cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Instrumental response model and detrending for the Dark Energy Camera
Creators: name: Bernstein, G. M.
name: Abbott, T. M. C.
name: Desai, S.
name: Gruen, D.
name: Gruendl, R. A.
name: Johnson, M. D.
name: Lin, H.
name: Menanteau, F.
name: Morganson, E.
name: Neilsen, E.
name: Paech, K.
name: Walker, A. R.
name: Wester, W.
name: Yanny, B.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: We describe the model for the mapping from sky brightness to the digital output of the Dark Energy Camera, and the algorithms adopted by the Dark Energy Survey (DES) for inverting this model to obtain photometric measures of celestial objects from the raw camera output. The calibration aims for fluxes that are uniform across the camera field of view and across the full angular and temporal span of the DES observations, approaching the accuracy limits set by shot noise for the full dynamic range of DES observations. The DES pipeline incorporates several substantive advances over standard detrending techniques, including: principal-components-based sky and fringe subtraction; correction of the "brighter-fatter" nonlinearity; use of internal consistency in on-sky observations to disentangle the influences of quantum efficiency, pixel-size variations, and scattered light in the dome flats; and pixel-by-pixel characterization of instrument spectral response, through combination of internal-consistency constraints with auxiliary calibration data. This article provides conceptual derivations of the detrending/calibration steps, and the procedures for obtaining the necessary calibration data. Other publications will describe the implementation of these concepts for the DES operational pipeline, the detailed methods, and the validation that the techniques can bring DECam photometry and astrometry within ~2 mmag and ~3 mas, respectively, of fundamental atmospheric and statistical limits. The DES techniques should be broadly applicable to wide-field imagers.
description: Submitted to PASP
Additional file 1: of Improved adherence adjustment in the Coronary Drug Project
Creators: name: Murray, Eleanor
name: Hernรกn, Miguel
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology
subject: 111714 Mental Health
subject: FOS: Health sciences

description: SAS 9.4 code for placebo-arm adherence analysis. A SAS code for all analyses is provided in this file. If you have any questions, comments, or discover an error, please contact Eleanor Murray at emurray@mail.harvard.edu. For the most updated versions of related SAS programs, please visit www.hsph.harvard.edu/causal/ . (PDF 316 kb)
MOESM2 of Predicting drug-target interactions from drug structure and protein sequence using novel convolutional neural networks
Creators: name: Hu, ShanShan
name: Zhang, Chenglin
name: Chen, Peng
name: Gu, Pengying
name: Zhang, Jun
name: Wang, Bing
Publisher: name: figshare
Year: 2019
Subjects: Biochemistry
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified

description: Additional file 2 In this file, to obtain the optimal learning rate of our model, a series of different learning rates are explored on each types of protein families of both Dataset1 and Dataset2.
Additional file 9: of IntLIM: integration using linear models of metabolomics and gene expression data
Creators: name: Siddiqui, Jalal
name: Baskin, Elizabeth
name: Mingrui Liu
name: Cantemir-Stone, Carmen
name: Bofei Zhang
name: Bonneville, Russell
name: McElroy, Joseph
name: Coombes, Kevin
name: MathĂŠ, Ewy
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Inorganic Chemistry
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Computational Biology

description: Table S3. Breast Cancer Data pathway analysis results of metabolites. Ingenuity Pathway Analysis Canonical Pathways from Metabolites involved in Gene-Metabolite Pairs of the Tumor Correlated Cluster. P-values are all calculated from right-tailed Fisherâ s Exact Test. (PDF 53Â kb)
Progressive Joint Modeling in Unsupervised Single-channel Overlapped Speech Recognition
Creators: name: Chen, Zhehuai
name: Droppo, Jasha
name: Li, Jinyu
name: Xiong, Wayne
Publisher: name: arXiv
Year: 2017
Subjects: subject: Computation and Language (cs.CL)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences
subject: I.2.7
subject: 68T10

description: Unsupervised single-channel overlapped speech recognition is one of the hardest problems in automatic speech recognition (ASR). Permutation invariant training (PIT) is a state of the art model-based approach, which applies a single neural network to solve this single-input, multiple-output modeling problem. We propose to advance the current state of the art by imposing a modular structure on the neural network, applying a progressive pretraining regimen, and improving the objective function with transfer learning and a discriminative training criterion. The modular structure splits the problem into three sub-tasks: frame-wise interpreting, utterance-level speaker tracing, and speech recognition. The pretraining regimen uses these modules to solve progressively harder tasks. Transfer learning leverages parallel clean speech to improve the training targets for the network. Our discriminative training formulation is a modification of standard formulations, that also penalizes competing outputs of the system. Experiments are conducted on the artificial overlapped Switchboard and hub5e-swb dataset. The proposed framework achieves over 30% relative improvement of WER over both a strong jointly trained system, PIT for ASR, and a separately optimized system, PIT for speech separation with clean speech ASR model. The improvement comes from better model generalization, training efficiency and the sequence level linguistic knowledge integration.
description: submitted to TASLP, 07/20/2017; accepted by TASLP, 10/13/2017
A new monoterpenoid glycoside and a new phenolic glycoside isolated from Dracocephalum moldavica and their anti-complementary activity
Creators: name: Wang, Jiaming
name: Sun, Jinfeng
name: Jin, Long
name: Wang, Mengjie
name: Huang, Yanyan
name: Jin, Mei
name: Zhou, Wei
name: Li, Gao
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Infectious Diseases
subject: FOS: Health sciences

