cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Atmospheric River Reconnaissance 2021: A Review
Creators: name: Cobb, Alison
name: Ralph, F. Martin
name: Tallapragada, Vijay
name: Wilson, Anna M.
name: Murphy, Michael
name: Et Al
Publisher: name: AMS
Year: 2022

description: Authors: Alison Cobb, F. Martin Ralph, Vijay Tallapragada, Anna M. Wilson, Christopher A. Davis, Luca Delle Monache, James D. Doyle, Florian Pappenberger, Carolyn A. Reynolds, Aneesh Subramanian, Peter G. Black, Forest Cannon, Chris Castellano, Jason M. Cordeira, Jennifer S. Haase, Chad Hecht, Brian Kawzenuk, David A. Lavers, Michael Murphy , Jack Parrish, Ryan Rickert, Jonathan J. Rutz, Ryan Torn, Xingren Wu, and Minghua Zheng
description: Atmospheric River Reconnaissance (AR Recon) is a targeted campaign that complements other sources of observational data, forming part of a diverse observing system. AR Recon 2021 operated for ten weeks from January 13 to March 22, with 29.5 Intensive Observation Periods (IOPs), 45 flights and 1142 successful dropsondes deployed in the northeast Pacific. With the availability of two WC-130J aircraft operated by the 53rd Weather Reconnaissance Squadron (53 WRS), Air Force Reserve Command (AFRC) and one National Oceanic and Atmospheric Administration (NOAA) Aircraft Operations Center (AOC) G-IVSP aircraft, six sequences were accomplished, in which the same synoptic system was sampled over several days. The principal aim was to gather observations to improve forecasts of landfalling atmospheric rivers on the U.S. West Coast. Sampling of other meteorological phenomena forecast to have downstream impacts over the U.S. was also considered. Alongside forecast improvement, observations were also gathered to address important scientific research questions, as part of a Research and Operations Partnership. Targeted dropsonde observations were focused on essential atmospheric structures, primarily atmospheric rivers. Adjoint and ensemble sensitivities, mainly focusing on predictions of U.S. West Coast precipitation, provided complementary information on locations where additional observations may help to reduce the forecast uncertainty. Additionally, Airborne Radio Occultation (ARO) and tail radar were active during some flights, 30 drifting buoys were distributed, and 111 radiosondes were launched from four locations in California. Dropsonde, radiosonde and buoy data were available for assimilation in real-time into operational forecast models. Future work is planned to examine the impact of AR Recon 2021 data on model forecasts.
title: ADCO, Comptes du Petit-Cîteaux (1477-1491) (11 H 1179), f. 00099
Creators: name: de la Côte d'Or, Archives départementales
name: Petot, Frédéric
name: Archives Départementales De La Côte-D'Or
name: Archives Départementales De La Côte D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CBMA/CG21/F.PETOT/2019
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: cartulaire
subject: comptes
subject: Corpus Burgundiae Medii Aevi
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris
subject: Chartes de la Bourgogne du Moyen Âge

description: Comptes du Petit-Cîteaux (1477-1491), Archives départementales de la Côte-d'Or, (11 H 1179). Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Comptes du Petit-Cîteaux (1477-1491), Archives départementales de la Côte-d'Or, (11 H 1179), f. 00099, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https://manuscrits.cbma-project.eu/
description: Provenance: abbaye de Cîteaux
description: Provenance: http://www.wikidata.org/entity/Q843261
description: Provenance: https://www.geonames.org/3024876
description: Provenance: http://www.idref.fr/030974844/id
description: Provenance: https://catalogue.bnf.fr/ark:/12148/cb12228351v
Improving Our Understanding of Dark Matter Halos with Machine Learning
Creators: name: Vladimir, Ze'ev
Publisher: name: Digital Repository at the University of Maryland
Year: 2024
Subjects: Astronomy
Dark Matter
Machine Learning

