bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mako: A Graph-Based Pattern Growth Approach to Detect Complex Structural Variants
Authors: Lin Jiadong , Yang Xiaofei , Kosters Walter , Xu Tun , Jia Yanyan , Wang Songbo , Zhu Qihui , Ryan Mallory , Guo Li , Gerstein Mark B. , Sanders Ashley D. , Zody Micheal C. , Talkowski Michael E. , Mills Ryan E. , Korbel Jan O. , Marschall Tobias , Ebert Peter , Audano Peter A. , Rodriguez-Martin Bernardo , Porubsky David , Jan Bonder Marc , Sulovari Arvis , Ebler Jana , Zhou Weichen , Serra Mari Rebecca , Yilmaz Feyza , Zhao Xuefang , Hsieh PingHsun , Lee Joyce , Kumar Sushant , Rausch Tobias , Chen Yu , Chong Zechen , Munson Katherine M. , Chaisson Mark J.P. , Chen Junjie , Shi Xinghua , Wenger Aaron M. , Harvey William T. , Hansenfeld Patrick , Regier Allison , Hall Ira M. , Flicek Paul , Hastie Alex R. , Fairely Susan , Zhang Chengsheng ,   The Human Genome Structural Variation Consortium, Lee Charles , Devine Scott E. , Eichler Evan E. , Ye Kai 
Published: July 2021

Abstract
Complex structural variants (CSVs) are genomic alterations that have more than two breakpoints and are considered as the simultaneous occurrence of simple structural variants. However, detecting the compounded mutational signals of CSVs is challenging through a commonly used model-match strategy. As a result, there has been limited progress for CSV discovery compared with simple structural variants. Here, we systematically analyzed the multi-breakpoint connection feature of CSVs, and proposed Mako, utilizing a bottom-up guided model-free strategy, to detect CSVs from paired-end short-read sequencing. Specifically, we implemented a graph-based pattern growth approach, where the graph depicts potential breakpoint connections, and pattern growth enables CSV detection without pre-defined models. Comprehensive evaluations on both simulated and real datasets revealed that Mako outperformed other algorithms. Notably, validation rates of CSVs on real data based on experimental and computational validations as well as manual inspections are around 70%, where the medians of experimental and computational breakpoint shift are 13 bp and 26 bp, respectively. Moreover, the Mako CSV subgraph effectively characterized the breakpoint connections of a CSV event and uncovered a total of 15 CSV types, including two novel types of adjacent segment swap and tandem dispersed duplication. Further analysis of these CSVs also revealed the impact of sequence homology on the formation of CSVs. Mako is publicly available at https://github.com/xjtu-omics/Mako.
New Radiocarbon Constraints on the Global Cycling of Solid‐Phase Extractable Dissolved Organic Carbon
Authors: Lewis Christian B. , Walker Brett D. , Druffel Ellen R. M. 
Published: July 2021

AbstractRadiocarbon (∆14C) measurements suggest the deep ocean stores marine dissolved organic carbon (DOC) on millennial timescales. The mechanisms that mediate this residence time remain unconstrained. Solid‐phase extraction (SPE) has emerged as a widely used technique to isolate DOC for subsequent analyses. We present SPE‐DOC concentrations and ∆14C values for three GO‐SHIP Repeat Hydrography transects, spanning the Pacific, Southern and Indian Oceans. Comparisons of SPE‐DOC with total DOC ∆14C values are used with an isotopic mass‐balance to estimate the size of the refractory DOC (RDOC) reservoir and changes in RDOC relative abundance in the global ocean. Estimated RDOC abundance is similar across the deep Pacific and Indian Oceans (average = 93 ± 5%, 35 ± 6 μM), whereas RDOC in the surface ocean varies as a function of total DOC concentration. Our results fill in spatial SPE‐DOC ∆14C sampling gaps for the global ocean, and our mass‐balance RDOC estimates are consistent with previous observations.
Southeast Indian Subantarctic Mode Water in the CMIP6 Coupled Models
Authors: Qiu Zishan , Wei Zexun , Nie Xunwei , Xu Tengfei 
Published: July 2021

