cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
MOESM1 of CSA: a web service for the complete process of ChIP-Seq analysis
Creators: name: Li, Min
name: Tang, Li
name: Wu, Fang-Xiang
name: Pan, Yi
name: Wang, Jianxin
Publisher: name: figshare
Year: 2019
Subjects: subject: Space Science
subject: Medicine
subject: Pharmacology
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: Additional file 1: Fig. S1. YAP/TAZ/TEAD (A) binding to promoter; (B) binding to enhancers. Fig. S2. YAP/TAZ/TEAD binding comparison of promoters and enhancers. Fig. S3. CASE STUDY 2: Motif discovery in ChIP-Seq peaks. Finding de novo motifs. Fig. S4. CASE STUDY 2: Motif discovery in ChIP-Seq peaks. Detail information about the motif 1. Fig. S5. CASE STUDY 2: GO enrichment analysis for ChIP-Seq peaks. Fig. S6. CASE STUDY 2: KEGG pathway analysis for ChIP-Seq peaks.
O(a) improvement of the axial current in lattice QCD to one-loop order of perturbation theory
Creators: name: Lüscher, M.
name: Weisz, P.
Publisher: name: arXiv
Year: 1996
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: The conservation of the isovector axial current in lattice QCD with massless Wilson quarks is studied to one-loop order of perturbation theory. Following a strategy described in a previous publication, the O($a$) counterterm required for on-shell improvement of the current is computed. We also confirm an earlier result of Wohlert for the coefficient in front of the SW term in the improved action.
description: 38 pages, postscript file
FTS improvements for LHC Run-3 and beyond
Creators: name: Manzi, Andrea
name: Keeble, Oliver
name: Rios, Maria Arsuaga
name: Karavakis, Edward
name: Angelogiannopoulos, Aris
Publisher: name: Zenodo
Year: 2019

description: The File Transfer Service developed at CERN and in production since 2014, has become fundamental component for LHC experiments workflows. Starting from the beginning of 2018 with the participation to the EU project Extreme Data Cloud (XDC) [1] and the activities carried out in the context of the DOMA TPC [2] and QoS [3] working groups, a series of new developments and improvements has been planned and performed taking also into account the requirements from the experiments. This talk will mainly focus on the support for OpenID Connect and the QoS integration via CDMI as output of the XDC project. The integration with OpenID Connect is also following the direction of the future Authentication and Authorisation Infrastructure (AAI) for WLCG experiments. The service scalability enhancements, the support for Xrootd and HTTP TPC and the first 'non-gridftp' transfers experiences via FTS between WLCG production sites will be also described, with an emphasis on performance comparison. The service enhancements are meeting the requirements for LHC Run-3 and facilitating the adoption for other HEP and non-HEP communities. [1] http://www.extreme-datacloud.eu/ [2] https://twiki.cern.ch/twiki/bin/view/LCG/ThirdPartyCopy [3] https://twiki.cern.ch/twiki/bin/view/LCG/QoS
A combination chaotic system and application in color image encryption
Creators: name: Parvaz, R.
name: Zarebnia, M.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Information Theory (cs.IT)
subject: Cryptography and Security (cs.CR)
subject: FOS: Computer and information sciences

description: In this paper, by using Logistic, Sine and Tent systems we define a combination chaotic system. Some properties of the chaotic system are studied by using figures and numerical results. A color image encryption algorithm is introduced based on new chaotic system. Also this encryption algorithm can be used for gray scale or binary images. The experimental results of the encryption algorithm show that the encryption algorithm is secure and practical.
Additional file 1 of Stress granule activation attenuates lipopolysaccharide-induced cardiomyocyte dysfunction
Creators: name: Wang, Yaqiao
name: Liu, Runmin
name: Wu, Kehan
name: Yang, Gaowei
name: Wang, Yusheng
name: Wang, Hao
name: Rui, Tao
Publisher: name: figshare
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Science Policy
subject: Immunology
subject: FOS: Clinical medicine

description: Supplementary Material 1
Experimental nonlocal steering of Bohmian trajectories
Creators: name: Xiao, Ya
name: Kedem, Yaron
name: Xu, Jin-Shi
name: Li, Chuan-Feng
name: Guo, Guang-Can
Publisher: name: arXiv
Year: 2017
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Interpretations of quantum mechanics (QM), or proposals for underlying theories, that attempt to present a definite realist picture, such as Bohmian mechanics, require strong non-local effects. Naively, these effects would violate causality and contradict special relativity. However if the theory agrees with QM the violation cannot be observed directly. Here, we demonstrate experimentally such an effect: we steer the velocity and trajectory of a Bohmian particle using a remote measurement. We use a pair of photons and entangle the spatial transverse position of one with the polarization of the other. The first photon is sent to a double-slit-like apparatus, where its trajectory is measured using the technique of Weak Measurements. The other photon is projected to a linear polarization state. The choice of polarization state, and the result, steer the first photon in the most intuitive sense of the word. The effect is indeed shown to be dramatic, while being easy to visualize. We discuss its strength and what are the conditions for it to occur.
description: 10 pages, 3 figures
Additional file 6: of Characterising resuscitation promoting factor fluorescent-fusions in mycobacteria
Creators: name: Uhía, Iria
name: Nitya Krishnan
name: Robertson, Brian
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology

description: Table S2. Primers used in this study. (PDF 14 kb)
A Model for the Global Quantum Efficiency for a TPB-based Wavelength-Shifting System used with Photomultiplier Tubes in Liquid Argon in MicroBooNE
Creators: name: Pate, S. F.
name: Wester, T.
name: Bugel, L.
name: Conrad, J.
name: Henderson, E.
name: Jones, B. J. P.
name: McLean, A. I. L.
name: Moon, J. S.
name: Toups, M.
name: Wongjirad, T.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: High Energy Physics - Experiment (hep-ex)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: We present a model for the Global Quantum Efficiency (GQE) of the MicroBooNE optical units. An optical unit consists of a flat, circular acrylic plate, coated with tetraphenyl butadiene (TPB), positioned near the photocathode of a 20.2-cm diameter photomultiplier tube. The plate converts the ultra-violet scintillation photons from liquid argon into visible-spectrum photons to which the cryogenic phototubes are sensitive. The GQE is the convolution of the efficiency of the plates that convert the 128 nm scintillation light from liquid argon to visible light, the efficiency of the shifted light to reach the photocathode, and the efficiency of the cryogenic photomultiplier tube. We develop a GEANT4-based model of the optical unit, based on first principles, and obtain the range of probable values for the expected number of detected photoelectrons ($N_{\rm PE}$) given the known systematic errors on the simulation parameters. We compare results from four measurements of the $N_{\rm PE}$ determined using alpha-particle sources placed at two distances from a TPB-coated plate in a liquid argon cryostat test stand. We also directly measured the radial dependence of the quantum efficiency, and find that this has the same shape as predicted by our model. Our model results in a GQE of $0.0055\pm0.0009$ for the MicroBooNE optical units. While the information shown here is MicroBooNE specific, the approach to the model and the collection of simulation parameters will be widely applicable to many liquid-argon-based light collection systems.
description: final version accepted for publication by JINST
An XMM-Newton view of the young open cluster NGC 6231 -- I. The catalogue
Creators: name: Sana, H.
name: Gosset, E.
name: Rauw, G.
name: Sung, H.
name: Vreux, J. -M.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: This paper is the first of a series dedicated to the X-ray properties of the young open cluster NGC 6231. Our data set relies on an XMM-Newton campaign of a nominal duration of 180 ks and reveals that NGC 6231 is very rich in the X-ray domain too. Indeed, 610 X-ray sources are detected in the present field of view, centered on the cluster core. The limiting sensitivity of our survey is approximately 6E-15 erg/s/cm^2 but clearly depends on the location in the field of view and on the source spectrum. Using different existing catalogues, over 85% of the X-ray sources could be associated with at least one optical and/or infrared counterpart within a limited cross-correlation radius of 3 arcsec at maximum. The surface density distribution of the X-ray sources presents a slight N-S elongation. Once corrected for the spatial sensitivity variation of the EPIC instruments, the radial profile of the source surface density is well described by a King profile with a central density of about 8 sources per arcmin^2 and a core radius close to 3.1arcmin. The distribution of the X-ray sources seems closely related to the optical source distribution. The expected number of foreground and background sources should represent about 9% of the detected sources, thus strongly suggesting that most of the observed X-ray emitters are physically belonging to NGC 6231. Finally, beside a few bright but soft objects -- corresponding to the early-type stars of the cluster -- most of the sources are relatively faint (~5E-15 erg/s/cm^2) with an energy distribution peaked around 1.0-2.0 keV.
description: 21 pages, 11 figures, 2 tables available at CDS, to appeared in Astronomy & Astrophysics
Asymmetric Andreev resonant state with a magnetic exchange field in spin-triplet superconducting monolayer $MoS_2$
Creators: name: Goudarzi, H.
name: Khezerlou, M.
name: Ebadzadeh, S. F.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Featuring spin-valley degree of freedom by a magnetic exchange field-induction to gain transport of charge carriers through a junction based on superconducting subgap tunneling can provide a new scenario for future electronics. Transmission of low-energy Dirac-like electron (hole) quasiparticles through a ferromagnet/superconductor (F/S) interface can be of noticeable importance due to strong spin-orbit coupling in the valence band of monolayer $MoS_2$ (ML-MDS). The magnetic exchange field (MEF) of a ferromagnetic section on top of ML-MDS may affect the electron (hole) excitations for spin-up and spin-down electrons, differently. Tuning the MEF enables one to control either electrical properties (such as band gap, SOC and etc.) or spin-polarized transport. We study the influence of MEF on the chirality of Andreev resonant state (ARS) appearing at the relating F/S interface, in which the induced pairing order parameter is chiral $p$-wave symmetry. The resulting normal conductance is found to be more sensitive to the magnitude of MEF and doping regime of F region. Unconventional spin-triplet $p$-wave symmetry features the zero-bias conductance, which strongly depends on $p$-doping level of F region in the relating NFS junction.
description: 11 pages, 7 figures
Jove & the PARROT: MeerKAT as a dynamic imaging machine
Creators: name: Smirnov, Oleg
Publisher: name: Zenodo
Year: 2024

description: With the increased sensitivity and field of view of SKA pathfinders, dynamic imaging (that is, imaging the time axis) is becoming a burgeoning field yielding rich new discoveries of transients and variable sources. MeerKAT is capable of reaching sub-150 $\upmu$Jy image rms in an 8s integration, which opens up studies of variability on much shorter timescales than  possible with any other past or present instruments. At the same time, imaging at such short timescales introduces its own substantial challenges. Instrumental effects that tend to average out in a traditional long synthesis observation can become limiting for dynamic imaging if not addressed correctly.

