julilili42/papers huggingface dataset:
eRHIC Design Study: An Electron-Ion Collider at BNL
2022-03-09

This document presents BNL's plan for an electron-ion collider, eRHIC, a major new research tool that builds on the existing RHIC facility to advance the long-term vision for Nuclear Physics to discover and understand the emergent phenomena of Quantum Chromodynamics (QCD), the fundamental theory of the strong interaction that binds the atomic nucleus. We describe the scientific requirements for such a facility, following up on the community-wide 2012 white paper, 'Electron-Ion Collider: the Next QCD Frontier', and present a design concept that incorporates new, innovative accelerator techniques to provide a cost-effective upgrade of RHIC with polarized electron beams colliding with the full array of RHIC hadron beams. The new facility will deliver electron-nucleon luminosity of 10^33-10^34 cm-1sec-1 for collisions of 15.9 GeV polarized electrons on either 250 GeV polarized protons or 100 GeV/u heavy ion beams. The facility will also be capable of providing an electron beam energy of 21.2 GeV, at reduced luminosity. We discuss the on-going R&amp;D effort to realize the project, and present key detector requirements and design ideas for an experimental program capable of making the 'golden measurements' called for in the EIC White Paper.
On the Recognition of Fan-Planar and Maximal Outer-Fan-Planar Graphs
2022-03-09

Fan-planar graphs were recently introduced as a generalization of 1-planar graphs. A graph is fan-planar if it can be embedded in the plane, such that each edge that is crossed more than once, is crossed by a bundle of two or more edges incident to a common vertex. A graph is outer-fan-planar if it has a fan-planar embedding in which every vertex is on the outer face. If, in addition, the insertion of an edge destroys its outer-fan-planarity, then it is maximal outer-fan-planar. In this paper, we present a polynomial-time algorithm to test whether a given graph is maximal outer-fan-planar. The algorithm can also be employed to produce an outer-fan-planar embedding, if one exists. On the negative side, we show that testing fan-planarity of a graph is NP-hard, for the case where the rotation system (i.e., the cyclic order of the edges around each vertex) is given.
The Influence of Decoding Accuracy on Perceived Control: A Simulated BCI Study
2022-03-09

Understanding the relationship between the decoding accuracy of a brain-computer interface (BCI) and a subject's subjective feeling of control is important for determining a lower limit on decoding accuracy for a BCI that is to be deployed outside a laboratory environment. We investigated this relationship by systematically varying the level of control in a simulated BCI task. We find that a binary decoding accuracy of 65% is required for users to report more often than not that they are feeling in control of the system. Decoding accuracies above 75%, on the other hand, added little in terms of the level of perceived control. We further find that the probability of perceived control does not only depend on the actual decoding accuracy, but is also in influenced by whether subjects successfully complete the given task in the allotted time frame.
Examination of the Nature of the ABC Effect
2022-03-09

Recently it has been shown by exclusive and kinematically complete experiments that the appearance of a narrow resonance structure in double-pionic fusion reactions is strictly correlated with the appearance of the so-called ABC effect, which denotes a pronounced low-mass enhancement in the -invariant mass spectrum. Whereas the resonance structure got its explanation by the dibaryonic resonance, a satisfactory explanation for the ABC effect is still pending. In this paper we discuss possible explanations of the ABC effect and their consequences for the internal structure of the dibaryon.
Clades and clans: a comparison study of two evolutionary models
2022-03-09

The Yule-Harding-Kingman (YHK) model and the proportional to distinguishable arrangements (PDA) model are two binary tree generating models that are widely used in evolutionary biology. Understanding the distributions of clade sizes under these two models provides valuable insights into macro-evolutionary processes, and is important in hypothesis testing and Bayesian analyses in phylogenetics. Here we show that these distributions are log-convex, which implies that very large clades or very small clades are more likely to occur under these two models. Moreover, we prove that there exists a critical value for each such that for a given clade with size , the probability that this clade is contained in a random tree with leaves generated under the YHK model is higher than that under the PDA model if $1
inPHAP: Interactive visualization of genotype and phased haplotype data
2022-03-09

Background: To understand individual genomes it is necessary to look at the variations that lead to changes in phenotype and possibly to disease. However, genotype information alone is often not sufficient and additional knowledge regarding the phase of the variation is needed to make correct interpretations. Interactive visualizations, that allow the user to explore the data in various ways, can be of great assistance in the process of making well informed decisions. But, currently there is a lack for visualizations that are able to deal with phased haplotype data. Results: We present inPHAP, an interactive visualization tool for genotype and phased haplotype data. inPHAP features a variety of interaction possibilities such as zooming, sorting, filtering and aggregation of rows in order to explore patterns hidden in large genetic data sets. As a proof of concept, we apply inPHAP to the phased haplotype data set of Phase 1 of the 1000 Genomes Project. Thereby, inPHAP's ability to show genetic variations on the population as well as on the individuals level is demonstrated for several disease related loci. Conclusions: As of today, inPHAP is the only visual analytical tool that allows the user to explore unphased and phased haplotype data interactively. Due to its highly scalable design, inPHAP can be applied to large datasets with up to 100 GB of data, enabling users to visualize even large scale input data. inPHAP closes the gap between common visualization tools for unphased genotype data and introduces several new features, such as the visualization of phased data.
A new approach for numerical simulation of the time-dependent Ginzburg-Landau equations
2022-03-09