AbstractThis study assesses the capability of 12 models in the Phase 6 of the Coupled Models Intercomparison Project (CMIP6) in simulating the Southeast Indian Subantarctic mode water (SEISAMW) by comparing to Argo observations. The results show that all of the analyzed CMIP6 coupled models can reproduce the SEISAMW and its seasonal cycle, albeit with discrepancies of formation region and properties among the models. The SEISAMW subduction rate shows significant interannual variability, which is primarily induced by lateral induction in these models, in agreement with observations. Furthermore, the longterm trends of the SEISAMW show volume loss in accordance with the descending trend of the subduction rate, which are co‐occurred with the ascending trend of the Southern Annular Mode (SAM) indices in most of the analyzed CMIP6 models, similar to those in the CMIP3 and CMIP5 coupled models. Meanwhile, the potential density of the SEISAMWs show decreasing trends in these volume loss models, which could be explained by the warming (SAM0‐UNICON, CESM2‐WACCM, CAS‐ESM2‐0 and CIESM), the freshening (IPSL‐CM6A‐LR, CAMS‐CSM1‐0, MRI‐ESM2‐0, and FGOALS‐f3‐L) or the both (FIO‐ESM‐2‐0, E3SM‐1‐0, and CanESM5) trends of the SEISAMWs in different CMIP6 coupled models. Decreases in the projected subduction rate and volume of SEISAMW imply a slowdown of Southern Indian Ocean circulation in the future, reducing the heat and carbon transport from atmosphere to ocean interior contributed by SEISAMW.
Reversing Sahelian Droughts
Authors: Ricke Katharine , Ivanova Detelina , McKie Taylor , Rugenstein Maria 
Published: July 2021

AbstractEarth system modeling of climate geoengineering proposals suggests that the physical outcomes of such interventions will depend on the particulars of the implementation. Here, we present a first attempt to “geoengineer” a well‐known teleconnection between sea surface temperatures (SSTs) and Sahelian precipitation. Using idealized earth system model simulations, we show that selectively cooling the Indian Ocean efficiently increases precipitation in the Sahel region, widening the seasonally migrating rainband over Africa. Applying the SST perturbations derived from the idealized experiments to observationally constrained historical ones, we find that our intervention can reverse conditions as extreme as the mid‐20th century Sahelian drought, albeit less efficiently than in the idealized simulations. Side effects include changes in the seasonal distribution of Sahelian precipitation and substantial precipitation reductions in sub‐Saharan East Africa. This work represents a proof‐of‐concept illustration of effects that might be expected with a tailored, regional approach to climate intervention.
Hydrological Effects on Seismic‐Noise Monitoring in Karstic Media
Authors: Almagro Vidal C. , Zaccarelli L. , Pintori F. , Bragato P. L. , Serpelloni E. 
Published: July 2021

AbstractFluctuations in groundwater content may produce surface deformation and affect the elastic properties of the Earth’s crust. In this study, we evaluate the temporal variations of the Earth’s crust elastic properties (in the form of relative seismic‐velocity variations) in a tectonically active region in Northern Italy characterized by the presence of karst systems. In this area, GPS measurements already revealed hydrologically‐induced deformation, modulated by changes in groundwater storage. We study the relation of our seismological observations with the geodetic and hydrological results and identify the effects of groundwater‐content variations in the seismic‐velocity perturbations. Our results show that hydrologically‐induced changes in karstic media produce significant seismic‐velocity perturbations, therefore its role in tectonic‐stress adjustment studies must not be ignored. Depth sensitivity analysis of our results constrain the crustal perturbations to range between 500 and 3,500 m depth. Results from scattering imaging locate the crustal perturbations along the main local karst systems.
Micromechanics of Sheared Granular Layers Activated by Fluid Pressurization
Authors: Nguyen Hien Nho Gia , Scholtès Luc , Guglielmi Yves , Donzé Frédéric Victor , Ouraga Zady , Souley Mountaka 
Published: July 2021

AbstractFluid pressurization of critically stressed sheared zones can trigger slip mechanisms at work in many geological processes. Using discrete element modeling, we simulate pore‐pressure‐step creep test experiments on a sheared granular layer under a sub‐critical stress state to investigate the micromechanical processes at stake during fluid induced reactivation. The global response is consistent with available experiments. The progressive increase of pore pressure promotes slow steady creep at sub‐critical stress states, and fast accelerated dynamic slip once the critical strength is overcome. Our multi‐scale analyses show that these two emergent behaviors correlate to characteristic deformation modes: diffuse deformation during creep, and highly localized deformation during rupture. Creep corresponds to bulk deformation while rupture results from grain rotations initiating from overpressure induced unlocking of contacts located within the shear band which, consequently, acts as a roller bearing for the surrounding bulk.
“Simpson's Law” and the Spectral Cancellation of Climate Feedbacks
Authors: Jeevanjee Nadir , Koll Daniel D. B. , Lutsko Nicholas 
Published: July 2021

