bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advection of Martian Crustal Magnetic Fields by Ionospheric Plasma Flow Observed by the MAVEN Spacecraft
Authors: de Oliveira I. , Fränz M. , Echer E. , Franco A. 
Published: September 2021

AbstractThe plasma environment of Mars is highly influenced by its crustal magnetic fields. In this work, we investigate whether the crustal magnetic fields can be displaced from their original positions due to advection by ionospheric plasma flow. The ranges of interest are altitudes between km and solar zenith angles between . We examine magnetic field data using measurements from the Magnetometer (MAG) onboard the Mars Atmosphere and Volatile EvolutioN (MAVEN) spacecraft. We conduct statistical analyses ( years of data) in order to investigate if horizontal shifts are observed between the data and the crustal magnetic field model by Langlais et al. (2019), https://doi.org/10.1029/2018je005854. We also show two case studies of individual measurements within a specific region of Mars. The results show statistical and observational evidence that the crustal magnetic fields are often being advected towards the night‐side of the planet. The displacement seems to increase exponentially as a function of altitude, reaching a horizontal shift of 100 km at 650 km altitude. Moreover, we use measurements from the SupraThermal And Thermal Ion Composition (STATIC) instrument in order to compare the dynamic pressure of ionospheric plasma flow to the magnetic pressure of the crustal magnetic fields. There are two possible causes for the displacement: a forcing by external magnetic pressure or an advection of the field to the electron fluid, which follows the ion fluid. In this paper, we argue that by the observed relation between ion fluid and displacement, the latter explanation is more probable.
High Mach Number Quasi‐Perpendicular Shocks: Spatial Versus Temporal Structure
Authors: Omidi N. , Desai M. , Russell C. T. , Howes G. G. 
Published: September 2021

AbstractPlanetary bow shocks are a natural laboratory for investigating the physics of collisionless shocks. Given that spacecraft observations provide us with information regarding the temporal structure of the shock, often multi‐spacecraft missions and kinetic simulations are needed to discern the nature of the dissipation processes at the shock and the resulting spatial structure. Such an approach through the ISEE mission and 1.5‐D hybrid (kinetic ions and fluid electrons) simulations led to an understanding of supercritical quasi‐perpendicular shocks. In such shocks, the reflection of a fraction of incident ions and their gyration back into the shock is part of the dissipation process resulting in the formation of a foot, ramp, overshoot, and undershoot. More recently, observations of high Mach number quasi‐perpendicular shocks show a seemingly turbulent structure in time series data. In this study, we use the results of 2.5‐D global hybrid simulation of a high Mach number quasi‐perpendicular shock to demonstrate the major differences between the spatial and temporal structure of such shocks. The spatial structure of the shock is the same as that of supercritical shocks while the temporal structure consists of fast magnetosonic pulses. The reason for this difference is attributed to the generation of surface waves at the shock which results in partial encounters between the shock and spacecraft. The surface waves are shown to be generated by large velocity shears present at the shock due to ion reflection and gyration into the upstream.
New Paleointensities From the Skinner Cove Formation, Newfoundland, Suggest a Changing State of the Geomagnetic Field at the Ediacaran‐Cambrian Transition
Authors: Thallner Daniele , Biggin Andrew J. , McCausland Phil J. A. , Fu Roger R. 
Published: September 2021

AbstractThe geomagnetic field in the Ediacaran period appears to be characterized by anomalous directions, high reversal frequencies, and ultra‐low field strength. At the Ediacaran‐Cambrian transition, apparent polar wander paths become less controversial, but hyper‐reversing fields with reversal frequencies similar to earlier in the Ediacaran have been reported until the mid‐Cambrian. To understand the long‐term behavior of the magnetic field during this transitional interval, information about the field strength is vital but currently lacking. To improve the intensity record at that time, samples of volcanic rocks from the 550 Ma Skinner Cove Formation, western Newfoundland, have been used for paleointensity determination. This multi‐method paleointensity study, utilizing thermal and microwave Thellier as well as double‐heating Shaw and pseudo‐Thellier experiments produces paleointensity estimates of 2.6–10.3 μT, corresponding to virtual dipole moments of 0.65–2.25 × 1022 Am2. Analyses using scanning electron microscopy and rock magnetic measurements, as well as a positive intraformational conglomerate test, suggest that the remanence is primary. These intensity estimates are higher than earlier Ediacaran intensities and could point to the geomagnetic field entering into a stronger, more dipole‐dominated state at the Ediacaran‐Cambrian boundary.
Hydrate Formation on Marine Seep Bubbles and the Implications for Water Column Methane Dissolution
Authors: Fu X. , Waite W. F. , Ruppel C. D. 
Published: September 2021

