cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Needles in the genetic haystack of lipid disorders: single nucleotide polymorphisms in the microRNA regulome
Creators: name: Sethupathy, Praveen
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: In recent years, microRNAs (miRNA) have emerged as important posttranscriptional regulators of gene expression in a wide variety of biological pathways. Since the discovery of the liver-specific miRNA-122 (miR-122) and its critical role in hepatic function, numerous additional miRNAs have been implicated in lipid metabolism. It is now apparent that lipid homeostasis is governed in part by an intricate web of miRNA activity. miRNAs are thought to confer robustness against environmental changes, such as diet modifications. Therefore, naturally occurring genetic variation that perturbs miRNA expression and/or function is likely to contribute to interindividual variability in lipid phenotypes. Although the field is still in its infancy, this review describes the growing evidence for miRNA-related genetic variation as etiological factors in lipid disorders. Specific examples, including a variant in a miRNA transcriptional control element that leads to dyslipidemia as well as a variant in a miRNA target site that modulates the effect of diet on plasma lipid levels, are discussed. Finally, the utility of recent systems genetics approaches to uncover hidden miRNA-related genetic associations with lipid disorders are considered, thereby illuminating the needles in the genetic haystack.
Stressed hyperplanes and Kazhdan-Lusztig gamma-positivity for matroids
Creators: name: Ferroni, Luis
name: Nasr, George D.
name: Vecchi, Lorenzo
Publisher: name: arXiv
Year: 2021
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics

description: In this article we make several contributions of independent interest. First, we introduce the notion of stressed hyperplane of a matroid, essentially a type of cyclic flat that permits to transition from a given matroid into another with more bases. Second, we prove that the framework provided by the stressed hyperplanes allows one to write very concise closed formulas for the Kazhdan--Lusztig, inverse Kazhdan--Lusztig and $Z$-polynomials of all paving matroids, a class which is conjectured to predominate among matroids. Third, noticing the palindromicity of the $Z$-polynomial, we address its $γ$-positivity, a midpoint between unimodality and real-rootedness. To this end, we introduce the \emph{$γ$-polynomial} associated to it, we study some of its basic properties and we find closed expressions for it in the case of paving matroids. Also, we prove that it has positive coefficients in many interesting cases, particularly in the large family of sparse paving matroids, and other smaller classes such as projective geometries, thagomizer matroids and other particular graphs. Our last contribution consists of providing explicit combinatorial interpretations for the coefficients of many of the polynomials addressed in this article by enumerating fillings in certain Young tableaux and skew Young tableaux.
description: 42 pages. Revised version
Knowledge Cross-Distillation for Membership Privacy
Creators: name: Chourasia, Rishav
name: Enkhtaivan, Batnyam
name: Ito, Kunihiro
name: Mori, Junki
name: Teranishi, Isamu
name: Tsuchida, Hikaru
Publisher: name: arXiv
Year: 2021
Subjects: subject: Cryptography and Security (cs.CR)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: A membership inference attack (MIA) poses privacy risks for the training data of a machine learning model. With an MIA, an attacker guesses if the target data are a member of the training dataset. The state-of-the-art defense against MIAs, distillation for membership privacy (DMP), requires not only private data for protection but a large amount of unlabeled public data. However, in certain privacy-sensitive domains, such as medicine and finance, the availability of public data is not guaranteed. Moreover, a trivial method for generating public data by using generative adversarial networks significantly decreases the model accuracy, as reported by the authors of DMP. To overcome this problem, we propose a novel defense against MIAs that uses knowledge distillation without requiring public data. Our experiments show that the privacy protection and accuracy of our defense are comparable to those of DMP for the benchmark tabular datasets used in MIA research, Purchase100 and Texas100, and our defense has a much better privacy-utility trade-off than those of the existing defenses that also do not use public data for the image dataset CIFAR10.
description: Accepted by PETS 2022
Probing the epoch of pre-reionization by cross-correlating cosmic microwave and infrared background anisotropies
Creators: name: Atrio-Barandela, Fernando
name: Kashlinsky, Alexander
Publisher: name: arXiv
Year: 2014
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: The epoch of first star formation and the state of the intergalactic medium (IGM) at that time are not directly observable with current telescopes. The radiation from those early sources is now part of the Cosmic Infrared Background (CIB) and, as these sources ionize the gas around them, the IGM plasma would produce faint temperature anisotropies in the Cosmic Microwave Background (CMB) via the thermal Sunyaev-Zeldovich (TSZ) effect. While these TSZ anisotropies are too faint to be detected, we show that the cross-correlation of maps of source-subtracted CIB fluctuations from {\it Euclid}, with suitably constructed microwave maps at different frequencies can probe the physical state of the gas during reionization and test/constrain models of the early CIB sources. We identify the frequency-combined CMB-subtracted microwave maps from space and ground-based instruments to show that they can be cross-correlated with the forthcoming all-sky {\it Euclid} CIB maps to detect the cross-power at scales $\sim 5'-60'$ with the signal/noise of up to $S/N\sim 4-8$ depending on the contribution to the Thomson optical depth during those pre-reionization epochs ($Δτ\simeq 0.05$) and the temperature of IGM (up to $\sim10^4$K). Such a measurement would offer a new window to explore emergence and physical properties of these first light sources.