description: Dark matter constitutes 80% of all matter and is key to understanding the structure of the universe. Dark matter impacts galaxy formation through the gravitational influence it exerts on baryonic matter. However, dark matter and the structures it forms are too complex to describe with an analytical solution. As a result numerical simulations have provided a way to learn about dark matter structures. Within these simulations, dark matter forms filaments, voids, and most notably halos. Halos are roughly spherical regions with a high concentration of dark matter that contain a galaxy which co-evolves alongside it. However, determining which particles form a halo is most commonly oversimplified with the spherical over-density model. This model defines a halo as all the particles present in a sphere around an over-dense region in space. However, a more physically accurate definition for halos has recently been proposed: only the particles that orbit a halo's center of mass constitute the halo. Unfortunately, current methods that determine if a particle is orbiting either lack a high level of accuracy or are computationally expensive. To fill this gap, we have developed a simple machine-learning model using the XGBoost library. Our model is trained on the velocity and position of the dark matter particles which are accessible from all simulations. To improve accuracy, we utilized velocity and position data from two snapshots in simulation time to capture how a particle moves. Our model achieves over 97\% accuracy at all radii on our validation set. In addition, our model's speed outperforms more complex orbiting classifiers on the order of seconds to minutes compared to hours.
Revisiting the Hybrid Quantum Monte Carlo Method for Hubbard and Electron-Phonon Models
Creators: name: Beyl, Stefan
name: Goth, Florian
name: Assaad, Fakher F.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: High Energy Physics - Lattice (hep-lat)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: A unique feature of the hybrid quantum Monte Carlo (HQMC) method is the potential to simulate negative sign free lattice fermion models with subcubic scaling in system size. Here we will revisit the algorithm for various models. We will show that for the Hubbard model the HQMC suffers from ergodicity issues and unbounded forces in the effective action. Solutions to these issues can be found in terms of a complexification of the auxiliary fields. This implementation of the HQMC that does not attempt to regularize the fermionic matrix so as to circumvent the aforementioned singularities does not outperform single spin flip determinantal methods with cubic scaling. On the other hand we will argue that there is a set of models for which the HQMC is very efficient. This class is characterized by effective actions free of singularities. Using the Majorana representation, we show that models such as the Su-Schrieffer-Heeger Hamiltonian at half filling and on a bipartite lattice belong to this class. For this specific model sub-cubic scaling is achieved.
title: 02_1114
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/
Kedrostis africana Cogn.
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Cucurbitales
Cucurbitaceae
Kedrostis
Kedrostis africana

description: Bryonia africana Linnaeus, Species Plantarum 2: 1013. 1753.
"Habitat in Aethiopia." RCN: 7345.
Type not designated.
 Original material: Herb. Linn. No. 395.9 (S); Herb. Linn. No. 1153.9 (LINN); Herb. Clifford: 453, Bryonia 4 (BM); [icon] in Hermann, Parad. Bat.: 107, 108. 1698.
 Current name: Kedrostis africana (L.) Cogn. (Cucurbitaceae).
 Note: Meeuse (in Bothalia 8: 33. 1962) interpreted the name via a Hermann illustration, which Newton & Njoroge (in Eggli, Ill. Handb. Succ. Pl., Dicots: 86. 2002) indicated as the type, but this choice was published after 1 Jan 2001 and so the omission of the phrase "designated here" or an equivalent (Art. 7.11) means that it is not effective.
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part B), pp. 343-369 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 363, DOI: 10.5281/zenodo.291971
Additional file 8 of Signature construction and molecular subtype identification based on immune-related genes for better prediction of prognosis in hepatocellular carcinoma
Creators: name: Sun, Liang
name: Wu, Zhengyi
name: Dong, Cairong
name: Yu, Shian
name: Huang, He
name: Chen, Zhendong
name: Wu, Zhipeng
name: Yin, Xiangbao
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer

description: Additional file 8: Figure S5. Clustering analyses in TCGA and ICGC.PCA results for two groups of patients in TCGA.ggalluvial of two clusters in TCGA displayed the correlation between clusters, risk, and survival status.PCA results for two groups of patients in ICGC.ggalluvial of two clusters in ICGC displayed the correlation between clusters, risk, and survival status.
Fully kinetic versus reduced-kinetic modelling of collisionless plasma turbulence
Creators: name: Groselj, D.
name: Cerri, S. S.
name: Navarro, A. Banon
name: Willmott, C.
name: Told, D.
name: Loureiro, N. F.
name: Califano, F.
name: Jenko, F.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: We report the results of a direct comparison between different kinetic models of collisionless plasma turbulence in two spatial dimensions. The models considered include a first principles fully-kinetic (FK) description, two widely used reduced models [gyrokinetic (GK) and hybrid-kinetic (HK) with fluid electrons], and a novel reduced gyrokinetic approach (KREHM). Two different ion beta ($β_i$) regimes are considered: 0.1 and 0.5. For $β_i=0.5$, good agreement between the GK and FK models is found at scales ranging from the ion to the electron gyroradius, thus providing firm evidence for a kinetic Alfvén cascade scenario. In the same range, the HK model produces shallower spectral slopes, presumably due to the lack of electron Landau damping. For $β_i=0.1$, a detailed analysis of spectral ratios reveals a slight disagreement between the GK and FK descriptions at kinetic scales, even though kinetic Alfvén fluctuations likely still play a significant role. The discrepancy can be traced back to scales above the ion gyroradius, where the FK and HK results seem to suggest the presence of fast magnetosonic and ion Bernstein modes in both plasma beta regimes, but with a more notable deviation from GK in the low-beta case. The identified practical limits and strengths of reduced-kinetic approximations, compared here against the fully-kinetic model on a case-by-case basis, may provide valuable insight into the main kinetic effects at play in turbulent collisionless plasmas, such as the solar wind.
Investigating the Role of Glutamine Metabolism on Bacteriophage Replication
Creators: name: Goodwin, Gabriel
name: Altberger, Hannah
name: Varghese, Riya
Publisher: name: Digital Repository at the University of Maryland
Year: 2024
Subjects: FIRE, microbiology, virology