AbstractMethane released from seafloor seeps contributes to a number of benthic, water column, and atmospheric processes. At seafloor seeps within the methane hydrate stability zone, crystalline gas hydrate shells can form on methane bubbles while the bubbles are still in contact with the seafloor or as the bubbles begin ascending through the water column. These shells reduce methane dissolution rates, allowing hydrate‐coated bubbles to deliver methane to shallower depths in the water column than hydrate‐free bubbles. Here, we analyze seafloor videos from six deepwater seep sites associated with a diverse range of bubble‐release processes involving hydrate formation. Bubbles that grow rapidly are often hydrate‐free when released from the seafloor. As bubble growth slows and seafloor residence time increases, a hydrate coating can form on the bubble's gas‐water interface, fully coating most bubbles within ∼10 s of the onset of hydrate formation at the seafloor. This finding agrees with water‐column observations that most bubbles become hydrate‐coated after their initial ∼150 cm of rise, which takes about 10 s. Whether a bubble is coated or not at the seafloor affects how much methane a bubble contains and how quickly that methane dissolves during the bubble's rise through the water column. A simplified model shows that, after rising 150 cm above the seafloor, a bubble that grew a hydrate shell before releasing from the seafloor will have ∼5% more methane than a bubble of initial equal volume that did not grow a hydrate shell after it traveled to the same height.
Impacts of Pore Network‐Scale Wettability Heterogeneity on Immiscible Fluid Displacement: A Micromodel Study
Authors: Chang Chun , Kneafsey Timothy J. , Tokunaga Tetsu K. , Wan Jiamin , Nakagawa Seiji 
Published: September 2021

AbstractThe mixed‐wet nature of reservoir formations imposes a wide range of rock wettability from strong resident‐fluid wetting to strong invading‐fluid wetting. The characteristics of two‐phase flow in porous media composed of mixed‐wetting surfaces remain poorly understood. In this study, we investigated the displacement of resident ethylene glycol (EG) by hexane in two mixed‐wet micromodels of identical 2.5‐D geometry heterogeneity, with uniformly or heterogeneously distributed patches strongly wetting to hexane. These patches are mixed among pores with unaltered EG‐wetting surfaces. Along with control tests in the originally EG‐wet micromodel, we show the classic fingering and transitions in flow regimes at (capillary number) from −7.2 to −3.9. Moreover, pore‐scale distributions of wettability and their spatial correlation influence displacement efficiency. In the two mixed‐wet micromodels, we found (a) an increase of steady‐state hexane saturation at the end of experiments by up to 0.12 in the capillary fingering regime and a decrease of at most by 0.06 in the viscous fingering regime, compared to the EG‐wet micromodel, and (b) dispersed and fragmented hexane distribution after displacement. Brine drainage during supercritical CO2 (scCO2) injections in these micromodels occurs with lower wettability contrasts, and under similar viscosity ratios and interfacial tensions resulted in higher displacement efficiency relative to displacement of EG by hexane. While mixed‐wettability can enhance displacement efficiency compared to uniform wettability, the dynamics of immiscible fluids in strong mixed‐wet reservoirs are expected to be less pronounced in contributing to the efficiency of geological CO2 sequestration, oil recovery, and remediation of hydrocarbon‐contaminated aquifers.
There is plenty of room at the top: generation of hot charge carriers and their applications in perovskite and other semiconductor-based optoelectronic devices
Authors: Ahmed Irfan , Shi Lei , Pasanen Hannu , Vivo Paola , Maity Partha , Hatamvand Mohammad , Zhan Yiqiang 
Published: September 2021

