and extratemporal regions may be an important part of the reorganization of episodic memory. However, it is currently unclear whether focal damage to the medial temporal lobe (MTL) induces gray matter (GM) volume changes in the intact contralateral hippocampus and in connected network regions on a shorter timescale. We therefore investigated whether unilateral resection of the MTL, including the hippocampus, induces measurable volumetric changes in the contralateral hippocampus and in the default mode network (DMN). We recruited 31 patients with unilateral left (N = 19) or right (N = 12) hippocampal sclerosis undergoing MTL resection for treatment of drug-resistant epilepsy. Structural MRI was acquired immediately before and 3 months after surgery. Longitudinal voxel-based morphometry (VBM) analysis revealed a significant increase of right hippocampal volume following resection of the left anterior MTL. Furthermore, this patient group showed GM volume increases in the DMN. These results demonstrate significant structural plasticity of the contralateral hippocampus, even in patients with a long-standing unilateral hippocampal dysfunction and structural reorganization processes extending to distant, but functionally connected brain regions.
Thermodynamics of the two-dimensional Hubbard model in the two-body scattering approximation
Creators: name: LeClair, Andre
Publisher: name: arXiv
Year: 2010
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: A new analytic treatment of the two-dimensional Hubbard model at finite temperature and chemical potential is presented. A next nearest neighbor hopping term of strength t' is included. This analysis is based upon a formulation of the statistical mechanics of particles in terms of the S-matrix. In the 2-body scattering approximation, the S-matrix allows a systematic expansion in t/U. We show that for U/t large enough, a region of attractive interactions exists near the Fermi surface due to 1-loop renormalization effects. For t'/t = -0.3, attractive interactions exist for U/t > 6.4. Our analysis suggests that superconductivity may not exist for t'=0. Based on the existence of solutions of the integral equation for the pseudo-energy, we provide evidence for the superconducting phase and estimate Tc/t = 0.02.
description: version 2: published version, additional explanations and references
Additional file 4 of Mechanical power during extracorporeal membrane oxygenation and hospital mortality in patients with acute respiratory distress syndrome
Creators: name: Chiu, Li-Chung
name: Shih-Wei Lin
name: Li-Pang Chuang
name: Hsin-Hsien Li
name: Liu, Pi-Hua
name: Tsai, Feng-Chun
name: Chih-Hao Chang
name: Chen-Yiu Hung
name: Chung-Shu Lee
name: Shaw-Woei Leu
name: Han-Chung Hu
name: Huang, Chung-Chi
name: Huang-Pin Wu
name: Kao, Kuo-Chin
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Computational Biology

description: Additional file 4: Table S4. Cox proportional hazard regression analysis of factors associated with 90-day hospital mortality.
Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law
Creators: name: Zou, Xudong
name: Schaefke, Bernhard
name: Li, Yisheng
name: Jia, Fujian
name: Sun, Wei
name: Li, Guipeng
name: Liang, Weizheng
name: Reif, Tristan
name: Heyd, Florian
name: Gao, Qingsong
Publisher: name: Freie Universität Berlin
Year: 2022
Subjects: subject: Mammalian splicing divergence
subject: alternative splicing
subject: mechanisms
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie

description: Alternative splicing is ubiquitous, but the mechanisms underlying its pattern of evolutionary divergence across mammalian tissues are still underexplored. Here, we investigated the cis-regulatory divergences and their relationship with tissue-dependent trans-regulation in multiple tissues of an F1 hybrid between two mouse species. Large splicing changes between tissues are highly conserved and likely reflect functional tissue-dependent regulation. In particular, micro-exons frequently exhibit this pattern with high inclusion levels in the brain. Cis-divergence of splicing appears to be largely non-adaptive. Although divergence is in general associated with higher densities of sequence variants in regulatory regions, events with high usage of the dominant isoform apparently tolerate more mutations, explaining why their exon sequences are highly conserved but their intronic splicing site flanking regions are not. Moreover, we demonstrate that non-adaptive mutations are often masked in tissues where accurate splicing likely is more important, and experimentally attribute such buffering effect to trans-regulatory splicing efficiency.
Additional file 1 of Integrated transcriptome and proteome revealed that the declined expression of cell cycle-related genes associated with follicular atresia in geese
Creators: name: Yang, Wanli
name: Chen, Xingyong
name: Liu, Zhengquan
name: Zhao, Yutong
name: Chen, Yufei
name: Geng, Zhaoyu
Publisher: name: figshare
Year: 2023
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Environmental Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology

description: Additional file 1: Fig. S1. Principal component analysis of DEGs in normal and atretic follicles.
The visibility of IQHE at sharp edges: Experimental proposals based on interactions and edge electrostatics
Creators: name: Erkarslan, U.
name: Oylumluoglu, G.
name: Grayson, M.
name: Siddiki, A.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: The influence of the incompressible strips on the integer quantized Hall effect (IQHE) is investigated, considering a cleaved-edge overgrown (CEO) sample as an experimentally realizable sharp edge system. We propose a set of experiments to clarify the distinction between the large-sample limit when bulk disorder defines the IQHE plateau width and the small-sample limit smaller than the disorder correlation length, when self-consistent edge electrostatics define the IQHE plateau width. The large-sample or bulk QH regime is described by the usual localization picture, whereas the small-sample or edge regime is discussed within the compressible/incompressible strips picture, known as the screening theory of QH edges. Utilizing the unusually sharp edge profiles of the CEO samples, a Hall bar design is proposed to manipulate the edge potential profile from smooth to extremely sharp. By making use of a side-gate perpendicular to the two dimensional electron system, it is shown that the plateau widths can be changed or even eliminated altogether. Hence, the visibility of IQHE is strongly influenced when adjusting the edge potential profile and/or changing the dc current direction under high currents in the non-linear transport regime. As a second investigation, we consider two different types of ohmic contacts, namely highly transmitting (ideal) and highly reflecting (non-ideal) contacts. We show that if the injection contacts are non-ideal, however still ohmic, it is possible to measure directly the non-quantized transport taking place at the bulk of the CEO samples. The results of the experiments we propose will clarify the influence of the edge potential profile and the quality of the contacts, under quantized Hall conditions.
description: Substantially revised version of manuscript arXiv:0906.3796v1, including new figures etc
Activity and components of the granulocyte colony‐stimulating factor pathway in hidradenitis suppurativa*
Creators: name: Wolk, Kerstin
name: Brembach, Theresa-Charlotte
name: Šimaitė, D.
name: Bartnik, E.
name: Cucinotta, S.
name: Pokrywka, A.
name: Irmer, Marie Luise
name: Triebus, Julia
name: Witte‐Händel, Ellen
name: Salinas, G.
name: Leeuw, T.
name: Volk, Hans-Dieter
name: Ghoreschi, Kamran
name: Sabat, Robert
Publisher: name: Charité - Universitätsmedizin Berlin
Year: 2021
Subjects: subject: Hidradenitis suppurativa
subject: chronic inflammatory disease
subject: granulocyte colony-stimulating factor
subject: 600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit::610 Medizin und Gesundheit

description: Background Hidradenitis suppurativa (HS) is a chronic inflammatory disease, characterized by painful, purulent and destructive skin alterations in intertriginous areas. Objectives We investigated the expression and role in HS of granulocyte colony-stimulating factor (G-CSF), the regulator of neutrophil biology, as clinical signs of a neutrophilic granulocyte-driven inflammation are distinctive in the disease. Methods Skin and blood samples obtained from different cohorts of patients with HS and control individuals were assessed by RNA sequencing, quantitative polymerase chain reaction on reverse transcribed mRNA, and/or enzyme-linked immunosorbent assay. Mechanistic studies using keratinocytes, dermal fibroblasts, immune cell populations and skin biopsies were performed. Results G-CSF was abundant in HS skin, particularly in inflamed nodules and abscesses. Its levels even exceeded those found in other inflammatory skin diseases. Interleukin (IL)-1 and IL-17, respectively, induced G-CSF production by fibroblasts and keratinocytes. These effects were enhanced by tumour necrosis factor (TNF)-alpha and IL-36. Accordingly, fibroblasts separated from HS lesions expressed G-CSF, and IL-1 receptor antagonist reduced G-CSF levels in explanted HS skin. G-CSF blood levels positively correlated with severity of HS. Elevated lesional G-CSF receptor levels were linked to upregulation of molecules that contribute to prolonged activation of neutrophils by components of bacteria and damaged host cells [formyl peptide receptor 1 (FPR1), FPR2 and free fatty acid receptor 2 (FFAR2)], neutrophil survival [TNF receptor superfamily member 10C (TNFRSF10C/TRAIL-R3) and TNF receptor superfamily member 6B], kinases (tyrosine-protein kinase HCK and hexokinase 3), and skin destruction [MMP25 (matrix metalloproteinase 25) and ADAM8 (disintegrin and metalloproteinase domain-containing protein 8)]. G-CSF elevated the expression of FPR1, FFAR2, and TNFRSF10C/TRAIL-R3 in neutrophils and synergized with bacterial components to induce skin-destructive enzymes. Conclusions The G-CSF pathway engages both tissue and immune cells, is strongly activated in HS lesions, and offers the opportunity to target the neutrophil-driven inflammation.
Functional validation of UGT1A6 in anthracycline-induced cardiotoxicity
Creators: name: Morrison, Alexander
Publisher: name: University of British Columbia
Year: 2022