description: The emergence of antimicrobial resistance demands more effective alternative treatments such as phage therapy. To further explore treatments, this research attempts to better understand bacteriophage replication. The TCA cycle is a crucial metabolic pathway in E. coli, responsible for providing bacteria with energy, which includes pathways such as glutamine-synthesis and glutamine degradation. It is known that bacteriophage requires energy and nutrients to perform viral replication. We chose to knock out genes glnA (present in glutamine-synthesis), glsA, and glsB (both present in glutamine degradation). This research examines the importance of glutamine in these metabolic pathways. To determine the role of glutamine in T4 bacteriophage replication, growth and phage replication dynamics in the different strains were compared. Growth and lysis curves were conducted in rich LB media to understand patterns in optimal nutrient conditions, while also in M9 minimal media with a small glucose concentration and varied glutamine concentrations. This data was used to determine optimal glutamine concentrations for growth and lysis. Phage replication differences in the strains were further analyzed via phage titer and burst size. The glsB strain showed increased phage replication, and glnA had decreased replication. These results indicate what genes are necessary for optimal phage replication. Our research will assess the selected knockout genes to understand which aspects of the metabolic pathway are more influential on bacterial lysis. Further research will help illuminate the role of glutamine metabolism in T4 phage replication and have implications for improving phage therapy.
Evaluation of GNSS Radio Occultation Profiles in the Vicinity of Atmospheric Rivers
Creators: name: Murphy, Michael
name: Haase, Jennifer S.
Publisher: name: MDPI
Year: 2022

description: Increasing the density of Global Navigation Satellite System radio occultation (RO) with commercial Smallsats and the next generation COSMIC-2 constellation is expected to improve analyses of the state of atmosphere, which is essential for numerical weather prediction. High vertical resolution RO profiles could be useful to observe atmospheric rivers (ARs) over the ocean, which transport water vapor in shallow, elongated corridors that frequently impact the west coasts of continents. The multi-year AR Reconnaissance campaign has extensively sampled ARs over the northeastern Pacific with dropsondes, providing an invaluable dataset to evaluate the reliability of RO retrievals. These dropsondes, and a reanalysis product that assimilates them, are compared to three RO datasets: (1) established operational missions, (2) COSMIC-2, and (3) the commercial Spire constellation. Each RO dataset has biases relative to reanalyses of less than 0.5% N in the upper troposphere and negative biases in the lower troposphere. Direct colocations with dropsondes indicate that vertical refractivity gradients present within ARs may be contributing to negative biases at higher altitudes inside than outside ARs, where the greatest variability and vertical gradients are at the well-defined boundary layer top. Observations from Spire are overly smooth, affecting the ability to resolve the low-level structure of an AR. Surprisingly, the depth of penetration into the lower troposphere is greater inside an AR than outside for all datasets. The results indicate that the observation errors used for assimilation of RO within ARs should consider the height dependent biases that are associated with the structure of the atmosphere.
Additional file 1: Table S1. of Cardiometabolic disorder reduces survival prospects more than suboptimal body mass index irrespective of age or gender: a longitudinal study of 377,929 adults in Taiwan
Creators: name: Chih-Cheng Hsu
name: Wahlqvist, Mark
name: I-Chien Wu
name: Yu-Hung Chang
name: I-Shou Chang
name: Yi-Fen Tsai
name: Liu, Ting-Ting
name: Chwen Tsao
name: Hsiung, Chao
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences

description: All-cause mortality risk for subjects overall and those who survived at least 1, 2, and 3 years after entry. Figure S1. Adjusted mortality risk for different BMI, high blood pressure, hyperglycemia, and waist circumference for overall subjects, non-smokers, men, and women, stratified by age. BMI classification: underweight: <18.5 kg/m2, low normal: 18.5–21.9 kg/m2, normal: 22–23.9 kg/m2, overweight: 24–26.9 kg/m2, obese1: 27–29.9 kg/m2, obese2: ≥ 30 kg/m2. The hazards ratios shown in Figure S1 were derived from Cox proportional hazards models adjusted for gender, age, education level, smoking status, physical activity, and drinking status. Table S2. Mortality rate (per 10,000 person-years) by body mass index, age, and status of metabolic syndrome for the study subjects including previous heart disease and stroke (N = 390,941). Table S3. Mortality risk, prevalence, and population attributable burden of mortality for different BMI, high blood pressure, and hyperglycemia in overall subjects and people in different age groups, for the study subjects including previous heart disease and stroke (N = 390,941). (DOCX 135 kb)
Computational Psychiatry in Borderline Personality Disorder
Creators: name: Fineberg, Sarah K
name: Stahl, Dylan
name: Corlett, Philip
Publisher: name: arXiv
Year: 2017
Subjects: subject: Neurons and Cognition (q-bio.NC)
subject: FOS: Biological sciences