AbstractHot charge carriers (HC) are photoexcited electrons and holes that exist in nonequilibrium high-energy states of photoactive materials. Prolonged cooling time and rapid extraction are the current challenges for the development of future innovative HC-based optoelectronic devices, such as HC solar cells (HCSCs), hot energy transistors (HETs), HC photocatalytic reactors, and lasing devices. Based on a thorough analysis of the basic mechanisms of HC generation, thermalization, and cooling dynamics, this review outlines the various possible strategies to delay the HC cooling as well as to speed up their extraction. Various materials with slow cooling behavior, including perovskites and other semiconductors, are thoroughly presented. In addition, the opportunities for the generation of plasmon-induced HC through surface plasmon resonance and their technological applications in hybrid nanostructures are discussed in detail. By judiciously designing the plasmonic nanostructures, the light coupling into the photoactive layer and its optical absorption can be greatly enhanced as well as the successful conversion of incident photons to HC with tunable energies can also be realized. Finally, the future outlook of HC in optoelectronics is highlighted which will provide great insight to the research community.
Label-free SARS-CoV-2 detection and classification using phase imaging with computational specificity
Authors: Goswami Neha , He Yuchen R. , Deng Yu-Heng , Oh Chamteut , Sobh Nahil , Valera Enrique , Bashir Rashid , Ismail Nahed , Kong Hyunjoon , Nguyen Thanh H. , Best-Popescu Catherine , Popescu Gabriel 
Published: September 2021

AbstractEfforts to mitigate the COVID-19 crisis revealed that fast, accurate, and scalable testing is crucial for curbing the current impact and that of future pandemics. We propose an optical method for directly imaging unlabeled viral particles and using deep learning for detection and classification. An ultrasensitive interferometric method was used to image four virus types with nanoscale optical path-length sensitivity. Pairing these data with fluorescence images for ground truth, we trained semantic segmentation models based on U-Net, a particular type of convolutional neural network. The trained network was applied to classify the viruses from the interferometric images only, containing simultaneously SARS-CoV-2, H1N1 (influenza-A virus), HAdV (adenovirus), and ZIKV (Zika virus). Remarkably, due to the nanoscale sensitivity in the input data, the neural network was able to identify SARS-CoV-2 vs. the other viruses with 96% accuracy. The inference time for each image is 60 ms, on a common graphic-processing unit. This approach of directly imaging unlabeled viral particles may provide an extremely fast test, of less than a minute per patient. As the imaging instrument operates on regular glass slides, we envision this method as potentially testing on patient breath condensates. The necessary high throughput can be achieved by translating concepts from digital pathology, where a microscope can scan hundreds of slides automatically.
Artificial sweeteners stimulate horizontal transfer of extracellular antibiotic resistance genes through natural transformation
Authors: Yu Zhigang , Wang Yue , Henderson Ian R , Guo Jianhua 
Published: September 2021

Abstract
Antimicrobial resistance has emerged as a global threat to human health. Natural transformation is an important pathway for horizontal gene transfer, which facilitates the dissemination of antibiotic resistance genes (ARGs) among bacteria. Although it is suspected that artificial sweeteners could exert antimicrobial effects, little is known whether artificial sweeteners would also affect horizontal transfer of ARGs via transformation. Here we demonstrate that four commonly used artificial sweeteners (saccharin, sucralose, aspartame, and acesulfame potassium) promote transfer of ARGs via natural transformation in Acinetobacter baylyi ADP1, a model organism for studying competence and transformation. Such phenomenon was also found in a Gram-positive human pathogen Bacillus subtilis and mice faecal microbiome. We reveal that exposure to these sweeteners increases cell envelope permeability and results in an upregulation of genes encoding DNA uptake and translocation (Com) machinery. In addition, we find that artificial sweeteners induce an increase in plasmid persistence in transformants. We propose a mathematical model established to predict the long-term effects on transformation dynamics under exposure to these sweeteners. Collectively, our findings offer insights into natural transformation promoted by artificial sweeteners and highlight the need to evaluate these environmental contaminants for their antibiotic-like side effects.
Genome-wide association study identifies QTL for eight fruit traits in cultivated tomato (Solanum lycopersicumL.)
Authors: Kim Minkyung , Nguyen Thuy Tien Phan , Ahn Joon-Hyung , Kim Gi-Jun , Sim Sung-Chur 
Published: September 2021

