cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
A new species of Xinpusaurus (Reptilia, Thalattosauria) from the Ladinian (Middle Triassic) of Xingyi, Guizhou, southwestern China
Creators: name: Li, Zhi-Guang
name: Jiang, Da-Yong
name: Rieppel, Olivier
name: Motani, Ryosuke
name: Tintori, Andrea
name: Sun, Zuo-Yu
name: Ji, Cheng
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Developmental Biology
subject: Cancer
subject: Science Policy
subject: Plant Biology

description: SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Li, Z.-G., D.-Y. Jiang, O. Rieppel, R. Motani, A. Tintori, Z.-Y. Sun, and C. Ji. 2016. A new species of Xinpusaurus (Reptilia, Thalattosauria) from the Ladinian (Middle Triassic) of Xingyi, Guizhou, southwestern China. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1218340.
Geometric Hamilton-Jacobi theory for systems with external forces
Creators: name: de León, Manuel
name: Lainz, Manuel
name: López-Gordón, Asier
Publisher: name: arXiv
Year: 2021
Subjects: subject: Mathematical Physics (math-ph)
subject: Symplectic Geometry (math.SG)
subject: Classical Physics (physics.class-ph)
subject: FOS: Physical sciences
subject: FOS: Mathematics
subject: 70H20, 70H33, 70F40, 53Z05

description: In this paper, we develop a Hamilton-Jacobi theory for forced Hamiltonian and Lagrangian systems. We study the complete solutions, particularize for Rayleigh systems and present some examples. Additionally, we present a method for the reduction and reconstruction of the Hamilton-Jacobi problem for forced Hamiltonian systems with symmetry. Furthermore, we consider the reduction of the Hamilton-Jacobi problem for a Čaplygin system to the Hamilton-Jacobi problem for a forced Lagrangian system.
description: 39 pages, submitted to J. Math. Phys
Analytic Form of a Two-Dimensional Critical Distribution
Creators: name: Bramwell, Steven T.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: This paper explores the possibility of establishing an analytic form of the distribution of the order parameter fluctuations in a two-dimensional critical spin wave model, or width fluctuations of a two dimensional Edwards-Wilkinson interface. It is shown that the characteristic function of the distribution can be expressed exactly as a Gamma function quotient, while a Charlier series, using the convolution of two Gumbel distributions as the kernel, converges to the exact result over a restricted domain. These results can also be extended to calculate the temperature dependence of the distribution and give an insight into the origin of Gumbel-like distributions in steady-state and equilibrium quantities that are not extreme values.
description: 6 pages, 3 figures
Bayesian structure learning and sampling of Bayesian networks with the R package BiDAG
Creators: name: Suter, Polina
name: Kuipers, Jack
name: Moffa, Giusi
name: Beerenwinkel, Niko
Publisher: name: ETH Zurich
Year: 2021
Subjects: Computation (stat.CO)
Machine Learning (stat.ML)
FOS: Computer and information sciences
Bayesian networks
Dynamic Bayesian networks
Structure learning
Bayesian inference
MCMC
R.

description: The R package BiDAG implements Markov chain Monte Carlo (MCMC) methods for structure learning and sampling of Bayesian networks. The package includes tools to search for a maximum a posteriori (MAP) graph and to sample graphs from the posterior distribution given the data. A new hybrid approach to structure learning enables inference in large graphs. In the first step, we define a reduced search space by means of the PC algorithm or based on prior knowledge. In the second step, an iterative order MCMC scheme proceeds to optimize within the restricted search space and estimate the MAP graph. Sampling from the posterior distribution is implemented using either order or partition MCMC. The models and algorithms can handle both discrete and continuous data. The BiDAG package also provides an implementation of MCMC schemes for structure learning and sampling of dynamic Bayesian networks.
description: arXiv
Validation of a DNA methylation reference panel for the estimation of nucleated cells types in cord blood
Creators: name: Cardenas, Andres
name: Allard, Catherine
name: Doyon, Myriam
name: E. Andres Houseman
name: Bakulski, Kelly M.
name: Perron, Patrice
name: Bouchard, Luigi
name: Marie-France Hivert
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Hematology

description: Cord blood is widely used as surrogate tissue in epigenome-wide association studies of prenatal conditions. Cell type composition variation across samples can be an important confounder of epigenome-wide association studies in blood that constitute a mixture of cells. We evaluated a newly developed cord blood reference panel to impute cell type composition from DNA methylation levels, including nucleated red blood cells (nRBCs). We estimated cell type composition from 154 unique cord blood samples with available DNA methylation data as well as direct measurements of nucleated cell types. We observed high correlations between the estimated and measured composition for nRBCs (r = 0.92, R2 = 0.85), lymphocytes (r = 0.77, R2 = 0.58), and granulocytes (r = 0.72, R2 = 0.52), and a moderate correlation for monocytes (r = 0.51, R2 = 0.25) as well as relatively low root mean square errors from the residuals ranging from 1.4 to 5.4%. These results validate the use of the cord blood reference panel and highlight its utility and limitations for epidemiological studies.
Does international “offshoring” of environmental impacts reflect consumer NIMBYism?
Creators: name: Presberger, David
name: Kolcava, Dennis
name: Bernauer, Thomas
Publisher: name: ETH Zurich
Year: 2022