description: Purpose of review: We review the literature on the use and potential use of computational psychiatry methods in Borderline Personality Disorder. Recent findings: Computational approaches have been used in psychiatry to increase our understanding of the molecular, circuit, and behavioral basis of mental illness. This is of particular interest in BPD, where the collection of ecologically valid data, especially in interpersonal settings, is becoming more common and more often subject to quantification. Methods that test learning and memory in social contexts, collect data from real-world settings, and relate behavior to molecular and circuit networks are yielding data of particular interest. Summary: Research in BPD should focus on collaborative efforts to design and interpret experiments with direct relevance to core BPD symptoms and potential for translation to the clinic.
Harold Daniels in the Fleet Air Arm
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: Harold joined the Royal Navy on 06/02/1940, aged 15. He gained an apprenticeship with the Royal Navy but trained with the RAF prior to going into the Fleet Air Arm. He worked in electrical and ordnance duties on the aircraft.He was sent to RAF Halton for training. He was sent to New York on the Queen Elizabeth on 19/11/1943; it was his birthday on the day he arrived. From New York, he went to an air force base near Boston to form up 853 Avenger Squadron, a torpedo/bomber/fighter unit that, Harold says, was 'way ahead of its time'. The squadron was formed from November 1943 to February 1944.From Boston, he was sent to Vancouver, Canada. On the journey, you had to amuse yourself across the USA. Harold and a Yorkshire friend gambled all the way across.At Vancouver, he joined the HMS Arbiter and sailed down from Vancouver to the Panama Canal. There was an accident at sea. On the boat, a plane crashed off the deck on a training flight, and the pilot was killed. He escorted a convoy back to England after the Panama Canal. He was then at the Orkneys with his ship until 13/09/1944.Then, the squadron picked up HMS Tracker. This was a convoy bound for the USSR. The boat went to Murmansk, where it was very cold. There were very rough weather conditions on the way. There was lots of US Lend-Lease equipment there, including American Jeeps. His experience with Soviet troops and people was positive. He got back to the Orkneys and was there from 05/12/1944 to 25/01/1945. He then joined HMS Queen.Harold served with the Fleet Air Arm and left on 19/11/1964. After the war, Harold served with the Royal Australian Navy and visited Japan (Hiroshima) and all over Australia. The Australians were starting a Fleet Air Arm, and Harold was sent to help them set it up. There were differences between the Australian and British Navy; for instance, Australians did not address people by their surnames.
Additional file 9 of Signature construction and molecular subtype identification based on immune-related genes for better prediction of prognosis in hepatocellular carcinoma
Creators: name: Sun, Liang
name: Wu, Zhengyi
name: Dong, Cairong
name: Yu, Shian
name: Huang, He
name: Chen, Zhendong
name: Wu, Zhipeng
name: Yin, Xiangbao
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer

description: Additional file 9: Figure S6. Correlation between immune cells and seven genes in TCGA. MAPT and NROB1 have no Significant correlation wirh immune cells in TCGA.
Equatorial waves resolved by balloon-borne Global Navigation Satellite System radio occultation in the Strateole-2 campaign
Creators: name: Cao, Bing
name: Haase, Jennifer S.
name: Murphy, Michael
name: Alexander, M. Joan
name: Bramberger, Martina
name: Hertzog, Albert
Publisher: name: EGU
Year: 2022

