bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unmasking Arrhythmogenic Hubs of Reentry Driving Persistent Atrial Fibrillation for Patient‐Specific Treatment
Authors: Hansen Brian J. , Zhao Jichao , Helfrich Katelynn M. , Li Ning , Iancau Alexander , Zolotarev Alexander M. , Zakharkin Stanislav O. , Kalyanasundaram Anuradha , Subr Megan , Dastagir Nawshin , Sharma Roshan , Artiga Esthela J. , Salgia Nicholas , Houmsse Mustafa M. , Kahaly Omar , Janssen Paul M. L. , Mohler Peter J. , Mokadam Nahush A. , Whitson Bryan A. , Afzal Muhammad R. , Simonetti Orlando P. , Hummel John D. , Fedorov Vadim V. 
Published: October 2020

Background
Atrial fibrillation (AF) driver mechanisms are obscured to clinical multielectrode mapping approaches that provide partial, surface‐only visualization of unstable 3‐dimensional atrial conduction. We hypothesized that transient modulation of refractoriness by pharmacologic challenge during multielectrode mapping improves visualization of hidden paths of reentrant AF drivers for targeted ablation.

Methods and Results
Pharmacologic challenge with adenosine was tested in ex vivo human hearts with a history of AF and cardiac diseases by multielectrode and high‐resolution subsurface near‐infrared optical mapping, integrated with 3‐dimensional structural imaging and heart‐specific computational simulations. Adenosine challenge was also studied on acutely terminated AF drivers in 10 patients with persistent AF. Ex vivo, adenosine stabilized reentrant driver paths within arrhythmogenic fibrotic hubs and improved visualization of reentrant paths, previously seen as focal or unstable breakthrough activation pattern, for targeted AF ablation. Computational simulations suggested that shortening of atrial refractoriness by adenosine may (1) improve driver stability by annihilating spatially unstable functional blocks and tightening reentrant circuits around fibrotic substrates, thus unmasking the common reentrant path; and (2) destabilize already stable reentrant drivers along fibrotic substrates by accelerating competing fibrillatory wavelets or secondary drivers. In patients with persistent AF, adenosine challenge unmasked hidden common reentry paths (9/15 AF drivers, 41±26% to 68±25% visualization), but worsened visualization of previously visible reentry paths (6/15, 74±14% to 34±12%). AF driver ablation led to acute termination of AF.

Conclusions
Our ex vivo to in vivo human translational study suggests that transiently altering atrial refractoriness can stabilize reentrant paths and unmask arrhythmogenic hubs to guide targeted AF driver ablation treatment.
Modes of Atmospheric Circulation Variability in the Northern Extratropics: A Comparison of Five Reanalyses
Authors: Hynčica Martin , Huth Radan 
Published: October 2020

AbstractModes of low-frequency circulation variability in the Northern Hemisphere extratropics are compared between five reanalyses. Circulation modes are detected by rotated principal component analysis (PCA) of monthly mean 500-hPa geopotential heights between 1957 and 2002, separately for individual seasons. The quantification of differences between reanalyses is based on the percentage of grid points (approximately corresponding to the percentage of area) where the spatial representations of a mode (loadings) significantly differ between reanalyses. The differences between surface-input reanalyses (20CRv2c, ERA-20C) and full-input reanalyses (NCEP-1, ERA-40, JRA-55) are larger than differences within the reanalysis groups in all seasons except for autumn. The causes of the differences are of two kinds. First, the differences may be inherent to PCA: namely, the spatial structure of the modes may be sensitive to the number of components rotated. This concerns only a few modes. Second, the differences may reflect real correlation structures in reanalysis data. We demonstrate that the differences concentrate in three or fewer modes in each season. The reanalysis most different from the rest is 20CRv2c, with the differences concentrating over the southern half of Asia and in the subtropical belt over the Pacific and adjacent southwestern North America. The 20CRv2c reanalysis disagrees from other reanalyses there predominantly before the 1980s, which points to the impact of insufficient amount of assimilated observations. On the contrary, ERA-20C exhibits a higher agreement with full-input reanalyses, which is why we recommend it for studies of atmospheric circulation over the entire twentieth century.
Siberian Snow Forcing in a Dynamically Bias-Corrected Model
Authors: Tyrrell Nicholas L. , Karpechko Alexey Yu. , Rast Sebastian 
Published: October 2020