description: Consumption of imported goods whose production affects the natural environment abroad implies international ``insourcing'' of consumer benefits and ``outsourcing'' of environmental impacts. We examine to what extent consumer choices driving such ecological outsourcing in the aggregate, often from the Global North to the Global South, are motivated by environmental NIMBY (not in my backyard) preferences. The analysis relies on an original survey-embedded choice experiment in three large, high-income economies (Germany, Japan, United States, total N=7,494). We find considerable support for environmental NIMBYism in consumer decisions. Whereas consumers generally tend to prefer domestically sourced products, this home bias becomes weaker with increasing environmental impacts of production. One important implication of this finding is that policy makers should address potential unintended side-effects of more stringent eco-labeling requirements. The latter may in fact contribute to further ecological outsourcing by making both information on environmental impacts and product provenance more explicit.
description: OSF Preprints
Experimental study on thermo-physical and rheological properties of stable and green reduced graphene oxide nanofluids: Hydrothermal assisted technique
Creators: name: Rad Sadri
name: K. Zangeneh Kamali
name: M. Hosseini
name: Nashrul Zubir
name: S. N. Kazi
name: Goodarz Ahmadi
name: Mahidzal Dahari
name: N. M. Huang
name: A. M. Golsheikh
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified

description: In this study a dehydration hydrothermal technique has been used to introduce a simple, environmentally friendly and facile method for manufacturing highly dispersed reduced graphene oxide for improving the thermo-physical and rheological properties of heat transfer liquids. The hydrothermal reduction of graphene oxide was verified by various characterizations methods such as UV–visible absorption spectroscopy, Zeta potential, Raman spectroscopy, X-ray photoemission spectroscopy, X-ray diffraction, Fourier transform infrared spectroscopy, and transmission electron microscopy. A thorough investigation was conducted on the thermo-physical properties of reduced graphene oxide at concentrations of 0.02, 0.04, 0.06, and 0.08 wt% under different temperatures. Significant improvements in electrical and thermal conductivity were obtained by adding a small amount of hydrothermal-assisted reduced graphene oxide (h-rGO) in the suspension. The viscosity and density remained relatively unchanged with the increase of concentrations where the pH was maintained within the desirable value, despite the fact that no additive was used during the reduction process. It is noteworthy to highlight that the h-rGO aqueous suspensions have shown Newtonian behavior. Results indicated that the h-rGO could be employed as a promising additive for conventional heat transfer liquids for different thermal applications.
Joint copy number and mutation phylogeny reconstruction from single-cell amplicon sequencing data
Creators: name: Sollier, Etienne
name: Kuipers, Jack
name: Takahashi, Koichi
name: Beerenwinkel, Niko
name: Jahn, Katharina
Publisher: name: ETH Zurich
Year: 2022

description: Reconstructing the history of somatic DNA alterations that occurred in a tumour can help understand its evolution and predict its resistance to treatment. Single-cell DNA sequencing (scDNAseq) can be used to investigate clonal heterogeneity and to inform phylogeny reconstruction. However, existing phylogenetic methods for scDNAseq data are designed either for point mutations or for large copy number variations, but not for both types of events simultaneously. Here, we develop COMPASS, a computational method for inferring the joint phylogeny of mutations and copy number alterations from targeted scDNAseq data. We evaluate COMPASS on simulated data and show that it outperforms existing methods. We apply COMPASS to a large cohort of 123 patients with acute myeloid leukemia (AML) and detect copy number alterations, including subclonal ones, which are in agreement with and extend current knowledge of AML development. We further used bulk sequencing and SNP array data to orthogonally validate our findings.
description: bioRxiv
Buffer gas cooling of ions in time-dependent traps using ultracold atoms
Creators: name: Trimby, E.
name: Hirzler, H.
name: Fürst, H.
name: Safavi-Naini, A.
name: Gerritsma, R.
name: Lous, R. S.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: For exploration of quantum effects with hybrid atom-ion systems, reaching ultracold temperatures is the major limiting factor. In this work, we present results on numerical simulations of trapped ion buffer gas cooling using an ultracold atomic gas in a large number of experimentally realistic scenarios. We explore the suppression of micromotion-induced heating effects through optimization of trap parameters for various radio-frequency (rf) traps and rf driving schemes including linear and octupole traps, digital Paul traps, rotating traps and hybrid optical/rf traps. We find that very similar ion energies can be reached in all of them even when considering experimental imperfections that cause so-called excess micromotion. Moreover we look into a quantum description of the system and show that quantum mechanics cannot save the ion from micromotion-induced heating in an atom-ion collision. The results suggest that buffer gas cooling can be used to reach close to the ion's groundstate of motion and is even competitive when compared to some sub-Doppler cooling techniques such as Sisyphus cooling. Thus, buffer gas cooling is a viable alternative for ions that are not amenable to laser cooling, a result that may be of interest for studies into quantum chemistry and precision spectroscopy.
Validation of a DNA Methylation Reference Panel for the Estimation of Nucleated Cells Types in Cord Blood
Creators: name: Cardenas, Andres
name: Allard, Catherine
name: Doyon, Myriam
name: E. Andres Houseman
name: Bakulski, Kelly M.
name: Perron, Patrice
name: Bouchard, Luigi
name: Marie-France Hivert
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Hematology