description: ApJ Lett, in press
PPARγ coactivator-1α contributes to exercise-induced regulation of intramuscular lipid droplet programming in mice and humans
Creators: name: Muoio, Deborah M.
name: Mosedale, Merrie
name: Kovalik, J. P.
name: Koves, Timothy R.
name: DeBalsi, Karen L.
name: Phielix, Esther
name: Kien, C. Lawrence
name: Hesselink, Matthijs K. C.
name: Schrauwen, Patrick
name: Thorne, Leigh
name: Arumugam, Ramamani
name: Sparks, Lauren M.
name: Meex, Ruth C.
name: Everingham, Karen
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Intramuscular accumulation of triacylglycerol, in the form of lipid droplets (LD), has gained widespread attention as a hallmark of metabolic disease and insulin resistance. Paradoxically, LDs also amass in muscles of highly trained endurance athletes who are exquisitely insulin sensitive. Understanding the molecular mechanisms that mediate the expansion and appropriate metabolic control of LDs in the context of habitual physical activity could lead to new therapeutic opportunities. Herein, we show that acute exercise elicits robust upregulation of a broad program of genes involved in regulating LD assembly, morphology, localization, and mobilization. Prominent among these was perilipin-5, a scaffolding protein that affects the spatial and metabolic interactions between LD and their surrounding mitochondrial reticulum. Studies in transgenic mice and primary human skeletal myocytes established a key role for the exercise-responsive transcriptional coactivator PGC-1α in coordinating intramuscular LD programming with mitochondrial remodeling. Moreover, translational studies comparing physically active versus inactive humans identified a remarkably strong association between expression of intramuscular LD genes and enhanced insulin action in exercise-trained subjects. These results reveal an intimate molecular connection between intramuscular LD biology and mitochondrial metabolism that could prove relevant to the etiology and treatment of insulin resistance and other disorders of lipid imbalance.
The Effects of Refraction on Transit Transmission Spectroscopy: Application to Earth-like Exoplanets
Creators: name: Misra, Amit
name: Meadows, Victoria
name: Crisp, Dave
Publisher: name: arXiv
Year: 2014
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We quantify the effects of refraction in transit transmission spectroscopy on spectral absorption features and on temporal variations that could be used to obtain altitude-dependent spectra for planets orbiting stars of different stellar types. We validate our model against altitude-dependent transmission spectra of the Earth from ATMOS and against lunar eclipse spectra from Palle et al. (2009). We perform detectability studies to show the potential effects of refraction on hypothetical observations of Earth analogs with the James Webb Space Telescope (JWST) Near-Infrared Spectrograph (NIRSPEC). Due to refraction, there will be a maximum tangent pressure level that can be probed during transit for each given planet-star system. We show that because of refraction, for an Earth-analog planet orbiting in the habitable zone of a Sun-like star only the top 0.3 bars of the atmosphere can be probed, leading to a decrease in the signal to noise ratio (SNR) of absorption features by 60%, while for an Earth-analog planet orbiting in the habitable zone of an M5V star it is possible to probe almost the entire atmosphere with minimal decreases in SNR. We also show that refraction can result in temporal variations in the transit transmission spectrum which may provide a way to obtain altitude-dependent spectra of exoplanet atmospheres. Additionally, the variations prior to ingress and subsequent to egress provide a way to probe pressures greater than the maximum tangent pressure that can be probed during transit. Therefore, probing the maximum range of atmospheric altitudes, and in particular the near-surface environment of an Earth-analog exoplanet, will require looking at out-of-transit refracted light in addition to the in-transit spectrum.
description: Added journal reference, minor proof corrections included
Spatiotemporal Impact Assessment of Hurricanes on Electric Power Systems
Creators: name: Poudyal, Abodh
name: Iyengar, Vishnu
name: Garcia-Camargo, Diego
name: Dubey, Anamika
Publisher: name: arXiv
Year: 2021
Subjects: subject: Systems and Control (eess.SY)
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Almost 90% of the major power outages in the US are caused due to hurricanes. Due to the highly uncertain nature of hurricanes in both spatial and temporal dimensions, it is essential to quantify the effect of such hurricanes on a power grid. In this paper, we provide a Monte-Carlo-based framework in which several hurricane scenarios and their impact on a power grid are analyzed in spatiotemporal dimensions. The hurricane simulations are performed using samples from previously occurred hurricanes in the US whereas probabilistic assessment of the transmission lines is performed through line fragility model. Finally, a loss metric based on the amount of load disconnected due to hurricanes traveling inland is calculated for each time step. The simulation is performed on ACTIVSg2000: 2000-bus synthetic Texas grid while mapping the transmission lines of the test case on the geographical footprint of Texas. The simulation results show that the loss increases significantly for a few time steps when the wind field of a hurricane is intense and almost saturates when the intensity of the hurricane decays while traversing further. The proposed analysis can provide some insights for proactive planning strategies on improving the resilience of the power grid.
