bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generation of gravity waves from thermal tides in the Venus atmosphere
Authors: Sugimoto Norihiko , Fujisawa Yukiko , Kashimura Hiroki , Noguchi Katsuyuki , Kuroda Takeshi , Takagi Masahiro , Hayashi Yoshi-Yuki 
Published: June 2021

AbstractGravity waves play essential roles in the terrestrial atmosphere because they propagate far from source regions and transport momentum and energy globally. Gravity waves are also observed in the Venus atmosphere, but their characteristics have been poorly understood. Here we demonstrate activities of small-scale gravity waves using a high-resolution Venus general circulation model with less than 20 and 0.25 km in the horizontal and vertical grid intervals, respectively. We find spontaneous gravity wave radiation from nearly balanced flows. In the upper cloud layer (~70 km), the thermal tides in the super-rotation are primary sources of small-scale gravity waves in the low-latitudes. Baroclinic/barotropic waves are also essential sources in the mid- and high-latitudes. The small-scale gravity waves affect the three-dimensional structure of the super-rotation and contribute to material mixing through their breaking processes. They propagate vertically and transport momentum globally, which decelerates the super-rotation in the upper cloud layer (~70 km) and accelerates it above ~80 km.
3D genome alterations associated with dysregulated HOXA13 expression in high-risk T-lineage acute lymphoblastic leukemia
Authors: Yang Lu , Chen Fengling , Zhu Haichuan , Chen Yang , Dong Bingjie , Shi Minglei , Wang Weitao , Jiang Qian , Zhang Leping , Huang Xiaojun , Zhang Michael Q. , Wu Hong 
Published: June 2021

Abstract3D genome alternations can dysregulate gene expression by rewiring enhancer-promoter interactions and lead to diseases. We report integrated analyses of 3D genome alterations and differential gene expressions in 18 newly diagnosed T-lineage acute lymphoblastic leukemia (T-ALL) patients and 4 healthy controls. 3D genome organizations at the levels of compartment, topologically associated domains and loop could hierarchically classify different subtypes of T-ALL according to T cell differentiation trajectory, similar to gene expressions-based classification. Thirty-four previously unrecognized translocations and 44 translocation-mediated neo-loops are mapped by Hi-C analysis. We find that neo-loops formed in the non-coding region of the genome could potentially regulate ectopic expressions of TLX3, TAL2 and HOXA transcription factors via enhancer hijacking. Importantly, both translocation-mediated neo-loops and NUP98-related fusions are associated with HOXA13 ectopic expressions. Patients with HOXA11-A13 expressions, but not other genes in the HOXA cluster, have immature immunophenotype and poor outcomes. Here, we highlight the potentially important roles of 3D genome alterations in the etiology and prognosis of T-ALL.
Charge carrier mapping for Z-scheme photocatalytic water-splitting sheet via categorization of microscopic time-resolved image sequences
Authors: Ebihara Makoto , Ikeda Takeshi , Okunaka Sayuri , Tokudome Hiromasa , Domen Kazunari , Katayama Kenji 
Published: June 2021

AbstractPhotocatalytic water splitting system using particulate semiconductor materials is a promising strategy for converting solar energy into hydrogen and oxygen. In particular, visible-light-driven ‘Z-scheme’ printable photocatalyst sheets are cost-effective and scalable. However, little is known about the fundamental photophysical processes, which are key to explaining and promoting the photoactivity. Here, we applied the pattern-illumination time-resolved phase microscopy for a photocatalyst sheet composed of Mo-doped BiVO4 and Rh-doped SrTiO3 with indium tin oxide as the electron mediator to investigate photo-generated charge carrier dynamics. Using this method, we successfully observed the position- and structure-dependent charge carrier behavior and visualized the active/inactive sites in the sheets under the light irradiation via the time sequence images and the clustering analysis. This combination methodology could provide the material/synthesis optimization methods for the maximum performance of the photocatalyst sheets.
Evolution of an assembly factor-based subunit contributed to a novel NDH-PSI supercomplex formation in chloroplasts
Authors: Kato Yoshinobu , Odahara Masaki , Shikanai Toshiharu 
Published: June 2021