description: Cord blood is widely used as surrogate tissue in epigenome-wide association studies of prenatal conditions. Cell type composition variation across samples can be an important confounder of epigenome-wide association studies in blood that constitute a mixture of cells. We evaluated a newly developed cord blood reference panel to impute cell type composition from DNA methylation levels, including nucleated red blood cells (nRBCs). We estimated cell type composition from 154 unique cord blood samples with available DNA methylation data as well as direct measurements of nucleated cell types. We observed high correlations between the estimated and measured composition for nRBCs (r = 0.92, R2 = 0.85), lymphocytes (r = 0.77, R2 = 0.58), and granulocytes (r = 0.72, R2 = 0.52), and a moderate correlation for monocytes (r = 0.51, R2 = 0.25) as well as relatively low root mean square errors from the residuals ranging from 1.4 to 5.4%. These results validate the use of the cord blood reference panel and highlight its utility and limitations for epidemiological studies.
SpyHammer: Using RowHammer to Remotely Spy on Temperature
Creators: name: Orosa, Lois
name: Rührmair, Ulrich
name: Yağlikçi, A. Giray
name: Luo, Haocong
name: Olgun, Ataberk
name: Jattke, Patrick
name: Patel, Minesh
name: Kim, Jeremie
name: Razavi, Kaveh
name: Mutlu, Onur
Publisher: name: ETH Zurich
Year: 2022
Subjects: Cryptography and Security (cs.CR)
Hardware Architecture (cs.AR)
FOS: Computer and information sciences

description: RowHammer is a DRAM vulnerability that can cause bit errors in a victim DRAM row by just accessing its neighboring DRAM rows at a high-enough rate. Recent studies demonstrate that new DRAM devices are becoming increasingly more vulnerable to RowHammer, and many works demonstrate system-level attacks for privilege escalation or information leakage. In this work, we leverage two key observations about RowHammer characteristics to spy on DRAM temperature: 1) RowHammer-induced bit error rate consistently increases (or decreases) as the temperature increases, and 2) some DRAM cells that are vulnerable to RowHammer cause bit errors only at a particular temperature. Based on these observations, we propose a new RowHammer attack, called SpyHammer, that spies on the temperature of critical systems such as industrial production lines, vehicles, and medical systems. SpyHammer is the first practical attack that can spy on DRAM temperature. SpyHammer can spy on absolute temperature with an error of less than 2.5 °C at the 90th percentile of tested temperature points, for 12 real DRAM modules from 4 main manufacturers.
description: arXiv
Anomalies of Cosmic Anisotropy from Holographic Universality of Great-Circle Variance
Creators: name: Selub, Nathaniel
name: Wehlen, Frederick
name: Hogan, Craig
name: Meyer, Stephan S.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We examine all-sky cosmic microwave background (CMB) temperature maps on large angular scales to compare their consistency with two scenarios: the standard inflationary quantum picture, and a distribution constrained to have a universal variance of primordial curvature perturbations on great circles. The latter symmetry is not a property of standard quantum inflation, but may be a symmetry of holographic models with causal quantum coherence on null surfaces. Since the variation of great-circle variance is dominated by the largest angular scale modes, in the latter case the amplitude and direction of the unobserved intrinsic dipole (that is, the $\ell=1$ harmonics) can be estimated from measured $\ell = 2, 3$ harmonics by minimizing the variance of great-circle variances including only $\ell =1, 2, 3$ modes. It is found that including the estimated intrinsic dipole leads to a nearly-null angular correlation function over a wide range of angles, in agreement with a null anti-hemispherical symmetry independently motivated by holographic causal arguments, but highly anomalous in standard cosmology. Simulations are used here to show that simultaneously imposing the constraints of universal great-circle variance and the vanishing of the angular correlation function over a wide range of angles tends to require patterns that are unusual in the standard picture, such as anomalously high sectorality of the $\ell = 3$ components, and a close alignment of principal axes of $\ell=2$ and $\ell = 3$ components, that have been previously noted on the actual sky. The precision of these results appears to be primarily limited by errors introduced by models of Galactic foregrounds.
Reacting multi-component fluids -- regular solutions in Lorentz spaces
Creators: name: Mucha, Piotr B.
name: Piasecki, Tomasz
Publisher: name: arXiv
Year: 2021
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: 76N10, 35Q30

description: The paper deals with analysis of a model of a multi-component fluid admitting chemical reactions. The flow is considered in the incompressible regime. The main result shows global existence of regular solutions under assumption of suitable smallness conditions. In order to control the solutions a special structure condition on the derivatives of chemical production functions determining the reactions is required. The existence is shown in a new critical functional framework of Lorentz spaces of type $L_{p,r}(0,T;L_q)$, which allows to control the integral $\int_0^\infty \|\nabla u(t)\|_{\infty} dt$.
DRAM Bender: An Extensible and Versatile FPGA-based Infrastructure to Easily Test State-of-the-art DRAM Chips
Creators: name: Olgun, Ataberk
name: Hassan, Hasan
name: Yağlıkçı, A. Giray
name: Tuğrul, Yahya Can
name: Orosa, Lois
name: Luo, Haocong
name: Patel, Minesh
name: Ergin, Oğuz
name: Mutlu, Onur
Publisher: name: ETH Zurich
Year: 2022
Subjects: Hardware Architecture (cs.AR)
Cryptography and Security (cs.CR)
FOS: Computer and information sciences
DRAM
Security
Reliability
Performance
Energy
Memory systems
FPGA
Open source
Testing