description: A new monoterpenoid glycoside (1 R, 2 R, 4S)-1,8-epoxy-p-menthan-2-O-β-D-glucopyranosyl-(1→4)-β-D-glucopyranoside (1) and a new phenolic glycoside, cis-1-(3-hydroxy-4-methoxyphenyl)-2-butene-4-O-α-L-rhamnopyranosyl-(1→3)-O-β-D-glucopyranoside (2) were isolated from the dried aerial parts of Dracocephalum moldavica, together with 12 known compounds. Compound 5 was isolated from the Lamiaceae family for the first time, compounds 3, 4, 6 and 8–12 were identified from the genus Dracocephalum for the first time and compounds 7 and 13–14 were reported from the D. moldavica for the first time. All the compounds were evaluated for anti-complementary activity against the classical and alternative pathways. Compounds 2–4, 8 and 11 showed anti-complementary activity to different extents, with CH50 and AP50 values ranging from 0.78–1.24 and 1.52–1.84 mM, respectively. The targets of compounds 2–4, 8 and 11 in complement activation cascade were identified as well.
Hydrodynamic mobility of a sphere moving on the centerline of an elastic tube
Creators: name: Daddi-Moussa-Ider, Abdallah
name: Lisicki, Maciej
name: Gekle, Stephan
Publisher: name: arXiv
Year: 2017
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: Biological Physics (physics.bio-ph)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: Elastic channels are an important component of many soft matter systems, in which hydrodynamic interactions with confining membranes determine the behavior of particles in flow. In this work, we derive analytical expressions for the Green's functions associated to a point-force (Stokeslet) directed parallel or perpendicular to the axis of an elastic cylindrical channel exhibiting resistance against shear and bending. We then compute the leading order self- and pair mobility functions of particles on the cylinder axis, finding that the mobilities are primarily determined by membrane shear and that bending does not play a significant role. In the quasi-steady limit of vanishing frequency, the particle self- and pair mobilities near a no-slip hard cylinder are recovered only if the membrane possesses a non-vanishing shear rigidity. We further compute the membrane deformation, finding that deformation is generally more pronounced in the axial (radial) directions, for the motion along (perpendicular) to the cylinder centerline, respectively. Our analytical calculations for the Green's functions in an elastic cylinder can serve as a fundamental building block for future studies and are verified by fully resolved boundary integral simulations where a very good agreement is obtained.
description: 28 pages, 7 figures and 129 references. Manuscript under review
title: DIALOGUES 1: Read dialogues designed for phonetic research into the influence of speaker attitude on the realization of two sentence-final particles in Hanoi Vietnamese. This audio file was created by MIXING two audio files (see description).
title: DIALOGUES 1: Dialogues lus, conçus pour une étude phonétique portant sur l'influence de l'attitude du locuteur sur la réalisation de deux particules finales du vietnamien de Hanoi
titleType: AlternativeTitle
title: ĐỐI THOẠI 1: Đối thoại được thiết kế cho việc nghiên cứu sự biến đổi đặc tính âm học của hai trợ từ tình thái cuối câu trong Tiếng Việt, thể hiện theo các thái độ khác nhau (Hà Nội)
titleType: AlternativeTitle
Creators: name: Michaud, Alexis
name: Nguyễn, Thị Lan
name: Trần, Đỗ Đạt
name: Mạc, Đăng Khoa
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2013
Subjects: subject: Hanoi dialect
subject: vie
subject: Vietnamese

description: Information on FORM: The present audio file was created simply for convenience of consultation. It was produced by combining audio signals from 2 different microphones: one for speaker M4, one for speaker M5. In addition to this 'mixed' file, there exist three 'real' data files: audio signal for speaker M4; EGG signal for speaker M4; and audio signal for speaker M5. These 3 files were also deposited in the archive. Information on CONTENTS: This is a set of read dialogues. They were designed for phonetic research into the influence of speaker attitude on the realization of two sentence-final particles in Hanoi Vietnamese. Further details are provided in a PDF document associated to this deposit.
description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
Additional file 1: of A combined linkage, microarray and exome analysis suggests MAP3K11 as a candidate gene for left ventricular hypertrophy
Creators: name: Silva, Claudia
name: Zorkoltseva, Irina
name: Niemeijer, Maartje
name: Berg, Marten Van Den
name: Najaf Amin
name: Ayşe Demirkan
name: Leeuwen, Elisa Van
name: Iglesias, Adriana
name: Piñeros-Hernández, Laura
name: Restrepo, Carlos
name: Kors, Jan
name: Kirichenko, Anatoly
name: Willemsen, Rob
name: Oostra, Ben
name: Stricker, Bruno
name: Uitterlinden, André
name: Axenovich, Tatiana
name: Duijn, Cornelia Van
name: Isaacs, Aaron
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy
subject: Computational Biology

