bluuebunny/crossref_metadata_2025_split huggingface dataset:
AI‐Based Unmixing of Medium and Source Signatures From Seismograms: Ground Freezing Patterns
Authors: Steinmann René , Seydoux Léonard , Campillo Michel 
Published: August 2022

AbstractSeismograms always result from mixing many sources and medium changes that are complex to disentangle, witnessing many physical phenomena within the Earth. With artificial intelligence (AI), we isolate the signature of surface freezing and thawing in continuous seismograms recorded in a noisy urban environment. We perform a hierarchical clustering of the seismograms and identify a pattern that correlates with ground frost periods. We further investigate the fingerprint of this pattern and use it to track the continuous medium change with high accuracy and resolution in time. Our method isolates the effect of the ground frost and describes how it affects the horizontal wavefield. Our findings show how AI‐based strategies can help to identify and understand hidden patterns within seismic data caused either by medium or source changes.
Upper Limit of Outer Radiation Belt Electron Acceleration Driven by Whistler‐Mode Chorus Waves
Authors: Hua Man , Bortnik Jacob , Ma Qianli 
Published: August 2022

AbstractWe investigate the outer radiation belt electron energy spectra of the highest fluxes observed during storms based on Van Allen Probes measurements, which demonstrate a similar shape despite various levels of geomagnetic activity. Using quasi‐linear diffusion simulations, we reproduce the observed electron acceleration by whistler‐mode chorus waves during the storm of 25 October 2016, when the maximum fluxes were close to the highest upper limit observed during the 2013–2018 period. The electrons below ∼1 MeV reached the upper limit of chorus acceleration within ∼1 day and then remained at a stable level, while the multi‐MeV electrons with sharper energy gradient were subject to the continuous acceleration process. Our results reveal the natural upper limit of electron acceleration by chorus, which strongly depends on the lower energy boundary, and the stable seed population at hundreds of keV (but not the chorus intensity) which is a prerequisite for the relativistic electron acceleration.
Forecasting Surface Velocity Fields Associated With Laboratory Seismic Cycles Using Deep Learning
Authors: Mastella G. , Corbi F. , Bedford J. , Funiciello F. , Rosenau M. 
Published: August 2022

AbstractIt has been recently demonstrated that Machine Learning (ML) can predict laboratory earthquakes. Here we propose a prediction framework that allows forecasting future surface velocity fields from past ones for analog experiments of megathrust seismic cycles. Using data from two types of experiments, we explore the prediction performances of multiple Deep Learning (DL) and ML algorithms. In such a self‐supervised regression, no feature extraction is required and the entire seismic cycle is forecasted. The onset, magnitude, and propagation of analog earthquakes can thus be predicted at different prediction horizons. From all architectures tested in this study, convolutional recurrent neural networks (CNN‐LSTM and CONVLSTM) provide the best predictions although their performances depend on experiment characteristics and hyperparameters tuning. Analog earthquakes can be successfully anticipated up to a horizon of the order of their duration. This laboratory‐based study may open new avenues for transfer learning applications with data from natural subduction zones.
Compositional Attributes of the Deep Continental Crust Inferred From Geochemical and Geophysical Data
Authors: Sammon Laura G. , McDonough William F. , Mooney Walter D. 
Published: August 2022

AbstractThis study provides a global assessment of the abundance of the major oxides in the deep continental crust. The combination of geochemistry and seismology better constrains the composition of the middle and lower continental crust better than either discipline can achieve alone. The inaccessible nature of the deep crust (typically >15 km) forces reliance on analog samples and modeling results to interpret its bulk composition, evolution, and physical properties. A common practice relates major oxide compositions of small‐ to medium‐scale samples (e.g., medium to high metamorphic grade terrains and xenoliths) to large scale measurements of seismic velocities (Vp, Vs, Vp/Vs) to determine the composition of the deep crust. We provide a framework for building crustal models with multidisciplinary constraints on composition. We present a global deep crustal model that documents compositional changes with depth and accounts for uncertainties in Moho depth, temperature, and physical and chemical properties. Our 3D compositional model of the deep crust uses the USGS Global Seismic Structure Catalog (Mooney, 2015) and a compilation of geochemical analyses on amphibolite and granulite facies lithologies (Sammon & McDonough, 2021, https://doi.org/10.1029/2021JB022791). We find a SiO2 gradient from 61.2 ± 7.3 to 53.3 ± 4.8 wt.% from the middle to the base of the crust, with the equivalent lithological gradient ranging from quartz monzonite to gabbronorite. In addition, we calculate trace element abundances as a function of depth from their correlations with major oxides. From here, other lithospheric properties, such as Moho heat flux ( mW/m2), are derived.
On the Influence of Antecedent Morphology on Development of Equilibrium Bathymetry in Estuaries Past and Future
Authors: Rahdarian Amin , Bryan Karin R. , Van Der Wegen Mick 
Published: August 2022