AbstractWe spectrally resolve the conventional clear‐sky temperature and water vapor feedbacks in an idealized single‐column framework, and show that the well‐known partial compensation of these feedbacks is actually due to an almost perfect cancellation of the spectral feedbacks at wavenumbers where H2O is optically thick. This cancellation is a natural consequence of “Simpson's Law”, which says that H2O emission temperatures do not change with surface warming if relative humidity (RH) is fixed. We provide an explicit formulation and validation of Simpson's Law, and furthermore show that this spectral cancellation of feedbacks is naturally incorporated in the alternative RH‐based framework proposed by Held and Shell (2012, https://doi.org/10.1175/jcli-d-11-00721.1) and Ingram (2012, https://doi.org/10.1029/2011jd017221, 2013b, https://doi.org/10.1007/s00382-012-1294-3), thus bolstering the case for switching from conventional to RH‐based feedbacks. We also find a negligible RH‐based clear‐sky lapse rate feedback, suggesting that the impact of changing lapse rates depends crucially on whether relative or specific humidity is held fixed.
Direct Evidence Reveals Transmitter Signal Propagation in the Magnetosphere
Authors: Gu Wenyao , Chen Lunjin , Xia Zhiyang , Horne Richard B. 
Published: July 2021

AbstractSignals from very‐low‐frequency transmitters on the ground are known to induce energetic electron precipitation from the Earth's radiation belts. The effectiveness of this mechanism depends on the propagation characteristics of those signals in the magnetosphere, and in particular whether the signals are ducted or nonducted along channels of enhanced plasma density, analogous to optical fibers. Here we perform a statistical analysis of in‐situ waveform data collected by the Van Allen Probes satellites that shows that nonducted propagation dominates over ducted propagation in both the occurrence and intensity of the waves. Ray tracing confirms that the latitudinal distribution of wavevectors corresponds to nonducted as opposed to ducted propagation. Our results show the dominant mode of propagation needed to quantify transmitter‐induced precipitation and improve the forecast of electron radiation belt dynamics for the safe operation of satellites.
Progress in Unraveling Atmospheric New Particle Formation and Growth Across the Arctic
Authors: Schmale Julia , Baccarini Andrea 
Published: July 2021

AbstractNew particle formation (NPF) and growth can be an important source of cloud condensation nuclei for the Arctic atmosphere, where cloud formation is sensitive to their availability. Low‐level clouds influence the Arctic energy budget, and likely contribute to amplified Arctic warming. Molecular information of NPF is rarely reported, despite its importance to determine sources of condensing vapors and nucleation mechanisms. Beck et al. (2020, https://doi.org/10.1029/2020gl091334) shed light on the complexity of NPF and growth at two Arctic locations. They reveal that chemical drivers and sources are diverse across the Arctic. This advance in knowledge calls for similar studies throughout all seasons and in various Arctic environments to obtain a more systematic understanding of NPF and growth.
Closure of the Paleo‐Asian Ocean in the Middle‐Late Triassic (Ladinian‐Carnian): Evidence From Provenance Analysis of Retroarc Sediments
Authors: Song Dongfang , Xiao Wenjiao , Windley Brian F. , Mao Qigui , Ao Songjian , Wang Hao Y. C. , Li Rui 
Published: July 2021

AbstractA major current debate in Asian tectonics concerns the time of closure of the Paleo‐Asian Ocean (PAO) and the collision between the Central Asian arcs and the Tarim and North China cratons (NCC). This has led to much uncertainty about the reconstruction of proto‐Asia and tectonic configuration of northeast Pangea. Here we report Triassic provenance change in the foreland of the Alxa Block by field‐based zircon U‐Pb and Hf isotopic analysis. Nonmarine sediments, unconformable on or in fault contact, with the Alxa basement yield Precambrian and Paleozoic–Triassic detrital zircon ages with maximum depositional ages of Middle‐Late Triassic (∼244–224 Ma). Hf isotopic data indicate that Middle Triassic sandstones were sourced from the NCC basement and a continental arc, whereas Late Triassic sediments received an additional input from a juvenile arc. This provenance change in the foreland sedimentation indicates that the final closure of the PAO was in the Middle‐Late Triassic.
Record‐Low WNP Tropical Cyclone Activity in Early Summer 2020 due to Indian Ocean Warming and Madden‐Julian Oscillation Activity
Authors: Liu Chao , Zhang Wenjun , Jiang Feng , Stuecker Malte F. , Huang Zongci 
Published: July 2021