description: Table S1. Coding variants under the linkage peaks for LVH proxy measurements. Table S2. Selected damaging variants in the coding regions contained in the linkage regions. Table S3. SKAT and burden tests for genes of interest. Table S4. Results of linkage analyses before (LOD1) and after (LOD2) regression on GWAS SNPs under the linkage peaks. Table S5. Descriptive statistics of the Rotterdam study population. Table S6. Replications results in the Rotterdam Study. Figure S1. Venn diagram showing the overlap between the different ERF genotyping experiments. Figure S2. Pedigrees segregating rs138968470. (DOCX 119 kb)
NLO Renormalization in the Hamiltonian Truncation
Creators: name: Elias-Miro, Joan
name: Rychkov, Slava
name: Vitale, Lorenzo G.
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Hamiltonian Truncation (a.k.a. Truncated Spectrum Approach) is a numerical technique for solving strongly coupled QFTs, in which the full Hilbert space is truncated to a finite-dimensional low-energy subspace. The accuracy of the method is limited only by the available computational resources. The renormalization program improves the accuracy by carefully integrating out the high-energy states, instead of truncating them away. In this paper we develop the most accurate ever variant of Hamiltonian Truncation, which implements renormalization at the cubic order in the interaction strength. The novel idea is to interpret the renormalization procedure as a result of integrating out exactly a certain class of high-energy "tail states". We demonstrate the power of the method with high-accuracy computations in the strongly coupled two-dimensional quartic scalar theory, and benchmark it against other existing approaches. Our work will also be useful for the future goal of extending Hamiltonian Truncation to higher spacetime dimensions.
description: 28pp + appendices, detailed version of arXiv:1706.06121
Soil washing of total petroleum and polycyclic aromatic hydrocarbons from crude oil-contaminated ultisol using aqueous extracts of waterleaf
Creators: name: Offiong, Nnanake-Abasi O.
name: Fatunla, Opeyemi K.
name: Essien, Joseph P.
name: Yang, Chaoge
name: Dong, Jun
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Plant Biology

description: Ultisols are acidic soils found in humid climates and are known for poor fertility. Crude oil impacted ultisols, therefore, require special treatment measures to account for nutrient loss during treatment. In this paper, we report the utilization of a food waste, aqueous extracts of waterleaf (Talinum triangulare), as a plant-derived surfactant to wash simulated crude oil-contaminated soils. The soils before and after washing were monitored for microbial loads, nutrient parameters, physicochemical characteristics, total petroleum hydrocarbons (TPHs) and polycyclic aromatic hydrocarbons (PAHs). Although higher amounts of PAHs (up to 100%) were removed compared to TPHs (up to 95.7%), the results revealed that the efficiency of the waterleaf extracts was comparable to that of a commercial surfactant sodium dodecyl sulphate. However, soils washed with the waterleaf extracts retained some significant amounts of nutrients and favourable pH moderation. In both surfactants, soil microbial loads reduced significantly. Overall, the aqueous waterleaf extracts showed potential as ecofriendly surfactants and nutrients retainer during soil washing of contaminated ultisols.
The Sources of Extreme Ultraviolet and Soft X-ray Backgrounds
Creators: name: Sanderbeck, Phoebe R. Upton
name: McQuinn, Matthew
name: D'Aloisio, Anson
name: Werk, Jessica K.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Radiation in the extreme ultraviolet (EUV) and soft X-ray holds clues to the location of the missing baryons, the energetics in stellar feedback processes, and the cosmic enrichment history. Additionally, EUV and soft X-ray photons help determine the ionization state of most intergalactic and circumgalactic metals, shaping the rate at which cosmic gas cools. Unfortunately, this band is extremely difficult to probe observationally due to absorption from the Galaxy. In this paper, we model the contributions of various sources to the cosmic EUV and soft X-ray backgrounds. We bracket the contribution from (1) quasars, (2) X-ray binaries, (3) hot interstellar gas, (4) circumgalactic gas, (5) virialized gas, and (6) supersoft sources, developing models that extrapolate into these bands using both empirical and theoretical inputs. While quasars are traditionally assumed to dominate these backgrounds, we discuss the substantial uncertainty in their contribution. Furthermore, we find that hot intrahalo gases likely emit an O(1) fraction of this radiation at low redshifts, and that interstellar and circumgalactic emission potentially contribute tens of percent to these backgrounds at all redshifts. We estimate that uncertainties in the angular-averaged background intensity impact the ionization corrections for common circumgalactic and intergalactic metal absorption lines by ~0.3-1 dex, and we show that local emissions are comparable to the cosmic background only at r_prox = 10-100 kpc from Milky Way-like galaxies.
description: 13 pages, 9 figures, accepted to ApJ. New calculation added in section 2.3
title: DIALOGUES 2: Read dialogues designed for phonetic research into the influence of speaker attitude on the realization of two sentence-final particles in Hanoi Vietnamese. This audio file was created by MIXING two audio files (see description).
title: DIALOGUES 2: Dialogues lus, conçus pour une étude phonétique portant sur l'influence de l'attitude du locuteur sur la réalisation de deux particules finales du vietnamien de Hanoi
titleType: AlternativeTitle
title: ĐỐI THOẠI 2: Đối thoại được thiết kế cho việc nghiên cứu sự biến đổi đặc tính âm học của hai trợ từ tình thái cuối câu trong Tiếng Việt, thể hiện theo các thái độ khác nhau (Hà Nội)
titleType: AlternativeTitle
Creators: name: Michaud, Alexis
name: Nguyễn, Thị Lan
name: Trần, Đỗ Đạt
name: Mạc, Đăng Khoa
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2013
Subjects: subject: Hanoi dialect
subject: vie
subject: Vietnamese