description: 6 pages, 7 figures, accepted in 2022 Power and Energy Society General Meeting
Metadata-informed community detection with lazy encoding using absorbing random walks
Creators: name: Bassolas, Aleix
name: Eriksson, Anton
name: Marot, Antoine
name: Rosvall, Martin
name: Nicosia, Vincenzo
Publisher: name: arXiv
Year: 2021
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Information Theory (cs.IT)
subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Integrating structural information and metadata, such as gender, social status, or interests, enriches networks and enables a better understanding of the large-scale structure of complex systems. However, existing approaches to metadata integration only consider immediately adjacent nodes, thus failing to identify and exploit long-range correlations between metadata and network structure, typical of many spatial and social systems. Here we show how a flow-based community-detection approach can integrate network information and distant metadata, providing a more nuanced picture of network structure and correlations. We analyse social and spatial networks using the map equation framework and find that our methodology can detect a variety of useful metadata-informed partitions in diverse real-world systems. This framework paves the way for systematically incorporating metadata in network analysis.
description: 15 pages, 15 figures
Thematic Review Series: Functional Regulation of Lipid Homeostasis by microRNA: Complexity of microRNA function and the role of isomiRs in lipid homeostasis
Creators: name: Vickers, Kasey C.
name: Remaley, Alan T.
name: Baran-Gale, Jeanette
name: Sethupathy, Praveen
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: MicroRNAs (miRNAs) are key posttranscriptional regulators of biological pathways that govern lipid metabolic phenotypes. Recent advances in high-throughput small RNA sequencing technology have revealed the complex and dynamic repertoire of miRNAs. Specifically, it has been demonstrated that a single genomic locus can give rise to multiple, functionally distinct miRNA isoforms (isomiR). There are several mechanisms by which isomiRs can be generated, including processing heterogeneity and posttranscriptional modifications, such as RNA editing, exonuclease-mediated nucleotide trimming, and/or nontemplated nucleotide addition (NTA). NTAs are dominant at the 3′-end of a miRNA, are most commonly uridylation or adenlyation events, and are catalyzed by one or more of several nucleotidyl transferase enzymes. 3′ NTAs can affect miRNA stability and/or activity and are physiologically regulated, whereas modifications to the 5′-ends of miRNAs likely alter miRNA targeting activity. Recent evidence also suggests that the biogenesis of specific miRNAs, or small RNAs that act as miRNAs, can occur through unconventional mechanisms that circumvent key canonical miRNA processing steps. The unveiling of miRNA diversity has significantly added to our view of the complexity of miRNA function. In this review we present the current understanding of the biological relevance of isomiRs and their potential role in regulating lipid metabolism.
Rethinking Connes' approach to the standard model of particle physics via non-commutative geometry
Creators: name: Farnsworth, Shane
name: Boyle, Latham
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: Connes' non-commutative geometry (NCG) is a generalization of Riemannian geometry that is particularly apt for expressing the standard model of particle physics coupled to Einstein gravity. In a previous paper, we suggested a reformulation of this framework that is: (i) simpler and more unified in its axioms, and (ii) allows the Lagrangian for the standard model of particle physics (coupled to Einstein gravity) to be specified in a way that is tighter and more explanatory than the traditional algorithm based on effective field theory. Here we explain how this same reformulation yields a new perspective on the symmetries of a given NCG. Applying this perspective to the NCG traditionally used to describe the standard model we find, instead, an extension of the standard model by an extra $U(1)_{B-L}$ gauge symmetry, and a single extra complex scalar field $σ$, which is a singlet under $SU(3)_{C}\times SU(2)_{L}\times U(1)_{Y}$, but has $B-L=2$. This field has cosmological implications, and offers a new solution to the discrepancy between the observed Higgs mass and the NCG prediction.
description: v2: 5 pages, no figures, minor changes matching NJP published version
Development of next-generation sequencing-based sterility test
Creators: name: 岳建辉(Jianhui Yue)
Publisher: name: CNGB
Year: 2023
Subjects: Raw sequence reads
Multispecies
Industrial

description: The sterility testing methods described in pharmacopoeias require an incubation period of 14 days to obtain analysis results. An alternative method that can significantly shorten the detection time and improve the accuracy is in urgent need to meet the sterility testing requirements of regenerative medicine products with a short shelf life. In this study, we developed the next-generation sequencing-based sterility test (NGSST) based on sequencing and multiple displacement amplification. The NGSST can be finished within 48 hours with five steps including whole genome amplification, sequencing, alignment, sterility testing report, and microorganism identification. We use RPKM ratio to minorize the influence of environmental bacteria and determine its cutoff based AUC curve. The NGSST showed high sensitivity in reporting contaminates at 0.1 CFU in supernatant of biological product or 1 CFU in cell suspension. Furthermore, we identified microorganisms in 5 primary umbilical cord mesenchymal stem cell samples that were tested positive by BacT/ALERTR 3D. Overall, the NGSST can serve as a promising alternative for sterility testing of biological products.