AbstractChloroplast NADH dehydrogenase-like (NDH) complex is structurally related to mitochondrial Complex I and forms a supercomplex with two copies of Photosystem I (the NDH-PSI supercomplex) via linker proteins Lhca5 and Lhca6. The latter was acquired relatively recently in a common ancestor of angiosperms. Here we show that NDH-dependent Cyclic Electron Flow 5 (NDF5) is an NDH assembly factor in Arabidopsis. NDF5 initiates the assembly of NDH subunits (PnsB2 and PnsB3) and Lhca6, suggesting that they form a contact site with Lhca6. Our analysis of the NDF5 ortholog in Physcomitrella and angiosperm genomes reveals the subunit PnsB2 to be newly acquired via tandem gene duplication of NDF5 at some point in the evolution of angiosperms. Another Lhca6 contact subunit, PnsB3, has evolved from a protein unrelated to NDH. The structure of the largest photosynthetic electron transport chain complex has become more complicated by acquiring novel subunits and supercomplex formation with PSI.
Suppression of mitochondrial ROS by prohibitin drives glioblastoma progression and therapeutic resistance
Authors: Huang Haohao , Zhang Songyang , Li Yuanyuan , Liu Zhaodan , Mi Lanjuan , Cai Yan , Wang Xinzheng , Chen Lishu , Ran Haowen , Xiao Dake , Li Fangye , Wu Jiaqi , Li Tingting , Han Qiuying , Chen Liang , Pan Xin , Li Huiyan , Li Tao , He Kun , Li Ailing , Zhang Xuemin , Zhou Tao , Xia Qing , Man Jianghong 
Published: June 2021

AbstractLow levels of reactive oxygen species (ROS) are crucial for maintaining cancer stem cells (CSCs) and their ability to resist therapy, but the ROS regulatory mechanisms in CSCs remains to be explored. Here, we discover that prohibitin (PHB) specifically regulates mitochondrial ROS production in glioma stem-like cells (GSCs) and facilitates GSC radiotherapeutic resistance. We find that PHB is upregulated in GSCs and is associated with malignant gliomas progression and poor prognosis. PHB binds to peroxiredoxin3 (PRDX3), a mitochondrion-specific peroxidase, and stabilizes PRDX3 protein through the ubiquitin-proteasome pathway. Knockout of PHB dramatically elevates ROS levels, thereby inhibiting GSC self-renewal. Importantly, deletion or pharmacological inhibition of PHB potently slows tumor growth and sensitizes tumors to radiotherapy, thus providing significant survival benefits in GSC-derived orthotopic tumors and glioblastoma patient-derived xenografts. These results reveal a selective role of PHB in mitochondrial ROS regulation in GSCs and suggest that targeting PHB improves radiotherapeutic efficacy in glioblastoma.
Fluorescent nanosensors reveal dynamic pH gradients during biofilm formation
Authors: Hollmann Birte , Perkins Mark , Chauhan Veeren M. , Aylott Jonathan W. , Hardie Kim R. 
Published: June 2021

AbstractUnderstanding the dynamic environmental microniches of biofilms will permit us to detect, manage and exploit these communities. The components and architecture of biofilms have been interrogated in depth; however, little is known about the environmental microniches present. This is primarily because of the absence of tools with the required measurement sensitivity and resolution to detect these changes. We describe the application of ratiometric fluorescent pH-sensitive nanosensors, as a tool, to observe physiological pH changes in biofilms in real time. Nanosensors comprised two pH-sensitive fluorophores covalently encapsulated with a reference pH-insensitive fluorophore in an inert polyacrylamide nanoparticle matrix. The nanosensors were used to analyse the real-time three-dimensional pH variation for two model biofilm formers: (i) opportunistic pathogen Pseudomonas aeruginosa and (ii) oral pathogen Streptococcus mutans. The detection of sugar metabolism in real time by nanosensors provides a potential application to identify therapeutic solutions to improve oral health.
Development and pilot of an online, personalized risk assessment tool for a breast cancer precision medicine trial
Authors: Keane Holly , Huilgol Yash S. , Shieh Yiwey , Tice Jeffrey A. , Belkora Jeff , Sepucha Karen , Shibley W. Patrick , Wang Tianyi , Che Mandy , Goodman Deborah , Ozanne Elissa , Fiscalini Allison Stover , Esserman Laura J. 
Published: June 2021