description: Information on FORM: The present audio file was created simply for convenience of consultation. It was produced by combining audio signals from 2 different microphones: one for speaker M4, one for speaker M5. In addition to this 'mixed' file, there exist three 'real' data files: audio signal for speaker M4; EGG signal for speaker M5; and audio signal for speaker M5. These 3 files were also deposited in the archive. Information on CONTENTS: This is a set of read dialogues. They were designed for phonetic research into the influence of speaker attitude on the realization of two sentence-final particles in Hanoi Vietnamese. Further details are provided in a PDF document associated to this deposit.
description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
Phase sensitive photonic flash
Creators: name: Cui, X. Y.
name: Wu, Jin-Hui
name: Wang, Z. H.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We theoretically propose a photonic flash based on a linearly coupled cavity system. Via driving the two side cavities by external fields, it forms a cyclic energy-level diagram and therefore the phase difference between the driving fields acts as a controller of the steady state due to the quantum interference effect. In the optical trimer structure, we show that the perfect photonic flash can be realized in the situation of resonant driving. The perfect photonic flash scheme is furthermore generalized to multiple coupled cavity system, where the cavities with odd and even number turn bright and dark alternatively. {Our proposal may be applied in the designing of quantum neon and realizing a controllable photonic localization.
Additional file 8: of IntLIM: integration using linear models of metabolomics and gene expression data
Creators: name: Siddiqui, Jalal
name: Baskin, Elizabeth
name: Mingrui Liu
name: Cantemir-Stone, Carmen
name: Bofei Zhang
name: Bonneville, Russell
name: McElroy, Joseph
name: Coombes, Kevin
name: MathĂŠ, Ewy
Publisher: name: figshare
Year: 2018
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Table S2. Breast Cancer Data pathway analysis results of genes. Ingenuity Pathway Analysis Canonical Pathways from Genes involved in Gene-Metabolite Pairs of the Tumor Correlated Cluster and Tumor Anti-Correlated Cluster. P-values are all calculated from right-tailed Fisherâ s Exact Test. (PDF 55Â kb)
An unusual civilian deployment in uniform
Creators: name: Project Team, Their Finest Hour
Publisher: name: University of Oxford
Year: 2024
Subjects: classificationCode: 430304
subject: British history
classificationCode: 430308
subject: European history (excl. British, classical Greek and Roman)
classificationCode: 430316
subject: International history