AbstractWe investigate the effect of systematic model biases on teleconnections influencing the Northern Hemisphere wintertime circulation. We perform a two-step nudging and bias-correcting scheme for the dynamic variables of the ECHAM6 atmospheric model to reduce errors in the model climatology relative to ERA-Interim. One result is a significant increase in the strength of the Northern Hemisphere wintertime stratospheric polar vortex, reducing errors in the December–February mean zonal stratospheric winds by up to 75%. The bias corrections are applied to the full atmosphere or the stratosphere only. We compare the response of the bias-corrected and control runs to an increase in Siberian snow cover in October—a surface forcing that, in our experiments, weakens the stratospheric polar vortex from October to December. We find that despite large differences in the vortex strength the magnitude of the stratospheric weakening is similar among the different climatologies, with some differences in the timing and length of the response. Differences are more pronounced in the stratosphere–troposphere coupling, and the subsequent surface response. The snow forcing with the stratosphere-only bias corrections results in a stratospheric response that is comparable to control, yet with an enhanced surface response that extends into early January. The full-atmosphere bias correction’s snow response also has a comparable stratospheric response but a somewhat suppressed surface response. Despite these differences, our results show an overall small sensitivity of the Eurasian snow teleconnection to the background climatology.
Extensive High-Resolution Synthetic Aperture Radar (SAR) Data Analysis of Tropical Cyclones: Comparisons with SFMR Flights and Best Track
Authors: Combot Clement , Mouche Alexis , Knaff John , Zhao Yili , Zhao Yuan , Vinour Leo , Quilfen Yves , Chapron Bertrand 
Published: October 2020

AbstractTo produce more precise descriptions of air–sea exchanges under tropical cyclones (TCs), spaceborne synthetic aperture radar (SAR) instruments provide unique capabilities to probe the ocean surface conditions, at very high spatial resolution, and on synoptic scales. Using highly resolved (3 km) wind fields, an extensive database is constructed fromRadarSat-2and Sentinel-1 SAR acquisitions. Spanning 161 tropical cyclones, the database covers all TC intensity categories that have occurred in 5 different TC basins, and include 29 cases coincident with SFMR measurements. After locating the TC center, a specific methodology is applied to filter out areas contaminated by heavy precipitation to help extract, for each acquisition, the maximum wind speed (Vmax), its associated radius (Rmax), and corresponding outer wind radii (R34/50/64 kt). These parameters are then systematically compared with best track (BTK), and when available, SFMR airborne measurements. For collocated SFMR and SAR observations, comparisons yield root-mean-squares of 3.86 m s−1and 3 km for ocean surface wind speeds and TC Rmax, respectively. High correlations remain for category-5 cases, with Vmax exceeding 60 m s−1. The largest discrepancies are found between BTK and SAR Rmax estimates, with Rmax fluctuations poorly captured by BTK, especially for rapidly evolving category-3, -4, and -5 TCs. In heavy precipitation (>35 mm h−1), the SAR C-band measurements may be impacted, with local ambiguities associated with rain features, as revealed by external rain measurements. Still, this large dataset demonstrates that SAR measurements have unique high-resolution capabilities, capturing the inner- and outer-core radial structure of the TC vortex, and provide independent and complementary measurements than those used for BTK estimates.
Assimilation of Satellite-Derived Soil Moisture for Improved Forecasts of the Great Plains Low-Level Jet
Authors: Ferguson Craig R. , Agrawal Shubhi , Beauharnois Mark C. , Xia Geng , Burrows D. Alex , Bosart Lance F. 
Published: October 2020