AbstractAlthough analytical and numerical models have been widely used to explore evolution and equilibrium morphology in tidal environments, less attention has been paid to examining the impact of initial bathymetry on the model outcomes. Here we use two‐dimensional idealized models with contrasting initial bathymetries to study how the interactions between antecedent morphology and tidal exchange processes determine the establishment of an estuarine equilibrium bathymetry, and how these interactions mediate the morphodynamic response to rising sea levels. In all model runs with sandy beds, inter‐tidal zones reach the equilibrium condition first and equilibrium profiles are similar for points close to mean seal level. However, key aspects like channel formation, residence time and energy dissipation do not evolve to the same state and are inherited from the initial bathymetry. This implies that responses to sea‐level rise (SLR) are different as well. Conversely, in cases with mud and sand input at the boundaries, equilibrium occurs more quickly and the equilibrium bathymetry and channel formation are dominated by the boundary mud concentration. General implications of the study are that predictions of coastal response to changes such as SLR depend on initial bathymetric conditions.
Storm‐Time Observations of Traveling Ionospheric Disturbances and Ionospheric Irregularities in East Africa
Authors: Moges Samson T. , Giday Nigussie Mezgebe , Chekole Daniel Atnafu , Ulich Thomas , Sherstyukov R. O. 
Published: August 2022

AbstractIn this paper equatorward propagating large scale traveling ionospheric disturbance (LSTID) on 17 March 2015 were investigated using the Statistical Angle‐of‐Arrival and Doppler Method for GPS (SADM‐GPS) radio interferometry technique in data‐scarce East Africa. To apply the SADM‐GPS method, 5 GPS arrays each with 3 GPS receivers arranged in a triangular geometry were used. Our results show that during 15:00–18:00 UT on 17 March, TIDs with mean horizontal velocities between 161.9 and 464.4 m/s were observed. Using the wavelet analysis, the periods of TIDs in a range of 51–69 min that qualify to LSTIDs were revealed. The peak‐to‐peak phase shift of detrended total electron content (TEC) over latitudes in this study confirms the equatorward TID propagation, which was obtained by the SADM‐GPS technique. A pair of magnetometers were used to infer E × B drift and an adequate agreement was found with Swarm satellites derived plasma density that enabled us to explain the behaviour of ionospheric irregularity during the main phase of the geomagnetic storm. Moreover, significant TEC enhancement (reaching ∼20%–105%) were captured by GPS arrays during the period of TID propagation. Nevertheless, the rate of change of TEC (ROT) and ROT index (ROTI) show wavy structures that reflect TID effects over ionospheric modulations during the post noon to evening hours of 17 March 2015.
Genomic landscape of patients with FLT3-mutated acute myeloid leukemia (AML) treated within the CALGB 10603/RATIFY trial
Authors: Jahn Nikolaus , Jahn Ekaterina , Saadati Maral , Bullinger Lars , Larson Richard A. , Ottone Tiziana , Amadori Sergio , Prior Thomas W. , Brandwein Joseph M. , Appelbaum Frederick R. , Medeiros Bruno C. , Tallman Martin S. , Ehninger Gerhard , Heuser Michael , Ganser Arnold , Pallaud Celine , Gathmann Insa , Krzykalla Julia , Benner Axel , Bloomfield Clara D. , Thiede Christian , Stone Richard M. , Döhner Hartmut , Döhner Konstanze 
Published: August 2022