description: To understand and improve DRAM performance, reliability, security and energy efficiency, prior works study characteristics of commodity DRAM chips. Unfortunately, state-of-the-art open source infrastructures capable of conducting such studies are obsolete, poorly supported, or difficult to use, or their inflexibility limit the types of studies they can conduct. We propose DRAM Bender, a new FPGA-based infrastructure that enables experimental studies on state-of-the-art DRAM chips. DRAM Bender offers three key features at the same time. First, DRAM Bender enables directly interfacing with a DRAM chip through its low-level interface. This allows users to issue DRAM commands in arbitrary order and with finer-grained time intervals compared to other open source infrastructures. Second, DRAM Bender exposes easy-to-use C++ and Python programming interfaces, allowing users to quickly and easily develop different types of DRAM experiments. Third, DRAM Bender is easily extensible. The modular design of DRAM Bender allows extending it to (i) support existing and emerging DRAM interfaces, and (ii) run on new commercial or custom FPGA boards with little effort. To demonstrate that DRAM Bender is a versatile infrastructure, we conduct three case studies, two of which lead to new observations about the DRAM RowHammer vulnerability. In particular, we show that data patterns supported by DRAM Bender uncovers a larger set of bit-flips on a victim row compared to the data patterns commonly used by prior work. We demonstrate the extensibility of DRAM Bender by implementing it on five different FPGAs with DDR4 and DDR3 support. DRAM Bender is freely and openly available at https://github.com/CMU-SAFARI/DRAM-Bender.
description: arXiv
Progression of hypertension and kidney disease in aging fawn-hooded rats is mediated by enhanced influence of renin–angiotensin system and suppression of nitric oxide system and epoxyeicosanoids
Creators: name: Šárka Doleželová
name: Šárka Jíchová
name: Husková, Zuzana
name: Alžběta Vojtíšková
name: Kujal, Petr
name: Hošková, Lenka
name: Kautzner, Josef
name: Sadowski, Janusz
name: Luděk Červenka
name: Kopkan, Libor
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: Pharmacology
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Marine Biology
subject: Computational Biology

description: The fawn-hooded hypertensive (FHH) rat serves as a genetic model of spontaneous hypertension associated with glomerular hyperfiltration and proteinuria. However, the knowledge of the natural course of hypertension and kidney disease in FHH rats remains fragmentary and the underlying pathophysiological mechanisms are unclear. In this study, over the animals’ lifetime, we followed the survival rate, blood pressure (telemetry), indices of kidney damage, the activity of renin–angiotensin (RAS) and nitric oxide (NO) systems, and CYP450-epoxygenase products (EETs). Compared to normotensive controls, no elevation of plasma and renal RAS was observed in prehypertensive and hypertensive FHH rats; however, RAS inhibition significantly reduced systolic blood pressure (137 ± 9 to 116 ± 8, and 159 ± 8 to 126 ± 4 mmHg, respectively) and proteinuria (62 ± 2 to 37 ± 3, and 132 ± 8 to 87 ± 5 mg/day, respectively). Moreover, pharmacological RAS inhibition reduced angiotensin (ANG) II and increased ANG 1–7 in the kidney and thereby may have delayed the progression of kidney disease. Furthermore, renal NO and EETs declined in the aging FHH rats but not in the control strain. The present results, especially the demonstration of exaggerated vascular responsiveness to ANG II, indicate that RAS may contribute to the development of hypertension and kidney disease in FHH rats. The activity of factors opposing the development of hypertension and protecting the kidney declined with age in this model. Therefore, therapeutic enhancement of this activity besides RAS inhibition could be attempted in the therapy of human hypertension associated with kidney disease.
Fundamentally Understanding and Solving RowHammer
Creators: name: Mutlu, Onur
name: Olgun, Ataberk
name: Yağlıkçı, A. Giray
Publisher: name: ETH Zurich
Year: 2022
Subjects: Cryptography and Security (cs.CR)
Hardware Architecture (cs.AR)
FOS: Computer and information sciences
DRAM
Security
Vulnerability
Technology scaling
Reliability
Safety
Errors
Memory systems
Fault attacks
RowHammer