Computation of solutions to linear difference and differential equations with a prescribed asymptotic behavior
Creators: name: Baumann, Hendrik
name: Hanschke, Thomas
Publisher: name: [Erscheinungsort nicht ermittelbar] : Springer International
Year: 2021
Subjects: subject: Asymptotic behavior of solutions of linear differential equations
subject: Kneser’s differential equation
subject: Linear systems of difference and differential equations
subject: Modified matrix-driven Jacobi–Perron algorithm
subject: Poincaré–Perron-type differential equation
subject: Dewey Decimal Classification::500 | Naturwissenschaften::510 | Mathematik
subject: Dewey Decimal Classification::600 | Technik::610 | Medizin, Gesundheit

description: Linear differential equations usually arise from mathematical modeling of physical experiments and real-world problems. In most applications these equations are linked to initial or boundary conditions. But sometimes the solution under consideration is characterized by its asymptotic behavior, which leads to the question how to infer from the asymptotic growth of a solution to its initial values. In this paper we show that under some mild conditions the initial values of the desired solution can be computed by means of a continuous-time analogue of a modified matrix continued fraction. For numerical applications we develop forward and backward algorithms which behave well in most situations. The topic is closely related to the theory of special functions and its extension to higher-dimensional problems. Our investigations result in a powerful tool for solving some classical mathematical problems. To demonstrate the efficiency of our method we apply it to Poincaré type and Kneser’s differential equation.
Moment expansion of polarized dust SED: a new path towards capturing the CMB $B$-modes with $\textit{LiteBIRD}$
Creators: name: Vacher, L.
name: Aumont, J.
name: Montier, L.
name: Azzoni, S.
name: Boulanger, F.
name: Remazeilles, M.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Characterizing the polarized dust emission from our Galaxy will be decisive for the quest for the Cosmic Microwave Background (CMB) primordial $B$-modes. The incomplete modelling of its potentially complex spectral properties could lead to biases in the CMB polarization analyses and to a spurious detection of the tensor-to-scalar ratio $r$. It is crucial for future surveys like the $LiteBIRD$ satellite, which aims at constraining the primordial signal leftover by Inflation with an accuracy on $r$ of the order 1e-3. Variations of the dust properties along and between lines of sight lead to distortions of the spectral energy distribution (SED) that can not be easily anticipated by standard component separation methods. This issue can be tackled with a moment expansion of the dust SED, an innovative parametrization method imposing minimal assumptions on the sky complexity. In this paper, we apply this formalism to the $B$-mode cross-angular power spectra computed from simulated $LiteBIRD$ polarization data at frequencies between 100 and 402 GHz, containing CMB, dust and instrumental noise. The spatial variation of the dust spectral parameters (spectral index $β$ and temperature $T$) in our simulations, lead to significant biases on $r$ if not properly taken into account. Performing the moment expansion in $β$, reduces the bias but do not lead to reliable enough estimates of $r$. We introduce for the first time the expansion of the cross-angular power spectra SED in $β$ and $T$, showing that, at the $LiteBIRD$ sensitivity, it is required to take into account the SED complexity due to temperature variations to prevent analysis biases on $r$. Thanks to this expansion and despite the existing correlations between some of the dust moments and the CMB signal, responsible for a rise of the error on $r$, we can measure an unbiased value of $r$ with an uncertainty of $σ(r)$=8.8e-4.
description: 23 pages,18 Figures, submitted to A&A
Functional characterization of cytochrome P450-derived epoxyeicosatrienoic acids in adipogenesis and obesity
Creators: name: Lee, Craig R.
name: Lih, Fred B.
name: Edin, Matthew L.
name: Schuck, Robert N.
name: DeGraff, Laura M.
name: Vendrov, Kimberly C.
name: Falck, John R.
name: Zeldin, Darryl C.
name: Hua, Kunjie
name: Zha, Weibin
name: Tomer, Kenneth B.
name: Jat, Jawahar Lal
name: Bradbury, J. Alyce
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Adipogenesis plays a critical role in the initiation and progression of obesity. Although cytochrome P450 (CYP)-derived epoxyeicosatrienoic acids (EETs) have emerged as a potential therapeutic target for cardiometabolic disease, the functional contribution of EETs to adipogenesis and the pathogenesis of obesity remain poorly understood. Our studies demonstrated that induction of adipogenesis in differentiated 3T3-L1 cells (in vitro) and obesity-associated adipose expansion in high-fat diet (HFD)-fed mice (in vivo) significantly dysregulate the CYP epoxygenase pathway and evoke a marked suppression of adipose-derived EET levels. Subsequent in vitro experiments demonstrated that exogenous EET analog administration elicits potent anti-adipogenic effects via inhibition of the early phase of adipogenesis. Furthermore, EET analog administration to mice significantly mitigated HFD-induced weight gain, adipose tissue expansion, pro-adipogenic gene expression, and glucose intolerance. Collectively, these findings suggest that suppression of EET bioavailability in adipose tissue is a key pathological consequence of obesity, and strategies that promote the protective effects of EETs in adipose tissue offer enormous therapeutic potential for obesity and its downstream pathological consequences.
