bluuebunny/crossref_metadata_2025_split huggingface dataset:
ABSTRACT FORMS OF QUANTIFICATION IN THE QUANTIFIED ARGUMENT CALCULUS
Authors: PAVLOVIĆ EDI , GRATZL NORBERT 
Published: March 2021

AbstractThe Quantified argument calculus (Quarc) has received a lot of attention recently as an interesting system of quantified logic which eschews the use of variables and unrestricted quantification, but nonetheless achieves results similar to the Predicate calculus (PC) by employing quantifiers applied directly to predicates instead. Despite this noted similarity, the issue of the relationship between Quarc and PC has so far not been definitively resolved. We address this question in the present paper, and then expand upon that result.Utilizing recent developments in structural proof theory, we develop a G3-style sequent calculus for Quarc and briefly demonstrate its structural properties. We put these properties to use immediately to construct direct proofs of the meta-theoretical properties of the system. We then incorporate an abstract (and, as we shall see, logical) predicate into the system in a way that preserves all the structural properties. This allows us to identify a system of Quarc which is deductively equivalent to PC, and also yields a constructive method of demonstrating the Craig interpolation theorem (which speaks in favor of the aforementioned predicate being logical). We further generalize this extension to develop a bivalent system of Quarc with defining clauses that still maintains all the desirable properties of a good proof system.
Analysis of the electromagnetic wave illumination on the transmission lines with nonlinear terminations
Authors: Seifi Z. , Ghorbani A. , Abdipour A. 
Published: March 2021

AbstractIn this paper, an unconditionally stable time-domain method is proposed to investigate the external electromagnetic (EM) field illumination on the nonlinearly loaded transmission lines. In the proposed algorithm, the field to line coupling equations and linear/nonlinear boundary conditions are incorporated and expressed in a matrix form. The derived differential matrix equations are then discretized and solved using the proposed finite difference time domain (FDTD) method approach. The discretized nonlinear matrix equations are also solved by applying a globally convergent iterative method to ensure the stability of the method. Moreover, the experimental investigations are conducted using a transverse EM (TEM) cell for a single microstrip line and a power detector circuit as a nonlinearly loaded transmission line to confirm the accuracy and stability of the proposed method. With the merit of satisfactory accuracy and unconditional stability for the entire range of time steps, the presented approach would be applicable for analyzing the microwave linear/nonlinear circuits subjected to the external incident EM wave.
Pan‐Arctic Riverine Dissolved Organic Matter: Synchronous Molecular Stability, Shifting Sources and Subsidies
Authors: Behnke M. I. , McClelland J. W. , Tank S. E. , Kellerman A. M. , Holmes R. M. , Haghipour N. , Eglinton T. I. , Raymond P. A. , Suslova A. , Zhulidov A. V. , Gurtovaya T. , Zimov N. , Zimov S. , Mutter E. A. , Amos E. , Spencer R. G. M. 
Published: March 2021

AbstractClimate change is dramatically altering Arctic ecosystems, leading to shifts in the sources, composition, and eventual fate of riverine dissolved organic matter (DOM) in the Arctic Ocean. Here we examine a 6‐year DOM compositional record from the six major Arctic rivers using Fourier‐transform ion cyclotron resonance mass spectrometry paired with dissolved organic carbon isotope data (Δ14C, δ13C) to investigate how seasonality and permafrost influence DOM, and how DOM export may change with warming. Across the pan‐Arctic, DOM molecular composition demonstrates synchrony and stability. Spring freshet brings recently leached terrestrial DOM with a latent high‐energy and potentially bioavailable subsidy, reconciling the historical paradox between freshet DOM's terrestrial bulk signatures and high biolability. Winter features undiluted baseflow DOM sourced from old, microbially degraded groundwater DOM. A stable core Arctic riverine fingerprint (CARF) is present in all samples and may contribute to the potential carbon sink of persistent, aged DOM in the global ocean. Future warming may lead to shifting sources of DOM and export through: (1) flattening Arctic hydrographs and earlier melt modifying the timing and role of the spring high‐energy subsidy; (2) increasing groundwater discharge resulting in a greater fraction of DOM export to the ocean occurring as stable and aged molecules; and (3) increasing contribution of nitrogen/sulfur‐containing DOM from microbial degradation caused by increased connectivity between groundwater and surface waters due to permafrost thaw. Our findings suggest the ubiquitous CARF (which may contribute to oceanic carbon sequestration) underlies predictable variations in riverine DOM composition caused by seasonality and permafrost extent.
How Atmospheric Chemistry and Transport Drive Surface Variability of N2O and CFC‐11
Authors: Ruiz Daniel J. , Prather Michael J. , Strahan Susan E. , Thompson Rona L. , Froidevaux Lucien , Steenrod Stephen D. 
Published: March 2021