description: The pursuit of precision medicine can be achieved via pharmacogenetic testing prior to treatment onset thanks to the genomic revolution. It has allowed for large-scale genetic testing to be done relatively inexpensively resulting in specific genetic variants to be linked with a phenotype or disease of interest. While beneficial, there remains a burden of proof before translation of knowledge from bench to bedside in order to provide the best possible healthcare. In this study, novel in vitro methods were used with the goal of functionally exploring the role of UGT1A6 in relation to a patient’s risk of the adverse drug reaction (ADR) known as anthracycline-induced cardiotoxicity. More specifically, the variant in UGT1A6 known as rs17863783 has been previously shown, along with other genetic and clinical risk factors, to put a patient at increased risk for cardiotoxicity following anthracycline treatment onset. HEK293 cells were used to create stably transfected expression systems of various haplotypes of UGT1A6. These cells were validated to be expressing the correct genotype via PCR and Sanger Sequencing and subsequently treated with the anthracycline known as doxorubicin (DOX) for viability investigation. Transiently transfected HEK293 cells were also used to express UGT1A6 haplotypes of interest for an investigation of cell viability in addition to UGT1A6 enzyme activity via a 4MU general glucuronidation assay. Despite inherent limitations of in vitro analysis, we conclude that UGT1A6 1) plays a role in anthracycline-induced cardiotoxicity 2) the various haplotypes, such as rs17863783, alter functionality providing additional evidence to support prospective pharmacogenomic testing of patients along with serving as a knowledge base for future research and 3) not all model systems effectively model in vivo phenomena. This thesis will detail the methods and results obtained over the course of investigation into the role of UGT1A6 and anthracycline-induced cardiotoxicity.
Applications of Tauberian Theorem for High-SNR Analysis of Performance over Fading Channels
Creators: name: Zhang, Yuan
name: Tepedelenlioglu, Cihan
Publisher: name: arXiv
Year: 2011
Subjects: subject: Information Theory (cs.IT)
subject: FOS: Computer and information sciences

description: This paper derives high-SNR asymptotic average error rates over fading channels by relating them to the outage probability, under mild assumptions. The analysis is based on the Tauberian theorem for Laplace-Stieltjes transforms which is grounded on the notion of regular variation, and applies to a wider range of channel distributions than existing approaches. The theory of regular variation is argued to be the proper mathematical framework for finding sufficient and necessary conditions for outage events to dominate high-SNR error rate performance. It is proved that the diversity order being $d$ and the cumulative distribution function (CDF) of the channel power gain having variation exponent $d$ at 0 imply each other, provided that the instantaneous error rate is upper-bounded by an exponential function of the instantaneous SNR. High-SNR asymptotic average error rates are derived for specific instantaneous error rates. Compared to existing approaches in the literature, the asymptotic expressions are related to the channel distribution in a much simpler manner herein, and related with outage more intuitively. The high-SNR asymptotic error rate is also characterized under diversity combining schemes with the channel power gain of each branch having a regularly varying CDF. Numerical results are shown to corroborate our theoretical analysis.
description: 22 pages, 4 figures, submitted to IEEE Transactions on Wireless Communications
Extremal functions for Caffarelli-Kohn-Nirenberg and logarithmic Hardy inequalities
Creators: name: Dolbeault, Jean
name: Esteban, Maria J.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: We consider a family of Caffarelli-Kohn-Nirenberg interpolation inequalities and weighted logarithmic Hardy inequalities which have been obtained recently as a limit case of the first ones. We discuss the ranges of the parameters for which the optimal constants are achieved by extremal functions. The comparison of these optimal constants with the optimal constants of Gagliardo-Nirenberg interpolation inequalities and Gross' logarithmic Sobolev inequality, both without weights, gives a general criterion for such an existence result in some particular cases.
description: Proc. Edinburgh A (2012) To appear