Measurement catastrophe and ballistic spread of charge density with vanishing current
Creators: name: Zadnik, Lenart
name: Bocini, Saverio
name: Bidzhiev, Kemal
name: Fagotti, Maurizio
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Physics (quant-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: One of the features of many-body quantum systems with Hilbert-space fragmentation is the existence of stationary states manifesting quantum jamming. It was recently shown that these are "states with memory", in which, e.g., measuring a localised observable has everlasting macroscopic effects. We study such a measurement catastrophe with an example that stands out for its clarity. We show in particular that at late times the expectation value of a charge density becomes a nontrivial function of the ratio between distance and time notwithstanding the corresponding current approaching zero.
description: 29 pages, 10 figures
Global fits to b -> s ll data and signs for lepton non-universality
Creators: name: Hurth, T.
name: Mahmoudi, F.
name: Neshatpour, S.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: There are some slight tensions with the SM predictions within the latest LHCb measurements. Besides the known anomaly in one angular observable of the rare decay B -> K* mu+ mu-, another small discrepancy recently occurred. The ratio R_K = BR(B+ -> K+ mu+ mu-) / BR(B+ -> K+ e+ e-) in the low-q^2 region has been measured by LHCb showing a 2.6 sigma deviation from the SM prediction. In contrast to the anomaly in the rare decay B -> K* mu+ mu- which is affected by power corrections, the ratio R_K is theoretically rather clean. We analyse all the b -> s ll data with global fits and in particular explore the possibility of breaking of lepton universality. Possible cross-checks with an analysis of the inclusive B -> X_s l+ l- decay are also explored.
description: 15 pages, 11 figures. v2: references added, to appear in JHEP
Acyl-CoA synthetase 1 deficiency alters cardiolipin species and impairs mitochondrial function
Creators: name: Coleman, Rosalind A.
name: Murphy, Robert C.
name: Anderson, Ethan J.
name: Cooper, Daniel E.
name: Martin, Sarah A.
name: Grevengoed, Trisha J.
name: Katunga, Lalage
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Long-chain acyl-CoA synthetase 1 (ACSL1) contributes more than 90% of total cardiac ACSL activity, but its role in phospholipid synthesis has not been determined. Mice with an inducible knockout of ACSL1 (Acsl1T−/−) have impaired cardiac fatty acid oxidation and rely on glucose for ATP production. Because ACSL1 exhibited a strong substrate preference for linoleate, we investigated the composition of heart phospholipids. Acsl1T−/− hearts contained 83% less tetralinoleoyl-cardiolipin (CL), the major form present in control hearts. A stable knockdown of ACSL1 in H9c2 rat cardiomyocytes resulted in low incorporation of linoleate into CL and in diminished incorporation of palmitate and oleate into other phospholipids. Overexpression of ACSL1 in H9c2 and HEK-293 cells increased incorporation of linoleate into CL and other phospholipids. To determine whether increasing the content of linoleate in CL would improve mitochondrial respiratory function in Acsl1T−/− hearts, control and Acsl1T−/− mice were fed a high-linoleate diet; this diet normalized the amount of tetralinoleoyl-CL but did not improve respiratory function. Thus, ACSL1 is required for the normal composition of several phospholipid species in heart. Although ACSL1 determines the acyl-chain composition of heart CL, a high tetralinoleoyl-CL content may not be required for normal function.
Flavin containing monooxygenase 3 exerts broad effects on glucose and lipid metabolism and atherosclerosis
Creators: name: Wu, Judy
name: Charugundla, Sarada
name: Che, Nam
name: Lusis, Aldons J.
name: Shih, Diana M.
name: Vallim, Thomas
name: Bennett, Brian J.
name: Pan, Calvin
name: Qi, Hannah
name: Graham, Mark
name: Brown, J. Mark
name: Lee, Richard
name: Meng, Yonghong
name: Hazen, Stanley L.
name: Wang, Zeneng
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: We performed silencing and overexpression studies of flavin containing monooxygenase (FMO) 3 in hyperlipidemic mouse models to examine its effects on trimethylamine N-oxide (TMAO) levels and atherosclerosis. Knockdown of hepatic FMO3 in LDL receptor knockout mice using an antisense oligonucleotide resulted in decreased circulating TMAO levels and atherosclerosis. Surprisingly, we also observed significant decreases in hepatic lipids and in levels of plasma lipids, ketone bodies, glucose, and insulin. FMO3 overexpression in transgenic mice, on the other hand, increased hepatic and plasma lipids. Global gene expression analyses suggested that these effects of FMO3 on lipogenesis and gluconeogenesis may be mediated through the PPARα and Kruppel-like factor 15 pathways. In vivo and in vitro results were consistent with the concept that the effects were mediated directly by FMO3 rather than trimethylamine/TMAO; in particular, overexpression of FMO3 in the human hepatoma cell line, Hep3B, resulted in significantly increased glucose secretion and lipogenesis. Our results indicate a major role for FMO3 in modulating glucose and lipid homeostasis in vivo, and they suggest that pharmacologic inhibition of FMO3 to reduce TMAO levels would be confounded by metabolic interactions.