We introduce a new approach for finite element simulations of the time-dependent Ginzburg-Landau equations (TDGL) in a general curved polygon, possibly with reentrant corners. Specifically, we reformulate the TDGL into an equivalent system of equations by decomposing the magnetic potential to the sum of its divergence-free and curl-free parts, respectively. Numerical simulations of vortex dynamics show that, in a domain with reentrant corners, the new approach is much more stable and accurate than the old approaches of solving the TDGL directly (under either the temporal gauge or the Lorentz gauge); in a convex domain, the new approach gives comparably accurate solutions as the old approaches.
Universal covers, color refinement, and two-variable counting logic: Lower bounds for the depth
2022-03-09

Given a connected graph and its vertex , let denote the universal cover of obtained by unfolding into a tree starting from . Let be the minimum number such that, for graphs and with at most vertices each, the isomorphism of and surely follows from the isomorphism of these rooted trees truncated at depth . Motivated by applications in theory of distributed computing, Norris [Discrete Appl. Math. 1995] asks if . We answer this question in the negative by establishing that . Our solution uses basic tools of finite model theory such as a bisimulation version of the Immerman-Lander 2-pebble counting game. The graphs and we construct to prove the lower bound for also show some other tight lower bounds. Both having vertices, and can be distinguished in 2-variable counting logic only with quantifier depth . It follows that color refinement, the classical procedure used in isomorphism testing and other areas for computing the coarsest equitable partition of a graph, needs rounds to achieve color stabilization on each of and . Somewhat surprisingly, this number of rounds is not enough for color stabilization on the disjoint union of and , where rounds are needed.
EF+EX Forest Algebras
2022-03-09

We examine languages of unranked forests definable using the temporal operators EF and EX. We characterize the languages definable in this logic, and various fragments thereof, using the syntactic forest algebras introduced by Bojanczyk and Walukiewicz. Our algebraic characterizations yield efficient algorithms for deciding when a given language of forests is definable in this logic. The proofs are based on understanding the wreath product closures of a few small algebras, for which we introduce a general ideal theory for forest algebras. This combines ideas from the work of Bojanczyk and Walukiewicz for the analogous logics on binary trees and from early work of Stiffler on wreath product of finite semigroups.
Some remarks on the use of effective Lagrangians in QED and QCD
2022-03-09

We discuss in this article the usefulness of the effective Lagrangians (L_eff) of QED and QCD within the one-loop approximation. Instead of calculating L_eff via complicated computations with Schwinger's proper-time technique or Feynman graphs, we prefer to employ the energy-momentum tensor and the leading-log model. The advantage is that we do not have to demand the external electromagnetic or color field to be constant. There are also some critical remarks added which cast doubt on the use of LQCD with covariant constant fields in explaining the nature of the QCD vacuum.
Quasi-Antichain Chermak-Delgado Lattices of Finite Groups
2022-03-09

The Chermak-Delgado lattice of a finite group is a dual, modular sublattice of the subgroup lattice of the group. This paper considers groups with a quasi-antichain interval in the Chermak-Delgado lattice, ultimately proving that if there is a quasi-antichain interval between and with then there exists a prime such that the quotient is an elementary abelian -group and the number of atoms in the quasi-antichain is one more than a power of . In the case where the Chermak-Delgado lattice of the entire group is a quasi-antichain, the relationship between the number of abelian atoms and the prime is examined; additionally several examples of group with a quasi-antichain Chermak-Delgado lattice are constructed.
Comment on acp-2021-935
2022-03-09

