bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solar Activity Driven 27‐Day Signatures in Ionospheric Electron and Molecular Oxygen Densities
Authors: Schmölter Erik , von Savigny Christian 
Published: September 2022

AbstractThe complex interactions in the upper atmosphere, which control the height‐dependent ionospheric response to the 27‐day solar rotation period, are investigated with the superposed epoch analysis technique. 27‐day signatures describing solar activity are calculated from a solar proxy (F10.7) and wavelength‐dependent extreme ultraviolet (EUV) fluxes (Thermosphere Ionosphere Mesosphere Energetics and Dynamics/Solar EUV Experiment), and the corresponding 27‐day signatures describing ionospheric conditions are calculated from electron density profiles (Pruhonice ionosonde station) and O2 density profiles (Global‐scale Observations of the Limb and Disk). The lag analysis of these extracted signatures is applied to characterize the delayed ionospheric response at heights from 100 to 300 km and the impact of major absorption processes in the lower (dominated by O2) and upper ionosphere (dominated by O) is discussed. The observed variations of the delay in these regions are in good agreement with model simulations in preceding studies. Additionally, the estimated significance and the correlation of the delays based on both ionospheric parameters are good. Thus, variations such as the strong shift in 27‐day signatures for the O2 density at low heights are also reliably identified (up to half a cycle). The analysis confirms the importance of ionospheric and thermospheric coupling to understand the variability of the delayed ionospheric response and introduces a method that could be applied to additional ionosonde stations in future studies. This would allow to describe the variability of the delayed ionospheric response spatially, vertically and temporally and therefore may contribute further to the understanding of processes and improve ionospheric modeling.
Biomarker correlates with response to NY-ESO-1 TCR T cells in patients with synovial sarcoma
Authors: Gyurdieva Alexandra , Zajic Stefan , Chang Ya-Fang , Houseman E. Andres , Zhong Shan , Kim Jaegil , Nathenson Michael , Faitg Thomas , Woessner Mary , Turner David C. , Hasan Aisha N. , Glod John , Kaplan Rosandra N. , D’Angelo Sandra P. , Araujo Dejka M. , Chow Warren A. , Druta Mihaela , Demetri George D. , Van Tine Brian A. , Grupp Stephan A. , Fine Gregg D. , Eleftheriadou Ioanna 
Published: September 2022

AbstractAutologous T cells transduced to express a high affinity T-cell receptor specific to NY-ESO-1 (letetresgene autoleucel, lete-cel) show promise in the treatment of metastatic synovial sarcoma, with 50% overall response rate. The efficacy of lete-cel treatment in 45 synovial sarcoma patients (NCT01343043) has been previously reported, however, biomarkers predictive of response and resistance remain to be better defined. This post-hoc analysis identifies associations of response to lete-cel with lymphodepleting chemotherapy regimen (LDR), product attributes, cell expansion, cytokines, and tumor gene expression. Responders have higher IL-15 levels pre-infusion (p = 0.011) and receive a higher number of transduced effector memory (CD45RA- CCR7-) CD8 + cells per kg (p = 0.039). Post-infusion, responders have increased IFNγ, IL-6, and peak cell expansion (p < 0.01, p < 0.01, and p = 0.016, respectively). Analysis of tumor samples post-treatment illustrates lete-cel infiltration and a decrease in expression of macrophage genes, suggesting remodeling of the tumor microenvironment. Here we report potential predictive and pharmacodynamic markers of lete-cel response that may inform LDR, cell dose, and strategies to enhance anticancer efficacy.
IFITM3 restricts virus-induced inflammatory cytokine production by limiting Nogo-B mediated TLR responses
Authors: Clement M. , Forbester J. L. , Marsden M. , Sabberwal P. , Sommerville M. S. , Wellington D. , Dimonte S. , Clare S. , Harcourt K. , Yin Z. , Nobre L. , Antrobus R. , Jin B. , Chen M. , Makvandi-Nejad S. , Lindborg J. A. , Strittmatter S. M. , Weekes M. P. , Stanton R. J. , Dong T. , Humphreys I. R. 
Published: September 2022