AbstractBreast cancer risk reduction has been validated by large-scale clinical trials, but uptake remains low. A risk communication tool could provide personalized risk-reduction information for high-risk women. A low-literacy-friendly, visual, and personalized tool was designed as part of the Women Informed to Screen Depending On Measures of risk (WISDOM) study. The tool integrates genetic, polygenic, and lifestyle factors, and quantifies the risk-reduction from undertaking medication and lifestyle interventions. The development and design process utilized feedback from clinicians, decision-making scientists, software engineers, and patient advocates. We piloted the tool with 17 study participants, collecting quantitative and qualitative feedback. Overall, participants felt they better understood their personalized breast cancer risk, were motivated to reduce their risk, and considered lifestyle interventions. The tool will be used to evaluate whether risk-based screening leads to more informed decisions and higher uptake of risk-reduction interventions among those most likely to benefit.
First-principles prediction of electronic transport in fabricated semiconductor heterostructures via physics-aware machine learning
Authors: Pimachev Artem K. , Neogi Sanghamitra 
Published: June 2021

AbstractFirst-principles techniques for electronic transport property prediction have seen rapid progress in recent years. However, it remains a challenge to predict properties of heterostructures incorporating fabrication-dependent variability. Machine-learning (ML) approaches are increasingly being used to accelerate design and discovery of new materials with targeted properties, and extend the applicability of first-principles techniques to larger systems. However, few studies exploited ML techniques to characterize relationships between local atomic structures and global electronic transport coefficients. In this work, we propose an electronic-transport-informatics (ETI) framework that trains on ab initio models of small systems and predicts thermopower of fabricated silicon/germanium heterostructures, matching measured data. We demonstrate application of ML approaches to extract important physics that determines electronic transport in semiconductor heterostructures, and bridge the gap between ab initio accessible models and fabricated systems. We anticipate that ETI framework would have broad applicability to diverse materials classes.
Evaluating the lettuce metatranscriptome with MinION sequencing for future spaceflight food production applications
Authors: Haveman Natasha J. , Khodadad Christina L. M. , Dixit Anirudha R. , Louyakis Artemis S. , Massa Gioia D. , Venkateswaran Kasthuri , Foster Jamie S. 
Published: June 2021

AbstractHealthy plants are vital for successful, long-duration missions in space, as they provide the crew with life support, food production, and psychological benefits. The microorganisms that associate with plant tissues play a critical role in improving plant health and production. To that end, we developed a methodology to investigate the transcriptional activities of the microbiome of red romaine lettuce, a key salad crop that was grown under International Space Station (ISS)-like conditions. Microbial transcripts enriched from host–microbe total RNA were sequenced using the Oxford Nanopore MinION sequencing platform. Results show that this enrichment approach was highly reproducible and could be an effective approach for the on-site detection of microbial transcriptional activity. Our results demonstrate the feasibility of using metatranscriptomics of enriched microbial RNA as a potential method for on-site monitoring of the transcriptional activity of crop microbiomes, thereby helping to facilitate and maintain plant health for on-orbit space food production.
A cautionary perspective regarding the isolation and serial propagation of SARS-CoV-2 in Vero cells
Authors: Funnell Simon G. P. , Afrough Babak , Baczenas John James , Berry Neil , Bewley Kevin R. , Bradford Rebecca , Florence Clint , Duff Yann Le , Lewis Mark , Moriarty Ryan V. , Connor Shelby L. O. , Osman Karen L. , Pullan Steven , Rashid Sujatha , Richards Kevin S. , Stemple Kimberly J. , Knezevic Ivana 
Published: June 2021