description: Walter Page was a telegraphist working in London for a private company, but attached to the British telecommunications giant Cable and Wireless. Walter started working for the company at 14, first as a messenger. After training in telegraphy, he worked with connections to New York and Paris. In 1943, aged 43 and leaving his young family (including daughter Jeanette) back in North London, he deployed to Algiers and Naples on a government contract to provide mobile communications. Due to it being a wartime deployment, Cable and Wireless devised a uniform and special cap badge for the men. Walter's daughter Jeanette was always led to believe this was to avoid them being shot as spies. Whilst in Naples, he purportedly saw Mount Vesuvius erupt. His deployment with Cable and Wireless lasted until 1946.
title: 03_0362
Creators: name: Wesley Baldwin, John
name: Baldwin, John W.
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2018
Subjects: subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: L'ensemble de ces notes ont été crée par John Baldwin lors d'une de ses premières périodes de résidence à Paris. Ces documents comprennent tous les magistri qu’il avait pu rencontrer dans ses sources. Aux XIIème et XIIIème siècles, les universités n'existant pas encore, le titre de magister s'il évoque certainement une compétence n'est pas rattaché de façon systématique au passage par les écoles. De surcroît, les magistris sont le plus souvent désignés par leur seul prénom. La lecture de ces données est donc difficile et suppose un long travail pour tenter d'identifier un individu auquel on pourrait rattacher plusieurs mentions. John Baldwin avait donc renoncé à utiliser ces données pour donner un prolongement à sa magnifique étude sur les gradués d'université et leur emploi par les Capétiens et les Plantagenêts. Néanmoins, il a conservé ces données et elles sont potentiellement très utile dans le cadre de Studium, comme le sont toutes les mentions dans les volumes des Fasti Ecclesiae Gallicanae de chanoines portant ce titre de magister sans autres précisions. L'ampleur des dépouillements rend ces données très utiles et nous devons une grande reconnaissance à John Baldwin pour avoir pris la peine de faire photocopier ses fiches et de nous les avoir transmises amicalement.
Les données ainsi que les images des fiches sont accessibles sur le site Internet à l'adresse suivante : http://studium-baldwin.lamop.fr/.
Les transcriptions des fiches ont été effectuées par des étudiants de Paris 1 Panthéon - Sorbonne mais elles n'ont pas été corrigées par la suite.
description: Relation: https://lamop.hypotheses.org/
Optimized Surface Code Communication in Superconducting Quantum Computers
Creators: name: Javadi-Abhari, Ali
name: Gokhale, Pranav
name: Holmes, Adam
name: Franklin, Diana
name: Brown, Kenneth R.
name: Martonosi, Margaret
name: Chong, Frederic T.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum computing (QC) is at the cusp of a revolution. Machines with 100 quantum bits (qubits) are anticipated to be operational by 2020 [googlemachine,gambetta2015building], and several-hundred-qubit machines are around the corner. Machines of this scale have the capacity to demonstrate quantum supremacy, the tipping point where QC is faster than the fastest classical alternative for a particular problem. Because error correction techniques will be central to QC and will be the most expensive component of quantum computation, choosing the lowest-overhead error correction scheme is critical to overall QC success. This paper evaluates two established quantum error correction codes---planar and double-defect surface codes---using a set of compilation, scheduling and network simulation tools. In considering scalable methods for optimizing both codes, we do so in the context of a full microarchitectural and compiler analysis. Contrary to previous predictions, we find that the simpler planar codes are sometimes more favorable for implementation on superconducting quantum computers, especially under conditions of high communication congestion.
description: 14 pages, 9 figures, The 50th Annual IEEE/ACM International Symposium on Microarchitecture
Additional file 2: of Altered DNA methylation is associated with aberrant gene expression in parenchymal but not airway fibroblasts isolated from individuals with COPD
Creators: name: Clifford, Rachel
name: Fishbane, Nick
name: Patel, Jamie
name: MacIsaac, Julia
name: McEwen, Lisa
name: Fisher, Andrew
name: Corry-Anke Brandsma
name: Nair, Parameswaran
name: Kobor, Michael
name: Tillie-Louise Hackett
name: Knox, Alan
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
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: Cancer
subject: Plant Biology

description: Table S2. (.MWD): DNA regions differentially methylated with COPD status in parenchymal fibroblasts. Summary of the three gene annotated regions containing a minimum of three CpG probes and a maximum difference in DNA methylation of at least 20% (difference in beta value of 0.2). A positive delta beta identifies decreased DNA methylation in cells isolated from individuals with COPD, while a negative value identifies increased DNA methylation in cells isolated from individuals with COPD. (DOCX 14Â kb)
kakapo: easy extraction and annotation of genes from raw RNA-seq reads
Creators: name: Ramanauskas, Karolis
name: Igić, Boris
Publisher: name: University of Illinois at Chicago
Year: 2024
Subjects: classificationCode: 32
subject: Biomedical and clinical sciences
classificationCode: 31
subject: Biological sciences
subject: FOS: Biological sciences
classificationCode: 3105
subject: Genetics
classificationCode: 3102
subject: Bioinformatics and computational biology

description: kakapo (kākāpō) is a Python-based pipeline that allows users to extract and assemble one or more specified genes or gene families. It flexibly uses original RNA-seq read or GenBank SRA accession inputs without performing global assembly of entire transcriptomes or metatranscriptomes. The pipeline identifies open reading frames in the assembled gene transcripts and annotates them. It optionally filters raw reads for ribosomal, plastid, and mitochondrial reads, or reads belonging to non-target organisms (e.g., viral, bacterial, human). kakapo can be employed for targeted assembly, to extract arbitrary loci, such as those commonly used for phylogenetic inference in systematics or candidate genes and gene families in phylogenomic and metagenomic studies. We provide example applications and discuss how its use can offset the declining value of GenBank's single-gene databases and help assemble datasets for a variety of phylogenetic analyses.
B1MG M2.3 Draft report on legal set-up including DPIA
Creators: name: Bovenberg, Jasper
name: Becker, Regina
name: Thorogood, Adrian
name: Tzortzatou, Olga
Publisher: name: Zenodo
Year: 2022
Subjects: B1MG
Beyond 1 Million Genomes
1+MG
1 Million Genomes Initiative
ELSI
DPIA
Data Protection
Data protection Impact assessment

description: B1MG Project Milestone - B1MG M2.3 Draft report on legal set-up including DPIA
Random affine simplexes
Creators: name: Götze, Friedrich
name: Gusakova, Anna
name: Zaporozhets, Dmitry
Publisher: name: arXiv
Year: 2017
Subjects: subject: Probability (math.PR)
subject: Metric Geometry (math.MG)
subject: FOS: Mathematics
subject: 60D05, 52A22, 60B20, 78A40, 52A39