AbstractInterferon-induced transmembrane protein 3 (IFITM3) is a restriction factor that limits viral pathogenesis and exerts poorly understood immunoregulatory functions. Here, using human and mouse models, we demonstrate that IFITM3 promotes MyD88-dependent, TLR-mediated IL-6 production following exposure to cytomegalovirus (CMV). IFITM3 also restricts IL-6 production in response to influenza and SARS-CoV-2. In dendritic cells, IFITM3 binds to the reticulon 4 isoform Nogo-B and promotes its proteasomal degradation. We reveal that Nogo-B mediates TLR-dependent pro-inflammatory cytokine production and promotes viral pathogenesis in vivo, and in the case of TLR2 responses, this process involves alteration of TLR2 cellular localization. Nogo-B deletion abrogates inflammatory cytokine responses and associated disease in virus-infected IFITM3-deficient mice. Thus, we uncover Nogo-B as a driver of viral pathogenesis and highlight an immunoregulatory pathway in which IFITM3 fine-tunes the responsiveness of myeloid cells to viral stimulation.
Multi-pathway DNA-repair reporters reveal competition between end-joining, single-strand annealing and homologous recombination at Cas9-induced DNA double-strand breaks
Authors: van de Kooij Bert , Kruswick Alex , van Attikum Haico , Yaffe Michael B. 
Published: September 2022

AbstractDNA double-strand breaks (DSB) are repaired by multiple distinct pathways, with outcomes ranging from error-free repair to mutagenesis and genomic loss. DSB-repair pathway cross-talk and compensation is incompletely understood, despite its importance for genomic stability, oncogenesis, and genome editing using CRISPR/Cas9. To address this, we constructed and validated three fluorescent Cas9-based reporters, named DSB-Spectrum, that simultaneously quantify the contribution of multiple DNA repair pathways at a DSB. DSB-Spectrum reporters distinguish between DSB-repair by error-free canonical non-homologous end-joining (c-NHEJ) versus homologous recombination (HR; reporter 1), mutagenic repair versus HR (reporter 2), and mutagenic end-joining versus single strand annealing (SSA) versus HR (reporter 3). Using these reporters, we show that inhibiting the c-NHEJ factor DNA-PKcs increases repair by HR, but also substantially increases mutagenic SSA. Our data indicate that SSA-mediated DSB-repair also occurs at endogenous genomic loci, driven by Alu elements or homologous gene regions. Finally, we demonstrate that long-range end-resection factors DNA2 and Exo1 promote SSA and reduce HR, when both pathways compete for the same substrate. These new Cas9-based DSB-Spectrum reporters facilitate the comprehensive analysis of repair pathway crosstalk and DSB-repair outcome.
A central arctic extreme aerosol event triggered by a warm air-mass intrusion
Authors: Dada Lubna , Angot Hélène , Beck Ivo , Baccarini Andrea , Quéléver Lauriane L. J. , Boyer Matthew , Laurila Tiia , Brasseur Zoé , Jozef Gina , de Boer Gijs , Shupe Matthew D. , Henning Silvia , Bucci Silvia , Dütsch Marina , Stohl Andreas , Petäjä Tuukka , Daellenbach Kaspar R. , Jokinen Tuija , Schmale Julia 
Published: September 2022

AbstractFrequency and intensity of warm and moist air-mass intrusions into the Arctic have increased over the past decades and have been related to sea ice melt. During our year-long expedition in the remote central Arctic Ocean, a record-breaking increase in temperature, moisture and downwelling-longwave radiation was observed in mid-April 2020, during an air-mass intrusion carrying air pollutants from northern Eurasia. The two-day intrusion, caused drastic changes in the aerosol size distribution, chemical composition and particle hygroscopicity. Here we show how the intrusion transformed the Arctic from a remote low-particle environment to an area comparable to a central-European urban setting. Additionally, the intrusion resulted in an explosive increase in cloud condensation nuclei, which can have direct effects on Arctic clouds’ radiation, their precipitation patterns, and their lifetime. Thus, unless prompt actions to significantly reduce emissions in the source regions are taken, such intrusion events are expected to continue to affect the Arctic climate.
Regulation associated modules reflect 3D genome modularity associated with chromatin activity
Authors: Zheng Lina , Wang Wei 
Published: September 2022