description: We provide an overview of recent developments and future directions in the RowHammer vulnerability that plagues modern DRAM (Dynamic Random Memory Access) chips, which are used in almost all computing systems as main memory. RowHammer is the phenomenon in which repeatedly accessing a row in a real DRAM chip causes bitflips (i.e., data corruption) in physically nearby rows. This phenomenon leads to a serious and widespread system security vulnerability, as many works since the original RowHammer paper in 2014 have shown. Recent analysis of the RowHammer phenomenon reveals that the problem is getting much worse as DRAM technology scaling continues: newer DRAM chips are fundamentally more vulnerable to RowHammer at the device and circuit levels. Deeper analysis of RowHammer shows that there are many dimensions to the problem as the vulnerability is sensitive to many variables, including environmental conditions (temperature \& voltage), process variation, stored data patterns, as well as memory access patterns and memory control policies. As such, it has proven difficult to devise fully-secure and very efficient (i.e., low-overhead in performance, energy, area) protection mechanisms against RowHammer and attempts made by DRAM manufacturers have been shown to lack security guarantees. After reviewing various recent developments in exploiting, understanding, and mitigating RowHammer, we discuss future directions that we believe are critical for solving the RowHammer problem. We argue for two major directions to amplify research and development efforts in: 1) building a much deeper understanding of the problem and its many dimensions, in both cutting-edge DRAM chips and computing systems deployed in the field, and 2) the design and development of extremely efficient and fully-secure solutions via system-memory cooperation.
description: arXiv
One-loop same helicity YM amplitudes from BG currents
Creators: name: Chattopadhyay, Pratik
name: Krasnov, Kirill
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We propose and prove a new formula for the one-loop all same helicity Yang-Mills amplitudes. These amplitudes are seen to arise as a sum of products of two tree-level Berends-Giele currents connected by an effective propagator. To make sense of the propagators one needs to introduce the so-called region, or dual momenta. The formula is proven by observing that it readily implies the correct collinear limit properties. The only non-trivial part of the proof is establishing that our formula for the amplitude is invariant under shifts of the region momenta.
description: 26 pages
Experimental Study on Thermo-Physical and Rheological Properties of Highly Stable and Green Reduced Graphene Oxide Nanofluids: Hydrothermal Assisted Technique
Creators: name: Rad Sadri
name: K. Zangeneh Kamali
name: M. Hosseini
name: Nashrul Zubir
name: S. N. Kazi
name: Goodarz Ahmadi
name: Mahidzal Dahari
name: N. M. Huang
name: Moradi, Amir
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine

description: In this research a dehydration hydrothermal technique has been used to introduce a simple, environmentally friendly and facile method for manufacturing highly dispersed reduced graphene oxide for improving the thermo-physical and rheological properties of heat transfer liquids. The hydrothermal reduction of graphene oxide was verified by various characterizations methods such as UV-visible absorption spectroscopy, Zeta potential, Raman spectroscopy, X-ray photoemission spectroscopy, X-ray Diffraction, Fourier transform infrared spectroscopy and Scanning electron microscopy. A thorough investigation was conducted on the thermo-physical properties of reduced graphene oxide at concentrations of 0.02, 0.04, 0.06 and 0.08 wt% under different temperatures. Significant Improvements on electrical and thermal conductivity were obtained by adding a small amount of hydrothermal-assisted reduced graphene oxide (h-rGO) in the suspension. The viscosity and density remained relatively unchanged with the increase of concentrations where the pH was maintained within the desirable value, despite the fact that no additive was used during the reduction process. It is noteworthy to highlight that the h-rGO aqueous suspensions have shown Newtonian behavior. Results indicated that the h-rGO could be employed as promising additive for conventional heat transfer liquids for different thermal applications.
Dynamics of targeted ransomware negotiation
Creators: name: Ryan, Pierce
name: Fokker, John
name: Healy, Sorcha
name: Amann, Andreas
Publisher: name: arXiv
Year: 2021
Subjects: subject: Dynamical Systems (math.DS)
subject: Computer Science and Game Theory (cs.GT)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: In this paper, we consider how the development of targeted ransomware has affected the dynamics of ransomware negotiations to better understand how to respond to ransomware attacks. We construct a model of ransomware negotiations as an asymmetric non-cooperative two-player game. In particular, our model considers the investments that a malicious actor must make in order to conduct a successful targeted ransomware attack. We demonstrate how imperfect information is a crucial feature for replicating observed real-world behaviour. Furthermore, we present optimal strategies for both the malicious actor and the target, and demonstrate how imperfect information results in a non-trivial optimal strategy for the malicious actor.
Synthesis, characterization, and crystal structure of macrocyclic nickel(II) complexes bearing a,e-cis-1,4-chdc and e,e-trans-1,4-chdc (chdc = cyclohexanedicarboxylate) ligands
Creators: name: Shin, Hyang Jin
name: Kim, Ju Chang
name: Lough, Alan J.
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences

description: Two macrocyclic nickel(II) complexes, [Ni(L)(a,e-cis-1,4-chdc)]·4H2O (1) and [{Ni(L)(H2O)}2(e,e-trans-1,4-chdc)](ClO4)2 (2) (L = 1,4,8,11-tetraazacyclotetradecane, cyclam), were prepared by the reaction of [Ni(L)](ClO4)2 and a,e-cis-/e,e-trans-1,4-chdcH2 in basic solvents. Both complexes were characterized by EA, IR, and TGA techniques. In addition, molecular structures were determined by single crystal X-ray diffraction methods. In 1, the a,e-cis-1,4-chdc ligand bridges nickel(II) macrocycles to form an undulated 1D coordination polymer, whereas the complex 2 shows a dimer in which the e,e-trans-1,4-chdc ligand bridges two nickel(II) cyclams.
Supporting Information: Quantum Chemical Roots of Machine-Learning Molecular Similarity Descriptors
Creators: name: Gugler, Stefan
name: Reiher, Markus
Publisher: name: ETH Zurich
Year: 2022