AbstractThe aim of this study was to characterize the mutational landscape of patients withFLT3-mutated acute myeloid leukemia (AML) treated within the randomized CALGB 10603/RATIFY trial evaluating intensive chemotherapy plus the multi-kinase inhibitor midostaurin versus placebo. We performed sequencing of 262 genes in 475 patients: mutations occurring concurrently with theFLT3-mutation were most frequent inNPM1(61%),DNMT3A(39%),WT1(21%),TET2(12%),NRAS(11%),RUNX1(11%),PTPN11(10%), andASXL1(8%) genes. To assess effects of clinical and genetic features and their possible interactions, we fitted random survival forests and interpreted the resulting variable importance. Highest prognostic impact was found forWT1andNPM1mutations, followed by white blood cell count,FLT3mutation type (internal tandem duplications vs. tyrosine kinase domain mutations), treatment (midostaurin vs. placebo),ASXL1mutation, and ECOG performance status. When evaluating two-fold variable combinations the most striking effects were found forWT1:NPM1(withNPM1mutation abrogating the negative effect ofWT1mutation), and forWT1:treatment (with midostaurin exerting a beneficial effect inWT1-mutated AML). This targeted gene sequencing study provides important, novel insights into the genomic background ofFLT3-mutated AML including the prognostic impact of co-mutations, specific gene–gene interactions, and possible treatment effects of midostaurin.
A history of visual acuity testing and optotypes
Authors: de Jong Paulus T. V. M. 
Published: August 2022

AbstractAfter going into the etymology of the word “optotype”, this article covers some tasks in ancient times that required good visual acuity (VA). Around 300 BCE, Euclid formulated the existence of a visual cone with a minimal visual angle at its tip. Trials to test VA appeared AD 1754. Around that time, texts were introduced by opticians in order to be able to prescribe more reliably. In the early nineteenth century, the need for VA tests in ophthalmology resulted in German and English test charts. Numerous variants emerged after the first edition of Snellen’s optotypes in 1862 in The Netherlands. However, 100 years later there was still no standard optotype to reliably test VA. Multidisciplinary approaches between ophthalmology, linguistics, psychology and psychophysics improved optotypes and VA testing, which led to the more reliable LogMAR charts. Recent advances in aids and therapies for the blind and severely visually handicapped, necessitate further development of new and standardized VA tests.
Explaining a series of models by propagating Shapley values
Authors: Chen Hugh , Lundberg Scott M. , Lee Su-In 
Published: August 2022

AbstractLocal feature attribution methods are increasingly used to explain complex machine learning models. However, current methods are limited because they are extremely expensive to compute or are not capable of explaining a distributed series of models where each model is owned by a separate institution. The latter is particularly important because it often arises in finance where explanations are mandated. Here, we present Generalized DeepSHAP (G-DeepSHAP), a tractable method to propagate local feature attributions through complex series of models based on a connection to the Shapley value. We evaluate G-DeepSHAP across biological, health, and financial datasets to show that it provides equally salient explanations an order of magnitude faster than existing model-agnostic attribution techniques and demonstrate its use in an important distributed series of models setting.
Optoelectronic system and device integration for quantum-dot light-emitting diode white lighting with computational design framework
Authors: Samarakoon Chatura , Choi Hyung Woo , Lee Sanghyo , Fan Xiang-Bing , Shin Dong-Wook , Bang Sang Yun , Jo Jeong-Wan , Ni Limeng , Yang Jiajie , Kim Yoonwoo , Jung Sung-Min , Occhipinti Luigi G. , Amaratunga Gehan A. J. , Kim Jong Min 
Published: August 2022

AbstractWe propose a computational design framework to design the architecture of a white lighting system having multiple pixelated patterns of electric-field-driven quantum dot light-emitting diodes. The quantum dot of the white lighting system has been optimised by a system-level combinatorial colour optimisation process with the Nelder-Mead algorithm used for machine learning. The layout of quantum dot patterns is designed precisely using rigorous device-level charge transport simulation with an electric-field dependent charge injection model. A theoretical maximum of 97% colour rendering index has been achieved with red, green, cyan, and blue quantum dot light-emitting diodes as primary colours. The white lighting system has been fabricated using the transfer printing technique to validate the computational design framework. It exhibits excellent lighting performance of 92% colour rendering index and wide colour temperature variation from 1612 K to 8903 K with only the four pixelated quantum dots as primary.
Dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022 in England
Authors: Elliott Paul , Eales Oliver , Bodinier Barbara , Tang David , Wang Haowei , Jonnerby Jakob , Haw David , Elliott Joshua , Whitaker Matthew , Walters Caroline E. , Atchison Christina , Diggle Peter J. , Page Andrew J. , Trotter Alexander J. , Ashby Deborah , Barclay Wendy , Taylor Graham , Ward Helen , Darzi Ara , Cooke Graham S. , Chadeau-Hyam Marc , Donnelly Christl A. 
Published: August 2022