AbstractGenome-wide association study (GWAS) is effective in identifying favorable alleles for traits of interest with high mapping resolution in crop species. In this study, we conducted GWAS to explore quantitative trait loci (QTL) for eight fruit traits using 162 tomato accessions with diverse genetic backgrounds. The eight traits included fruit weight, fruit width, fruit height, fruit shape index, pericarp thickness, locule number, fruit firmness, and brix. Phenotypic variations of these traits in the tomato collection were evaluated with three replicates in field trials over three years. We filtered 34,550 confident SNPs from the 51 K Axiom® tomato array based on &lt; 10% of missing data and &gt; 5% of minor allele frequency for association analysis. The 162 tomato accessions were divided into seven clusters and their membership coefficients were used to account for population structure along with a kinship matrix. To identify marker-trait associations (MTAs), four phenotypic data sets representing each of three years and combined were independently analyzed in the multilocus mixed model (MLMM). A total of 30 significant MTAs was detected over data sets for eight fruit traits at P &lt; 0.0005. The number of MTA per trait ranged from one (brix) to seven (fruit weight and fruit width). Two SNP markers on chromosomes 1 and 2 were significantly associated with multiple traits, suggesting pleiotropic effects of QTL. Furthermore, 16 of 30 MTAs suggest potential novel QTL for eight fruit traits. These results facilitate genetic dissection of tomato fruit traits and provide a useful resource to develop molecular tools for improving fruit traits via marker-assisted selection and genomic selection in tomato breeding programs.
A novel de novo androgen receptor nonsense mutation in a sex-reversed 46,XY infant
Authors: Poon Kok-Siong , Tan Karen Mei-Ling , Loke Kah Yin 
Published: September 2021

AbstractAn infant with 46,XY karyotype, and unambiguous female phenotype was found to have testes in the inguinal regions. Capillary sequencing of the androgen receptor (AR) gene identified a hemizygous de novo mutation (NM_000044.6:c.1621G > T) in exon 2 resulting in a termination codon p.(Glu541*) at the DNA binding domain (DBD). This novel nonsense mutation adds to the compendium of AR mutations which result in complete androgen insensitivity syndrome (AIS).
Cortical overgrowth in a preclinical forebrain organoid model of CNTNAP2-associated autism spectrum disorder
Authors: de Jong Job O. , Llapashtica Ceyda , Genestine Matthieu , Strauss Kevin , Provenzano Frank , Sun Yan , Zhu Huixiang , Cortese Giuseppe P. , Brundu Francesco , Brigatti Karlla W. , Corneo Barbara , Migliori Bianca , Tomer Raju , Kushner Steven A. , Kellendonk Christoph , Javitch Jonathan A. , Xu Bin , Markx Sander 
Published: September 2021

AbstractWe utilized forebrain organoids generated from induced pluripotent stem cells of patients with a syndromic form of Autism Spectrum Disorder (ASD) with a homozygous protein-truncating mutation in CNTNAP2, to study its effects on embryonic cortical development. Patients with this mutation present with clinical characteristics of brain overgrowth. Patient-derived forebrain organoids displayed an increase in volume and total cell number that is driven by increased neural progenitor proliferation. Single-cell RNA sequencing revealed PFC-excitatory neurons to be the key cell types expressing CNTNAP2. Gene ontology analysis of differentially expressed genes (DEgenes) corroborates aberrant cellular proliferation. Moreover, the DEgenes are enriched for ASD-associated genes. The cell-type-specific signature genes of the CNTNAP2-expressing neurons are associated with clinical phenotypes previously described in patients. The organoid overgrowth phenotypes were largely rescued after correction of the mutation using CRISPR-Cas9. This CNTNAP2-organoid model provides opportunity for further mechanistic inquiry and development of new therapeutic strategies for ASD.
Defining the RBPome of primary T helper cells to elucidate higher-order Roquin-mediated mRNA regulation
Authors: Hoefig Kai P. , Reim Alexander , Gallus Christian , Wong Elaine H. , Behrens Gesine , Conrad Christine , Xu Meng , Kifinger Lisa , Ito-Kureha Taku , Defourny Kyra A. Y. , Geerlof Arie , Mautner Josef , Hauck Stefanie M. , Baumjohann Dirk , Feederle Regina , Mann Matthias , Wierer Michael , Glasmacher Elke , Heissmeyer Vigo 
Published: September 2021

AbstractPost-transcriptional gene regulation in T cells is dynamic and complex as targeted transcripts respond to various factors. This is evident for the Icos mRNA encoding an essential costimulatory receptor that is regulated by several RNA-binding proteins (RBP), including Roquin-1 and Roquin-2. Here, we identify a core RBPome of 798 mouse and 801 human T cell proteins by utilizing global RNA interactome capture (RNA-IC) and orthogonal organic phase separation (OOPS). The RBPome includes Stat1, Stat4 and Vav1 proteins suggesting unexpected functions for these transcription factors and signal transducers. Based on proximity to Roquin-1, we select ~50 RBPs for testing coregulation of Roquin-1/2 targets by induced expression in wild-type or Roquin-1/2-deficient T cells. Besides Roquin-independent contributions from Rbms1 and Cpeb4 we also show Roquin-1/2-dependent and target-specific coregulation of Icos by Celf1 and Igf2bp3. Connecting the cellular RBPome in a post-transcriptional context, we find contributions from multiple RBPs to the prototypic regulation of mRNA targets by individual trans-acting factors.
Spatial rearrangement of the Streptomyces venezuelae linear chromosome during sporogenic development
Authors: Szafran Marcin J. , Małecki Tomasz , Strzałka Agnieszka , Pawlikiewicz Katarzyna , Duława Julia , Zarek Anna , Kois-Ostrowska Agnieszka , Findlay Kim C. , Le Tung B. K. , Jakimowicz Dagmara 
Published: September 2021