I will present MeerKAT dynamic imaging of Jupiter's radiation belts, which has led to the serendipitous discovery of a new neutron star tentatively called a PARROT (pulsar with abnormal refraction occurring on odd timescales). I will discuss the calibration and imaging challenges inherent to dynamic imaging. I will also present imaging pipelines that are capable of yielding light curves and, potentially, dynamic spectra for thousands of field sources en masse, potentially turning MeerKAT into a ``variability mining" machine.
Additional file 1: of Personalized objects can optimize the diagnosis of EMCS in the assessment of functional object use in the CRS-R: a double blind, randomized clinical trial
Creators: name: Yuxiao Sun
name: Jianan Wang
name: Heine, Lizette
name: Wangshan Huang
name: Wang, Jing
name: Nantu Hu
name: Xiaohua Hu
name: Xiaohui Fang
name: Supeng Huang
name: Laureys, Steven
name: Haibo Di
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Neuroscience
subject: Cancer
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: CONSORT 2010 checklist of information to include when reporting a randomised trial. (DOC 217 kb)
(Anti-)Chiral Superfield Approach to Interacting Abelian 1-Form Gauge Theories: Nilpotent and Absolutely Anticommuting Charges
Creators: name: Chauhan, B.
name: Kumar, S.
name: Malik, R. P.
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We derive the off-shell nilpotent (fermionic) (anti-)BRST symmetry transformations by exploiting the (anti-)chiral superfield approach (ACSA) to Becchi-Rouet-Stora-Tyutin (BRST) formalism for the interacting Abelian 1-form gauge theories where there is a coupling between the U(1) Abelian 1-form gauge field and Dirac as well as complex scalar fields. We exploit the (anti-)BRST invariant restrictions on the (anti-)chiral superfields to derive the fermionic symmetries of our present D-dimensional Abelian 1-form gauge theories. The novel observation of our present investigation is the derivation of the absolute anticommutativity of the nilpotent (anti-)BRST charges despite the fact that our ordinary D-dimensional theories are generalized onto the (D, 1)-dimensional (anti-)chiral super submanifolds (of the general (D, 2)-dimensional supermanifold) where only the (anti-)chiral expansions of the (anti-)chiral superfields have been taken into account. We also discuss the nilpotency of the (anti-)BRST charges and (anti-)BRST invariance of the Lagrangian densities of our present theories within the framework of ACSA to BRST formalism.
description: LaTeX file, 20 pages, journal version
Additional file 1: of Patterns of caesarean section in HIV infected and non-infected women in Malawi: is caesarean section used for PMTCT?
Creators: name: Lyson Tenthani
name: Oosterhout, Joep Van
name: Haas, Andreas
name: Malango Msukwa
name: Nozgechi Phiri
name: Chimbwandira, Frank
name: Tal, Kali
name: Aebi-Popp, Karoline
name: Estill, Janne
name: Keiser, Olivia
Publisher: name: figshare
Year: 2018
Subjects: subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: FOS: Biological sciences
subject: Computational Biology

description: Appendix 1. Word document describing the sampling strategy used in the study. (DOCX 24 kb)
Outdoor Domestication Cultivation and Survival Mechanism for Tissue Culture Seedlings of Paeonia suffruticosa
Creators: name: MA Xianglong
name: WU Jingxu
name: LIANG Yixin
name: LIU Shaohua
name: WANG Yongmei
name: MA Xianglong
name: WU Jingxu
name: LIANG Yixin
name: LIU Shaohua
name: WANG Yongmei
Publisher: name: Unknown
Year: 2019
Subjects: subject: Agribusiness
subject: Tissue culture seedlings of Paeonia suffruticosa, Outdoor domestication cultivation, Survival rate, Survival mechanism

description: In order to reveal the differences between different peony varieties and facilities, thousands of tissue culture seedlings of 21 Itoh peony varieties imported from abroad were used as test materials, and the peony domestication cultivation method used in the past was used as a control. The technical measures and mechanisms for the outdoor domestication of seedlings and the survival of field transplantation were studied. The results indicate that the main factors and measures for effectively protecting the outdoor transplanting of tissue culture seedlings include cultivating sound and strong seedlings, transplanting in proper period of spring, and providing good ventilating places and facilities, removing leaves, keeping buds and releasing dormancy before transplantation, planting depth should be exposed to the root neck, changing the pots according to the size of seedlings, the substrate should be loose and permeable, seriously disinfected and sterilized, scientific management, and prevention and control of diseases and insect pests. In addition, the survival mechanism was also analyzed, and the reasons and countermeasures for the successful application of peony tissue culture in China were found. Finally, the differences in survival rates between different varieties and facilities were summarized.
MAKTABGACHA YOSHDAGI BOLALAR NUTQINI RIVOJLANTIRISH YO'LLARI HAMDA ERTAK TERAPIYANING AHAMIYATI
Creators: name: Absalamova, Feruza
Publisher: name: Zenodo
Year: 2025