AbstractDuring early boreal summer 2020, the western North Pacific (WNP) was characterized by record‐low tropical cyclone (TC) activity, reaching the lowest historical level since 1979. Only one short‐lived TC was observed in June and the whole of July underwent an unprecedented quiescent TC period. Concurrent Indian Ocean warming provided unfavorable conditions for cyclogenesis over the WNP, which partly (∼40%) explains the extremely low TC number from a statistical standpoint. Accompanied with the Indian Ocean warming, an unprecedentedly long‐lasting Madden‐Julian Oscillation (MJO) event stalled over the Indian Ocean sector, persisting almost through the entire June and July. This simultaneous quasi‐stationary MJO activity further caused unfavorable background conditions for cyclogenesis in the WNP. The Indian Ocean warming combined with the anomalous MJO conditions together largely (>80%) explain the record‐low TC number over the WNP during early summer 2020.
First Results on E Region Irregularities From a 53 MHz Radar Experiment From Haringhata, India
Authors: Paul Ashik , Chaitanya P. Pavan , Patra A. K. , Nandakumar P. , Das Tanmay 
Published: July 2021

AbstractWe present the first results on E region field‐aligned irregularities (FAIs) observed using a 53 MHz radar experiment conducted from Ionosphere Field Station, Haringhata (geographic latitude 22.93°N; geographic longitude 88.5°E; magnetic dip angle 35.2°N) of University of Calcutta, a location just on the Tropic of Cancer and below the Equatorial Ionization Anomaly. Results show that the E region FAI echoes, which occur with signal intensity as high as 35 dB above noise, are mostly confined to altitudes of 90–120 km with daytime FAI being confined to 100 km. The FAI echoes are often found to occur in the form of descending echoing region that includes continuous, quasi periodic and discrete patches of echoes. The FAI echoes display large day‐to‐day variations and tend to occur more during the morning (06–09 IST) and evening (18–21 IST) with relative less occurrence during the noon and midnight. Doppler spectra are type‐2 in nature with mean Doppler velocity in the range of −100–120 m s−1 and spectral width limited to 100 m s−1. While these characteristics are very similar to those of off‐equatorial low latitudes and mid‐latitudes, comparison of these results with those concurrently observed at Gadanki reveals remarkable difference in the echo occurrence, day‐to‐day variability and Doppler velocity, in spite of the small difference in ionospheric pierce points between these two stations. These results are discussed and the prospective of these observations in understanding the E region FAI over a convective active meteorological region is outlined.
Microbiome diversity and host immune functions influence survivorship of sponge holobionts under future ocean conditions
Authors: Posadas Niño , Baquiran Jake Ivan P , Nada Michael Angelou L , Kelly Michelle , Conaco Cecilia 
Published: July 2021

Abstract
The sponge-associated microbial community contributes to the overall health and adaptive capacity of the sponge holobiont. This community is regulated by the environment and the immune system of the host. However, little is known about the effect of environmental stress on the regulation of host immune functions and how this may, in turn, affect sponge–microbe interactions. In this study, we compared the bacterial diversity and immune repertoire of the demosponge, Neopetrosia compacta, and the calcareous sponge, Leucetta chagosensis, under varying levels of acidification and warming stress based on climate scenarios predicted for 2100. Neopetrosia compacta harbors a diverse microbial community and possesses a rich repertoire of scavenger receptors while L. chagosensis has a less diverse microbiome and an expanded range of pattern recognition receptors and immune response-related genes. Upon exposure to RCP 8.5 conditions, the microbiome composition and host transcriptome of N. compacta remained stable, which correlated with high survival (75%). In contrast, tissue necrosis and low survival (25%) of L. chagosensis was accompanied by microbial community shifts and downregulation of host immune-related pathways. Meta-analysis of microbiome diversity and immunological repertoire across poriferan classes further highlights the importance of host–microbe interactions in predicting the fate of sponges under future ocean conditions.
SNP-mediated lncRNA-ENTPD3-AS1 upregulation suppresses renal cell carcinoma via miR-155/HIF-1α signaling
Authors: Wang Jiangyi , Zou Yun , Du Bowen , Li Wenzhi , Yu Guopeng , Li Long , Zhou Lin , Gu Xin , Song Shangqing , Liu Yushan , Zhou Wenquan , Xu Bin , Wang Zhong 
Published: July 2021