description: This document contains the supporting information published together with the article "Quantum Chemical Roots of Machine-Learning Molecular Similarity Descriptors" (J. Chem. Theory Comput., 2022, 18, 6670).
description: Zenodo
Fragmentation fraction $f_{Ω_b}$ and the $Ω_b\to ΩJ/ψ$ decay in the light-front formalism
Creators: name: Hsiao, Yu-Kuo
name: Lih, Chong-Chung
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: One has measured $f_{Ω_b}{\cal B}(Ω_b^-\to Ω^- J/Ψ)$ at the level of $10^{-6}$, where the fragmentation faction $f_{Ω_b}$ is to evaluate the $b$-quark to $Ω_b^-$ production rate. Using the $Ω_b\to Ω$ transition form factors calculated in the light-front quark model, we predict ${\cal B}(Ω_b^-\to Ω^- J/Ψ) =(5.3^{+3.3+3.8}_{-2.1-2.7})\times 10^{-4}$. In particular, we extract $f_{Ω_b}=(0.54^{+0.34+0.39+0.21}_{-0.22-0.28-0.15})\times 10^{-2}$, demonstrating that the $b$ to $Ω_b$ productions are much more difficult than the $b$ to $Λ_b(Ξ_b)$ ones. Since $f_{Ω_b}$ has not been determined experimentally, $f_{Ω_b}$ added to theoretical branching fractions can be compared to future measurements of the $Ω_b$ decays.
description: 10 pages, 2 figures, 1 table, published version in PRD
Stellar multiplicity and stellar rotation: Insights from APOGEE
Creators: name: Daher, Christine Mazzola
name: Badenes, Carles
name: Tayar, Jamie
name: Pinsonneault, Marc
name: Koposov, Sergey E.
name: Kratter, Kaitlin
name: Moe, Maxwell
name: Anguiano, Borja
name: Godoy-Rivera, Diego
name: Majewski, Steven
name: Carlberg, Joleen K.
name: Walker, Matthew G.
name: Buttry, Rachel
name: Dixon, Don
name: Serna, Javier
name: Stassun, Keivan G.
name: De Lee, Nathan
name: Hernández, Jesús
name: Nitschelm, Christian
name: Stringfellow, Guy S.
name: Troup, Nicholas W.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We measure rotational broadening in spectra taken by the Apache Point Observatory Galactic Evolution Experiment (APOGEE) survey to characterise the relationship between stellar multiplicity and rotation. We create a sample of 2786 giants and 24 496 dwarfs with stellar parameters and multiple radial velocities from the APOGEE pipeline, projected rotation speeds \vsini\ determined from our own pipeline, and distances, masses, and ages measured by Sanders \& Das. We use the statistical distribution of the maximum shift in the radial velocities, \drvm, as a proxy for the close binary fraction to explore the interplay between stellar evolution, rotation, and multiplicity. Assuming that the minimum orbital period allowed is the critical period for Roche Lobe overflow and rotational synchronization, we calculate theoretical upper limits on expected \vsini\ and \drvm\ values. These expectations agree with the positive correlation between the maximum \drvm\ and \vsini\ values observed in our sample as a function of \logg. We find that the fast rotators in our sample have a high occurrence of short-period ($\log(P/\text{d})\lesssim 4$) companions. We also find that old, rapidly-rotating main sequence stars have larger completeness-corrected close binary fractions than their younger peers. Furthermore, rapidly-rotating stars with large \drvm\ consistently show differences of 1-10 Gyr between the predicted gyrochronological and measured isochronal ages. These results point towards a link between rapid rotation and close binarity through tidal interactions. We conclude that stellar rotation is strongly correlated with stellar multiplicity in the field, and caution should be taken in the application of gyrochronology relations to cool stars.
description: 12 pages, 9 figures; accepted by MNRAS
Geometrical discretisations for unfitted finite elements on explicit boundary representations
Creators: name: Badia, Santiago
name: Martorell, Pere A.
name: Verdugo, Francesc
Publisher: name: arXiv
Year: 2021
Subjects: subject: Numerical Analysis (math.NA)
subject: Computational Engineering, Finance, and Science (cs.CE)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: Unfitted (also known as embedded or immersed) finite element approximations of partial differential equations are very attractive because they have much lower geometrical requirements than standard body-fitted formulations. These schemes do not require body-fitted unstructured mesh generation. In turn, the numerical integration becomes more involved, because one has to compute integrals on portions of cells (only the interior part). In practice, these methods are restricted to level-set (implicit) geometrical representations, which drastically limit their application. Complex geometries in industrial and scientific problems are usually determined by (explicit) boundary representations. In this work, we propose an automatic computational framework for the discretisation of partial differential equations on domains defined by oriented boundary meshes. The geometrical kernel that connects functional and geometry representations generates a two-level integration mesh and a refinement of the boundary mesh that enables the straightforward numerical integration of all the terms in unfitted finite elements. The proposed framework has been applied with success on all analysis-suitable oriented boundary meshes (almost 5,000) in the Thingi10K database and combined with an unfitted finite element formulation to discretise partial differential equations on the corresponding domains.
Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing for personalized oncology
Creators: name: Dondi, Arthur
name: Lischetti, Ulrike
name: Jacob, Francis
name: Singer, Franziska
name: Borgsmüller, Nico
name: Tumor Profiler Consortium
name: Heinzelmann-Schwarz, Viola
name: Beisel, Christian
name: Beerenwinkel, Niko
Publisher: name: ETH Zurich
Year: 2022
Subjects: Full-length single-cell RNA sequencing
Long-read PacBio sequencing
Transcript concatenation
Isoforms
Mutations
Gene fusions
Ovarian cancer