description: maktabgacha yoshdagi bolalar nutqini rivojlantirish, ularning kommunikativ ko‘nikmalarini shakllantirishda muhim ahamiyatga ega. Ushbu tadqiqotda bolalarning nutq rivojlanishiga ta'sir etuvchi omillar, o‘yinlar, muloqot va ertaklar orqali nutqni rivojlantirish yo‘llari ko‘rib chiqiladi. Ertak terapiyasi esa bolalarning hissiy va ruhiy holatini yaxshilash, tasavvur va ijodkorlikni rivojlantirishda muhim vosita sifatida e'tirof etiladi. Ushbu ishda ertaklarning tarbiyaviy ahamiyati va bolalar nutqini rivojlantirishdagi o‘rni batafsil tahlil qilinadi.
dCache - keeping up with the evolution of science
Creators: name: Rossi, Albert
name: Litvintsev, Dmitry
name: Juergen Starek
name: Morschel, Lea
name: Sahakyan, Marina
name: Olufemi Adeyemi
name: Fuhrmann, Patrick
name: Millar, Paul
name: Yasar, Sibel
name: Mkrtchyan, Tigran
name: Garonne, Vincent
Publisher: name: Zenodo
Year: 2019

description: The dCache project provides open-source software deployed internationally to satisfy ever more demanding storage requirements of various scientific communities. Its multifaceted approach provides an integrated way of supporting different use-cases with the same storage, from high throughput data ingest, through wide access and easy integration with existing systems, including event driven workflow management. With this presentation, we will show some of the recent developments that optimize data management and access to maximise the gain from stored data.
Terahertz field control of interlayer transport modes in cuprate superconductors
Creators: name: Schlawin, Frank
name: Dietrich, Anastasia S. D.
name: Kiffner, Martin
name: Cavalleri, Andrea
name: Jaksch, Dieter
Publisher: name: arXiv
Year: 2017
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We theoretically show that terahertz pulses with controlled amplitude and frequency can be used to switch between stable transport modes in layered superconductors, modelled as stacks of Josephson junctions. We find pulse shapes that deterministically switch the transport mode between superconducting, resistive and solitonic states. We develop a simple model that explains the switching mechanism as a destablization of the centre of mass excitation of the Josephson phase, made possible by the highly non-linear nature of the light-matter coupling.
Where are All the Gas-Bearing Local Dwarf Galaxies? Quantifying Possible Impacts of Reionization
Creators: name: Tollerud, Erik J.
name: Peek, J. E. G.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present an approach for comparing the detections and non-detections of Local Group (LG) dwarf galaxies in large HI surveys to the predictions of a suite of n-body simulations of the LG. This approach depends primarily on a set of empirical scaling relations to connect the simulations to the observations, rather than making strong theoretical assumptions. We then apply this methodology to the Galactic Arecibo L-band Feed Array HI Compact Cloud Catalog (GALFA-HI CCC), and compare it to the ELVIS suite of simulations. This approach reveals a strong tension between the naïve results of the model and the observations: while there are no LG dwarfs in the GALFA-HI CCC, the simulations predict $\sim 10$. Applying a simple model of reionization can resolve this tension by preventing low-mass halos from forming gas. However, and if this effect operates as expected, the observations provide a constraint on the mass scale of dwarf galaxy that reionization impacts. Combined with the observed properties of Leo T, the halo virial mass scale at which reionization impacts dwarf galaxy gas content is constrained to be $\sim 10^{8.5} M_\odot$, independent of any assumptions about star formation.
description: 10 pages, 7 figures, accepted to ApJ
The sharp $L^p$ decay of oscillatory integral operators with certain homogeneous polynomial phases in several variables
Creators: name: Xu, Shaozhen
name: Yan, Dunyan
Publisher: name: arXiv
Year: 2017
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics

description: We obtain the $L^p$ decay of oscillatory integral operators $T_λ$ with certain homogeneous polynomial phase of degree $d$ in $(n+n)$-dimensions. In this paper we require that $d>2n$. If $d/(d-n)
Space-time slicing in Horndeski theories and its implications for non-singular bouncing solutions
Creators: name: Ijjas, Anna
Publisher: name: arXiv
Year: 2017
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this paper, we show how the proper choice of gauge is critical in analyzing the stability of non-singular cosmological bounce solutions based on Horndeski theories. We show that it is possible to construct non-singular cosmological bounce solutions with classically stable behavior for all modes with wavelengths above the Planck scale where: (a) the solution involves a stage of null-energy condition violation during which gravity is described by a modification of Einstein's general relativity; and (b) the solution reduces to Einstein gravity both before and after the null-energy condition violating stage. Similar considerations apply to galilean genesis scenarios.
description: 33 pages, 3 figures; accepted for publication in JCAP; v2: updated to match journal version
Additional file 6: of Effectiveness of ultrasonography and nerve conduction studies in the diagnosing of carpal tunnel syndrome: clinical trial on accuracy
Creators: name: Pimentel, Benedito
name: FlĂĄvio Faloppa
name: Tamaoki, Marcel
name: JoĂŁo Belloti
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Table S11. Positive and negative predictive value of the US in relation to the reference standard. (DOCX 14Â kb)
Disentangling the Circumnuclear Environs of Centaurus A: III. An Inner Molecular Ring, Nuclear Shocks and the CO to warm H2 interface
Creators: name: Espada, D.
name: Matsushita, S.
name: Miura, R. E.
name: Israel, F. P.
name: Neumayer, N.
name: Martin, S.
name: Henkel, C.
name: Izumi, T.
name: Iono, D.
name: Aalto, S.
name: Ott, J.
name: Peck, A. B.
name: Quillen, A. C.
name: Kohno, K.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present the distribution and kinematics of the molecular gas in the circumnuclear disk (CND, 400 pc x 200 pc) of Centaurus A with resolutions of ~5 pc (0.3 arcsec) and shed light onto the mechanism feeding the Active Galactic Nucleus (AGN) using CO(3-2), HCO+(4-3), HCN(4-3), and CO(6-5) observations obtained with ALMA. Multiple filaments or streamers of tens to a hundred parsec scale exist within the CND, which form a ring-like structure with an unprojected diameter of 9 x 6 arcsec (162pc x 108pc) and a position angle PA = 155deg. Inside the nuclear ring, there are two leading and straight filamentary structures with lengths of about 30-60pc at PA = 120deg on opposite sides of the AGN, with a rotational symmetry of 180deg and steeper position-velocity diagrams, which are interpreted as nuclear shocks due to non-circular motions. Along the filaments, and unlike other nearby AGNs, several dense molecular clumps present low HCN/HCO+(4-3) ratios (~0.5). The filaments abruptly end in the probed transitions at r = 20pc from the AGN, but previous near-IR H2 (J=1-0) S(1) maps show that they continue in an even ~1000 K), winding up in the form of nuclear spirals, and forming an inner ring structure with another set of symmetric filaments along the N-S direction and within r = 10pc. The molecular gas is governed primarily by non-circular motions, being the successive shock fronts at different scales where loss of angular momentum occurs, a mechanism which may feed efficiently powerful radio galaxies down to parsec scales.
description: 46 pages. Accepted for publication in ApJ
Debugging Compute Clusters with Techniques from Functional Programming and Text Stream Processing
Creators: name: Adler, Alexander
name: Kebschull, Udo Wolfgang
Publisher: name: Zenodo
Year: 2019

description: Monitoring is an indispensable tool for the operation of any large installment of grid or cluster computing, be it high energy physics or elsewhere. Usually, monitoring is configured to collect a small amount of data, just enough to enable detection of abnormal conditions. Once detected, the abnormal condition is handled by gathering all information from the affected components. This data is processed by querying it in a manner similar to a database. This contribution shows how the metaphor of a debugger (for software applications) can be transferred to a compute cluster. The concepts of variables, assertions and breakpoints that are used in debugging can be applied to monitoring by defining variables as the quantities recorded by monitoring and breakpoints as invariants formulated through these variables. It is found that embedding fragments of a data extracting and reporting tool such as the UNIX tool _awk_ facilitates concise notations for commonly used variables since tools like _awk_ are designed to process large event streams (in textual representations) with bounded memory. Additionally, it is found that a functional notation similar to both the pipe notation used in the UNIX shell and the pointfree style used in functional programming simplifies the combining of variables that commonly occur when formulating breakpoints.
Online rapid prototyping of 3D objects using GPU-based 3D cloud computing: Application to 3D face modelling
Creators: name: GASTELUM-STROZZI, Alfonso
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 460304
subject: Computer vision
classificationCode: 460702
subject: Computer graphics