description: Current climate models have difficulty representing realistic wave–mean flow interactions, partly because the contribution from waves with fine vertical scales is poorly known. There are few direct observations of these waves, and most models have difficulty resolving them. This observational challenge cannot be addressed by satellite or sparse ground-based methods. The Strateole-2 long-duration stratospheric superpressure balloons that float with the horizontal wind on constant-density surfaces provide a unique platform for wave observations across a broad range of spatial and temporal scales. For the first time, balloon-borne Global Navigation Satellite System (GNSS) radio occultation (RO) is used to provide high-vertical-resolution equatorial wave observations. By tracking navigation signal refractive delays from GPS satellites near the horizon, 40–50 temperature profiles were retrieved daily, from balloon flight altitude (∼20 km) down to 6–8 km altitude, forming an orthogonal pattern of observations over a broad area (±400–500 km) surrounding the flight track. The refractivity profiles show an excellent agreement of better than 0.2 % with co-located radiosonde, spaceborne COSMIC-2 RO, and reanalysis products. The 200–500 m vertical resolution and the spatial and temporal continuity of sampling make it possible to extract properties of Kelvin waves and gravity waves with vertical wavelengths as short as 2–3 km. The results illustrate the difference in the Kelvin wave period (20 vs. 16 d) in the Lagrangian versus ground-fixed reference and as much as a 20 % difference in amplitude compared to COSMIC-2, both of which impact estimates of momentum flux. A small dataset from the extra Galileo, GLONASS, and BeiDou constellations demonstrates the feasibility of nearly doubling the sampling density in planned follow-on campaigns when data with full equatorial coverage will contribute to a better estimate of wave forcing on the quasi-biennial oscillation (QBO) and improved QBO representation in models.
Additional file 1: Figure S1. of Validation of genotype imputation in Southeast Asian populations and the effect of single nucleotide polymorphism annotation on imputation outcome
Creators: name: Worachart Lert-Itthiporn
name: Bhoom Suktitipat
name: Grove, Harald
name: Anavaj Sakuntabhai
name: Prida Malasit
name: Nattaya Tangthawornchaikul
name: Matsuda, Fumihiko
name: Prapat Suriyaphol
Publisher: name: figshare
Year: 2018
Subjects: 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: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics

description: Long distance LD pr. Mb separated by the chromosome for each population LD for each SNP pair with a distance between 10Â kb and 1Â Mb taken into account. Figure S2. Accuracy and yield of imputation between each location of SNPs. Figure S3. Comparing minor allele frequencies of SNPs between imputed and actual genotypes before quality control of imputed results separately plot by each SNP location. Figure S4. Comparing allele frequencies of SNPs between imputed and actual genotypes after quality control of imputed results separately plotted by each SNP location. Figure S5. Proportion of SNPs with lower AF after imputation vs initial AF. Figure S6. Comparing p-values between cases and controls of SNPs between imputed and actual genotypes before quality control of imputed results separately plotted by each SNP location. Figure S7. Comparing p-values between cases and controls of SNPs between imputed and actual genotypes after quality control of imputed results separately plotted according to each SNP location. Figure S8. Average linkage disequilibrium as r-squared for each region. SNPs were assigned to gene locations. Figure S9. LD, measured as r2, plotted against physical distance. (PDF 1286Â kb)
Sensitivity Analysis of Chaotic Systems using Unstable Periodic Orbits
Creators: name: Lasagna, Davide
Publisher: name: arXiv
Year: 2017
Subjects: subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Physical sciences

description: A well-behaved adjoint sensitivity technique for chaotic dynamical systems is presented. The method arises from the specialisation of established variational techniques to the unstable periodic orbits of the system. On such trajectories, the adjoint problem becomes a time periodic boundary value problem. The adjoint solution remains bounded in time and does not exhibit the typical unbounded exponential growth observed using traditional methods over unstable non-periodic trajectories (Lea et al., Tellus 52 (2000)). This enables the sensitivity of period averaged quantities to be calculated exactly, regardless of the orbit period, because the stability of the tangent dynamics is decoupled effectively from the sensitivity calculations. We demonstrate the method on two prototypical systems, the Lorenz equations at standard parameters and the Kuramoto-Sivashinky equation, a one-dimensional partial differential equation with chaotic behaviour. We report a statistical analysis of the sensitivity of these two systems based on databases of unstable periodic orbits of size 10^5 and 4x10^4, respectively. The empirical observation is that most orbits predict approximately the same sensitivity. The effects of symmetries, bifurcations and intermittency are discussed and future work is outlined in the conclusions.
INVESTIGATING THE ROLE OF E. COLI TCA CYCLE METABOLISM IN BACTERIOPHAGE REPLICATION
Creators: name: Kavalov, Lilith
name: Weaver, Trinity
Publisher: name: Digital Repository at the University of Maryland
Year: 2024
Subjects: subject: FIRE
subject: Microbiology
subject: FOS: Biological sciences
subject: Virology

description: Bacteriophages are viruses that specifically infect and hijack Escherichia coli's metabolic processes to proliferate, ultimately destroying the host cell in the process. The Tricarboxylic Acid Cycle (TCA Cycle) is a multi-step aerobic enzyme-catalyzed pathway that occurs in the cytoplasm of E. coli and is responsible for generating the electron-carrier molecules NADH and FADH2 which are crucial for generating ATP for the cell in future steps of cellular respiration. The E. coli genes, acnB, and acnA, encode enzymes that catalyze different reactions that are necessary for the TCA cycle. We hypothesize that the removal of these genes would negatively impact the growth rate and ATP levels of E. coli and, as a result, inhibit or slow the replication of bacteriophage. To determine the effects of the removal of these genes, enzyme assays, comparative growth curves of the knockout strains, and plaque assays of bacteriophage replication were measured and investigated. Furthermore, we quantified the knockout’s effects by collecting lysis curves as well as performing an ATP assay using bioluminescence.
Additional file 2: of A novel LRAT mutation affecting splicing in a family with early onset retinitis pigmentosa
Creators: name: Chen, Yabin
name: Huang, Li
name: Jiao, Xiaodong
name: Riazuddin, Sheikh
name: Riazuddin, S.
name: Fielding Hetmancik, J.
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Science Policy