AbstractBacteria of the genus Streptomyces have a linear chromosome, with a core region and two ‘arms’. During their complex life cycle, these bacteria develop multi-genomic hyphae that differentiate into chains of exospores that carry a single copy of the genome. Sporulation-associated cell division requires chromosome segregation and compaction. Here, we show that the arms of Streptomyces venezuelae chromosomes are spatially separated at entry to sporulation, but during sporogenic cell division they are closely aligned with the core region. Arm proximity is imposed by segregation protein ParB and condensin SMC. Moreover, the chromosomal terminal regions are organized into distinct domains by the Streptomyces-specific HU-family protein HupS. Thus, as seen in eukaryotes, there is substantial chromosomal remodelling during the Streptomyces life cycle, with the chromosome undergoing rearrangements from an ‘open’ to a ‘closed’ conformation.
A versatile genetic engineering toolkit for E. coli based on CRISPR-prime editing
Authors: Tong Yaojun , Jørgensen Tue S. , Whitford Christopher M. , Weber Tilmann , Lee Sang Yup 
Published: September 2021

AbstractCRISPR base editing is a powerful method to engineer bacterial genomes. However, it restricts editing to single-nucleotide substitutions. Here, to address this challenge, we adapt a CRISPR-Prime Editing-based, DSB-free, versatile, and single-nucleotide resolution genetic manipulation toolkit for prokaryotes. It can introduce substitutions, deletions, insertions, and the combination thereof, both in plasmids and the chromosome of E. coli with high fidelity. Notably, under optimal conditions, the efficiency of 1-bp deletions reach up to 40%. Moreover, deletions of up to 97 bp and insertions up to 33 bp were successful with the toolkit in E. coli, however, efficiencies dropped sharply with increased fragment sizes. With a second guide RNA, our toolkit can achieve multiplexed editing albeit with low efficiency. Here we report not only a useful addition to the genome engineering arsenal for E. coli, but also a potential basis for the development of similar toolkits for other bacteria.
The homogenous alternative to biomineralization: Zn- and Mn-rich materials enable sharp organismal “tools” that reduce force requirements
Authors: Schofield R. M. S. , Bailey J. , Coon J. J. , Devaraj A. , Garrett R. W. , Goggans M. S. , Hebner M. G. , Lee B. S. , Lee D. , Lovern N. , Ober-Singleton S. , Saephan N. , Seagal V. R. , Silver D. M. , Som H. E. , Twitchell J. , Wang X. , Zima J. S. , Nesson M. H. 
Published: September 2021

AbstractWe measured hardness, modulus of elasticity, and, for the first time, loss tangent, energy of fracture, abrasion resistance, and impact resistance of zinc- and manganese-enriched materials from fangs, stings and other “tools” of an ant, spider, scorpion and nereid worm. The mechanical properties of the Zn- and Mn-materials tended to cluster together between plain and biomineralized “tool” materials, with the hardness reaching, and most abrasion resistance values exceeding, those of calcified salmon teeth and crab claws. Atom probe tomography indicated that Zn was distributed homogeneously on a nanometer scale and likely bound as individual atoms to more than ¼ of the protein residues in ant mandibular teeth. This homogeneity appears to enable sharper, more precisely sculpted “tools” than materials with biomineral inclusions do, and also eliminates interfaces with the inclusions that could be susceptible to fracture. Based on contact mechanics and simplified models, we hypothesize that, relative to plain materials, the higher elastic modulus, hardness and abrasion resistance minimize temporary or permanent tool blunting, resulting in a roughly 2/3 reduction in the force, energy, and muscle mass required to initiate puncture of stiff materials, and even greater force reductions when the cumulative effects of abrasion are considered. We suggest that the sharpness-related force reductions lead to significant energy savings, and can also enable organisms, especially smaller ones, to puncture, cut, and grasp objects that would not be accessible with plain or biomineralized “tools”.