AbstractNitrous oxide (N2O) is a long‐lived greenhouse gas that affects atmospheric chemistry and climate. In this work, we use satellite measurements of N2O, ozone (O3), and temperature from the Aura Microwave Limb Sounder (MLS) instrument to calculate stratospheric loss of N2O, and thus its atmospheric lifetime. Using three chemistry transport models simulating the Aura period 2005–2017, we verify the stratospheric sink using MLS data and follow that loss signal down to the surface and compare with surface observations. Stratospheric loss has a strong seasonal cycle and is further modulated by the Quasi‐Biennial Oscillation (QBO); these cycles are seen equally in both observations and the models. When filtered for interannual variability, the modeled surface signal is QBO‐caused, and it reproduces the observed pattern, highlighting the potential role of the QBO in tropospheric chemistry and composition, as well as in model evaluation. The observed annual surface signal in the northern hemisphere matches well with the models run without emissions, indicating the annual cycle is driven mostly by stratosphere‐troposphere exchange (STE) flux of N2O‐depleted air and not surface N2O emissions. In the southern hemisphere (SH), all three models disagree and thus provide no guidance, except for indicating that modeling annual STE in the SH remains a major model uncertainty. Parallel model simulations of CFCl3, which has greater stratospheric loss that N2O and possibly surreptitious emissions, show that its interannual variations parallel those of N2O, and thus the observed N2O variability can identify the stratospheric component of the observed CFCl3variability.
The SET HASDM Density Database
Authors: Tobiska W. Kent , Bowman Bruce R. , Bouwer S. David , Cruz Alfredo , Wahl Kaiya , Pilinski Marcin D. , Mehta Piyush M. , Licata Richard J. 
Published: March 2021

AbstractThe SET HASDM density database is available for scientific studies through a SQL database with open community access. The information in the SET HASDM density database covers the period from January 1, 2000 through December 31, 2019. Data records exist every 3 h during solar cycles 23 and 24. The database has a grid size of 10° × 15° (latitude, longitude) with 25 km altitude steps between 175 and 825 km. A description of the source of the database, its validation, its information content, and its accessibility are provided.
Irrigation of biomass plantations may globally increase water stress more than climate change
Authors: Stenzel Fabian , Greve Peter , Lucht Wolfgang , Tramberend Sylvia , Wada Yoshihide , Gerten Dieter 
Published: March 2021

AbstractBioenergy with carbon capture and storage (BECCS) is considered an important negative emissions (NEs) technology, but might involve substantial irrigation on biomass plantations. Potential water stress resulting from the additional withdrawals warrants evaluation against the avoided climate change impact. Here we quantitatively assess potential side effects of BECCS with respect to water stress by disentangling the associated drivers (irrigated biomass plantations, climate, land use patterns) using comprehensive global model simulations. By considering a widespread use of irrigated biomass plantations, global warming by the end of the 21st century could be limited to 1.5 °C compared to a climate change scenario with 3 °C. However, our results suggest that both the global area and population living under severe water stress in the BECCS scenario would double compared to today and even exceed the impact of climate change. Such side effects of achieving substantial NEs would come as an extra pressure in an already water-stressed world and could only be avoided if sustainable water management were implemented globally.
Deep learning-based enhancement of epigenomics data with AtacWorks
Authors: Lal Avantika , Chiang Zachary D. , Yakovenko Nikolai , Duarte Fabiana M. , Israeli Johnny , Buenrostro Jason D. 
Published: March 2021