description: Table S2. Primer list (DOCX 12Â kb).
title: ADCO, Ordre cistercien et abbaye de Cîteaux : comptes pour l'ordre (1337-1347), comptes du boursier (1377-1402) (11 H 1160), f. 00399
Creators: name: de la Côte-d'Or, Archives départementales
name: Petot, Frédéric
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CBMA/CG21/F.PETOT/2017
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge
subject: comptes
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: Ordre cistercien et abbaye de Cîteaux : comptes pour l'ordre (1337-1347), comptes du boursier (1377-1402), Archives départementales de la Côte-d'Or, (11 H 1160). Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Ordre cistercien et abbaye de Cîteaux : comptes pour l'ordre (1337-1347), comptes du boursier (1377-1402), Archives départementales de la Côte-d'Or, (11 H 1160), f. 00399, in Projet CBMA - Corpus Burgundiae Medii Aevi \[Ressource en ligne\], https:// manuscrits.cbma-project.eu/
description: Provenance: https://www.geonames.org/3024876
description: Provenance: http://www.idref.fr/030974844/id
description: Provenance: https://catalogue.bnf.fr/ark:/12148/cb12228351v
description: Provenance: abbaye de Cîteaux
description: Provenance: http://www.wikidata.org/entity/Q843261
Bryonia alba Linnaeus 1753
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Cucurbitales
Cucurbitaceae
Bryonia
Bryonia alba

description: Bryonia alba Linnaeus, Species Plantarum 2: 1012. 1753.
"Habitat in Europa ad pagos & sepes." RCN: 7340.
 Lectotype (Jeffrey in Kew Bull. 23: 455. 1969): Herb. Linn. No. 1153.1 (LINN).
 Generitype of Bryonia Linnaeus (vide Green, Prop. Brit. Bot.: 190. 1929).
 Current name: Bryonia alba L. (Cucurbitaceae).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part B), pp. 343-369 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 363, DOI: 10.5281/zenodo.291971
Asymmetry of leaf internal structure affects PLSR modelling of anatomical traits using VIS-NIR leaf level spectra
Creators: name: Neuwirthová, Eva
name: Lhotáková, Zuzana
name: ?Ervená, Lucie
name: Lukeš, Petr
name: Campbell, Petya Entcheva
name: Albrechtová, Jana
Publisher: name: Taylor & Francis
Year: 2023
Subjects: contact probe
leaf optical properties
leaf thickness
leaf traits
palisade
Planar leaves
spongy parenchyma
two-sided reflectance
vegetation function

description: Leaf traits can be used to elucidate vegetation functional responses to global climate change. Pigments, water and leaf mass per area are the most used traits. However, detailed anatomical traits such as leaf thickness, the thickness of palisade and spongy parenchyma are often neglected, although they affect leaf physiological function and optical properties. Our aim was to produce partial least squares regression (PLSR) models for estimating leaf traits using biconical reflectance factor (BCRF). We established that estimation of leaf anatomical properties differs when using BCRF obtained from the upper and lower surface of the leaf. PLSR explained that 90% of the variability was based on total chlorophyll content (R2 = 0.95), spongy parenchyma to leaf thickness ratio (R2 = 0.94), equivalent water thickness (R2 = 0.93) and leaf mass per area (R2 = 0.91) or leaf thickness (R2 = 0.90). We conclude that internal asymmetry in leaf structure affects significantly leaf optical properties and should not be neglected in radiative transfer modelling at the leaf level and when upscaling leaf properties to the canopy.
Soft Hair as a Soft Wig
Creators: name: Bousso, Raphael
name: Porrati, Massimo
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We consider large gauge transformations of gravity and electromagnetism in D=4 asymptotically flat spacetime. Already at the classical level, we identify a canonical transformation that decouples the soft variables from the hard dynamics. We find that only the soft dynamics is constrained by BMS or large U(1) charge conservation. Physically this corresponds to the fact that sufficiently long-wavelength photons or gravitons that are added to the in-state will simply pass through the interaction region; they scatter trivially in their own sector. This implies in particular that the large gauge symmetries bear no relevance to the black hole information paradox. We also present the quantum version of soft decoupling. As a consistency check, we show that the apparent mixing of soft and hard modes in the original variables arises entirely from the long range field of the hard charges, which is fixed by gauge invariance and so contains no additional information.
description: One reference added and other references updated. To appear in Classical and Quantum Gravity, focus issue on BMS asymptotic symmetries
Additional file 2: of A novel LRAT mutation affecting splicing in a family with early onset retinitis pigmentosa
Creators: name: Chen, Yabin
name: Huang, Li
name: Jiao, Xiaodong
name: Riazuddin, Sheikh
name: Amer Riazuddin, S.
name: Fielding Hetmancik, J.
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Science Policy