AbstractIn the context of forecasting societally impactful Great Plains low-level jets (GPLLJs), the potential added value of satellite soil moisture (SM) data assimilation (DA) is high. GPLLJs are both sensitive to regional soil moisture gradients and frequent drivers of severe weather, including mesoscale convective systems. An untested hypothesis is that SM DA is more effective in forecasts of weakly synoptically forced, or uncoupled GPLLJs, than in forecasts of cyclone-induced coupled GPLLJs. Using the NASA Unified Weather Research and Forecasting (NU-WRF) Model, 75 GPLLJs are simulated at 9-km resolution both with and without NASA Soil Moisture Active Passive SM DA. Differences in modeled SM, surface sensible (SH) and latent heat (LH) fluxes, 2-m temperature (T2), 2-m humidity (Q2), PBL height (PBLH), and 850-hPa wind speed (W850) are quantified for individual jets and jet-type event subsets over the south-central Great Plains, as well as separately for each GPLLJ sector (entrance, core, and exit). At the GPLLJ core, DA-related changes of up to 5.4 kg m−2in SM can result in T2, Q2, LH, SH, PBLH, and W850 differences of 0.68°C, 0.71 g kg−2, 59.9 W m−2, 52.4 W m−2, 240 m, and 4 m s−1, respectively. W850 differences focus along the jet axis and tend to increase from south to north. Jet-type differences are most evident at the GPLLJ exit where DA increases and decreases W850 in uncoupled and coupled GPLLJs, respectively. Data assimilation marginally reduces negative wind speed bias for all jets, but the correction is greater for uncoupled GPLLJs, as hypothesized.
Using ZDR Columns in Forecaster Conceptual Models and Warning Decision-Making
Authors: Kuster Charles M. , Schuur Terry J. , Lindley T. Todd , Snyder Jeffrey C. 
Published: October 2020

ABSTRACTResearch has shown that dual-polarization (dual-pol) data currently available to National Weather Service forecasters could provide important information about changes in a storm’s structure and intensity. Despite these new data being used gradually by forecasters more over time, they are still not used extensively to inform warning decisions because it is unclear how to apply dual-pol radar data to specific warning decisions. To address this knowledge gap, rapid-update (i.e., volumetric update time of 2.3 min or less) radar data of 45 storms in Oklahoma are used to examine one dual-pol signature, known as the differential reflectivity (ZDR) column, to relate this signature to warning decisions. Base data (i.e., ZDR, reflectivity, velocity) are used to relate ZDR columns to storm intensity, radar signatures such as upper-level reflectivity cores, and scientific conceptual models used by forecasters during the warning decision process. Analysis shows that 1) differences exist between the ZDR columns of severe and nonsevere storms, 2) ZDR columns develop and evolve prior to upper-level reflectivity cores, 3) rapid-update radar data provide a more complete picture of ZDR column evolution than traditional-update radar data (i.e., volumetric update time of about 5 min), and 4) ZDR columns provide a clearer and earlier indication of changes in updraft strength compared to reflectivity signatures. These findings suggest that ZDR columns can be used to inform warning decisions, increase warning confidence, and potentially increase warning lead time especially when they are integrated into existing conceptual models about a storm’s updraft and intensity.
Temporal airway microbiome changes related to ventilator-associated pneumonia in children
Authors: Mourani Peter M. , Sontag Marci K. , Williamson Kayla M. , Harris J. Kirk , Reeder Ron , Locandro Chris , Carpenter Todd C. , Maddux Aline B. , Ziegler Katherine , Simões Eric A.F. , Osborne Christina M. , Ambroggio Lilliam , Leroue Matthew K. , Robertson Charles E. , Langelier Charles , DeRisi Joseph L. , Kamm Jack , Hall Mark W. , Zuppa Athena F. , Carcillo Joseph , Meert Kathleen , Sapru Anil , Pollack Murray M. , McQuillen Patrick , Notterman Daniel A. , Dean J. Michael , Wagner Brandie D. 
Published: October 2020