AbstractThe 3D genome has been shown to be organized into modules including topologically associating domains (TADs) and compartments that are primarily defined by spatial contacts from Hi-C. There exists a gap to investigate whether and how the spatial modularity of the chromatin is related to the functional modularity resulting from chromatin activity. Despite histone modifications reflecting chromatin activity, inferring spatial modularity of the genome directly from the histone modification patterns has not been well explored. Here, we report that histone modifications show a modular pattern (referred to as regulation associated modules, RAMs) that reflects spatial chromatin modularity. Enhancer-promoter interactions, loop anchors, super-enhancer clusters and extrachromosomal DNAs (ecDNAs) are found to occur more often within the same RAMs than within the same TADs. Consistently, compared to the TAD boundaries, deletions of RAM boundaries perturb the chromatin structure more severely (may even cause cell death) and somatic variants in cancer samples are more enriched in RAM boundaries. These observations suggest that RAMs reflect a modular organization of the 3D genome at a scale better aligned with chromatin activity, providing a bridge connecting the structural and functional modularity of the genome.
Never-homozygous genetic variants in healthy populations are potential recessive disease candidates
Authors: Schmenger Torsten , Diwan Gaurav D. , Singh Gurdeep , Apic Gordana , Russell Robert B. 
Published: September 2022

AbstractThe rapid pace with which genetic variants are now being determined means there is a pressing need to understand how they affect biological systems. Variants from healthy individuals have previously been used to study blood groups or HLA diversity and to identify genes that can apparently be nonfunctional in healthy people. These studies and others have observed a lower than expected frequency of homozygous individuals for potentially deleterious alleles, which would suggest that several of these alleles can lead to recessive disorders. Here we exploited this principle to hunt for potential disease variants in genomes from healthy people. We identified at least 108 exclusively heterozygous variants with evidence for an impact on biological function. We discuss several examples of candidate variants/genes including CCDC8, PANK3, RHD and NLRP12. Overall, the results suggest there are many, comparatively frequent, potentially lethal or disease-causing variants lurking in healthy human populations.
Enhancing quantum cryptography with quantum dot single-photon sources
Authors: Bozzio Mathieu , Vyvlecka Michal , Cosacchi Michael , Nawrath Cornelius , Seidelmann Tim , Loredo Juan C. , Portalupi Simone L. , Axt Vollrath M. , Michler Peter , Walther Philip 
Published: September 2022

AbstractQuantum cryptography harnesses quantum light, in particular single photons, to provide security guarantees that cannot be reached by classical means. For each cryptographic task, the security feature of interest is directly related to the photons’ non-classical properties. Quantum dot-based single-photon sources are remarkable candidates, as they can in principle emit deterministically, with high brightness and low multiphoton contribution. Here, we show that these sources provide additional security benefits, thanks to the tunability of coherence in the emitted photon-number states. We identify the optimal optical pumping scheme for the main quantum-cryptographic primitives, and benchmark their performance with respect to Poisson-distributed sources such as attenuated laser states and down-conversion sources. In particular, we elaborate on the advantage of using phonon-assisted and two-photon excitation rather than resonant excitation for quantum key distribution and other primitives. The presented results will guide future developments in solid-state and quantum information science for photon sources that are tailored to quantum communication tasks.
Model-informed experimental design recommendations for distinguishing intrinsic and acquired targeted therapeutic resistance in head and neck cancer
Authors: Cárdenas Santiago D. , Reznik Constance J. , Ranaweera Ruchira , Song Feifei , Chung Christine H. , Fertig Elana J. , Gevertz Jana L. 
Published: September 2022