description: Table S2. Primer list (DOCX 12Â kb).
Additional file 1: of A model to predict disease progression in patients with autosomal dominant polycystic kidney disease (ADPKD): the ADPKD Outcomes Model
Creators: name: McEwan, Phil
name: Wilton, Hayley Bennett
name: Ong, Albert
name: Ørskov, Bjarne
name: Sandford, Richard
name: Scolari, Francesco
name: Maria-Cristina Cabrera
name: Walz, Gerd
name: O’Reilly, Karl
name: Robinson, Paul
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: 20199 Astronomical and Space Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Statistics
subject: Plant Biology
subject: 60506 Virology

description: Variance covariance matrices for TKV and eGFR progression equation coefficients. Table S1. Variance covariance matrix for the TEMPO 3:4 TKV equation coefficients. Table S2. Variance covariance matrix for the TEMPO 3:4 eGFR equation coefficients. Example of using the TKV and eGFR progression equations to predict annual ADPKD progression. Applying the ADPKD-OM to alternative patient populations. Using CKD-Epi measurements to model eGFR progression. Table S3. Comparison of eGFR progression equation coefficient estimates. Table S4. Variance covariance matrix for the TEMPO 3:4 eGFR equation coefficients. Validation against CRISP I-derived progression equations. CRISP I-derived equations for TKV (Equation S1) and eGFR (Equation S2) progression. Table S5. TKV progression equation coefficient estimates, as derived from CRISP I. Table S6. eGFR progression equation coefficient estimates, as derived from CRISP I. Validation against HALT-PKD trial data. Validation against THIN data. Validation against Thong and Ong [40]. Equation S3. eGFR progression equation, derived by Thong and Ong [40]. Table S7. eGFR progression equation coefficient estimates, as derived from Thong and Ong [40]. (DOCX 51 kb)
10 simple rules to create a serious game, illustrated with examples from structural biology
Creators: name: Baaden, Marc
name: Delalande, Olivier
name: Ferey, Nicolas
name: Pasquali, Samuela
name: Waldispühl, Jérôme
name: Taly, Antoine
Publisher: name: arXiv
Year: 2017
Subjects: subject: Computers and Society (cs.CY)
subject: FOS: Computer and information sciences

description: Serious scientific games are games whose purpose is not only fun. In the field of science, the serious goals include crucial activities for scientists: outreach, teaching and research. The number of serious games is increasing rapidly, in particular citizen science games, games that allow people to produce and/or analyze scientific data. Interestingly, it is possible to build a set of rules providing a guideline to create or improve serious games. We present arguments gathered from our own experience ( Phylo , DocMolecules , HiRE-RNA contest and Pangu) as well as examples from the growing literature on scientific serious games.
Return to Sport After Osteochondral Lesions in Pediatric Patients: A systematic review
Creators: name: Baumann, Anthony
name: Anaspure, Omkar
name: Lininger, Jake
name: Patel, Shiv
Publisher: name: OSF Registries
Year: 2024
Subjects: subject: Medicine and Health Sciences

description: This systematic review aims to determine the best protocol for return to sport after osteochondral lesions in children.
Mukia maderaspatana M. Roem.
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Angiospermae
Dicotyledoneae
Cucurbitales
Cucurbitaceae
Mukia
Mukia maderaspatana

description: Bryonia cordifolia Linnaeus, Species Plantarum 2: 1012. 1753.
"Habitat in Zeylona." RCN: 7343.
 Lectotype (Jeffrey in Milne-Redhead & Polhill, Fl. Trop. E. Africa, Cucurbitaceae: 117. 1967): Herb. Hermann 2: 22, No. 354 (BM- 000621582).
 Current name: Mukia maderaspatana (L.) M. Roem. (Cucurbitaceae).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part B), pp. 343-369 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 363, DOI: 10.5281/zenodo.291971
DNA Aptamers Against Airway Mucin Proteins for Therapeutics and Diagnostics
Creators: name: Dwomoh, Deborah
name: Welte, Linara
name: Savage, Colin
name: McDonald, Cyan
name: Shpilman, Zackary
name: Srinath, Priyanka
Publisher: name: Digital Repository at the University of Maryland
Year: 2024
Subjects: First-Year Innovation and Research Experience
FIRE
Molecular Diagnostics
Aptamer Selection

