cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Josephson thermal memory
Creators: name: Guarcello, Claudio
name: Solinas, Paolo
name: Braggio, Alessandro
name: Di Ventra, Massimiliano
name: Giazotto, Francesco
Publisher: name: arXiv
Year: 2017
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We propose a superconducting thermal memory device that exploits the thermal hysteresis in a flux-controlled, temperature-biased superconducting quantum-interference device (SQUID). This system reveals a flux-controllable temperature bistability, which can be used to define two well-distinguishable thermal logic states. We discuss a suitable writing-reading procedure for these memory states. The time of the memory writing operation is expected to be on the order of ~0.2 ns, for a Nb-based SQUID in thermal contact with a phonon bath at 4:2 K. We suggest a non-invasive readout scheme for the memory states based on the measurement of the effective resonance frequency of a tank circuit inductively coupled to the SQUID. The proposed device paves the way for a practical implementation of thermal logic and computation. The advantage of this proposal is that it represents also an example of harvesting thermal energy in superconducting circuits.
description: 10 pages, 7 figures
Additional file 1 of Polycomb group genes are required for neuronal pruning in Drosophila
Creators: name: Bu, Shufeng
name: Lau, Samuel Song Yuan
name: Yong, Wei Lin
name: Zhang, Heng
name: Thiagarajan, Sasinthiran
name: Bashirullah, Arash
name: Yu, Fengwei
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Scm is required for dendrite pruning in ddaC neurons.
The non-monotypic status of the neotropical fish genus Hemiodontichthys (Siluriformes, Loricariidae) evidenced by genetic approaches
Creators: name: Carvalho, Margarida Lima
name: Silva, Guilherme José Da Costa
name: Melo, Silvana
name: Ashikaga, Fernando Yuldi
name: Cristiane Kioko Shimabukuro-Dias
name: Scacchetti, Priscilla Cardim
name: Devidé, Renato
name: Foresti, Fausto
name: Oliveira, Claudio
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: The combination of cytogenetic and molecular data with those traditionally obtained in areas like systematics and taxonomy created interesting perspectives for the analysis of natural populations under different aspects. In this context, this study aimed to evaluate the genetic differentiation among populations of the genus Hemiodontichthys Bleeker, 1862, through combined genetic techniques and included the analysis of populations sampled in the Araguaia River, Guamá River, Madeira River and two populations from the Purus River. Hemiodontichthys samples from the two localities in Purus River were also karyotyped in order to address the degree of chromosomal variation between populations. Through GMYC analysis of the COI tree, the patterns of genetic variation among local populations revealed to be higher than the ones found among distinct species from other genera of the subfamily Loricariinae, suggesting the existence of probable four cryptic species in this genus. The possible existence of a species complex in the genus is corroborated by the different cytogenetic patterns between Hemiodontichthys sp. 1 and sp. 2, revealing the necessity of a deep taxonomic review of the group.
Complete mitogenomes from Kurdistani sheep: abundant centromeric nuclear copies representing diverse ancestors
Creators: name: Sarbast Ihsan Mustafa
name: Schwarzacher, Trude
name: J. S. Heslop-Harrison
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 60506 Virology

description: The geographical centre of domestication and species diversity for sheep (Ovis aries) lies around the Kurdistan region of Northern Iraq, within the ‘Fertile Crescent’. From whole genome sequence reads, we assembled the mitochondrial genomes (mtDNA or mitogenome) of five animals of the two main Kurdistani sheep breeds Hamdani and Karadi and found they fitted into known sheep haplogroups (or matrilineages), with some SNPs. Haplotyping 31 animals showed presence of the main Asian (hpgA) and European (hpgB) haplogroups, as well as the rarer Anatolian haplogroup hpgC. From the sequence reads, near-complete genomes of mitochondria from wild sheep species (or subspecies), and even many sequences similar to goat (Capra) mitochondria, could be extracted. Analysis suggested that these polymorphic reads were nuclear mitochondrial DNA segments (numts). In situ hybridization with seven regions of mitochondria chosen from across the whole genome showed strong hybridization to the centromeric regions of all autosomal sheep chromosomes, but not the Y. Centromeres of the three submetacentric pairs and the X chromosomes showed fewer copies of numts, with varying abundance of different mitochondrial regions. Some mitochondrial-nuclear transfer presumably occurred before species divergence within the genus, and there has been further introgression of sheep mitochondrial sequences more recently. This high abundance of nuclear mitochondrial sequences is not reflected in the whole nuclear genome assemblies, and the accumulation near major satellite sequences at centromeres was unexpected. Mitochondrial variants including SNPs, numts and heteroplasmy must be rigorously validated to interpret correctly mitochondrial phylogenies and SNPs.
Low-cost datalogger for environmental and physiological data collection with Arduino®
Creators: name: Muzzini, Valerio Giorgio
name: Mattioni, Michele
name: Giovannelli, Alessio
name: Traversi, Maria Laura
name: Leonardi, Luca
name: De Cinti, Bruno
Publisher: name: Zenodo
Year: 2024