description: Understanding the complex background of cancer requires genotype-phenotype information in single-cell resolution. Long-read single-cell RNA sequencing (scRNA-seq), capturing full-length transcripts, lacked the depth to provide this information so far. Here, we increased the PacBio sequencing depth to 12,000 reads per cell, leveraging multiple strategies, including artifact removal and transcript concatenation, and applied the technology to samples from three human ovarian cancer patients. Our approach captured 152,000 isoforms, of which over 52,000 were novel, detected cell type- and cell-specific isoform usage, and revealed differential isoform expression in tumor and mesothelial cells. Furthermore, we identified gene fusions, including a novel scDNA sequencing-validated IGF2BP2::TESPA1 fusion, which was misclassified as high TESPA1 expression in matched short-read data, and called somatic and germline mutations, confirming targeted NGS cancer gene panel results. With multiple new opportunities, especially for cancer biology, we envision long-read scRNA-seq to become increasingly relevant in oncology and personalized medicine.
description: bioRxiv
Thermalization of non-abelian gauge theories at next-to-leading order
Creators: name: Fu, Yu
name: Ghiglieri, Jacopo
name: Iqbal, Shahin
name: Kurkela, Aleksi
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We provide the first next-to-leading-order (NLO) weak-coupling description of the thermalization process of far-from-equilibrium systems in non-abelian gauge theory. We study isotropic systems starting from either over- or under-occupied initial conditions and follow their time evolution towards thermal equilibrium by numerically solving the QCD effective kinetic theory at NLO accuracy. We find that the NLO corrections remain well under control for a wide range of couplings and that the overall effect of NLO corrections is to reduce the time needed to reach thermal equilibrium in the systems considered.
description: 9 Pages and two figures
${\cal N}=(1,1)$ supersymmetric AdS$_3$ in 10 dimensions
Creators: name: Macpherson, Niall T.
name: Tomasiello, Alessandro
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Warped AdS$_3$ solutions in 10 dimensional supergravity that preserve ${\cal N}=(1,1)$ supersymmetry are considered. Sufficient geometric conditions for their existence, and to stop the AdS$_3$ factor experiencing an enhancement to AdS$_4$, are presented. The internal space of such solutions decomposes as a foliation of M$_6$ over an interval where M$_6$ supports either an SU(3)- or SU(2)-structure. The former case is classified in terms of torsion classes and new solutions are found
description: 49 pages, 4 figures. v2: references, typos, new appendix on general N=(1,0) conditions, correction to sufficient N=(1,1) conditions when spinor norms are non equal
Rapidly quenched galaxies in the Simba cosmological simulation and observations
Creators: name: Zheng, Yirui
name: Dave, Romeel
name: Wild, Vivienne
name: Montero, Francisco Rodríguez
Publisher: name: arXiv
Year: 2021
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: A wide range of mechanisms have been put forward to explain the quenching of star formation in galaxies with cosmic time, however, the true balance of responsible mechanisms remains unknown. The identification and study of galaxies that have shut down their star formation on different timescales might elucidate which mechanisms dominate at different epochs and masses. Here we study the population of rapidly quenched galaxies (RQGs) in the SIMBA cosmological hydrodynamic simulation at $0.5
description: accepted on 29/Mar/2022, to appear on MNRAS, 13 pages, 9 figures, plus 2 appendices
The 3D dust and opacity distribution of protoplanets in multi-fluid global simulations
Creators: name: Krapp, Leonardo
name: Kratter, Kaitlin M.
name: Youdin, Andrew N.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: The abundance and distribution of solids inside the Hill sphere are central to our understanding of the giant planet dichotomy. Here, we present a three-dimensional characterization of the dust density, mass flux, and mean opacities in the envelope of sub-thermal and super-thermal mass planets. We simulate the dynamics of multiple dust species in a global protoplanetary disk model accounting for dust feedback. We find that the meridional flows do not effectively stir dust grains at scales of the Bondi sphere. Thus the dust-settling driven by the stellar gravitational potential sets the latitudinal dust density gradient within the planet envelope. Not only does the planet's potential enhance this gradient, but also the spiral wakes serve as another source of asymmetry. These asymmetries substantially alter the inferred mean Rosseland and Planck opacities. In cases with the moderate-to-strong dust settling, the opacity gradient can range from a few percent to more than two orders of magnitude between the mid-plane and the polar regions of the Bondi sphere. Finally, we show that this strong latitudinal opacity gradient can introduce a transition between optically thick and thin regimes at the scales of the planet envelope. We suggest that this transition is likely to occur when the equilibrium scale height of hundred-micron-sized particles is smaller than the Hill radius of the forming planet. This work calls into question the adoption of a constant opacity derived from well-mixed distributions and demonstrates the need for global radiation hydrodynamics models of giant planet formation which account for dust dynamics.
description: 19 pages, 13 figures, accepted for publication in The Astrophysical Journal
Gravitational soft theorem from emergent soft gauge symmetries
Creators: name: Beneke, Martin
name: Hager, Patrick
name: Szafron, Robert
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We consider and derive the gravitational soft theorem up to the sub-subleading power from the perspective of effective Lagrangians. The emergent soft gauge symmetries of the effective Lagrangian provide a transparent explanation of why soft graviton emission is universal to sub-subleading power, but gauge boson emission is not. They also suggest a physical interpretation of the form of the soft factors in terms of the charges related to the soft transformations and the kinematics of the multipole expansion. The derivation is done directly at Lagrangian level, resulting in an operatorial form of the soft theorems. In order to highlight the differences and similarities of the gauge-theory and gravitational soft theorems, we include an extensive discussion of soft gauge-boson emission from scalar, fermionic and vector matter at subleading power.
description: v2: 48 pages, 5 figures. Added sec. 6.6 discussing loop corrections of the soft theorem. Matches published version
The JWST Early Release Science Program for Direct Observations of Exoplanetary Systems I: High Contrast Imaging of the Exoplanet HIP 65426 b from 2-16  μ m
Creators: name: Carter, Aarynn L.
name: Hinkley, Sasha
name: Kammerer, Jens
name: Skemer, Andrew
name: Biller, Beth A.
name: Leisenring, Jarron M.
name: Millar-Blanchaer, Maxwell A.
name: Petrus, Simon
name: Stone, Jordan M.
name: Ward-Duong, Kimberly
name: Wang, Jason J.
name: Girard, Julien H.
name: Hines, Dean C.
name: Perrin, Marshall D.
name: Pueyo, Laurent
name: Balmer, William O.
name: Bonavita, Mariangela
name: Bonnefoy, Mickaël
name: Chauvin, Gaël
name: Choquet, Elodie
name: Patapis, Polychronis
name: Quanz, Sascha Patrick
name: et. al.
Publisher: name: ETH Zurich
Year: 2022