<strong class="journal-contentHeaderColor">Abstract.</strong> We collected surface snow samples from three different glaciers – Yala, Thana, and Sachin – in the central and western Himalayas to understand the spatial variability and radiative impacts of light-absorbing particles. The Yala and Thana glaciers in Nepal and Bhutan, respectively, were selected to represent the central Himalayas. The Sachin glacier in Pakistan was selected to represent the western Himalayas. The samples were collected during the pre- and post-monsoon seasons of the year 2016. The samples were analyzed for black carbon (BC) and water-insoluble organic carbon (OC) through the thermal optical method. The average mass concentrations (BC 2381 ng g<span class="inline-formula"><sup>−1</sup></span>; OC 3896 ng g<span class="inline-formula"><sup>−1</sup></span>; dust 101 <span class="inline-formula">μ</span>g g<span class="inline-formula"><sup>−1</sup>)</span> in the western Himalayas (Sachin glacier) were quite high compared to the mass concentrations (BC 358 ng g<span class="inline-formula"><sup>−1</sup></span>, OC 904 ng g<span class="inline-formula"><sup>−1</sup></span>, dust 22 <span class="inline-formula">μ</span>g g<span class="inline-formula"><sup>−1</sup>)</span> in the central Himalayas (Yala glacier). The difference in mass concentration may be due to the difference in elevation, snow age, local pollution sources, and meteorological conditions. BC in surface snow was also estimated through Weather Research and Forecasting (WRF) model coupled with Chemistry (WRF-Chem) simulations at the three glacier sites during the sampling periods. Simulations reasonably capture the spatial and seasonal patterns of the observed BC in snow but with a relatively smaller magnitude. Absolute snow albedo was estimated through the Snow, Ice, and Aerosol Radiative (SNICAR) model. The absolute snow albedo reduction ranged from 0.48 % (Thana glacier during September) to 24 % (Sachin glacier during May) due to BC and 0.13 % (Yala glacier during September) to 5 % (Sachin glacier during May) due to dust. The instantaneous radiative forcing due to BC and dust was estimated in the range of 0 to 96.48 and 0 to 25 W m<span class="inline-formula"><sup>−2</sup></span>, respectively. The lowest and highest albedo reduction and radiative forcing were observed in central and western Himalayan glaciers, respectively. The potential source regions of the deposited pollutants were inferred using WRF-Chem tagged-tracer simulations. Selected glaciers in the western Himalayas were mostly affected by long-range transport from the Middle East and central Asia; however, the central Himalayan glaciers were mainly affected by local and south Asia emissions (from Nepal, India, and China) especially during the pre-monsoon season. Overall, south Asia and west Asia were the main contributing source regions of pollutants.
Secreted Glycoside Hydrolase Proteins as Effectors and Invasion Patterns of Plant-Associated Fungi and Oomycetes
2022-03-10

During host colonization, plant-associated microbes, including fungi and oomycetes, deliver a collection of glycoside hydrolases (GHs) to their cell surfaces and surrounding extracellular environments. The number and type of GHs secreted by each organism is typically associated with their lifestyle or mode of nutrient acquisition. Secreted GHs of plant-associated fungi and oomycetes serve a number of different functions, with many of them acting as virulence factors (effectors) to promote microbial host colonization. Specific functions involve, for example, nutrient acquisition, the detoxification of antimicrobial compounds, the manipulation of plant microbiota, and the suppression or prevention of plant immune responses. In contrast, secreted GHs of plant-associated fungi and oomycetes can also activate the plant immune system, either by acting as microbe-associated molecular patterns (MAMPs), or through the release of damage-associated molecular patterns (DAMPs) as a consequence of their enzymatic activity. In this review, we highlight the critical roles that secreted GHs from plant-associated fungi and oomycetes play in plant–microbe interactions, provide an overview of existing knowledge gaps and summarize future directions.
Field experiments underestimate aboveground biomass response to drought
2022-03-10

Abstract Researchers use both experiments and observations to study the impacts of climate change on ecosystems, but results from these contrasting approaches have not been systematically compared for droughts. Using a meta-analysis and accounting for potential confounding factors, we demonstrate that aboveground biomass responded only about half as much to experimentally imposed drought events as to natural droughts. Our findings indicate that experimental results may underestimate climate change impacts and highlight the need to integrate results across approaches.
Time-resolved hadronic particle acceleration in the recurrent nova RS Ophiuchi
2022-03-10

Recurrent novae are repeating thermonuclear explosions in the outer layers of white dwarfs, due to the accretion of fresh material from a binary companion. The shock generated when ejected material slams into the companion star’s wind can accelerate particles. We report very-high-energy (VHE; <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" overflow="scroll"> <mml:mrow> <mml:mo>≳</mml:mo> <mml:mn>100</mml:mn> <mml:mtext> giga–electron volts</mml:mtext> </mml:mrow> </mml:math> ) gamma rays from the recurrent nova RS Ophiuchi, up to 1 month after its 2021 outburst, observed using the High Energy Stereoscopic System (H.E.S.S.). The temporal profile of VHE emission is similar to that of lower-energy giga–electron volt emission, indicating a common origin, with a 2-day delay in peak flux. These observations constrain models of time-dependent particle energization, favoring a hadronic emission scenario over the leptonic alternative. Shocks in dense winds provide favorable environments for efficient acceleration of cosmic rays to very high energies.
Coping with the COVID-19 Pandemic: Perceived Changes in Psychological Vulnerability, Resilience and Social Cohesion before, during and after Lockdown
2022-03-10