description: Physiological and environmental data are essential for understanding ecological relationships. Dataloggers, capable of long-term data acquisition and storage, are important tools for subsequent analysis. This work aimed to develop a low-cost, Arduino-based datalogger to capture both environmental (air temperature, humidity, and brightness) and physiological signals with sufficient precision for extended periods of several months to a year.
title: ADCO, Cartulaire de Cîteaux pour les possessions de Chaugey et Maison-Dieu (Fin XVe siècle), Cart. 181 (11 H 754), 165 folios, f. 0092
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: CG21/F.PETOT/2017
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: cartulaire
subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: Cartulaire de Cîteaux pour les possessions de Chaugey et Maison-Dieu (Fin XVe siècle), Archives départementales de la Côte-d'Or, Cart. 181 (11 H 754), 165 folios, f. 0092, Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Cartulaire de Cîteaux pour les possessions de Chaugey et Maison-Dieu (Fin XVe siècle), Archives départementales de la Côte-d'Or, Cart. 181 (11 H 754), 165 folios, f. 0092, 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
The magnetar model for Type I superluminous supernovae I: Bayesian analysis of the full multicolour light curve sample with MOSFiT
Creators: name: Nicholl, Matt
name: Guillochon, James
name: Berger, Edo
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We use the new Modular Open Source Fitter for Transients (MOSFiT) to model 38 hydrogen-poor superluminous supernovae (SLSNe). We fit their multicolour light curves with a magnetar spin-down model and present the posterior distributions of magnetar and ejecta parameters. The colour evolution can be well matched with a simple absorbed blackbody. We find the following medians (1$σ$ ranges): spin period 2.4 ms (1.2-4 ms); magnetic field $0.8\times 10^{14}$ G (0.2-1.8 $\times 10^{14}$ G); ejecta mass 4.8 Msun (2.2-12.9 Msun); kinetic energy $3.9\times 10^{51}$ erg (1.9-9.8 $\times 10^{51}$ erg). This significantly narrows the parameter space compared to our priors, showing that although the model is flexible, the parameter space relevant to SLSNe is well constrained by existing data. The requirement that the instantaneous engine power is $\sim 10^{44}$ erg at the light curve peak necessitates either a large rotational energy (P<2 ms), or more commonly that the spin-down and diffusion timescales be well-matched. We find no evidence for separate populations of fast- and slow-declining SLSNe, which instead form a continuum both in light curve widths and inferred parameters. Variations in the spectra are well explained through differences in spin-down power and photospheric radii at maximum-light. We find no correlations between any model parameters and the properties of SLSN host galaxies. Comparing our posteriors to stellar evolution models, we show that SLSNe require rapidly rotating (fastest 10%) massive stars (> 20 Msun), and that this is consistent with the observed SLSN rate. High mass, low metallicity, and likely binary interaction all serve to maintain rapid rotation essential for magnetar formation. By reproducing the full set of SLSN light curves, our posteriors can be used to inform photometric searches for SLSNe in future survey data.
Performance of prediction models for short-term outcome in COVID-19 patients in the emergency department: a retrospective study
Creators: name: van Dam, Paul M. E. L.
name: Zelis, Noortje
name: van Kuijk, Sander M. J.
name: Linkens, Aimée E. M. J. H.
name: Brüggemann, Renée A. G.
name: Spaetgens, Bart
name: van der Horst, Iwan C. C.
name: Stassen, Patricia M.
Publisher: name: Taylor & Francis
Year: 2021
Subjects: Medicine
Biological Sciences not elsewhere classified
Science Policy

description: Coronavirus disease 2019 (COVID-19) has a high burden on the healthcare system. Prediction models may assist in triaging patients. We aimed to assess the value of several prediction models in COVID-19 patients in the emergency department (ED). In this retrospective study, ED patients with COVID-19 were included. Prediction models were selected based on their feasibility. Primary outcome was 30-day mortality, secondary outcomes were 14-day mortality and a composite outcome of 30-day mortality and admission to medium care unit (MCU) or intensive care unit (ICU). The discriminatory performance of the prediction models was assessed using an area under the receiver operating characteristic curve (AUC). We included 403 patients. Thirty-day mortality was 23.6%, 14-day mortality was 19.1%, 66 patients (16.4%) were admitted to ICU, 48 patients (11.9%) to MCU, and 152 patients (37.7%) met the composite endpoint. Eleven prediction models were included. The RISE UP score and 4 C mortality scores showed very good discriminatory performance for 30-day mortality (AUC 0.83 and 0.84, 95% CI 0.79-0.88 for both), significantly higher than that of the other models. The RISE UP score and 4 C mortality score can be used to recognise patients at high risk for poor outcome and may assist in guiding decision-making and allocating resources.
Flexible fitting to cryo-electron microscopy maps with coarse-grained elastic network models
Creators: name: Tekpinar, Mustafa
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Computational Biology