AbstractThe promise of precision medicine has been limited by the pervasive resistance to many targeted therapies for cancer. Inferring the timing (i.e., pre-existing or acquired) and mechanism (i.e., drug-induced) of such resistance is crucial for designing effective new therapeutics. This paper studies cetuximab resistance in head and neck squamous cell carcinoma (HNSCC) using tumor volume data obtained from patient-derived tumor xenografts. We ask if resistance mechanisms can be determined from this data alone, and if not, what data would be needed to deduce the underlying mode(s) of resistance. To answer these questions, we propose a family of mathematical models, with each member of the family assuming a different timing and mechanism of resistance. We present a method for fitting these models to individual volumetric data, and utilize model selection and parameter sensitivity analyses to ask: which member(s) of the family of models best describes HNSCC response to cetuximab, and what does that tell us about the timing and mechanisms driving resistance? We find that along with time-course volumetric data to a single dose of cetuximab, the initial resistance fraction and, in some instances, dose escalation volumetric data are required to distinguish among the family of models and thereby infer the mechanisms of resistance. These findings can inform future experimental design so that we can best leverage the synergy of wet laboratory experimentation and mathematical modeling in the study of novel targeted cancer therapeutics.
Event-triggered STED imaging
Authors: Alvelid Jonatan , Damenti Martina , Sgattoni Chiara , Testa Ilaria 
Published: September 2022

AbstractMonitoring the proteins and lipids that mediate all cellular processes requires imaging methods with increased spatial and temporal resolution. STED (stimulated emission depletion) nanoscopy enables fast imaging of nanoscale structures in living cells but is limited by photobleaching. Here, we present event-triggered STED, an automated multiscale method capable of rapidly initiating two-dimensional (2D) and 3D STED imaging after detecting cellular events such as protein recruitment, vesicle trafficking and second messengers activity using biosensors. STED is applied in the vicinity of detected events to maximize the temporal resolution. We imaged synaptic vesicle dynamics at up to 24 Hz, 40 ms after local calcium activity; endocytosis and exocytosis events at up to 11 Hz, 40 ms after local protein recruitment or pH changes; and the interaction between endosomal vesicles at up to 3 Hz, 70 ms after approaching one another. Event-triggered STED extends the capabilities of live nanoscale imaging, enabling novel biological observations in real time.
Cenozoic origins of the genus Calliarcys (Insecta, Ephemeroptera) revealed by Micro-CT, with DNA barcode gap analysis of Leptophlebiinae and Habrophlebiinae
Authors: Godunko Roman J. , Alba-Tercedor Javier , Grabowski Michal , Rewicz Tomasz , Staniczek Arnold H. 
Published: September 2022

AbstractMayflies (Ephemeroptera) are among the oldest pterygote insects, with the earliest fossils dating back to the Late Carboniferous. Within mayflies, Leptophlebiidae are a highly diverse and widespread group, with approximately 140 genera and 640 species. Whereas taxonomy, systematics, and phylogeny of extant Leptophlebiidae are in the focus of extensive studies, little is known about leptophlebiid fossil taxa. Because fossil remains of Ephemeroptera in sedimentary rocks are relatively rare, inclusions of mayflies in amber are a unique source of information on their evolution and diversity in the past. Leptophlebiidae found in Cenozoic resins mostly belong to the subfamilies Leptophlebiinae (in Eocene Baltic amber) and Atalophlebiinae (in Miocene Dominican and Mexican ambers). In the present contribution, we confirm the first finding of the genusCalliarcysfrom Eocene Baltic amber by using Micro-CT, which allowed confirming its generic placement by visualizing diagnostic key characters otherwise hidden by a cloud of turbidity. Additionally, we present first molecular data on the extant speciesCalliarcys humilisEaton, 1881 from the Iberian Peninsula and the barcode gap analysis for Leptophlebiinae and Habrophlebiinae.
Temperature evolution of dense gold and diamond heated by energetic laser-driven aluminum ions
Authors: Song C. , Lee S. , Bang W. 
Published: September 2022

AbstractRecent studies have shown that energetic laser-driven ions with some energy spread can heat small solid-density samples uniformly. The balance among the energy losses of the ions with different kinetic energies results in uniform heating. Although heating with an energetic laser-driven ion beam is completed within a nanosecond and is often considered sufficiently fast, it is not instantaneous. Here we present a theoretical study of the temporal evolution of the temperature of solid-density gold and diamond samples heated by a quasimonoenergetic aluminum ion beam. We calculate the temporal evolution of the predicted temperatures of the samples using the available stopping power data and the SESAME equation-of-state tables. We find that the temperature distribution is initially very uniform, which becomes less uniform during the heating process. Then, the temperature uniformity gradually improves, and a good temperature uniformity is obtained toward the end of the heating process.
Vaccination willingness in association with personality traits in patients with multiple sclerosis in the course of SARS-CoV-2 pandemic
Authors: Heidler Felicita , Baldt Julia , Frahm Niklas , Langhorst Silvan Elias , Mashhadiakbar Pegah , Streckenbach Barbara , Burian Katja , Zettl Uwe Klaus , Richter Jörg 
Published: September 2022