AbstractRapid transmission of the SARS-CoV-2 Omicron variant has led to record-breaking case incidence rates around the world. Since May 2020, the REal-time Assessment of Community Transmission-1 (REACT-1) study tracked the spread of SARS-CoV-2 infection in England through RT-PCR of self-administered throat and nose swabs from randomly-selected participants aged 5 years and over. In January 2022, we found an overall weighted prevalence of 4.41% (n = 102,174), three-fold higher than in November to December 2021; we sequenced 2,374 (99.2%) Omicron infections (19 BA.2), and only 19 (0.79%) Delta, with a growth rate advantage for BA.2 compared to BA.1 or BA.1.1. Prevalence was decreasing overall (reproduction number R = 0.95, 95% credible interval [CrI], 0.93, 0.97), but increasing in children aged 5 to 17 years (R = 1.13, 95% CrI, 1.09, 1.18). In England during January 2022, we observed unprecedented levels of SARS-CoV-2 infection, especially among children, driven by almost complete replacement of Delta by Omicron.
Teixobactin kills bacteria by a two-pronged attack on the cell envelope
Authors: Shukla Rhythm , Lavore Francesca , Maity Sourav , Derks Maik G. N. , Jones Chelsea R. , Vermeulen Bram J. A. , Melcrová Adéla , Morris Michael A. , Becker Lea Marie , Wang Xiaoqi , Kumar Raj , Medeiros-Silva João , van Beekveld Roy A. M. , Bonvin Alexandre M. J. J. , Lorent Joseph H. , Lelli Moreno , Nowick James S. , MacGillavry Harold D. , Peoples Aaron J. , Spoering Amy L. , Ling Losee L. , Hughes Dallas E. , Roos Wouter H. , Breukink Eefjan , Lewis Kim , Weingarth Markus 
Published: August 2022

AbstractAntibiotics that use novel mechanisms are needed to combat antimicrobial resistance1–3. Teixobactin4 represents a new class of antibiotics with a unique chemical scaffold and lack of detectable resistance. Teixobactin targets lipid II, a precursor of peptidoglycan5. Here we unravel the mechanism of teixobactin at the atomic level using a combination of solid-state NMR, microscopy, in vivo assays and molecular dynamics simulations. The unique enduracididine C-terminal headgroup of teixobactin specifically binds to the pyrophosphate-sugar moiety of lipid II, whereas the N terminus coordinates the pyrophosphate of another lipid II molecule. This configuration favours the formation of a β-sheet of teixobactins bound to the target, creating a supramolecular fibrillar structure. Specific binding to the conserved pyrophosphate-sugar moiety accounts for the lack of resistance to teixobactin4. The supramolecular structure compromises membrane integrity. Atomic force microscopy and molecular dynamics simulations show that the supramolecular structure displaces phospholipids, thinning the membrane. The long hydrophobic tails of lipid II concentrated within the supramolecular structure apparently contribute to membrane disruption. Teixobactin hijacks lipid II to help destroy the membrane. Known membrane-acting antibiotics also damage human cells, producing undesirable side effects. Teixobactin damages only membranes that contain lipid II, which is absent in eukaryotes, elegantly resolving the toxicity problem. The two-pronged action against cell wall synthesis and cytoplasmic membrane produces a highly effective compound targeting the bacterial cell envelope. Structural knowledge of the mechanism of teixobactin will enable the rational design of improved drug candidates.
A mitotic chromatin phase transition prevents perforation by microtubules
Authors: Schneider Maximilian W. G. , Gibson Bryan A. , Otsuka Shotaro , Spicer Maximilian F. D. , Petrovic Mina , Blaukopf Claudia , Langer Christoph C. H. , Batty Paul , Nagaraju Thejaswi , Doolittle Lynda K. , Rosen Michael K. , Gerlich Daniel W. 
Published: August 2022

AbstractDividing eukaryotic cells package extremely long chromosomal DNA molecules into discrete bodies to enable microtubule-mediated transport of one genome copy to each of the newly forming daughter cells1–3. Assembly of mitotic chromosomes involves DNA looping by condensin4–8 and chromatin compaction by global histone deacetylation9–13. Although condensin confers mechanical resistance to spindle pulling forces14–16, it is not known how histone deacetylation affects material properties and, as a consequence, segregation mechanics of mitotic chromosomes. Here we show how global histone deacetylation at the onset of mitosis induces a chromatin-intrinsic phase transition that endows chromosomes with the physical characteristics necessary for their precise movement during cell division. Deacetylation-mediated compaction of chromatin forms a structure dense in negative charge and allows mitotic chromosomes to resist perforation by microtubules as they are pushed to the metaphase plate. By contrast, hyperacetylated mitotic chromosomes lack a defined surface boundary, are frequently perforated by microtubules and are prone to missegregation. Our study highlights the different contributions of DNA loop formation and chromatin phase separation to genome segregation in dividing cells.
A full year of turbulence measurements from a drift campaign in the Arctic Ocean 2019–2020
Authors: Schulz Kirstin , Mohrholz Volker , Fer Ilker , Janout Markus , Hoppmann Mario , Schaffer Janin , Koenig Zoé 
Published: August 2022