description: Cryo-electron microscopy has become an important tool for protein structure determination in recent decades. Since proteins may exist in multiple conformational states, combining high resolution X-ray or NMR structures with cryo-electron microscopy maps is a useful approach to obtain proteins in different functional states. Flexible fitting methods used in cryo-electron microscopy aim to obtain an unknown protein conformation from a high resolution structure and a cryo-electron microscopy map. Since all-atom flexible fitting is computationally expensive, many efficient flexible fitting algorithms that utilize coarse-grained elastic network models have been proposed. In this study, we investigated performance of three coarse-grained elastic network model-based flexible fitting methods (EMFF, iModFit, NMFF) using 25 protein pairs at four resolutions. This study shows that the application of coarse-grained elastic network models to flexible fitting of cryo-electron microscopy maps can provide fast and fruitful models of various conformational states of proteins.
Exploring belief systems regarding COVID-19 conspiracy myths using mental maps.
Creators: name: Thiele, Gundula
name: Scherbaum, Stefan
name: Richter, Franz
name: Dutschke, René
Publisher: name: OSF Registries
Year: 2024
Subjects: subject: Cognitive Psychology
subject: Social and Behavioral Sciences
subject: Psychology
subject: FOS: Psychology

description: The aim of this study is to further explore mental belief systems of people regarding COVID-19 conspiracy myths. Visualising different belief systems using a triad test and cognitive-affective maps might play a role in conflict resolution and lead towards bigger understanding of conspiracy myths.
A Robust Interrupted Time Series Model for Analyzing Complex Healthcare Intervention Data
Creators: name: Cruz, Maricela
name: Bender, Miriam
name: Ombao, Hernando
Publisher: name: arXiv
Year: 2017
Subjects: subject: Applications (stat.AP)
subject: FOS: Computer and information sciences

description: Current health policy calls for greater use of evidence based care delivery services to improve patient quality and safety outcomes. Care delivery is complex, with interacting and interdependent components that challenge traditional statistical analytic techniques, in particular when modeling a time series of outcomes data that might be "interrupted" by a change in a particular method of health care delivery. Interrupted time series (ITS) is a robust quasi-experimental design with the ability to infer the effectiveness of an intervention that accounts for data dependency. Current standardized methods for analyzing ITS data do not model changes in variation and correlation following the intervention. This is a key limitation since it is plausible for data variability and dependency to change because of the intervention. Moreover, present methodology either assumes a pre-specified interruption time point with an instantaneous effect or removes data for which the effect of intervention is not fully realized. In this paper, we describe and develop a novel `Robust-ITS' model that overcomes these omissions and limitations. The Robust-ITS model formally performs inference on: (a) identifying the change point; (b) differences in pre- and post-intervention correlation; (c) differences in the outcome variance pre- and post-intervention; and (d) differences in the mean pre- and post-intervention. We illustrate the proposed method by analyzing patient satisfaction data from a hospital that implemented and evaluated a new nursing care delivery model as the intervention of interest. The Robust-ITS model is implemented in a R Shiny toolbox which is freely available to the community.
description: 37 pages and 6 figures
title: ADCO, Grènetier de Cîteaux : comptes (1497-1504) (11 H 1172), f. 00218
Creators: name: de la Côte-d'Or, Archives départementales
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: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge
subject: comptes
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: Grènetier de Cîteaux : comptes (1497-1504), Archives départementales de la Côte-d'Or, (11 H 1172). Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Grènetier de Cîteaux : comptes (1497-1504), Archives départementales de la Côte-d'Or, (11 H 1172), f. 00218, 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
Preoperative predictors that impact the survival and outcome of patients undergoing secondary cytoreduction for ovarian cancer
Creators: name: Katsnelson, Marina
name: Hwang, Wei-Ting
name: Tahirovic, Emin
name: Rubin, Stephen C.
name: Janos L. Tanyi
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: This study aimed to examine the factors affecting feasibility of optimal and complete secondary cytoreductive surgery (SCRS) and to characterise the prognostic factors that correlate with improved survival in patients who underwent SCRS. This is a retrospective single-institutional cohort study of patients who underwent SCRS for recurrent epithelial ovarian cancer (EOC). One hundred and forty-eight patients met inclusion criteria. Platinum sensitivity was associated with complete cytoreduction at SCRS. Factors associated with suboptimal cytoreduction (SOC) were age >55 years, serous histology, largest tumour implant size >4 cm, and SOC at primary surgery. Overall survival analysis showed significantly longer survival with complete cytoreduction compared to optimal and SOC. Surgical outcome of SCRS was an independent predictor of survival regardless of the outcome of primary cytoreduction. Location of the largest implant, DFI and timing of chemotherapy also impact on survival.
Tameness from two successive good frames
Creators: name: Vasey, Sebastien
Publisher: name: arXiv
Year: 2017
Subjects: subject: Logic (math.LO)
subject: FOS: Mathematics
subject: 03C48 (Primary), 03C45, 03C52, 03C55, 03C75 (Secondary)