We sought to determine whether temporal changes in the lower airway microbiome are associated with ventilator-associated pneumonia (VAP) in children.Using a multicentre prospective study of children aged 31 days to 18 years requiring mechanical ventilation support for >72 h, daily tracheal aspirates were collected and analysed by sequencing of the 16S rRNA gene. VAP was assessed using 2008 Centers for Disease Control and Prevention paediatric criteria. The association between microbial factors and VAP was evaluated using joint longitudinal time-to-event modelling, matched case–control comparisons and unsupervised clustering.Out of 366 eligible subjects, 66 (15%) developed VAP at a median of 5 (interquartile range 3–5) days post intubation. At intubation, there was no difference in total bacterial load (TBL), but Shannon diversity and the relative abundance ofStreptococcus, Lactobacillales andPrevotellawere lower for VAP subjectsversusnon-VAP subjects. However, higher TBL on each sequential day was associated with a lower hazard (hazard ratio 0.39, 95% CI 0.23–0.64) for developing VAP, but sequential values of diversity were not associated with VAP. Similar findings were observed from the matched analysis and unsupervised clustering. The most common dominant VAP pathogens includedPrevotellaspecies (19%),Pseudomonas aeruginosa(14%) andStreptococcus mitis/pneumoniae(10%).MycoplasmaandUreaplasmawere also identified as dominant organisms in several subjects.In mechanically ventilated children, changes over time in microbial factors were marginally associated with VAP risk, although these changes were not suitable for predicting VAP in individual patients. These findings suggest that focusing exclusively on pathogen burden may not adequately inform VAP diagnosis.
Subduction of a rifted passive continental margin: the Pohorje case of Eastern Alps–constraints from geochronology and geochemistry
Authors: Chang Ruihong , Neubauer Franz , Liu Yongjiang , Genser Johann , Jin Wei , Yuan Sihua , Guan Qingbin , Huang Qianwen , Li Weimin 
Published: October 2020

AbstractThis study presents geochronological and geochemical data from newly dated Permian granitic orthogneisses associated with the Eclogite-Gneiss unit (EGU) from the southernmost part of the Austroalpine nappe stack, exposed within the Pohorje Mountains (Slovenia). LA-ICP-MS zircon U–Pb ages of two samples of the augen-gneisses are 255 ± 2.2 Ma and 260 ± 0.81 Ma, which are interpreted as the age of magmatic crystallization of zircon. In contrast, all round zircons from leucogneisses give Cretaceous ages (89.3 ± 0.7 Ma and 90.8 ± 1.2 Ma), considered as the age of UHP/HP metamorphism. The round zircons overgrew older euhedral zircons of Permian and rare older ages tentatively indicating that these rocks are of latest Permian age, too. Zircon εHf(t) values of the four orthogneiss samples are between − 13.7 and − 1.7 with an initial176Hf/177Hf ratio ranging from 0.282201 to 0.282562; TDMCis Proterozoic. The augen-gneisses show geochemical features, e.g. high (La/Lu)Nratios and strong negative Eu anomalies, of an evolved granitic magma derived from continental crust. The leucogneisses are more heterogeneously composed and are granitic to granodioritic in composition and associated with eclogites and ultramafic cumulates of oceanic affinity. We argue that the Permian granitic orthogneisses might be derived from partial melting of lower crust in a rift zone. We consider, therefore, that segment of the EGU is part of the distal Late Permian rift zone, which finally led to the opening of the Meliata Ocean during Middle Triassic times. If true, the new data also imply that the Permian stretched continental crust was potentially not much wider than ca. 100 km, was subducted and then rapidly exhumed during early Late Cretaceous times.
microRNA-18a from M2 Macrophages Inhibits TGFBR3 to Promote Nasopharyngeal Carcinoma Progression and Tumor Growth via TGF-β Signaling Pathway
Authors: Peng Ya , Li Xiangsheng , Liu Huowang , Deng Xiaowen , She Chang , Liu Chenxi , Wang Xinxing , Liu An 
Published: October 2020

Abstract
Objectives
Nasopharyngeal carcinoma (NPC) is a type of nasopharyngeal disease with high metastasis and invasion properties. Tumor-associated alternative activated (M2) macrophages are evidenced to connect with NPC. Based on this, this study purposes to explore the mechanism and participation of microRNA-18a (miR-18a) from M2 macrophages in NPC.

Methods
Peripheral blood mononuclear cells were differentiated to macrophages and macrophages were polarized to M2 type by interleukin-4. SUNE-1 and CNE2 cells were transfected with restored or depleted miR-18a or transforming growth factor-beta III receptor (TGFBR3) to explore their roles in NPC progression with the involvement of the TGF-β signaling pathway. Next, SUNE-1 and CNE2 cells were co-cultured with M2 macrophages that had been treated with restored or depleted miR-18a or TGFBR3 to comprehend their combined roles in NPC with the involvement of the TGF-β signaling pathway.