First genome edited poinsettias: targeted mutagenesis of flavonoid 3′-hydroxylase using CRISPR/Cas9 results in a colour shift
Creators: name: Nitarska, Daria
name: Boehm, Robert
name: Debener, Thomas
name: Lucaciu, Rares Calin
name: Halbwirth, Heidi
Publisher: name: Dordrecht [u.a.] : Springer Science + Business Media B.V
Year: 2021
Subjects: subject: Breeding
subject: Euphorbia pulcherrima
subject: Orange bract colour
subject: Pelargonidin
subject: Dewey Decimal Classification::600 | Technik::630 | Landwirtschaft, Veterinärmedizin
subject: Dewey Decimal Classification::600 | Technik::640 | Hauswirtschaft und Familienleben
subject: Dewey Decimal Classification::500 | Naturwissenschaften::570 | Biowissenschaften, Biologie
subject: Dewey Decimal Classification::500 | Naturwissenschaften::540 | Chemie

description: The CRISPR/Cas9 system is a remarkably promising tool for targeted gene mutagenesis, and becoming ever more popular for modification of ornamental plants. In this study we performed the knockout of flavonoid 3′-hydroxylase (F3′H) with application of CRISPR/Cas9 in the red flowering poinsettia (Euphorbia pulcherrima) cultivar ‘Christmas Eve’, in order to obtain plants with orange bract colour, which accumulate prevalently pelargonidin. F3′H is an enzyme that is necessary for formation of cyanidin type anthocyanins, which are responsible for the red colour of poinsettia bracts. Even though F3′H was not completely inactivated, the bract colour of transgenic plants changed from vivid red (RHS 45B) to vivid reddish orange (RHS 33A), and cyanidin levels decreased significantly compared with the wild type. In the genetically modified plants, an increased ratio of pelargonidin to cyanidin was observed. By cloning and expression of mutated proteins, the lack of F3′H activity was confirmed. This confirms that a loss of function mutation in the poinsettia F3′H gene is sufficient for obtaining poinsettia with orange bract colour. This is the first report of successful use of CRISPR/Cas9 for genome editing in poinsettia.
Transcriptomes of roots of crispr-PagGLR3.3ab
Creators: name: 韩潇(Xiao Han)
Publisher: name: CNGB
Year: 2023
Subjects: Raw sequence reads
Transcriptome or Gene expression
Monoisolate
Agricultural

description: Transcriptomic comparison of roots of crispr-PagGLR3.3ab and wild type
Genetic meta-analysis of 15,901 African Americans identifies variation in EXOC3L1 is associated with HDL concentration
Creators: name: North, Kari E.
name: Keating, Brendan J.
name: Drenos, Fotios
name: Tragante, Vinicius
name: Asselbergs, Folkert W.
name: Lanktree, Matthew B.
name: Wilson, James G.
name: Zhang, Guosheng
name: Duan, Qing
name: Guo, Yiran
name: Lange, Leslie A.
name: Cushman, Mary
name: Barnes, Michael R.
name: Reiner, Alex P.
name: Li, Yun
name: Elbers, Clara C.
name: Karczewski, Konrad J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Meta-analyses of European populations has successfully identified genetic variants in over 150 loci associated with lipid levels, but results from additional ethnicities remain limited. Previously, we reported two novel lipid loci identified in a sample of 7,657 African Americans using a gene-centric array including 50,000 SNPs in 2,100 candidate genes. Initial discovery and follow-up of signals with P < 10−5 in additional African American samples confirmed CD36 and ICAM1. Using an additional 8,244 African American female samples from the Women’s Health Initiative SNP Health Association Resource genome-wide association study dataset, we further examined the previous meta-analyses results by attempting to replicate 20 additional putative lipid signals with P < 10−4. Replication confirmed rs868213, located in a splice donor region of exocyst complex component 3-like 1 (EXOC3L1) as a novel signal for HDL (additive allelic effect β = 0.02; P = 1.4 × 10−8; meta-analyses of discovery and replication). EXOC3L1 is strongly expressed in vascular endothelium and forms part of the exocyst complex, a key facilitator of the trafficking of lipid receptors. Increasing sample sizes for genetic studies in nonEuropean populations will continue to improve our understanding of lipid metabolism.
Politics of Comedy
Creators: name: Jones, Calvert
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Social and Behavioral Sciences

description: Authoritarian regimes are hardly known for their comedic output, but humor can be a useful medium for political expression within repressive conditions due to its multivalent and ostensibly unserious nature. Comedians may plausibly deny responsibility for any political impact, even as their messaging goes viral. At the same time, authoritarian regimes are engaging in increasingly sophisticated social engineering, using state branding and other techniques to control narratives and project a positive global image. In this project we investigate how such diverse information sources may influence international public opinion toward a particularly closed authoritarian regime—Saudi Arabia. To do so, we combine fieldwork evidence from Saudi Arabia with media effects experiments. This study will be a follow-up and extension of a prior study involving a student sample in the US. The online experiment will randomly assign subjects to one of four groups: three treatment groups and one control. For each treatment, subjects read a short news article about Saudi Arabia, followed by a video that aligns with the article’s topic. In Comedy treatment group, respondents read a short article about a political satire video, “No Woman, No Drive,” that rapidly gained global popularity, followed by a presentation of the video itself. The article and the video show how a Saudi comedian spoofs the driving ban imposed on women in that country. In the Activist treatment group, respondents read a traditional news story and then watch a video clip on the female activists who defied the driving ban, with the video showing selfies of women driving. In the Tourism treatment group, respondents view a promotional video with an English-speaking voiceover created by the Saudi government to accompany the decision to offer tourist visas for the first time. In keeping with broader state-branding efforts that we uncovered in our fieldwork, this treatment aimed to project a positive and inviting image of the country, with no mention of politics. All three videos went viral and were widely viewed both inside and outside Saudi Arabia. The fourth group of respondents form the control group and do not read any article or view any video before the dependent variables are assessed. This study will also include an extension to assess the effects of a negative “News Update” on favorability ratings, occurring after the initial treatments and collection of initial DVs (see below).