description: For a fixed $k\in\{1,\dots,d\}$ consider random vectors $X_0,\dots, X_{k}\in\mathbb R^d$ with an arbitrary spherically symmetric joint density function. Let $A$ be any non-singular $d\times d$ matrix. We show that the $k$-dimensional volume of the convex hull of affinely transformed $X_{i}$'s satisfies \[ |\mathrm{conv}(AX_0,\dots,AX_{k})|\stackrel{d}{=}\frac{|P_ξ\mathcal{E}|}{κ_k}\cdot|\mathrm{conv}(X_0,\dots,X_{k})|, \] where $\mathcal{E}:=\{\mathbf{x}\in\mathbb R^d:{\mathbf{x}^\top (A^\top A)^{-1}\mathbf{x}}\leq 1\}$ is an ellipsoid, $P_ξ$ denotes the orthogonal projection to a random uniformly chosen $k$-dimensional linear subspace $ξ$ independent of $X_0,\dots, X_{k}$, and $κ_k$ is the volume of the unit $k$-dimensional ball. We express $|P_ξ\mathcal{E}|$ in terms of Gaussian random matrices. The important special case $k=1$ corresponds to the distance between two random points: \[ |AX_0-AX_1|\stackrel{d}{=}\sqrt{\frac{λ_1^2N_1^2+\dots+λ_d^2N_d^2}{N_1^2+\dots+N_d^2}}\cdot|X_0-X_1|, \] where $N_1,\dots,N_d$ are i.i.d. standard Gaussian variables independent of $X_0,X_1$ and $λ_1,\dots,λ_d$ are the singular values of $A$. As an application, we derive the following integral geometry formula for ellipsoids: \[ \frac{κ_{d}^{k+1}}{κ_k^{d+1}}\,\frac{κ_{k(d+p)+k}}{κ_{k(d+p)+d}}\,\int\limits_{A_{d,k}}|\mathcal{E}\cap E|^{p+d+1}\,μ_{d,k}(dE)=|\mathcal{E}|^{k+1}\,\int\limits_{G_{d,k}}|P_L\mathcal{E}|^p\,ν_{d,k}(dL), \] where $p> -d+k-1$ and $A_{d,k}$ and $G_{d,k}$ are the affine and the linear Grassmannians equipped with their respective Haar measures. The case $p=0$ reduces to an affine version of the integral formula of Furstenberg and Tzkoni.
title: SmoothTones: The six tones of sonorant-ending syllables of Hanoi Vietnamese, on the syllables /a/ and /ɗa/. Speaker M4
Creators: name: Michaud, Alexis
name: Nguyễn, Thị Lan
name: Trần, Đỗ Đạt
name: Mạc, Đăng Khoa
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2013
Subjects: subject: Hanoi dialect
subject: vie
subject: Vietnamese

description: SmoothTones: The six tones of sonorant-ending syllables of Hanoi Vietnamese, on the syllables /a/ and /ɗa/. Speaker M4
description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
Radical increase of the parametric X-ray intensity under condition of extremely asymmetric diffraction
Creators: name: Skoromnik, O. D.
name: Baryshevsky, V. G.
name: Ulyanenkov, A. P.
name: Feranchuk, I. D.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Accelerator Physics (physics.acc-ph)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Parametric X-ray radiation (PXR) from relativistic electrons moving in a crystal along the crystal-vacuum interface is considered. In this geometry the emission of photons is happening in the regime of extremely asymmetric diffraction (EAD). In the EAD case the whole crystal length contributes to the formation of X-ray radiation opposed to Laue and Bragg geometries, where the emission intensity is defined by the X-ray absorption length. We demonstrate that this phenomenon should be described within the dynamical theory of diffraction and predict a radical increase of the PXR intensity. In particular, under realistic electron-beam parameters, an increase of two orders of magnitude in PXR-EAD intensity can be obtained in comparison with conventional experimental geometries of PXR. In addition we discuss in details the experimental feasibility of the detection of PXR-EAD.
description: 9 pages, 5 figures
Additional file 6: of Digital storytelling as a method in health research: a systematic review protocol
Creators: name: Rieger, Kendra
name: West, Christina
name: Kenny, Amanda
name: Rishma Chooniedass
name: Demczuk, Lisa
name: Mitchell, Kim
name: Chateau, Joanne
name: Scott, Shannon
Publisher: name: figshare
Year: 2018
Subjects: Medicine
Developmental Biology
Science Policy

description: Quality Appraisal Instrument for Quantitative Studies. (DOCX 777 kb)
title: SmoothTones: The six tones of sonorant-ending syllables of Hanoi Vietnamese, on the syllables /a/ and /ɗa/. Speaker M5
Creators: name: Michaud, Alexis
name: Nguyễn, Thị Lan
name: Trần, Đỗ Đạt
name: Mạc, Đăng Khoa
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2013
Subjects: subject: Hanoi dialect
subject: vie
subject: Vietnamese

description: SmoothTones: The six tones of sonorant-ending syllables of Hanoi Vietnamese, on the syllables /a/ and /ɗa/. Speaker M5
description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
Soil washing of total petroleum and polycyclic aromatic hydrocarbons from crude oil contaminated ultisol using aqueous extracts of waterleaf
Creators: name: Offiong, Nnanake-Abasi O.
name: Fatunla, Opeyemi K.
name: Essien, Joseph P.
name: Yang, Chaoge
name: Dong, Jun
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Plant Biology