description: An on-line web application that interacts with an Internet user's 3D webcam (e.g. Minoru stereo web-camera) is described. The application instantly captures and processes stereo images to retrieve 3D object coordinates for further 3D modelling tasks. It offers on-demand semi-automatic camera calibration and automatic image pair rectification for further stereo matching operations. The reconstructed 3D objects are displayed on a Java3D panel with free observational navigation. The extracted 3D coordinates are saved for further use in a professional 3D graphical tool such as Blender. Real objects geometry was extracted from stereo images processed by a custom matching algorithm using either server-side (CUDA on high-end server) or client-side (Java Applet on user computer) processing. Specific applications in 3D face animation are described. Depth map and associated face texture were parsed into our animated 3D face system to rapidly generate specific facial expressions. The described application is portable, easy to set up and operate. Its current version is available at: http://www.ivs.auckland.ac.nz.
Additional file 6 of Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics
Creators: name: Maddirevula, Sateesh
name: Kuwahara, Hiroyuki
name: Ewida, Nour
name: Shamseldin, Hanan E.
name: Patel, Nisha
name: Alzahrani, Fatema
name: AlSheddi, Tarfa
name: AlObeid, Eman
name: Alenazi, Mona
name: Alsaif, Hessa S.
name: Alqahtani, Maha
name: AlAli, Maha
name: Al Ali, Hatoon
name: Helaby, Rana
name: Ibrahim, Niema
name: Abdulwahab, Firdous
name: Hashem, Mais
name: Hanna, Nadine
name: Monies, Dorota
name: Derar, Nada
name: Alsagheir, Afaf
name: Alhashem, Amal
name: Alsaleem, Badr
name: Alhebbi, Hamoud
name: Wali, Sami
name: Umarov, Ramzan
name: Gao, Xin
name: Alkuraya, Fowzan S.
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 6. Figure S1. Pedigree of a family which is mapped to a single locus and identified a very deep (+ 335) variant in ABCB4 causing cholestatic disease. Figure S2. A) A sashimi plot showing base-level densities of reads mapped to a genomic region containing exons 11 and 12 of KCTD3 transcripts from three samples. The x-axis represents the genomic coordinate in hg19. The y-axis represents per-base read counts, and the range is specified in the upper-left corner of the plot for each sample. Arcs connecting exons represent splice junction reads. The horizontal bar lines on the bottom indicate isoforms (exons as rectangle boxes and introns as line with arrow heads). The distribution in blue shows the sample with aberrant KCTD3 transcript, while the other two distributions are from randomly selected samples of lymphocytes (red from a patient and green from the GTEx cohort). B) A sashimi plot showing base-level densities of reads mapped to a genomic region in the positive control cases.
CMS Event-Builder Performance on State-of-the-Art Hardware
Creators: name: CMS Collaboration
name: Mommsen, Remi
Publisher: name: Zenodo
Year: 2019

description: We report on performance measurements and optimizations of the event-builder software for the CMS experiment at the CERN Large Hadron Collider (LHC). The CMS event builder collects event fragments from several hundred sources. It assembles them into complete events that are then handed to the High-Level Trigger (HLT) processes running on O(1000) computers. We use a test system with 16 dual-socket Skylake-based computers interconnected with 100 Gbps Infiniband and Ethernet networks. The main challenge is the demanding message rate and memory performance required of the event-builder node to fully exploit the network capabilities. Each event-builder node has to process several TCP/IP streams from the detector backends at an aggregated bandwidth of 100 Gbps, distribute event fragments to other event-builder nodes at the fist level trigger rate of 100 kHz, verify and build complete events using fragments received from all other nodes, and finally make the complete events available to the HLT processors. The achievable performance on today's hardware and different system architectures is described. Furthermore, we compare native Infiniband with RoCE (RDMA over Converged Ethernet). We discuss the required optimizations and highlight some of the problems encountered. We conclude with an outlook on the baseline CMS event-builder design for the LHC Run 3 starting in 2021.
End-to-End Modeling for Abstractive Speech Summarization
Creators: name: Sharma, Roshan
Publisher: name: Carnegie Mellon University
Year: 2024
Subjects: Electrical and Electronic Engineering not elsewhere classified

description:  In our increasingly interconnected world, where speech remains the most intuitive and natural form of communication, spoken language processing systems face a crucial challenge: they must do more than just categorize speech, they need to truly understand it to generate meaningful responses. One key aspect of this understanding is speech summarization, where a system condenses the important information from spoken input into a concise summary. This thesis delves into the challenge of generating abstractive textual summaries directly from speech.
The classical approach involves cascade systems that realize speech summarization by first transcribing speech, and then summarizing the resulting transcript. However, this comes with many challenges including computational efficiency, domain mismatches, and error propagation. In this thesis, we propose an alternative—an end-to-end framework that directly optimizes a single sequence model for speech summarization. To implement such end-to-end models with constrained computing resources, we address challenges such as abstract learning, learning global acoustic context, dealing with paucity of data, and improving the quality of summaries using multiple references. We also shed light on observations from human annotation for speech summarization. We present multi-stage training using speech transcription as a pre-training task to address abstract learning and facilitate improved performance of end-to-end models. We describe multiple solutions to address the problem of global acoustic context—restricted self-attention, replacing self-attention with the Fourier transform, and two block-wise adaptation solutions BASS and R-BASS that reframe speech summarization through the lens of block-wise processing. To address the challenge of data paucity, we introduce work on two new datasets—SLUE-TED and Interview for abstractive speech summarization. An exploration of human annotation provides insights into best practices and the nature of differences between speech-based and transcript-based summaries. Finally, we propose a novel method called AugSumm to improve the diversity and fluency of speech summaries by leveraging auxiliary references from generative text models.
Editor’s Note
Creators: Fogg, Thomas
Publisher: name: Columbia University
Year: 2014
Subjects: Music
Gratitude
Editors