Dip coating of thin polymer optical fibers
Creators: name: Evertz, Andreas
name: Schrein, Daniel
name: Olsen, Ejvind
name: Hoffmann, Gerd-Albert
name: Overmeyer, Ludger
Publisher: name: Orlando, Fla. : Academic Press
Year: 2021
Subjects: subject: Continuous dip coating
subject: Extruded optical fibers
subject: Polymer optical fiber
subject: Dewey Decimal Classification::000 | Allgemeines, Wissenschaft::000 | Informatik, Wissen, Systeme::004 | Informatik

description: To produce polymer optical fibers in research environments, a flexible cladding material-application process is required. Further, to functionalize the waveguide, the fiber core-production step needs to be separated from the cladding application, contrasting conventional polymer optical fiber production processes. In this study, we developed a solution using continuous dip-coating technique to apply cladding material onto previously extruded polymer optical fiber cores with diameters as low as 16 µm. The process was designed considering the fluid-dynamic behavior of the cladding material and fiber to achieve a radially symmetric coating thickness. We examined UV-curable resin as cladding and polymethyl-methacrylate (PMMA)-based extruded optical fibers with diameters of up to 16 µm. The proposed method helped continuously coat optical fiber cores with cladding material with diameters in the range of 1 mm and achieve the lowest optical attenuation (<3 dB/m).
The Pantheon+ Analysis: SuperCal-Fragilistic Cross Calibration, Retrained SALT2 Light Curve Model, and Calibration Systematic Uncertainty
Creators: name: Brout, Dillon
name: Taylor, Georgie
name: Scolnic, Dan
name: Wood, Charlotte M.
name: Rose, Benjamin M.
name: Vincenzi, Maria
name: Dwomoh, Arianna
name: Lidman, Christopher
name: Riess, Adam
name: Ali, Noor
name: Qu, Helen
name: Dai, Mi
Publisher: name: arXiv
Year: 2021
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: We present here a re-calibration of the photometric systems used in the Pantheon+ sample of Type Ia supernovae (SNe Ia) including those used for the SH0ES distance-ladder measurement of H$_0$. We utilize the large and uniform sky coverage of the public Pan-STARRS stellar photometry catalog to cross-calibrate against tertiary standards released by individual SN Ia surveys. The most significant updates over the `SuperCal' cross-calibration used for the previous Pantheon and SH0ES analyses are: 1) expansion of the number of photometric systems (now 25) and filters (now 105), 2) solving for all filter offsets in all systems simultaneously in order to produce a calibration uncertainty covariance matrix that can be used in cosmological-model constraints, and 3) accounting for the change in the fundamental flux calibration of the HST CALSPEC standards from previous versions on the order of $1.5\%$ over a $Δλ$ of 4000~Å. The re-calibration of samples used for light-curve fitting has historically been decoupled from the retraining of the light-curve model. Here, we are able to retrain the SALT2 model using this new calibration and find the change in the model coupled with the change to the calibration of the light-curves themselves causes a net distance modulus change ($dμ/dz$) of 0.04 mag over the redshift range $0
description: Published in ApJ. Comments welcome. Papers and data release here PantheonPlusSH0ES.github.io
Winter Daytime Warming and Shift in Summer Monsoon Increase Plant Cover and Net CO2 Uptake in a Central Tibetan Alpine Steppe Ecosystem
Creators: name: Nieberding, Felix
name: Wille, Christian
name: Ma, Yaoming
name: Wang, Yuyang
name: Maurischat, Philipp
name: Lehnert, Lukas
name: Sachs, Torsten
Publisher: name: Hoboken, NJ : Wiley
Year: 2021
Subjects: subject: alpine steppe
subject: carbon dioxide
subject: climate change
subject: eddy covariance
subject: plant cover
subject: tibetan plateau
subject: Dewey Decimal Classification::500 | Naturwissenschaften::550 | Geowissenschaften

description: Over the past decades, human-induced climate change has led to a widespread wetting and warming of the Tibetan Plateau (TP), affecting both ecosystems and the carbon cycling therein. Whether the previously observed climate changes stimulate carbon uptake via enhanced photosynthesis or carbon loss via enhanced soil respiration remains unclear. Here we present 14 years of observations of carbon fluxes, meteorological variables and remotely sensed plant cover estimations from a central Tibetan alpine steppe ecosystem at Nam Co, the third largest lake on the TP. Using modified Mann-Kendall trend tests, we found a significant increasing daily net carbon uptake of 0.5 g C m−2 decade−1, which can be explained by a widespread greening at the southern shore of lake Nam Co. The Plateau-wide changes in temperature and precipitation are locally expressed as an increasing diurnal temperature range during winter, higher water availability during spring, higher cloud cover during early summer and less water availability during late summer. While these changes differ over the course of the year, they tend to stimulate plant growth more than microbial respiration, leading to an increased carbon uptake during all seasons. This study indicates that during the 14 years study period, a higher amplitude in winter temperatures and an earlier summer monsoon promote carbon uptake in a central Tibetan alpine steppe ecosystem.