AbstractATAC-seq is a widely-applied assay used to measure genome-wide chromatin accessibility; however, its ability to detect active regulatory regions can depend on the depth of sequencing coverage and the signal-to-noise ratio. Here we introduce AtacWorks, a deep learning toolkit to denoise sequencing coverage and identify regulatory peaks at base-pair resolution from low cell count, low-coverage, or low-quality ATAC-seq data. Models trained by AtacWorks can detect peaks from cell types not seen in the training data, and are generalizable across diverse sample preparations and experimental platforms. We demonstrate that AtacWorks enhances the sensitivity of single-cell experiments by producing results on par with those of conventional methods using ~10 times as many cells, and further show that this framework can be adapted to enable cross-modality inference of protein-DNA interactions. Finally, we establish that AtacWorks can enable new biological discoveries by identifying active regulatory regions associated with lineage priming in rare subpopulations of hematopoietic stem cells.
Spatiotemporal persistence of multiple, diverse clades and toxins of Corynebacterium diphtheriae
Authors: Will Robert C. , Ramamurthy Thandavarayan , Sharma Naresh Chand , Veeraraghavan Balaji , Sangal Lucky , Haldar Pradeep , Pragasam Agila Kumari , Vasudevan Karthick , Kumar Dhirendra , Das Bhabatosh , Heinz Eva , Melnikov Vyacheslav , Baker Stephen , Sangal Vartul , Dougan Gordon , Mutreja Ankur 
Published: March 2021

AbstractDiphtheria is a respiratory disease caused by the bacterium Corynebacterium diphtheriae. Although the development of a toxin-based vaccine in the 1930s has allowed a high level of control over the disease, cases have increased in recent years. Here, we describe the genomic variation of 502 C. diphtheriae isolates across 16 countries and territories over 122 years. We generate a core gene phylogeny and determine the presence of antimicrobial resistance genes and variation within the tox gene of 291 tox+ isolates. Numerous, highly diverse clusters of C. diphtheriae are observed across the phylogeny, each containing isolates from multiple countries, regions and time of isolation. The number of antimicrobial resistance genes, as well as the breadth of antibiotic resistance, is substantially greater in the last decade than ever before. We identified and analysed 18 tox gene variants, with mutations estimated to be of medium to high structural impact.
Optimal proteome allocation and the temperature dependence of microbial growth laws
Authors: Mairet Francis , Gouzé Jean-Luc , de Jong Hidde 
Published: March 2021

AbstractAlthough the effect of temperature on microbial growth has been widely studied, the role of proteome allocation in bringing about temperature-induced changes remains elusive. To tackle this problem, we propose a coarse-grained model of microbial growth, including the processes of temperature-sensitive protein unfolding and chaperone-assisted (re)folding. We determine the proteome sector allocation that maximizes balanced growth rate as a function of nutrient limitation and temperature. Calibrated with quantitative proteomic data forEscherichia coli, the model allows us to clarify general principles of temperature-dependent proteome allocation and formulate generalized growth laws. The same activation energy for metabolic enzymes and ribosomes leads to an Arrhenius increase in growth rate at constant proteome composition over a large range of temperatures, whereas at extreme temperatures resources are diverted away from growth to chaperone-mediated stress responses. Our approach points at risks and possible remedies for the use of ribosome content to characterize complex ecosystems with temperature variation.
Bioinformatis analysis reveals possible molecular mechanism of PXR on regulating ulcerative colitis
Authors: Guo Hanze , Chi Yan , Chi Naiyu 
Published: March 2021