description: The Acknowledgment—in which this note is, at least in part, an exercise—is a tricky genre: there are always too many people to thank but too few words fit for the task. A game presents itself: to avoid where possible repetitions of the golden word—the T–word—and its few synonyms; in other words, no thanks, no gratitude. Keith Richards (2010, 549), in his autobiography Life, has a tidy solution: a single “my thanks to . . .” and then two sober columns of alphabetically ordered names. Similarly, in one of the more moving exemplars, Roger Parker (2006, xi–xii) follows “thanks to . . .” with a sentence almost two pages long, where he honors each addressee with a personalized vignette held between semicolons. With tongue presumably in cheek, Tamara Levitz (2012, xvii) interrupts the steady toll of T–words when, rather than thank her proofreaders, she “thinks” them.
Probing Velocity Dependent Self-Interacting Dark Matter with Neutrino Telescopes
Creators: name: Robertson, Denis S.
name: Albuquerque, Ivone F. M.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Experiment (hep-ex)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Self-interacting dark matter models constitute an attractive solution to problems in structure formation on small scales. A simple realization of these models considers the dark force mediated by a light particle which can couple to the Standard Model through mixings with the photon or the $Z$ boson. Within this scenario we investigate the sensitivity of the IceCube-DeepCore and PINGU neutrino telescopes to the associated muon neutrino flux produced by dark matter annihilations in the Sun. Despite the model's simplicity, several effects naturally appear: momentum suppressed capture by nuclei, velocity dependent dark matter self-capture, Sommerfeld enhanced annihilation, as well as the enhancement on the neutrino flux due to mediator late decays. Taking all these effects into account, we find that most of the model relevant parameter space can be tested by the three years of data already collected by the IceCube-DeepCore. We show that indirect detection through neutrinos can compete with the strong existing limits from direct detection experiments, specially in the case of isospin violation.
description: 7 figures, Published version
What have we learnt with MeerKAT on the densest Groups of Galaxies
Creators: name: Verdes-Montenegro, Lourdes
Publisher: name: Zenodo
Year: 2024

description: Hickson Compact Groups (HCGs) are defined to be galaxy groups composed of ~ 4-10 tightly bound galaxies found in a low-density environment. Their high galaxy density, similar to the centres of rich clusters, leads to strong gravitational interactions among members and acceleration of their evolution. This makes them ideal laboratories for studying galaxy transformation, such as mass assembly pathways and star formation quenching. HCGs can show extreme atomic gas (HI) deficiency. Previous HI studies with the VLA have established an evolutionary sequence: in Phase 1 the gas is mainly within galaxies, while in Phases 2 and 3 more HI gas is progressively missing, either distributed in tidal tails, or missing altogether.  The missing gas is (partly) detected by deep GBT observations (spread over up to 1000 km/s), suggesting the presence of diffuse gas in the intragroup medium (IGrM). MeerKAT has the unique capability required to locate and analyse this elusive, diffuse HI. Here we will present the results of our PI program to observe of a sample of HCGs in the intermediate and most advanced evolutionary phases, trying to shed light on how HCGs transition from a complex of HI tidal structures to the stage where all member galaxies completely lose their HI. The MeerKAT sensitivity will tell us whether the transition from Intermediate to late stage groups is accelerated, as suggested by other observations.  The large FOV will also give us information on the environment in which the groups are embedded on 1 Mpc scales and how the properties of HCGs correlated with their large scale environment. Our results show a surprising conclusion on the missing HI in the most advanced stage.
The Historical Soundscape of Monophonic Hi–Fidelity
Creators: Dineen, Murray
Publisher: name: Columbia University
Year: 2014
Subjects: Imagination
Technology
Sound recordings
Music

description: An article in High Fidelity magazine, entitled “Listening is Believing?” and dated July/August 1953, sets forth the contemporary limits of sound reproduction in the inimitable style of advertisement copy: “Technical electronics can go only so far. The rest of the job must be done by the imaginative mind of the listener. That’s not a platitude; it’s a technical specification” (Campbell 1953, 28).
The connection drawn between imagination and sound reproduction, that the imagination can be an aspect of “technical electronics,” is meant to salve the “imaginative mind of the listener.” In doing so, however, it betrays an anxiety: the relationship has gotten out of balance, with human imagination falling short in the face of advances in “technical electronics.” The author, John Campbell, puts a firm boundary around the latter: it “can go only so far” (Campbell 1953, 28). But in this arrangement, human imagination is a supplement, an accessory to technology, not vice versa.
Additional file 5: of Characterising resuscitation promoting factor fluorescent-fusions in mycobacteria
Creators: name: Uhía, Iria
name: Nitya Krishnan
name: Robertson, Brian
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Table S1. Bacterial strains and plasmids used in this study. (PDF 27 kb)
Lifetime of nuclear velocity dispersion drops in barred galaxies
Creators: name: Wozniak, Herve
name: Champavert, Nicolas
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We have made hydro/N-body simulations with and without star formation to shed some light on the conditions under which a central kinematically cold stellar component (characterized by a velocity dispersion drop or σ-drop) could be created in a hot medium (e.g. a bulge) and survive enough time to be observed. We found that the timescale for a σ-drop formation could be short (less than 500 Myr) whereas its lifetime could be long (more than 1 Gyr) provided that the central region is continuously or regularly fed by fresh gas which leads to a continuous star formation activity. Star formation in the central region, even at a low rate as 1M_{sol} yr^{-1}, is mandatory to sustain a permanent σ-drop by replacing heated particles by new low-σones. We moreover show that as soon as star formation is switched off, the σ-drop begins to disappear.
description: 7 pages, 7 figures, accepted for publication in MNRAS
Additional file 1 of Comparison of the pathological response to 2 or 4 cycles of neoadjuvant CAPOX in II/III rectal cancer patients with low/intermediate risks: study protocol for a prospective, non-inferior, randomized control trial (COPEC trial)
Creators: name: Shen, Yu
name: Shi, Wanyue
name: Huang, Cui
name: Gong, Xiaoling
name: Wei, Mingtian
name: Meng, Wenjian
name: Deng, Xiangbing
name: Wang, Ziqiang
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Cell Biology
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Developmental Biology
subject: Cancer
subject: Mental Health
subject: Computational Biology