description: We show, assuming a mild set-theoretic hypothesis, that if an abstract elementary class (AEC) has a superstable-like forking notion for models of cardinality $λ$ and a superstable-like forking notion for models of cardinality $λ^+$, then orbital types over models of cardinality $λ^+$ are determined by their restrictions to submodels of cardinality $λ$. By a superstable-like forking notion, we mean here a good frame, a central concept of Shelah's book on AECs. It is known that locality of orbital types together with the existence of a superstable-like notion for models of cardinality $λ$ implies the existence of a superstable-like notion for models of cardinality $λ^+$, but here we prove the converse. An immediate consequence is that forking in $λ^+$ can be described in terms of forking in $λ$.
description: 27 pages
Additional file 1: of Differences in flavonoid pathway metabolites and transcripts affect yellow petal colouration in the aquatic plant Nelumbo nucifera
Creators: name: Zhu, Huan-huan
name: Yang, Ju-xiang
name: Xiao, Chu-han
name: Mao, Tian-yu
name: Zhang, Jie
name: Zhang, Hong-yan
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Virology
subject: Computational Biology

description: Table S1. Primer sequences for qRT-PCR of flavonoid pathway structural genes. (DOC 14 kb)
Serum miRNAs in women affected by hyperandrogenic polycystic ovary syndrome: the potential role of miR-155 as a biomarker for monitoring the estroprogestinic treatment
Creators: name: Arancio, Walter
name: Amato, Marco Calogero
name: Magliozzo, Miriam
name: Pizzolanti, Giuseppe
name: Vesco, Rosalia
name: Giordano, Carla
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: MicroRNAs can be used as very efficient circulating biomarkers. The role of microRNAs in polycystic ovary syndrome (PCOS) and the effects of antiandrogen therapy on microRNA expression is still not fully understood. A panel of serum microRNAs were retrotranscribed via looped reverse primer transcription specific for each miRNA and quantified via probe specific RT-PCR in 16 Caucasian hyperandrogenic PCOS women selected according to the Rotterdam criteria and in a subset of seven patients after four months of sequential reverse antiandrogenic therapy. All women recruited underwent an oral glucose tolerance test (OGTT) and a baseline total cholesterol, high density lipoproteins cholesterol, triglycerides, AST and ALT dosage. In the follicular phase women were evaluated for total testosterone, Δ4-androstenedione, DHEAS, 17OHpg, FSH, LH, and 17-β-E2. The AUC2hglucose, ISI Matsuda, oral disposition index (DIo) and visceral adipose index (VAI) were also calculated. We suggest that miR-155 might have a role as biomarker in hyperandrogenic PCOS patients to monitor the effect of antiandrogen therapy.
Outcome of acute myocardial infarction versus stable coronary artery disease patients treated with coronary bypass surgery
Creators: name: Malmberg, Markus
name: Gunn, Jarmo
name: Rautava, Päivi
name: Sipilä, Jussi
name: Kytö, Ville
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Medicine
subject: Biotechnology
subject: Ecology
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer

description: To study the long-term outcome differences between acute myocardial infarction (MI) and stable coronary artery disease (CAD) patients treated with coronary artery bypass grafting (CABG). We studied retrospectively patients with MI (n = 1882) or stable CAD (n = 13117) treated with isolated CABG between 2004 and 2014. Inverse propensity probability weight adjustment for baseline features was used. Median follow-up was 7.9 years. In-hospital mortality (8.6% vs. 1.6%; OR 5.94; p < .0001) and re-sternotomy (5.5% vs. 2.7%; OR 2.07; p < .0001) were more common in MI patients compared to stable CAD patients. Hospital surviving MI patients had higher all-cause mortality (28.2% vs. 22.2%; HR 1.37; p = .002) and MACE rate (34.4% vs. 27.4%; HR 1.22; CI 1.00–1.50; p = .049) at 10-year follow-up. Cardiovascular mortality (15.9% vs. 12.7%; HR 1.36; p = .017) and rate of new myocardial infarction (12.0% vs. 9.8%; HR 1.40; p = .034) were also higher in MI patients during follow-up. In follow-up of stabilized first-year survivors, the difference in all-cause (26.5% vs. 20.7%; HR 1.40; p = .003) and cardiovascular (14.2% vs. 11.4%; HR 1.37; p = .027) mortality continued to increase between MI and stable CAD patients. MI patients have poorer short- and long-term outcomes compared to stable CAD patients after CABG and risk difference continues to increase with time.Key MessagesPatients with myocardial infarction have poorer short- and long-term outcomes compared to stable coronary artery disease patients after coronary artery bypass grafting (CABG).Higher risk of death continues also in stabilized first-year myocardial infarct survivors.The importance of efficient secondary prevention and follow-up highlights in post-myocardial infarct population after CABG. Patients with myocardial infarction have poorer short- and long-term outcomes compared to stable coronary artery disease patients after coronary artery bypass grafting (CABG). Higher risk of death continues also in stabilized first-year myocardial infarct survivors. The importance of efficient secondary prevention and follow-up highlights in post-myocardial infarct population after CABG.
Computing from projections of random points: a dense hierarchy of subideals of the $K$-trivial degrees
Creators: name: Greenberg, Noam
name: Miller, Joseph S.
name: Nies, Andre
Publisher: name: arXiv
Year: 2017
Subjects: subject: Logic (math.LO)
subject: FOS: Mathematics
subject: 03D32, 68Q30

description: We study the sets that are computable from both halves of some (Martin-Löf) random sequence, which we call \emph{$1/2$-bases}. We show that the collection of such sets forms an ideal in the Turing degrees that is generated by its c.e.\ elements. It is a proper subideal of the $K$-trivial sets. We characterise $1/2$-bases as the sets computable from both halves of Chaitin's $Ω$, and as the sets that obey the cost function $\mathbf c(x,s) = \sqrt{Ω_s - Ω_x}$. Generalising these results yields a dense hierarchy of subideals in the $K$-trivial degrees: For $k< n$, let $B_{k/n}$ be the collection of sets that are below any $k$ out of $n$ columns of some random sequence. As before, this is an ideal generated by its c.e.\ elements and the random sequence in the definition can always be taken to be $Ω$. Furthermore, the corresponding cost function characterisation reveals that $B_{k/n}$ is independent of the particular representation of the rational $k/n$, and that $B_p$ is properly contained in $B_q$ for rational numbers $p< q$. These results are proved using a generalisation of the Loomis--Whitney inequality, which bounds the measure of an open set in terms of the measures of its projections. The generality allows us to analyse arbitrary families of orthogonal projections. As it turns out, these do not give us new subideals of the $K$-trivial sets, we can calculate from the family which $B_p$ it characterises. We finish by showing that the the union of $B_p$ for $p<1$ is the collection of sets which are robustly computable from a random, a class previously studied by Hirschfeldt, Jockusch, Kuyper, and Schupp.
Large time behavior of a generalized Oseen evolution operator, with applications to the Navier-Stokes flow past a rotating obstacle
Creators: name: Hishida, Toshiaki
Publisher: name: arXiv
Year: 2017
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: 35Q30

description: Consider the motion of a viscous incompressible fluid in a 3D exterior domain when a rigid body moves with prescribed time-dependent translational and angular velocities. For the linearized non-autonomous system, $L^q$-$L^r$ smoothing action near the initial time as well as generation of the evolution operator was shown by Hansel and Rhandi (J. Reine Angew. Math. 2014) under reasonable conditions. In this paper we develop the $L^q$-$L^r$ decay estimates of the evolution operator and then apply them to the Navier-Stokes initial value problem.
description: 38 pages, Corrected typos, to appear in Math. Ann
An unexpected switch in peptide binding mode: from simulation to substrate specificity
Creators: name: Kahler, Ursula
name: Fuchs, Julian E.
name: Goettig, Peter
name: Liedl, Klaus R.
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Biophysics
subject: Biochemistry
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Computational Biology