AbstractAn array of SARS-CoV-2 virus variants have been isolated, propagated and used in in vitro assays, in vivo animal studies and human clinical trials. Observations of working stocks of SARS-CoV-2 suggest that sequential propagation in Vero cells leads to critical changes in the region of the furin cleavage site, which significantly reduce the value of the working stock for critical research studies. Serially propagating SARS-CoV-2 in Vero E6 cells leads to rapid increases in genetic variants while propagation in other cell lines (e.g. Vero/hSLAM) appears to mitigate this risk thereby improving the overall genetic stability of working stocks. From these observations, investigators are urged to monitor genetic variants carefully when propagating SARS-CoV-2 in Vero cells.
Lower crustal earthquake associated with highly pressurized frictional melts
Authors: Zhong Xin , Petley-Ragan Arianne J. , Incel Sarah H. M. , Dabrowski Marcin , Andersen Niels H. , Jamtveit Bjørn 
Published: June 2021

AbstractEarthquakes at lower crustal depths are common during continental collision. However, the coseismic weakening mechanisms required to propagate an earthquake at high pressures are poorly understood. Transient high-pressure fluids or melts have been proposed as a viable mechanism, but verifying this requires direct in situ measurement of fluid or melt overpressure along fault planes that have hosted dynamic ruptures. Here, we report direct measurement of highly overpressurized frictional melts along a seismic fault surface. Using Raman spectroscopy, we identified high-pressure quartz inclusions sealed in dendritic garnets that grew from frictional melts formed by lower crustal earthquakes in the Bergen Arcs, Western Norway. Melt pressure was estimated to be 1.8–2.3 GPa on the basis of an elastic model for the quartz-in-garnet system. This is ~0.5 GPa higher than the pressure recorded by the surrounding pseudotachylyte matrix and wall rocks. The recorded melt pressure could not arise solely from the volume expansion of melting, and we propose that it was generated when melt pressure approached the maximum principal stress in a system subject to high differential stress. The associated palaeostress field demonstrates that a strong lower crust accommodated up to 1 GPa differential stress during the compressive stage of the Caledonian orogeny.
Epigenetics Identifier screens reveal regulators of chromatin acylation and limited specificity of acylation antibodies
Authors: Kollenstart Leonie , van der Horst Sophie C. , Vreeken Kees , Janssen George M. C. , Martino Fabrizio , Vlaming Hanneke , van Veelen Peter A. , van Leeuwen Fred , van Attikum Haico 
Published: June 2021

AbstractThe collection of known posttranslational modifications (PTMs) has expanded rapidly with the identification of various non-acetyl histone lysine acylations, such as crotonylation, succinylation and butyrylation, yet their regulation is still not fully understood. Through an unbiased chromatin immunoprecipitation (ChIP)-based approach called Epigenetics-IDentifier (Epi-ID), we aimed to identify regulators of crotonylation, succinylation and butyrylation in thousands of yeast mutants simultaneously. However, highly correlative results led us to further investigate the specificity of the pan-K-acyl antibodies used in our Epi-ID studies. This revealed cross-reactivity and lack of specificity of pan-K-acyl antibodies in various assays. Our findings suggest that the antibodies might recognize histone acetylation in vivo, in addition to histone acylation, due to the vast overabundance of acetylation compared to other acylation modifications in cells. Consequently, our Epi-ID screen mostly identified factors affecting histone acetylation, including known (e.g. GCN5, HDA1, and HDA2) and unanticipated (MET7, MTF1, CLB3, and RAD26) factors, expanding the repertoire of acetylation regulators. Antibody-independent follow-up experiments on the Gcn5-Ada2-Ada3 (ADA) complex revealed that, in addition to acetylation and crotonylation, ADA has the ability to butyrylate histones. Thus, our Epi-ID screens revealed limits of using pan-K-acyl antibodies in epigenetics research, expanded the repertoire of regulators of histone acetylation, and attributed butyrylation activity to the ADA complex.
Lorentz force induced shear waves for magnetic resonance elastography applications
Authors: Flé Guillaume , Gilbert Guillaume , Grasland-Mongrain Pol , Cloutier Guy 
Published: June 2021