description: We present JWST Early Release Science (ERS) coronagraphic observations of the super-Jupiter exoplanet, HIP 65426 b, with the Near-Infrared Camera (NIRCam) from 2−5 µm, and with the MidInfrared Instrument (MIRI) from 11−16 µm. At a separation of ∼0.8200 (87+108 −31 au), HIP 65426 b is clearly detected in all seven of our observational filters, representing the first images of an exoplanet to be obtained by JWST, and the first ever direct detection of an exoplanet beyond 5 µm. These observations demonstrate that JWST is exceeding its nominal predicted performance by up to a factor of 10, with measured 5σ contrast limits of ∼4×10−6 (∼2.4 µJy) and ∼2×10−4 (∼10 µJy) at 100 for NIRCam at 3.6 µm and MIRI at 11.3 µm, respectively. These contrast limits provide sensitivity to sub-Jupiter companions with masses as low as 0.3MJup beyond separations of ∼100 au. Together with existing ground-based near-infrared data, the JWST photometry are well fit by a BT-SETTL atmospheric model from 1−16 µm, and span ∼97% of HIP 65426 b’s luminous range. Independent of the choice of forward model atmosphere we measure an empirical bolometric luminosity that is tightly constrained between log(Lbol/L)=−4.35 to −4.21, which in turn provides a robust mass constraint of 7.1±1.1 MJup. In totality, these observations confirm that JWST presents a powerful and exciting opportunity to characterise the population of exoplanets amenable to direct imaging in greater detail.
description: arXiv
Tracking SARS-CoV-2 genomic variants in wastewater sequencing data with LolliPop
Creators: name: Dreifuss, David
name: Topolsky, Ivan
name: Icer Baykal, Pelin
name: Beerenwinkel, Niko
Publisher: name: ETH Zurich
Year: 2022

description: During the COVID-19 pandemic, wastewater-based epidemiology has progressively taken a central role as a pathogen surveillance tool. Tracking viral loads and variant outbreaks in sewage offers advantages over clinical surveillance methods by providing unbiased estimates and enabling early detection. However, wastewater-based epidemiology poses new computational research questions that need to be solved in order for this approach to be implemented broadly and successfully. Here, we address the variant deconvolution problem, where we aim to estimate the relative abundances of genomic variants from next-generation sequencing data of a mixed wastewater sample. We introduce LolliPop, a computational method to solve the variant deconvolution problem by simultaneously solving least squares problems and kernel-based smoothing of relative variant abundances from wastewater time series sequencing data. We derive multiple approaches to compute confidence bands, and demonstrate the application of our method to data from the Swiss wastewater surveillance efforts
description: medRxiv