description: A ten microsecond molecular dynamics simulation of a kallikrein-related peptidase 7 peptide complex revealed an unexpected change in binding mode. After more than two microseconds unrestrained sampling we observe a spontaneous transition of the binding pose including a 180° rotation around the P1 residue. Subsequently, the substrate peptide occupies the prime side region rather than the cognate non-prime side in a stable conformation. We characterize the unexpected binding mode in terms of contacts, solvent-accessible surface area, molecular interactions and energetic properties. We compare the new pose to inhibitor-bound structures of kallikreins with occupied prime side and find that a similar orientation is adopted. Finally, we apply in silico mutagenesis based on the alternative peptide binding position to explore the prime side specificity of kallikrein-related peptidase 7 and compare it to available experimental data. Our study provides the first microsecond time scale simulation data on a kallikrein protease and shows previously unexplored prime side interactions. Therefore, we expect our study to advance the rational design of inhibitors targeting kallikrein-related peptidase 7, an emerging drug target involved in several skin diseases as well as cancer.
50 Years of the Golomb--Welch Conjecture
Creators: name: Horak, Peter
name: Kim, Dongryul
Publisher: name: arXiv
Year: 2017
Subjects: subject: Information Theory (cs.IT)
subject: Combinatorics (math.CO)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics
subject: 94B60

description: Since 1968, when the Golomb--Welch conjecture was raised, it has become the main motive power behind the progress in the area of the perfect Lee codes. Although there is a vast literature on the topic and it is widely believed to be true, this conjecture is far from being solved. In this paper, we provide a survey of papers on the Golomb--Welch conjecture. Further, new results on Golomb--Welch conjecture dealing with perfect Lee codes of large radii are presented. Algebraic ways of tackling the conjecture in the future are discussed as well. Finally, a brief survey of research inspired by the conjecture is given.
description: 28 pages, 2 figures
An unexpected switch in peptide binding mode: from simulation to substrate specificity
Creators: name: Kahler, Ursula
name: Fuchs, Julian E.
name: Goettig, Peter
name: Liedl, Klaus R.
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Biophysics
subject: Biochemistry
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Computational Biology

description: A ten microsecond molecular dynamics simulation of a kallikrein-related peptidase 7 peptide complex revealed an unexpected change in binding mode. After more than two microseconds unrestrained sampling we observe a spontaneous transition of the binding pose including a 180° rotation around the P1 residue. Subsequently, the substrate peptide occupies the prime side region rather than the cognate non-prime side in a stable conformation. We characterize the unexpected binding mode in terms of contacts, solvent-accessible surface area, molecular interactions and energetic properties. We compare the new pose to inhibitor-bound structures of kallikreins with occupied prime side and find that a similar orientation is adopted. Finally, we apply in silico mutagenesis based on the alternative peptide binding position to explore the prime side specificity of kallikrein-related peptidase 7 and compare it to available experimental data. Our study provides the first microsecond time scale simulation data on a kallikrein protease and shows previously unexplored prime side interactions. Therefore, we expect our study to advance the rational design of inhibitors targeting kallikrein-related peptidase 7, an emerging drug target involved in several skin diseases as well as cancer.
Theory for frequent measurements of spontaneous emissions in non-Markovian environment: beyond Lorentzian spectrum
Creators: name: Xu, Luting
name: Li, Xin-Qi
Publisher: name: arXiv
Year: 2017
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The measurement-result-conditioned evolution of a system (e.g. an atom) with spontaneous emissions of photons is well described by the quantum trajectory (QT) theory. In this work we generalize the associated QT theory from infinitely wide bandwidth Markovian environment to the case of finite bandwidth non-Markovian environment. In particular, we generalize the treatment for arbitrary spectrum, which is not restricted by the specific Lorentzian case. We rigorously prove a general existence of a perfect scaling behavior jointly defined by the bandwidth of environment and the time interval between successive photon detections. For a couple of examples, we obtain analytic results to facilitate QT simulations based on the Monte-Carlo algorithm. For the case where analytical result is not available, numerical scheme is proposed for practical simulations.
description: 9 pages, 4 figures
Response to “Clinical implications of assay-specific differences in f-calprotectin when monitoring inflammatory bowel disease activity over time”
Creators: name: Moore, Christian
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Biochemistry
subject: Neuroscience
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases

description: Response to “Clinical implications of assay-specific differences in f-calprotectin when monitoring inflammatory bowel disease activity over time”
Association between the liver fat score (LFS) and cardiovascular diseases in the national health and nutrition examination survey 1999–2016
Creators: name: Lee, Chun-On
name: Li, Hang-Long
name: Tsoi, Man-Fung
name: Cheung, Ching-Lung
name: Cheung, Bernard Man Yung
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Cancer
subject: Computational Biology