AbstractVaccination is a key strategy for controlling the SARS-CoV-2 pandemic. Acceptance of SARS-CoV-2 vaccines by chronically ill patients, such as multiple sclerosis (MS) patients, plays an important role in prevention of complicated disease course. This longitudinal, prospective, multi-centre-study of German MS-patients aimed to detect socio-demographic, clinical, or psychological determinants of attitudes towards standard vaccines, SARS-CoV-2 vaccines, and governmental measures before/during the pandemic. Exactly 404 MS-patients were investigated by standardized questionnaires and structured interviews on socio-demographic, clinical-neurological, and psychological characteristics, vaccination status, and vaccination from June 2019. Data on SARS-CoV-2 vaccination willingness were collected in two follow-up assessments (1st: June to July 2020, before SARS-CoV-2 vaccine availability, N = 200; 2nd: March to May 2021, after SARS-CoV-2 vaccine availability, N = 157). Age, sex, MS course type, depression, and personality characteristics (Extraversion, Novelty seeking, Self-directedness, and Cooperativeness) were significantly associated with vaccination willingness. Although the majority of MS-patients showed SARS-CoV-2 vaccination willingness at both follow-ups (1st: 60%, 2nd: 61%), a substantial proportion had concerns and were undecided or opposed to vaccination. Socio-demographic variables like age and sex, psychopathological status, and various personality characteristics might influence vaccination willingness and should be considered when discussing with MS-patients about SARS-CoV-2 vaccination.
Preferential growth of (001)-oriented Bi2SiO5 thin films deposited on (101)-oriented rutile substrates and their ferroelectric and dielectric properties
Authors: Kodera Masanori , Ishihama Keisuke , Shimizu Takao , Funakubo Hiroshi 
Published: September 2022

AbstractFerroelectric thin films are important because of their great potential for use in various electric devices such as ferroelectric random-access memory. It was expected that Bi2SiO5, a Si-containing ferroelectric material, would show improved ferroelectricity by targeting a film with the (001)-orientation (polar-axis) on the substrate. Although there was a narrow process window for the deposition of the (010)/(001)-oriented Bi2SiO5 thin film, it was successfully prepared on a (101)-oriented TiO2 single substrate using the pulsed layer deposition technique. The optimum film deposition conditions and film thickness were found, and in this material, the volume fraction of the (001)-oriented domain reached about 70%. By controlling film orientation to the polar axis, the remanent polarization value of this film was 4.8 μC cm−2, which is the highest value among reported Bi2SiO5.
Deep learning based optimal energy management for photovoltaic and battery energy storage integrated home micro-grid system
Authors: Alam Md. Morshed , Rahman Md. Habibur , Ahmed Md. Faisal , Chowdhury Mostafa Zaman , Jang Yeong Min 
Published: September 2022

AbstractThe development of the advanced metering infrastructure (AMI) and the application of artificial intelligence (AI) enable electrical systems to actively engage in smart grid systems. Smart homes with energy storage systems (ESS) and renewable energy sources (RES)-known as home microgrids-have become a critical enabling technology for the smart grid. This article proposes a new model for the energy management system of a home microgrid integrated with a battery ESS (BESS). The proposed dynamic model integrates a deep learning (DL)-based predictive model, bidirectional long short-term memory (Bi-LSTM), with an optimization algorithm for optimal energy distribution and scheduling of a BESS-by determining the characteristics of distributed resources, BESS properties, and the user’s lifestyle. The aim is to minimize the per-day electricity cost charged by time-of-use (TOU) pricing while considering the day-basis peak demand penalty. The proposed system also considers the operational constraints of renewable resources, the BESS, and electrical appliances. The simulation results from realistic case studies demonstrate the validation and responsibility of the proposed system in reducing a household’s daily electricity cost.