AbstractInflammatory bowel disease (IBD) is a chronic, recurrent inflammatory disease of the gastrointestinal (GI) tract. Ulcerative colitis (UC) is a type of IBD. Pregnane X Receptor (PXR) is a member of the nuclear receptor superfamily. In order to deepen understanding and exploration of the molecular mechanism of regulation roles of PXR on UC, biological informatics analysis was performed. First, 878 overlapping differentially expressed genes (DEGs) between UC and normal samples were obtained from the Gene Expression Omnibus (GEO) database (GSE59071 and GSE38713) by using the "limma" R language package. Then WGCNA analysis was performed by 878 DEGs to obtain co-expression modules that were positively and negatively correlated with clinical traits. GSEA analysis of PXR results obtained the signal pathways enriched in the PXR high and low expression group and the active genes of each signal pathway. Then the association of PXR with genes that are both active in high expression group and negatively related to diseases (gene set 1), or both active in low expression group and negatively related to diseases (gene set 2) was analyzed by String database. Finally, carboxylesterase 2 (CES2), ATP binding cassette subfamily G member 2 (ABCG2), phosphoenolpyruvate carboxykinase (PCK1), PPARG coactivator 1 alpha (PPARGC1A), cytochrome P450 family 2 subfamily B member 6 (CYP2B6) from gene set 1 and C-X-C motif chemokine ligand 8 (CXCL8) from gene set 2 were screened out. After the above analysis and reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) verification, we speculated that PXR may exert a protective role on UC by promoting CES2, ABCG2, PCK1, PPARGC1A, CYP2B6 expression and inhibiting CXCL8 expression in their corresponding signal pathway in intestinal tissue.
Modelling and predicting the spatio-temporal spread of COVID-19, associated deaths and impact of key risk factors in England
Authors: Sartorius B. , Lawson A. B. , Pullan R. L. 
Published: March 2021

AbstractCOVID-19 caseloads in England have passed through a first peak, and at the time of this analysis appeared to be gradually increasing, potentially signalling the emergence of a second wave. To ensure continued response to the epidemic is most effective, it is imperative to better understand both retrospectively and prospectively the geographical evolution of COVID-19 caseloads and deaths at small-area resolution, identify localised areas in space–time at significantly higher risk, quantify the impact of changes in localised population mobility (or movement) on caseloads, identify localised risk factors for increased mortality and project the likely course of the epidemic at high spatial resolution in coming weeks. We applied a Bayesian hierarchical space–time SEIR model to assess the spatiotemporal variability of COVID-19 caseloads (transmission) and deaths at small-area scale in England [Middle Layer Super Output Area (MSOA), 6791 units] and by week (using observed data from week 5 to 34 of 2020), including key determinants, the modelled transmission dynamics and spatial–temporal random effects. We also estimate the number of cases and deaths at small-area resolution with uncertainty projected forward in time by MSOA (up to week 51 of 2020), the impact mobility reductions (and subsequent easing) have had on COVID-19 caseloads and quantify the impact of key socio-demographic risk factors on COVID-19 related mortality risk by MSOA. Reductions in population mobility during the course of the first lockdown had a significant impact on the reduction of COVID-19 caseloads across England, however local authorities have had a varied rate of reduction in population movement which our model suggest has substantially impacted the geographic heterogeneity in caseloads at small-area scale. The steady gain in population mobility, observed from late April, appears to have contributed to a slowdown in caseload reductions towards late June and subsequent start of the second wave. MSOA with higher proportions of elderly (70+ years of age) and elderly living in deprivation, both with very distinct geographic distributions, have a significantly elevated COVID-19 mortality rates. While non-pharmaceutical interventions (that is, reductions in population mobility and social distancing) had a profound impact on the trajectory of the first wave of the COVID-19 outbreak in England, increased population mobility appears to have significantly contributed to the second wave. A number of contiguous small-areas appear to be at a significant elevated risk of high COVID-19 transmission, many of which are also at increased risk for higher mortality rates. A geographically staggered re-introduction of intensified social distancing measures is advised and limited cross MSOA movement if the magnitude and geographic extent of the second wave is to be reduced.
Use of catheter with 2-methacryloyloxyethyl phosphorylcholine polymer coating is associated with long-term availability of central venous port
Authors: Iida Yuuki , Hongo Kumiko , Onoda Takanobu , Kita Yusuke , Ishihara Yukio , Takabayashi Naoki , Kobayashi Ryo , Hiramatsu Takeyuki 
Published: March 2021