description: The liver fat score (LFS) has been proposed to be a simple non-invasive marker of non-alcoholic fatty liver disease (NAFLD), which is highly prevalent in the general population. We tested its association with cardiovascular diseases (CVDs) and prognosis. 17,244 adult participants from the National Health and Nutrition Examination Survey 1999–2016 were included. LFS is calculated from variables including serum aspartate transaminase/alanine transaminase (AST/ALT) ratio, fasting serum aspartate transaminase (AST) level, fasting serum insulin level, presence of metabolic syndrome and diabetes mellitus. In cross-sectional analysis, logistic regression was used to examine the association of the LFS with coronary heart disease (CHD), myocardial infarction (MI), congestive heart failure (CHF), stroke and angina pectoris. Mortality during follow-up was analysed using Cox proportional hazard regression. LFS was associated with CHD (adjusted odds ratio [OR]: 1.09 per standard deviation [SD], 95% confidence interval [95% CI]: 1.03–1.15) (p = .003), CHF (1.11, 1.04–1.18) (p = .003) and angina pectoris (1.08, 1.02–1.13) (p = .005). LFS was not associated with MI or stroke, but was associated with increased all-cause and cardiovascular mortality with hazard ratios (HRs) of 1.10 (95% CI: 1.07–1.13) (p < .001) and 1.12 (95% CI: 1.06–1.17) (p < .001), respectively. NAFLD is usually asymptomatic, but this large study of a large general population shows that LFS is associated with CHD, CHF, angina pectoris, cardiovascular and all-cause mortality. Determining the LFS is worthwhile, as it identifies people with NAFLD, who may also be at increased cardiovascular risk.Key MessagesLiver fat score (LFS), a non-invasive marker of non-alcoholic fatty liver disease (NAFLD), is associated with coronary heart disease (CHD), congestive heart failure (CHF) and angina.LFS is also associated with increased cardiovascular and all-cause mortality.Determining the LFS is worthwhile as it identifies people with NAFLD as well as increased cardiovascular risk. Liver fat score (LFS), a non-invasive marker of non-alcoholic fatty liver disease (NAFLD), is associated with coronary heart disease (CHD), congestive heart failure (CHF) and angina. LFS is also associated with increased cardiovascular and all-cause mortality. Determining the LFS is worthwhile as it identifies people with NAFLD as well as increased cardiovascular risk.
Detecting singular weak-dissipation limit for flutter onset in reversible systems
Creators: name: Bigoni, Davide
name: Kirillov, Oleg N.
name: Misseroni, Diego
name: Noselli, Giovanni
name: Tommasini, Mirko
Publisher: name: arXiv
Year: 2017
Subjects: subject: Classical Physics (physics.class-ph)
subject: Dynamical Systems (math.DS)
subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: A `flutter machine' is introduced for the investigation of a singular interface between the classical and reversible Hopf bifurcations that is theoretically predicted to be generic in nonconservative reversible systems with vanishing dissipation. In particular, such a singular interface exists for the Pflüger viscoelastic column moving in a resistive medium, which is proven by means of the perturbation theory of multiple eigenvalues with the Jordan block. The laboratory setup, consisting of a cantilevered viscoelastic rod loaded by a positional force with non-zero curl produced by dry friction, demonstrates high sensitivity of the classical Hopf bifurcation onset {to the ratio between} the weak air drag and Kelvin-Voigt damping in the Pflüger column. Thus, the Whitney umbrella singularity is experimentally confirmed, responsible for discontinuities accompanying dissipation-induced instabilities in a broad range of physical contexts.
description: 17 pages, 10 figures, typos corrected, refs added. Accepted to PRE
A non-parametric maximum test for the Behrens–Fisher problem
Creators: name: Welz, Anke
name: Ruxton, Graeme D.
name: Neuhäuser, Markus
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Science Policy

description: Non-normality and heteroscedasticity are common in applications. For the comparison of two samples in the non-parametric Behrens–Fisher problem, different tests have been proposed, but no single test can be recommended for all situations. Here, we propose combining two tests, the Welch t test based on ranks and the Brunner–Munzel test, within a maximum test. Simulation studies indicate that this maximum test, performed as a permutation test, controls the type I error rate and stabilizes the power. That is, it has good power characteristics for a variety of distributions, and also for unbalanced sample sizes. Compared to the single tests, the maximum test shows acceptable type I error control.
P38 MAPK/AKT signalling is involved in IL-33-mediated anti-apoptosis in childhood acute lymphoblastic leukaemia blast cells
Creators: name: Wang, Yiqian
name: Hou, Hanyi
name: Liang, Zhongping
name: Chen, Xuexin
name: Lian, Xindan
name: Yang, Jie
name: Zhu, Zeyu
name: Luo, Huanmin
name: Su, Haibo
name: Gong, Qing
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Cancer
subject: Hematology