description: Ultisols are acidic soils found in humid climates and are known for poor fertility. Crude oil impacted ultisols therefore require special treatment measures to account for nutrient loss during treatment. In this paper, we report the utilization of a food waste, aqueous extracts of waterleaf (Talinum triangulare), as a plant-derived surfactant to wash simulated crude oil contaminated soils. The soils before and after washing were monitored for microbial loads, nutrient parameters, physicochemical characteristics, total petroleum hydrocarbons (TPHs) and polycyclic aromatic hydrocarbons (PAHs). Although higher amounts of PAHs (up to 100%) was removed compared to TPHs (up to 95.7%), the results revealed that the efficiency of the waterleaf extracts was comparable to that of a commercial surfactant sodium dodecyl sulphate. However, soils washed with the waterleaf extracts retained some significant amounts of nutrients and favorable pH moderation. In both surfactants, soil microbial loads reduced significantly. Overall, the aqueous waterleaf extracts showed potential as ecofriendly surfactants and nutrients retainer during soil washing of contaminated ultisols.
title: SmoothTones: The six tones of sonorant-ending syllables of Hanoi Vietnamese, on the syllables /a/ and /ɗa/. Speaker M6
Creators: name: Michaud, Alexis
name: Nguyễn, Thị Lan
name: Trần, Đỗ Đạt
name: Mạc, Đăng Khoa
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2013
Subjects: subject: Hanoi dialect
subject: vie
subject: Vietnamese

description: SmoothTones: The six tones of sonorant-ending syllables of Hanoi Vietnamese, on the syllables /a/ and /ɗa/. Speaker M6
description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
Global description of action-angle duality for a Poisson-Lie deformation of the trigonometric $\mathrm{BC}_n$ Sutherland system
Creators: name: Feher, L.
name: Marshall, I.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Mathematical Physics (math-ph)
subject: High Energy Physics - Theory (hep-th)
subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: FOS: Physical sciences

description: Integrable many-body systems of Ruijsenaars--Schneider--van Diejen type displaying action-angle duality are derived by Hamiltonian reduction of the Heisenberg double of the Poisson-Lie group $\mathrm{SU}(2n)$. New global models of the reduced phase space are described, revealing non-trivial features of the two systems in duality with one another. For example, after establishing that the symplectic vector space $\mathbb{C}^n\simeq\mathbb{R}^{2n}$ underlies both global models, it is seen that for both systems the action variables generate the standard torus action on $\mathbb{C}^n$, and the fixed point of this action corresponds to the unique equilibrium positions of the pertinent systems. The systems in duality are found to be non-degenerate in the sense that the functional dimension of the Poisson algebra of their conserved quantities is equal to half the dimension of the phase space. The dual of the deformed Sutherland system is shown to be a limiting case of a van Diejen system.
description: 39 pages, some stylistic changes and typos removed in v2
Analytic description of inversion vibrational mode for ammonia molecule
Creators: name: Sitnitsky, A. E.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: The one-dimensional Schrödinger equation with symmetric trigonometric double-well potential is exactly solved via angular prolate spheroidal function. Although it is inferior compared with multidimensional counterparts and its limitations are obvious nevertheless its solution is shown to be analytic rather than commonly used numerical or approximate semiclassical (WKB) one. This comprises the novelty and the merit of the present work. Our exact analytic description of the ground state splitting can well be a referee point for comparison of the accuracy of numerous WKB formulas suggested in the literature. The approach reasonably well suits for the inversion mode in the ammonia molecule $NH_3$ and thus yields a new theoretical tool for its description. The results obtained provide good quantitative description of relevant experimental data on microwave and IR spectroscopy of $NH_3$.
description: 16 pages, 2 figures, Final version, misprint in Appendix 1 has been corrected
Additional file 1 of Construction of competing endogenous RNA networks from paired RNA-seq data sets by pointwise mutual information
Creators: name: Lan, Chaowang
name: Peng, Hui
name: Hutvagner, Gyorgy
name: Li, Jinyan
Publisher: name: figshare
Year: 2019
Subjects: Biophysics
Molecular Biology
Biological Sciences not elsewhere classified
Mathematical Sciences not elsewhere classified

description: Additional file 1 Comprehensive Comparison with Other Methods, Supplementary Figures and Tables.
Additional file 1: of DNA methylation holds prognostic information in relapsed precursor B-cell acute lymphoblastic leukemia
Creators: name: Borssén, Magnus
name: Nordlund, Jessica
name: Haider, Zahra
name: Landfors, Mattias
name: Larsson, Pär
name: Kanerva, Jukka
name: Schmiegelow, Kjeld
name: Flaegstad, Trond
name: Jónsson, Ólafur
name: Britt-Marie Frost
name: Palle, Josefine
name: Forestier, Erik
name: Heyman, Mats
name: Hultdin, Magnus
name: Gudmar Lönnerholm
name: Degerman, Sofie
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Hematology