AbstractOver the last decade, more than 10 independent SNPs have been discovered to be associated with the risk of renal cell carcinoma among different populations. However, the biological functions of them remain poorly understood. In this study, we performed eQTL analysis, ChIP-PCR, luciferase reporter assay, and Cox regression analysis to identify the functional role and underlying mechanism of rs67311347 in RCC. The ENCORI database, which contains the lncRNA–miRNA–mRNA interactions, was used to explore the possible target miRNA of ENTPD3-AS1. The results showed that the G > A mutation of rs67311347 created a binding motif of ZNF8 and subsequently upregulated ENTPD3-AS1 expression by acting as an enhancer. The TCGA-KIRC and our cohorts both confirmed the downregulation of ENTPD3-AS1 in RCC tissues and demonstrated that increased ENTPD3-AS1 expression was associated with good OS and PFS. Furthermore, ENTPD3-AS1 interacted with miR-155-5p and activated the expression of HIF-1α, which was an important tumor suppressor gene in the development of RCC. The functional experiments revealed that overexpression of ENTPD3-AS1 inhibited cell proliferation in RCC cell lines and the effect could be rescued by knocking down HIF-1α. Our findings reveal that SNP-mediated lncRNA-ENTPD3-AS1 upregulation suppresses renal cell carcinoma via miR-155/HIF-1α signaling.
A novel GaN MIS‐HEMT with a floating clamp electrode for suppressing short‐channel effect
Authors: Shi Yijun , Wang Hongyue 
Published: July 2021

AbstractIn this work, a novel GaN MIS‐HEMT (metal‐insulator‐semiconductor high electron mobility transistors) featuring a floating clamp (FC) electrode is proposed for suppressing the short‐channel effect. By inserting the FC electrode near to the drain‐side gate edge, the transverse potential at the gate edge can be clamped to less than 2 V, thereby the short‐channel effect can be suppressed. Compared to the conventional short‐channel GaN MIS‐HEMT, the proposed device exhibits much decreased off‐state electron density at the drain voltage of 10 V, which leads to the off‐state leakage current decreasing from 10–1 to 10–7 A/mm, without an obvious sacrifice of the on‐state current. Meanwhile, the proposed GaN MIS‐HEMT also delivers a much lower reverse gate‐to‐drain capacitor. The excellent characteristics of the proposed GaN MIS‐HEMT show that the device is promising for the future power applications.
First dust measurements with the Solar Orbiter Radio and Plasma Wave instrument
Authors: Zaslavsky A. , Mann I. , Soucek J. , Czechowski A. , Píša D. , Vaverka J. , Meyer-Vernet N. , Maksimovic M. , Lorfèvre E. , Issautier K. , Rackovic Babic K. , Bale S. D. , Morooka M. , Vecchio A. , Chust T. , Khotyaintsev Y. , Krasnoselskikh V. , Kretzschmar M. , Plettemeier D. , Steller M. , Štverák Š. , Trávníček P. , Vaivads A. 
Published: July 2021

Context.Impacts of dust grains on spacecraft are known to produce typical impulsive signals in the voltage waveform recorded at the terminals of electric antennas. Such signals (as may be expected) are routinely detected by the Time Domain Sampler (TDS) system of the Radio and Plasma Waves (RPW) instrument on board Solar Orbiter.Aims.We investigate the capabilities of RPW in terms of interplanetary dust studies and present the first analysis of dust impacts recorded by this instrument. Our purpose is to characterize the dust population observed in terms of size, flux, and velocity.Methods.We briefly discuss previously developed models of voltage pulse generation after a dust impact onto a spacecraft and present the relevant technical parameters for Solar Orbiter RPW as a dust detector. Then we present the statistical analysis of the dust impacts recorded by RPW/TDS from April 20, 2020 to February 27, 2021 between 0.5 AU and 1 AU.Results.The study of the dust impact rate along Solar Orbiter’s orbit shows that the dust population studied presents a radial velocity component directed outward from the Sun. Its order of magnitude can be roughly estimated asvr, dust ≃ 50 km s−1, which is consistent with the flux of impactors being dominated byβ-meteoroids. We estimate the cumulative flux of these grains at 1 AU to be roughlyFβ ≃ 8 × 10−5m−2s−1for particles of a radiusr ≳ 100 nm. The power law indexδof the cumulative mass flux of the impactors is evaluated by two differents methods, namely: direct observations of voltage pulses and indirect effect on the impact rate dependency on the impact speed. Both methods give the following result:δ ≃ 0.3 − 0.4.Conclusions.Solar Orbiter RPW proves to be a suitable instrument for interplanetary dust studies, and the dust detection algorithm implemented in the TDS subsystem an efficient tool for fluxes estimation. These first results are promising for the continuation of the mission, in particular, for the in situ study of the inner Solar System dust cloud outside of the ecliptic plane, which Solar Orbiter will be the first spacecraft to explore.