AbstractOcean turbulent mixing is a key process in the global climate system, regulating ocean circulation and the uptake and redistribution of heat, carbon, nutrients, oxygen and other tracers. In polar oceans, turbulent heat transport additionally affects the sea ice mass balance. Due to the inaccessibility of polar regions, direct observations of turbulent mixing are sparse in the Arctic Ocean. During the year-long drift expedition “Multidisciplinary drifting Observatory for the Study of Arctic Climate” (MOSAiC) from September 2019 to September 2020, we obtained an unprecedented data set of vertical profiles of turbulent dissipation rate and water column properties, including oxygen concentration and fluorescence. Nearly 1,700 profiles, covering the upper ocean down to approximately 400 m, were collected in sets of 3 or more consecutive profiles every day, and complemented with several intensive sampling periods. This data set allows for the systematic assessment of upper ocean mixing in the Arctic, and the quantification of turbulent heat and nutrient fluxes, and can help to better constrain turbulence parameterizations in ocean circulation models.
Histopathological evaluation of a retinoic acid eluting stent in a rabbit iliac artery model
Authors: Samara Ioanna , Katsouras Christos S. , Semertzioglou Arsen , Vratimos Athanassios , Moula Amalia I. , Dimitriou Constantinos A. , Theofanis Michail , Papadimitropoulou Triantafyllia , Bouratzis Vasileios , Karanasiou Georgia , Fotiadis Dimitrios , Michalis Lampros K. , Moulas Anargyros N. 
Published: August 2022

AbstractThis study aimed to evaluate the safety and efficacy of innovative retinoic acid (RA) eluting stents with bioabsorbable polymer. Sixty stents divided in ten groups were implanted in the iliac arteries of 30 rabbits. Two polymers (“A”, poly (lactic-co-glycolic acid) and “B”, polylactic acid), and three doses (“Low”, “Medium” and “High”) of RA (groups: AL, AM, AH, BL, BM, BH) were used on cobalt chromium stents (Rontis Corporation), one group of bare stent (C), one group (D) of Everolimus eluting stent (Xience-Pro, Abbot Vascular), and two groups of Rontis Everolimus eluting stents coated with polymer A (EA) and B (EB). Treated arteries were explanted after 4 weeks, processed by methyl methacrylate resin and evaluated by histopathology. None of the implanted stents was related with thrombus formation or extensive inflammation. Image analysis showed limited differences between groups regarding area stenosis (BH, D and EB groups had the lower values). Group BH had lower intimal mean thickness than AH (105.1 vs 75.3 μm, p = 0.024). Stents eluting RA, a non-cytotoxic drug, were not related with thrombus formation and had an acceptable degree of stenosis 4 weeks post implantation. RA dose and type of polymer may play role in the biocompatibility of the stents.
A time-series approach to mapping livestock density using household survey data
Authors: Meisner Julianne , Kato Agapitus , Lemerani Marshall , Miaka Erick Mwamba , Ismail Acaga Taban , Wakefield Jonathan , Rowhani-Rahbar Ali , Pigott David , Mayer Jonathan , Rabinowitz Peter 
Published: August 2022

AbstractMore than one billion people rely on livestock for income, nutrition, and social cohesion, however livestock keeping can facilitate disease transmission and contribute to climate change. While data on the distribution of livestock have broad utility across a range of applications, efforts to map the distribution of livestock on a large scale are limited to the Gridded Livestock of the World (GLW) project. We present a complimentary effort to map the distribution of cattle and pigs in Malawi, Uganda, Democratic Republic of Congo, and South Sudan. In contrast to GLW, which uses dasymmetric modeling applied to census data to produce time-stratified estimates of livestock counts and spatial density, our work uses complex survey data and distinct modeling methods to generate a time-series of livestock distribution, defining livestock density as the ratio of animals to humans. In addition to favorable cross-validation results and general agreement with national density estimates derived from external data on national human and livestock populations, our results demonstrate extremely good agreement with GLW-3 estimates, supporting the validity of both efforts. Our results furthermore offer a high-resolution time series result and employ a definition of density which is particularly well-suited to the study of livestock-origin zoonoses.