description: Methods description, figures, and tables can be found at the Clinical Epigenetics webpage. (DOCX 282 kb)
Simultaneous constraints on the mass and radius of Aql X-1 from quiescence and X-ray burst observations
Creators: name: Li, Zhaosheng
name: Falanga, Maurizio
name: Chen, Li
name: Qu, Jinlu
name: Xu, Renxin
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: The measurement of neutron star mass and radius is one of the most direct way to distinguish between various dense matter equations of state. The mass and radius of accreting neutron stars hosted in low mass X-ray binaries can be constrained by several methods, including photospheric radius expansion from type-I X-ray bursts and from quiescent spectra. In this paper, we apply for the first time these two methods simultaneously to constrain the mass and radius of Aql X-1, as a reliable distance estimation, high signal-to-noise ratio quiescent spectra from Chandra and XMM-Newton, and photospheric radius expansion bursts from RXTE are available. This is also used to verify the consistency between the two methods, and to narrow down the uncertainties of the neutron star mass and radius. It is found that the distance to Aql X-1 should be in the range of $4.0-5.75$ kpc, based on the overlapping confidence regions between photospheric radius expansion burst and quiescent spectra methods. In addition, we show that the mass and radius determined for the compact star in Aql X-1 are compatible with strange star equations of state and conventional neutron star models.
description: 16 pages, 9 figures, accepted by ApJ
title: SmoothTones: The six tones of sonorant-ending syllables of Hanoi Vietnamese, on the syllables /a/ and /ɗa/. Speaker M7
Creators: name: Michaud, Alexis
name: Nguyễn, Thị Lan
name: Trần, Đỗ Đạt
name: Mạc, Đăng Khoa
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2013
Subjects: subject: Hanoi dialect
subject: vie
subject: Vietnamese

description: SmoothTones: The six tones of sonorant-ending syllables of Hanoi Vietnamese, on the syllables /a/ and /ɗa/. Speaker M7
description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
title: Monats-Berichte des Statistischen Amtes der Stadt Zürich 1917
title: Monatsberichte des Statistischen Amtes der Stadt Zürich
titleType: AlternativeTitle
Creators: name: (:Unkn) Unknown
Publisher: name: Statistisches Amt
Year: 1918
Subjects: subject: 314 Allgemeine Statistiken zu Europa
subject: 330 Wirtschaft
subject: Zürich
subject: Amtliche Statistik
subject: Bevölkerungsstatistik

description: Monatsberichte
description: Früheres enth. in: Tagblatt der Stadt Zürich
Dirac Fermions with Competing Orders: Non-Landau Transition with Emergent Symmetry
Creators: name: Sato, Toshihiro
name: Hohenadler, Martin
name: Assaad, Fakher F.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We consider a model of Dirac fermions in $2+1$ dimensions with dynamically generated, anticommuting SO(3) Néel and Z$_2$ Kekulé mass terms that permits sign-free quantum Monte Carlo simulations. The phase diagram is obtained from finite-size scaling and includes a direct and continuous transition between the Néel and Kekulé phases. The fermions remain gapped across the transition, and our data support an emergent SO(4) symmetry unifying the two order parameters. While the bare symmetries of our model do not allow for spinon-carrying Z$_3$ vortices in the Kekulé mass, the emergent SO(4) invariance permits an interpretation of the transition in terms of deconfined quantum criticality. The phase diagram also features a tricritical point at which Néel, Kekulé, and semimetallic phases meet. The present, sign-free approach can be generalized to a variety of other mass terms and thereby provides a new framework to study exotic critical phenomena.
description: 5 pages, 5 figures, to appear in Phys. Rev. Lett
Additional file 2 of LSM2 is associated with a poor prognosis and promotes cell proliferation, migration, and invasion in skin cutaneous melanoma
Creators: name: Sun, Xiaofang
name: Zhang, Jianping
name: Hu, Jiayuan
name: Han, Qingdong
name: Ge, Zili
Publisher: name: figshare
Year: 2023
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Figure S2: Film 1, 2, and 3 were exposed at the same time. The three films were used to show western blot (WB) results of LSM2 and GAPDH in A2058 cells. The red labeled bands are the WB bands of Figure 6C in this paper.
Local models of astrophysical discs
Creators: name: Latter, Henrik N.
name: Papaloizou, John
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Local models of gaseous accretion discs have been successfully employed for decades to describe an assortment of small-scale phenomena, from instabilities and turbulence, to dust dynamics and planet formation. For the most part, they have been derived in a physically motivated but essentially ad hoc fashion, with some of the mathematical assumptions never made explicit nor checked for consistency. This approach is susceptible to error, and it is easy to derive local models that support spurious instabilities or fail to conserve key quantities. In this paper we present rigorous derivations, based on an asympototic ordering, and formulate a hierarchy of local models (incompressible, Boussinesq, and compressible), making clear which is best suited for a particular flow or phenomenon while spelling out explicitly the assumptions and approximations of each. We also discuss the merits of the anelastic approximation, emphasising that anelastic systems struggle to conserve energy unless strong restrictions are imposed on the flow. The problems encountered by the anelastic approximation are exacerbated by the disk's differential rotation, but also attend non-rotating systems such as stellar interiors. We conclude with a defence of local models and their continued utility in astrophysical research.
description: MNRAS, accepted