description: Additional file 1. List of coordinating center.
Dipole: Diagnosis Prediction in Healthcare via Attention-based Bidirectional Recurrent Neural Networks
Creators: name: Ma, Fenglong
name: Chitta, Radha
name: Zhou, Jing
name: You, Quanzeng
name: Sun, Tong
name: Gao, Jing
Publisher: name: arXiv
Year: 2017
Subjects: subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Predicting the future health information of patients from the historical Electronic Health Records (EHR) is a core research task in the development of personalized healthcare. Patient EHR data consist of sequences of visits over time, where each visit contains multiple medical codes, including diagnosis, medication, and procedure codes. The most important challenges for this task are to model the temporality and high dimensionality of sequential EHR data and to interpret the prediction results. Existing work solves this problem by employing recurrent neural networks (RNNs) to model EHR data and utilizing simple attention mechanism to interpret the results. However, RNN-based approaches suffer from the problem that the performance of RNNs drops when the length of sequences is large, and the relationships between subsequent visits are ignored by current RNN-based approaches. To address these issues, we propose {\sf Dipole}, an end-to-end, simple and robust model for predicting patients' future health information. Dipole employs bidirectional recurrent neural networks to remember all the information of both the past visits and the future visits, and it introduces three attention mechanisms to measure the relationships of different visits for the prediction. With the attention mechanisms, Dipole can interpret the prediction results effectively. Dipole also allows us to interpret the learned medical code representations which are confirmed positively by medical experts. Experimental results on two real world EHR datasets show that the proposed Dipole can significantly improve the prediction accuracy compared with the state-of-the-art diagnosis prediction approaches and provide clinically meaningful interpretation.
Particle identification algorithms for the Panda Barrel DIRC
Creators: name: Dzhygadlo, Roman
name: PANDA Cherenkov Group
Publisher: name: Zenodo
Year: 2019

description: The innovative Barrel DIRC (Detection of Internally Reflected Cherenkov light) counter will provide hadronic particle identification (PID) in the central region of the PANDA experiment at the new Facility for Antiproton and Ion Research (FAIR), Darmstadt, Germany. This detector is designed to separate charged pions and kaons with at least 3 standard deviations for momenta up to 3.5 GeV/c covering the polar angle range of 22-140 degree. An array of microchannel plate photomultiplier tubes is used to detect the location and arrival time of the Cherenkov photons with a position resolution of 2 mm and time precision of about 100 ps. Two reconstruction algorithms have been developed to make optimum use of the observables and to determine the performance of the detector. The "geometrical reconstruction" performs PID by reconstructing the value of the Cherenkov angle and using it in a track-by-track maximum likelihood fit. This method mostly relies on the position of the detected photons in the reconstruction, while the "time imaging" utilizes both, position and time information, and directly performs the maximum likelihood fit using probability density functions determined analytically or from detailed simulations. Geant4 simulations and data from the particle beams where used to optimize both algorithms in terms of PID performance and reconstruction speed. We will present current status of development and discuss advantages of each algorithm.
Awe, the Small Self, and Prosocial Behavior: Replication and Extension
Creators: name: Nguyen, Christine
name: Quinn, Kimberly
Publisher: name: Open Science Framework
Year: 2022

description: This study is a replication of research reported in "Awe, the Small Self, and Prosocial Behavior" by Piff, Dietze, Feinberg, Stancato, and Keltner (2015), which demonstrated an influence of awe on several indicators of prosociality (generosity, ethical decision-making, prosocial tendencies, and lowered entitlement). The study will also extend the research to explore whether collective awe—sharing an awe experience with others—heightens these effects, based on evidence that sharing experiences with others increases the intensity of those experiences (e.g., Boothby, Clark, & Bargh, 2014; Wagner et al., 2015).
Additional file 5: of Effectiveness of ultrasonography and nerve conduction studies in the diagnosing of carpal tunnel syndrome: clinical trial on accuracy
Creators: name: Pimentel, Benedito
name: FlĂĄvio Faloppa
name: Tamaoki, Marcel
name: JoĂŁo Belloti
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Table S10. Sensitivity and Specificity of the NCS in relation to the reference standard. (DOCX 14Â kb)