description: Mucus is a viscous bodily fluid composed of mucin proteins, inorganic salts, and water. MUC5AC and MUC5B are the two mucin proteins that makeup airway mucus. Elevated levels of MUC5AC can indicate certain diseases, like asthma and Chronic Obstructive Pulmonary Disease (COPD). Current treatments for mucus-associated respiratory diseases include using enzymes and chemical agents to clear mucus buildup. These existing treatments are limited in their ability to selectively target specific mucin proteins within mucus. Our research aims to select DNA aptamers that bind to MUC5AC or MUC5B, within mucus samples. We are optimizing a One-Pot SELEX or in vitro selection methodology previously used by other researchers to select aptamers against MUC16. Selected DNA aptamers with high binding affinity and specificity can detect airway mucin proteins and deliver engineered proteases to cleave and destroy them.
A glassy phase in quenched disordered graphene and crystalline membranes
Creators: name: Coquand, O.
name: Essafi, K.
name: Kownacki, J. -P.
name: Mouhanna, D.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We investigate the flat phase of $D$-dimensional crystalline membranes embedded in a $d$-dimensional space and submitted to both metric and curvature quenched disorders using a nonperturbative renormalization group approach. We identify a second order phase transition controlled by a finite-temperature, finite-disorder fixed point unreachable within the leading order of $ε=4-D$ and $1/d$ expansions. This critical point divides the flow diagram into two basins of attraction: that associated to the finite-temperature fixed point controlling the long distance behaviour of disorder-free membranes and that associated to the zero-temperature, finite-disorder fixed point. Our work thus strongly suggests the existence of a whole low-temperature glassy phase for quenched disordered graphene, graphene-like compounds and, more generally, crystalline membranes.
description: 6 pages, 1 figure
Bryonia cretica subsp. cretica Linnaeus 1753
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Cucurbitales
Cucurbitaceae
Bryonia
Bryonia cretica
Bryonia cretica l. subsp. cretica

description: Bryonia cretica Linnaeus, Species Plantarum 2: 1013. 1753.
"Habitat in Creta." RCN: 7346.
Type not designated.
 Original material: Herb. Clifford: 453, Bryonia 2 (BM).
 Current name: Bryonia cretica L. subsp. cretica (Cucurbitaceae).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part B), pp. 343-369 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 363, DOI: 10.5281/zenodo.291971
Response theory of the ergodic many-body delocalized phase: Keldysh Finkel'stein sigma models and the 10-fold way
Creators: name: Liao, Yunxiang
name: Levchenko, Alex
name: Foster, Matthew S.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We derive the finite temperature Keldysh response theory for interacting fermions in the presence of quenched disorder, as applicable to any of the 10 Altland-Zirnbauer classes in an Anderson delocalized phase with at least a U(1) continuous symmetry. In this formulation of the interacting Finkel'stein nonlinear sigma model, the statistics of one-body wave functions are encoded by the constrained matrix field, while physical correlations follow from the hydrodynamic density or spin response field, which decouples the interactions. Integrating out the matrix field first, we obtain weak (anti)localization and Altshuler-Aronov quantum conductance corrections from the hydrodynamic response function. This procedure automatically incorporates the correct infrared physics, and in particular gives the Altshuler-Aronov-Khmelnitsky (AAK) equations for dephasing of weak (anti)localization due to electron-electron collisions. We explicate the method by deriving known quantum corrections in two dimensions for the symplectic metal class AII, as well as the spin-SU(2) invariant superconductor classes C and CI. We show that conductance corrections due to the special modes at zero energy in nonstandard classes are automatically cut off by temperature, as previously expected, while the Wigner-Dyson class Cooperon modes that persist to all energies are cut by dephasing. We also show that for short-ranged interactions, the standard self-consistent solution for the dephasing rate is equivalent to a diagrammatic summation via the self-consistent Born approximation. This should be compared to the AAK solution for long-ranged Coulomb interactions, which exploits the Markovian noise correlations induced by thermal fluctuations of the electromagnetic field. We discuss prospects for exploring the many-body localization transition from the ergodic side as a dephasing catastrophe in short-range interacting models.
description: 68 pages, 23 figures
Coccinia grandis Voigt 1845
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Cucurbitales
Cucurbitaceae
Coccinia
Coccinia grandis

description: Bryonia grandis Linnaeus, Systema Naturae, ed. 12, 2: 640; Mantissa Plantarum: 126. 1767.
"Habitat in India." RCN: 7342.
 Lectotype (Jeffrey in Milne-Redhead & Polhill, Fl. Trop. E. Africa, Cucurbitaceae: 68. 1967): Herb. Linn. No. 1153.2 (LINN).
 Current name: Coccinia grandis (L.) Voigt (Cucurbitaceae).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part B), pp. 343-369 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 363, DOI: 10.5281/zenodo.291971