Results
MiR-18a was highly expressed and TGFBR3 was lowly expressed in NPC cells. MiR-18a restoration, TGFBR3 knockdown or co-culture with miR-18a mimics, or si-TGFBR3-transfected M2 macrophages promoted SUNE-1 cell progression, tumor growth in mice, decreased p-Smad1/t-Smad1, and elevated p-Smad3/t-Smad3. miR-18a downregulation, TGFBR3 overexpression, or co-culture with miR-18a inhibitors or OE-TGFBR3-transfected M2 macrophages depressed CNE2 cell progression, tumor growth in mice, increased p-Smad1/t-Smad1, and decreased p-Smad3/t-Smad3.

Conclusion
Our study elucidates that miR-18a from M2 macrophages results in promoted NPC cell progression and tumor growth in nude mice via TGFBR3 repression, along with the Smad1 inactivation and Smad3 activation.
Real-time audio and visual display of the Coronavirus genome
Authors: Temple Mark D. 
Published: October 2020

Abstract
Background
This paper describes a web based tool that uses a combination of sonification and an animated display to inquire into the SARS-CoV-2 genome. The audio data is generated in real time from a variety of RNA motifs that are known to be important in the functioning of RNA. Additionally, metadata relating to RNA translation and transcription has been used to shape the auditory and visual displays. Together these tools provide a unique approach to further understand the metabolism of the viral RNA genome. This audio provides a further means to represent the function of the RNA in addition to traditional written and visual approaches.

Results
Sonification of the SARS-CoV-2 genomic RNA sequence results in a complex auditory stream composed of up to 12 individual audio tracks. Each auditory motive is derived from the actual RNA sequence or from metadata. This approach has been used to represent transcription or translation of the viral RNA genome. The display highlights the real-time interaction of functional RNA elements. The sonification of codons derived from all three reading frames of the viral RNA sequence in combination with sonified metadata provide the framework for this display. Functional RNA motifs such as transcription regulatory sequences and stem loop regions have also been sonified. Using the tool, audio can be generated in real-time from either genomic or sub-genomic representations of the RNA. Given the large size of the viral genome, a collection of interactive buttons has been provided to navigate to regions of interest, such as cleavage regions in the polyprotein, untranslated regions or each gene. These tools are available through an internet browser and the user can interact with the data display in real time.

Conclusion
The auditory display in combination with real-time animation of the process of translation and transcription provide a unique insight into the large body of evidence describing the metabolism of the RNA genome. Furthermore, the tool has been used as an algorithmic based audio generator. These audio tracks can be listened to by the general community without reference to the visual display to encourage further inquiry into the science.
C3: connect separate connected components to form a succinct disease module
Authors: Wang Bingbo , Hu Jie , Wang Yajun , Zhang Chenxing , Zhou Yuanjun , Yu Liang , Guo Xingli , Gao Lin , Chen Yunru 
Published: October 2020

Abstract
Background
Precise disease module is conducive to understanding the molecular mechanism of disease causation and identifying drug targets. However, due to the fragmentization of disease module in incomplete human interactome, how to determine connectivity pattern and detect a complete neighbourhood of disease based on this is still an open question.

Results
In this paper, we perform exploratory analysis leading to an important observation that through a few intermediate nodes, most separate connected components formed by disease-associated proteins can be effectively connected and eventually form a complete disease module. And based on the topological properties of these intermediate nodes, we propose a connect separate connected components (C3) method to detect a succinct disease module by introducing a relatively small number of intermediate nodes, which allows us to obtain more pure disease module than other methods. Then we apply C3 across a large corpus of diseases to validate this connectivity pattern of disease module. Furthermore, the connectivity of the perturbed genes in multi-omics data such as The Cancer Genome Atlas also fits this pattern.

Conclusions
C3 tool is not only useful in detecting a clearly-defined connected disease neighbourhood of 299 diseases and cancer with multi-omics data, but also helpful in better understanding the interconnection of phenotypically related genes in different omics data and studying complex pathological processes.