AbstractQuantitative mechanical properties of biological tissues can be mapped using the shear wave elastography technique. This technology has demonstrated a great potential in various organs but shows a limit due to wave attenuation in biological tissues. An option to overcome the inherent loss in shear wave magnitude along the propagation pathway may be to stimulate tissues closer to regions of interest using alternative motion generation techniques. The present study investigated the feasibility of generating shear waves by applying a Lorentz force directly to tissue mimicking samples for magnetic resonance elastography applications. This was done by combining an electrical current with the strong magnetic field of a clinical MRI scanner. The Local Frequency Estimation method was used to assess the real value of the shear modulus of tested phantoms from Lorentz force induced motion. Finite elements modeling of reported experiments showed a consistent behavior but featured wavelengths larger than measured ones. Results suggest the feasibility of a magnetic resonance elastography technique based on the Lorentz force to produce an shear wave source.
Reflectivity relates differently to pro sociality in naïve and strategic subjects
Authors: Pancotto Francesca , Righi Simone 
Published: June 2021

AbstractIs pro sociality a natural impulse or the result of a self-controlled behavior? We investigate this issue in a lab in the field experiment with participants from the general adult population in Italy. We find two key results: first, that there is a positive relationship between pro sociality and strategic reasoning. Second, that reflectivity relates to lower pro sociality but only among strategic subjects, indicating that the intuitive view of pro sociality is valid only among strategic individuals. Non-strategic individuals are instead intuitively selfish. We surmise that these results emerge due to a common cognitive root between strategizing and pro sociality, namely empathy.
Genome sequencing and de novo assembly of the giant unicellular alga Acetabularia acetabulum using droplet MDA
Authors: Andresen Ina J. , Orr Russell J. S. , Krabberød Anders K. , Shalchian-Tabrizi Kamran , Bråte Jon 
Published: June 2021

AbstractThe macroscopic single-celled green alga Acetabularia acetabulum has been a model system in cell biology for more than a century. However, no genomic information is available from this species. Since the alga has a long life cycle, is difficult to grow in dense cultures, and has an estimated diploid genome size of almost 2 Gb, obtaining sufficient genomic material for genome sequencing is challenging. Here, we have attempted to overcome these challenges by amplifying genomic DNA using multiple displacement amplification (MDA) combined with microfluidics technology to distribute the amplification reactions across thousands of microscopic droplets. By amplifying and sequencing DNA from five single cells we were able to recover an estimated ~ 7–11% of the total genome, providing the first draft of the A. acetabulum genome. We highlight challenges associated with genome recovery and assembly of MDA data due to biases arising during genome amplification, and hope that our study can serve as a reference for future attempts on sequencing the genome from non-model eukaryotes.
Electro-oxidation of formoterol fumarate on the surface of novel poly(thiazole yellow-G) layered multi-walled carbon nanotube paste electrode
Authors: Hareesha N. , Manjunatha J. G. 
Published: June 2021

AbstractThe current study explicates the electro-oxidation behavior of formoterol fumarate (FLFT) in the presence of uric acid (UA) on the surface of poly thiazole yellow-G (TY-G) layered multi-walled carbon nanotube paste electrode (MWCNTPE). The modified (Poly(TY-G)LMWCNTPE) and unmodified (MWCNTPE) electrode materials were characterized through electrochemical impedance spectroscopy (EIS), field emission scanning electron microscopy (FE-SEM), and cyclic voltammetry (CV) approaches. The characterization data confirms the good conducting and electrocatalytic nature with more electrochemical active sites on the Poly(TY-G)LMWCNTPE than MWCNTPE towards the FLFT analysis in the presence of UA. Poly(TY-G)LMWCNTPE easily separates the two drugs (FLFT and UA) even though they both have nearer oxidation peak potential. The electro-catalytic activity of the developed electrode is fast and clear for FLFT electro-oxidation in 0.2 M phosphate buffer (PB) of pH 6.5. The Poly(TY-G)LMWCNTPE offered a well-resolved peak with the highest electro-oxidation peak current at the peak potential of 0.538 V than MWCNTPE. The potential scan rate and oxidation peak growth time studies show the electrode reaction towards FLFT electro-oxidation is continued through a diffusion-controlled step. The variation of concentration of FLFT in the range from 0.2 to 1.5 µM (absence of UA) and 3.0 to 8.0 μM (presence of UA) provides a good linear relationship with increased peak current and a lower limit of detection (LOD) values of 0.0128 µM and 0.0129 µM, respectively. The prepared electrode gives a fine recovery for the detection of FLFT in the medicinal sample with acceptable repeatability, stability, and reproducibility.