Selective suppression of adipose tissue apoE expression impacts systemic metabolic phenotype and adipose tissue inflammation
Creators: name: Mazzone, Theodore
name: Huang, Zhi H.
name: Maeda, Nobuyo
name: Getz, Godfrey S.
name: Reardon, Catherine A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: apoE is a multi-functional protein expressed in several cell types and in several organs. It is highly expressed in adipose tissue, where it is important for modulating adipocyte lipid flux and gene expression in isolated adipocytes. In order to investigate a potential systemic role for apoE that is produced in adipose tissue, mice were generated with selective suppression of adipose tissue apoE expression and normal circulating apoE levels. These mice had less adipose tissue with smaller adipocytes containing fewer lipids, but no change in adipocyte number compared with control mice. Adipocyte TG synthesis in the presence of apoE-containing VLDL was markedly impaired. Adipocyte caveolin and leptin gene expression were reduced, but adiponectin, PGC-1, and CPT-1 gene expression were increased. Mice with selective suppression of adipose tissue apoE had lower fasting lipid, insulin, and glucose levels, and glucose and insulin tolerance tests were consistent with increased insulin sensitivity. Lipid storage in muscle, heart, and liver was significantly reduced. Adipose tissue macrophage inflammatory activation was markedly diminished with suppression of adipose tissue apoE expression. Our results establish a novel effect of adipose tissue apoE expression, distinct from circulating apoE, on systemic substrate metabolism and adipose tissue inflammatory state.
Qubit noise deconvolution
Creators: name: Mangini, Stefano
name: Maccone, Lorenzo
name: Macchiavello, Chiara
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We present a noise deconvolution technique to remove a wide class of noises when performing arbitrary measurements on qubit systems. In particular, we derive the inverse map of the most common single qubit noisy channels and exploit it at the data processing step to obtain noise-free estimates of observables evaluated on a qubit system subject to known noise. We illustrate a self-consistency check to ensure that the noise characterization is accurate providing simulation results for the deconvolution of a generic Pauli channel, as well as experimental evidence of the deconvolution of decoherence noise occurring on Rigetti quantum hardware.
description: 17 pages, 3 figures. Updated version taking into account the referee's comments. Added references and minor changes
Adenovirus metagenomic next-generation sequencing
Creators: name: 赖娟(Juan Lai)
Publisher: name: CNGB
Year: 2023
Subjects: Metagenome
Metagenomic assembly
Multispecies

description: We detected the adenovirus infection in nasopharyngeal swab samples from patients with respiratory tract infection. mNGS was performed on NextSeq 550 and GenoLab M sequencing platforms to study viral phylogenetics and recombination.
Impacts of Drying and Rewetting on the Radiocarbon Signature of Respired CO2 and Implications for Incubating Archived Soils
Creators: name: Beem‐Miller, Jeffrey
name: Schrumpf, Marion
name: Hoyt, Alison M.
name: Guggenberger, Georg
name: Trumbore, Susan
Publisher: name: Hoboken, NJ : Wiley
Year: 2021
Subjects: subject: climate change
subject: incubation
subject: radiocarbon
subject: soil archives
subject: soil carbon
subject: soil carbon modeling
subject: Dewey Decimal Classification::500 | Naturwissenschaften::550 | Geowissenschaften

description: The radiocarbon signature of respired CO2 (∆14C-CO2) measured in laboratory soil incubations integrates contributions from soil carbon pools with a wide range of ages, making it a powerful model constraint. Incubating archived soils enriched by “bomb-C” from mid-20th century nuclear weapons testing would be even more powerful as it would enable us to trace this pulse over time. However, air-drying and subsequent rewetting of archived soils, as well as storage duration, may alter the relative contribution to respiration from soil carbon pools with different cycling rates. We designed three experiments to assess air-drying and rewetting effects on ∆14C-CO2 with constant storage duration (Experiment 1), without storage (Experiment 2), and with variable storage duration (Experiment 3). We found that air-drying and rewetting led to small but significant (α < 0.05) shifts in ∆14C-CO2 relative to undried controls in all experiments, with grassland soils responding more strongly than forest soils. Storage duration (4–14 y) did not have a substantial effect. Mean differences (95% CIs) for experiments 1, 2, and 3 were: 23.3‰ (±6.6), 19.6‰ (±10.3), and 29.3‰ (±29.1) for grassland soils, versus −11.6‰ (±4.1), 12.7‰ (±8.5), and −24.2‰ (±13.2) for forest soils. Our results indicate that air-drying and rewetting soils mobilizes a slightly older pool of carbon that would otherwise be inaccessible to microbes, an effect that persists throughout the incubation. However, as the bias in ∆14C-CO2 from air-drying and rewetting is small, measuring ∆14C-CO2 in incubations of archived soils appears to be a promising technique for constraining soil carbon models.
Maldoror et moi
Creators: name: Saliou, Kevin
Publisher: name: Classiques Garnier
Year: 2022
Subjects: subject: Maldoror
subject: Ducasse
subject: Lautréamont
subject: Bande dessinée
subject: Compte rendu
subject: Broyart
subject: Richard
subject: Influence
subject: Tueur.
subject: Maldoror
subject: Ducasse
subject: Lautréamont
subject: Graphic novel
subject: Review
subject: Broyart
subject: Richard
subject: Influence
subject: Killer.

description: Compte rendu de la bande dessinée parue en 2022 et mettant en scène un adolescent torturé fasciné par Les Chants de Maldoror.
description: A review of the graphic novel published in 2022 that features a troubled teenager fascinated by Les Chants de Maldoror.