The COVID-19 pandemic and associated lockdowns have posed unique and severe challenges to our global society. To gain an integrative understanding of pervasive social and mental health impacts in 3522 Berlin residents aged 18 to 65, we systematically investigated the structural and temporal relationship between a variety of psychological indicators of vulnerability, resilience and social cohesion before, during and after the first lockdown in Germany using a retrospective longitudinal study design. Factor analyses revealed that (a) vulnerability and resilience indicators converged on one general bipolar factor, (b) residual variance of resilience indicators formed a distinct factor of adaptive coping capacities and (c) social cohesion could be reliably measured with a hierarchical model including four first-order dimensions of trust, a sense of belonging, social interactions and social engagement, and one second-order social cohesion factor. In the second step, latent change score models revealed that overall psychological vulnerability increased during the first lockdown and decreased again during re-opening, although not to baseline levels. Levels of social cohesion, in contrast, first decreased and then increased again during re-opening. Furthermore, participants who increased in vulnerability simultaneously decreased in social cohesion and adaptive coping during lockdown. While higher pre-lockdown levels of social cohesion predicted a stronger lockdown effect on mental health, individuals with higher social cohesion during the lockdown and positive change in coping abilities and social cohesion during re-opening showed better mental health recovery, highlighting the important role of social capacities in both amplifying but also overcoming the multiple challenges of this collective crisis.
In vivo growth of Staphylococcus lugdunensis is facilitated by the concerted function of heme and non-heme iron acquisition mechanisms
2022-03-10

Staphylococcus lugdunensis has increasingly been recognized as a pathogen that can cause serious infection indicating this bacterium overcomes host nutritional immunity. Despite this, there exists a significant knowledge gap regarding the iron acquisition mechanisms employed by S. lugdunensis, especially during infection of the mammalian host. Here we show that S. lugdunensis can usurp hydroxamate siderophores and staphyloferrin A and B from Staphylococcus aureus. These transport activities all required a functional FhuC ATPase. Moreover, we show that the acquisition of catechol siderophores and catecholamine stress hormones by S. lugdunensis required the presence of the sst-1 transporter-encoding locus, but not the sst-2 locus. Iron-dependent growth in acidic culture conditions necessitated the ferrous iron transport system encoded by feoAB. Heme iron was acquired via expression of the iron-regulated surface determinant (isd) locus. During systemic infection of mice, we demonstrated that while S. lugdunensis does not cause overt illness, it does colonize and proliferate to high numbers in the kidneys. By combining mutations in the various iron acquisition loci (isd, fhuC, sst-1, and feo), we demonstrate that only a strain deficient for all of these systems was attenuated in its ability to proliferate to high numbers in the murine kidney. We propose the concerted action of heme and non-heme iron acquisition systems also enable S. lugdunensis to cause human infection.
Angpt2/Tie2 autostimulatory loop controls tumorigenesis
2022-03-10

Invasive nonfunctioning (NF) pituitary neuroendocrine tumors (PitNETs) are non-resectable neoplasms associated with frequent relapses and significant comorbidities. As the current therapies of NF-PitNETs often fail, new therapeutic targets are needed. The observation that circulating angiopoietin-2 (ANGPT2) is elevated in patients with NF-PitNET and correlates with tumor aggressiveness prompted us to investigate the ANGPT2/TIE2 axis in NF-PitNETs in the GH3 PitNET cell line, primary human NF-PitNET cells, xenografts in zebrafish and mice, and in MENX rats, the only autochthonous NF-PitNET model. We show that PitNET cells express a functional TIE2 receptor and secrete bioactive ANGPT2, which promotes, besides angiogenesis, tumor cell growth in an autocrine and paracrine fashion. ANGPT2 stimulation of TIE2 in tumor cells activates downstream cell proliferation signals, as previously demonstrated in endothelial cells (ECs). Tie2 gene deletion blunts PitNETs growth in xenograft models, and pharmacological inhibition of Angpt2/Tie2 signaling antagonizes PitNETs in primary cell cultures, tumor xenografts in mice, and in MENX rats. Thus, the ANGPT2/TIE2 axis provides an exploitable therapeutic target in NF-PitNETs and possibly in other tumors expressing ANGPT2/TIE2. The ability of tumor cells to coopt angiogenic signals classically viewed as EC-specific expands our view on the microenvironmental cues that are essential for tumor progression.
Incidental Tuberculosis in sudden, unexpected, and violent deaths in the community Lusaka, Zambia - A descriptive forensic post-mortem examination study
2022-03-10

Incidental cases of active tuberculosis undiagnosed antemortem seen at forensic autopsy reflects major gaps in the national TB control programs. More investments into proactive screening, testing, treatment activities, and accurate data collection are required.