description: Acute lymphoblastic leukaemia (ALL) is often characterized by broad clinical and biological heterogeneity, as well as recurrent genetic aberrations. Despite remarkable improvements in the treatment outcome in paediatric ALL over the past several decades, it remains a leading cause of morbidity and mortality among children. Cytokines have been extensively studied in haematologic diseases; however, the mechanisms by which cytokines contribute to ALL pathogenesis remain poorly understood. IL-33 levels were measured by enzyme-linked immunosorbent assay (ELISA). IL1RL1 expression on ALL cell surface was accessed by flow cytometry. Expression of phosphorylated p38 MAPK, p38, pAKT, AKT and GAPDH were quantified by western blot. Cell survival signals were evaluated by apoptosis using flow cytometry. BM samples from ALL patients at diagnosis upregulated their cell surface expression of IL1RL1, and a higher interleukin (IL)-33 level in the serum was observed as compared to the healthy individuals. Moreover, exogenous IL-33 treatment significantly inhibited apoptosis by activating p38 mitogen-activated protein kinase (MAPK) and AKT pathway, while the inhibitor for p38 MAPK, SB203580, counteracted IL-33-induced anti-apoptosis via inactivation of p38 MAPK and AKT. Furthermore, IL-33 negatively regulates cyclin B1 protein level while increasing the expression of CDK1, with SB203580 inhibiting the effect. Our study reveals an important role for IL-33/IL1RL1 axis in supporting ALL which may represent a novel treatment for paediatric patients.KEY MESSAGESBoth IL-33 and IL1RL1 levels are upregulated in primary ALL samples.IL-33 increased both p38 MAPK and AKT activation in ALL.IL-33 promotes survival and cell cycle progression of ALL cells via activating p38 MAPK. Both IL-33 and IL1RL1 levels are upregulated in primary ALL samples. IL-33 increased both p38 MAPK and AKT activation in ALL. IL-33 promotes survival and cell cycle progression of ALL cells via activating p38 MAPK.
Designing a highly efficient graphene quantum spin heat engine
Creators: name: Mani, Arjun
name: Pal, Subhajit
name: Benjamin, Colin
Publisher: name: arXiv
Year: 2017
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We design a quantum spin heat engine using spin polarized ballistic modes generated in a strained graphene monolayer doped with a magnetic impurity. We observe remarkably large efficiency and large thermoelectric figure of merit both for the charge as well as spin variants of the quantum heat engine. This suggests the use of this device as a highly efficient quantum heat engine for charge as well as spin-based transport. Further, a comparison is drawn between the device characteristics of a graphene spin heat engine against a quantum spin Hall heat engine. The reason being edge modes because of their origin should give much better performance. In this respect, we observe our graphene-based spin heat engine can almost match the performance characteristics of a quantum spin Hall heat engine. Finally, we show that a pure spin current can be transported in our device in absence of any charge current.
description: 22 pages, 12 figures, accepted for publication in Scientific Reports (2019)
Depletion of gut microbiota induces skeletal muscle atrophy by FXR-FGF15/19 signalling
Creators: name: Qiu, Yixuan
name: Yu, Jiaming
name: Li, Yi
name: Yang, Fan
name: Yu, Huiyuan
name: Xue, Mengjuan
name: Zhang, Fan
name: Jiang, Xin
name: Ji, Xueying
name: Bao, Zhijun
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Background: Recent evidence indicates that host-gut microbiota crosstalk has nonnegligible effects on host skeletal muscle, yet gut microbiota-regulating mechanisms remain obscure. Methods: C57BL/6 mice were treated with a cocktail of antibiotics (Abx) to depress gut microbiota for 4 weeks. The profiles of gut microbiota and microbial bile acids were measured by 16S rRNA sequencing and ultra-performance liquid chromatography (UPLC), respectively. We performed qPCR, western blot and ELISA assays in different tissue samples to evaluate FXR-FGF15/19 signaling. Results: Abx treatment induced skeletal muscle atrophy in mice. These effects were associated with microbial dysbiosis and aberrant bile acid (BA) metabolism in intestine. Ileal farnesoid X receptor (FXR)-fibroblast growth factor 15 (FGF15) signaling was inhibited in response to microbial BA disturbance. Mechanistically, circulating FGF15 was decreased, which downregulated skeletal muscle protein synthesis through the extracellular-signal-regulated protein kinase 1/2 (ERK1/2) signaling pathway. Treating Abx mice with FGF19 (human FGF15 ortholog) partly reversed skeletal muscle loss. Conclusions: These findings indicate that the BA-FXR-FGF15/19 axis acts as a regulator of gut microbiota to mediate host skeletal muscle.