AbstractCentral venous port (CVP) is a widely used totally implantable venous access device. Recognition of risks associated with CVP-related complications is clinically important for safe, reliable, and long-term intravenous access. We therefore investigated factors associated with CVP infection and evulsion, including the device type. A total of 308 consecutive patients with initial CVP implantation between January 2011 and December 2017 were retrospectively reviewed, and the association of clinical features with CVP-related complications were analyzed. Intraoperative and postoperative complications occurred in 11 (3.6%) and 39 (12.7%) patients, respectively. The overall rate of CVP availability at six months was 91.4%. Malignancy and 2-Methacryloyloxyethyl phosphorylcholine (MPC) polymer-coated catheter use were negatively associated with the incidence of CVP infections. Accordingly, malignancy and MPC polymer-coated catheter use were independent predictors for lower CVP evulsion rate (odds ratio, 0.23 and 0.18, respectively). Furthermore, both factors were significantly associated with longer CVP availability (hazard ratio, 0.24 and 0.27, respectively). This retrospective study identified factors associated with CVP-related complications and long-term CVP availability. Notably, MPC polymer-coated catheter use was significantly associated with a lower rate of CVP infection and longer CVP availability, suggesting the preventive effect of MPC coating on CVP infection.
Learning the best nanoscale heat engines through evolving network topology
Authors: Ashida Yuto , Sagawa Takahiro 
Published: March 2021

AbstractThe quest to identify the best heat engine has been at the center of science and technology. Considerable studies have so far revealed the potentials of nanoscale thermal machines to yield an enhanced thermodynamic efficiency in noninteracting regimes. However, the full benefit of many-body interactions is yet to be investigated; identifying the optimal interaction is a hard problem due to combinatorial explosion of the search space, which makes brute-force searches infeasible. We tackle this problem with developing a framework for reinforcement learning of network topology in interacting thermal systems. We find that the maximum possible values of the figure of merit and the power factor can be significantly enhanced by electron-electron interactions under nondegenerate single-electron levels with which, in the absence of interactions, the thermoelectric performance is quite low in general. This allows for an alternative strategy to design the best heat engines by optimizing interactions instead of single-electron levels. The versatility of the developed framework allows one to identify full potential of a broad range of nanoscale systems in terms of multiple objectives.
Peripheral arteriopathy caused by Notch3 gain-of-function mutation involves ER and oxidative stress and blunting of NO/sGC/cGMP pathway
Authors: Neves Karla B. , Morris Hannah E. , Alves-Lopes Rhéure , Muir Keith W. , Moreton Fiona , Delles Christian , Montezano Augusto C. , Touyz Rhian M. 
Published: March 2021

Abstract
Notch3 mutations cause Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy (CADASIL), which predisposes to stroke and dementia. CADASIL is characterised by vascular dysfunction and granular osmiophilic material (GOM) accumulation in cerebral small vessels. Systemic vessels may also be impacted by Notch3 mutations. However vascular characteristics and pathophysiological processes remain elusive. We investigated mechanisms underlying the peripheral vasculopathy mediated by CADASIL-causing Notch3 gain-of-function mutation. We studied: (i) small arteries and vascular smooth muscle cells (VSMCs) from TgNotch3R169C mice (CADASIL model), (ii) VSMCs from peripheral arteries from CADASIL patients, and (iii) post-mortem brains from CADASIL individuals. TgNotch3R169C vessels exhibited GOM deposits, increased vasoreactivity and impaired vasorelaxation. Hypercontractile responses were normalised by fasudil (Rho kinase inhibitor) and 4-phenylbutyrate (4-PBA; endoplasmic-reticulum (ER) stress inhibitor). Ca2+ transients and Ca2+ channel expression were increased in CADASIL VSMCs, with increased expression of Rho guanine nucleotide-exchange factors (GEFs) and ER stress proteins. Vasorelaxation mechanisms were impaired in CADASIL, evidenced by decreased endothelial nitric oxide synthase (eNOS) phosphorylation and reduced cyclic guanosine 3′,5′-monophosphate (cGMP) levels, with associated increased soluble guanylate cyclase (sGC) oxidation, decreased sGC activity and reduced levels of the vasodilator hydrogen peroxide (H2O2). In VSMCs from CADASIL patients, sGC oxidation was increased and cGMP levels decreased, effects normalised by fasudil and 4-PBA. Cerebral vessels in CADASIL patients exhibited significant oxidative damage. In conclusion, peripheral vascular dysfunction in CADASIL is associated with altered Ca2+ homoeostasis, oxidative stress and blunted eNOS/sGC/cGMP signaling, processes involving Rho kinase and ER stress. We identify novel pathways underlying the peripheral arteriopathy induced by Notch3 gain-of-function mutation, phenomena that may also be important in cerebral vessels.