bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental Insights on the Propagation of Fine‐Grained Geophysical Flows Entering Water
Authors: Bougouin Alexis , Roche Olivier , Paris Raphaël , Huppert Herbert E. 
Published: March 2021

AbstractGranular flows that propagate down a mountainside, then reach the sea, a lake or a river and finally, travel underwater, is a common event on the Earth's surface. To help the description of such events, laboratory experiments on gas‐fluidized granular flows entering water are performed, analyzed, and compared to those propagating in air. The originality of this study lies in the fluidization process, which improves the laboratory modeling of geophysical flows by taking their high mobility into account. Qualitatively, the presence of the water body promotes the generation of a granular jet over the water surface, a leading and largest wave, and a particle‐driven gravity current underwater. Hydrodynamic forces mainly play a dissipative role by slowing and reducing the spreading of the granular mass underwater, but a low amount of grains are still transported by the turbulent fluid as a gravity current far away. The temporal evolution of the granular jet and the particle‐driven gravity current are well described by ballistic motion theory and scaling laws of homogeneous gravity currents, respectively. Most currents propagate with a constant flow‐front velocity along the horizontal bottom, which is controlled by the flow height depending on the water depth. In contrast, the bulk volume concentration of particles in the current is estimated to be nearly constant, interpreted as a critical concentration above which the excess of particles cannot be maintained by the turbulent fluid. This experimental study highlights the complexity of the dynamics and deposits of granular masses when they encounter a water body.
Unexpected High Absorption of Atmospheric Aerosols Over a Western Tibetan Plateau Site in Summer
Authors: Zhang Lei , Tang Chenguang , Huang Jianping , Du Tao , Guan Xu , Tian Pengfei , Shi Jinsen , Cao Xianjie , Huang Zhongwei , Guo Qi , Zhang Haotian , Wang Min , Zeng Huiyu , Wang Feiyang , Dolkar Pema 
Published: March 2021

AbstractThe assessment of atmospheric aerosol radiative effects in the Tibetan Plateau (TP) suffers from large uncertainties due to limited understanding of aerosol physicochemical properties. To quantify aerosol optical properties, size distributions, and chemical compositions in the western TP, an intensive field campaign was carried out at Shiquanhe National Reference Climatological Station from July 8 to August 2, 2019. Unexpected low single scattering albedo (SSA) at 870 nm was found for the fine aerosols with an average value of 0.73 ± 0.18. SSA was even lower than 0.60 in the morning when fine aerosols peaked, indicating high absorption of the fine aerosols induced by anthropogenic activities. Coarse mode aerosols accounted for 70.58% ± 14.98% of the total volume concentration and mineral dust was the most abundant species in total suspended particles with a mass fraction of 48.7%. Fine mode aerosol concentrations showed little dependence on wind speed while coarse mode aerosols and metallic element concentrations exhibited strong positive correlations with wind speed, indicating the importance of wind‐blown dust particles. The present study for the first time quantified key aerosol parameters in the western TP and unexpected high absorption of atmospheric aerosols were found over the site in summer. Our results suggest the need to carefully consider the radiative effects caused by aerosol absorption in the TP region.
Machine learning powered ellipsometry
Authors: Liu Jinchao , Zhang Di , Yu Dianqiang , Ren Mengxin , Xu Jingjun 
Published: March 2021

AbstractEllipsometry is a powerful method for determining both the optical constants and thickness of thin films. For decades, solutions to ill-posed inverse ellipsometric problems require substantial human–expert intervention and have become essentially human-in-the-loop trial-and-error processes that are not only tedious and time-consuming but also limit the applicability of ellipsometry. Here, we demonstrate a machine learning based approach for solving ellipsometric problems in an unambiguous and fully automatic manner while showing superior performance. The proposed approach is experimentally validated by using a broad range of films covering categories of metals, semiconductors, and dielectrics. This method is compatible with existing ellipsometers and paves the way for realizing the automatic, rapid, high-throughput optical characterization of films.
Expanding the repertoire of electron acceptors for the anaerobic oxidation of methane in carbonates in the Atlantic and Pacific Ocean
Authors: Beckmann Sabrina , Farag Ibrahim F , Zhao Rui , Christman Glenn D , Prouty Nancy G , Biddle Jennifer F 
Published: March 2021

Abstract
Authigenic carbonates represent a significant microbial sink for methane, yet little is known about the microbiome responsible for the methane removal. We identify carbonate microbiomes distributed over 21 locations hosted by seven different cold seeps in the Pacific and Atlantic Oceans by carrying out a gene-based survey using 16S rRNA- and mcrA gene sequencing coupled with metagenomic analyses. Based on 16S rRNA gene amplicon analyses, these sites were dominated by bacteria affiliated to the Firmicutes, Alpha- and Gammaproteobacteria. ANME-1 and -2 archaeal clades were abundant in the carbonates yet their typical syntrophic partners, sulfate-reducing bacteria, were not significantly present. Based on mcrA amplicon analyses, the Candidatus Methanoperedens clades were also highly abundant. Our metagenome analysis indicated that methane oxidizers affiliated to the ANME-1 and -2, may be capable of performing complete methane- and potentially short-chain alkane oxidation independently using oxidized sulfur and nitrogen compounds as terminal electron acceptors. Gammaproteobacteria are hypothetically capable of utilizing oxidized nitrogen compounds and may be involved in syntrophy with methane-oxidizing archaea. Carbonate structures represent a window for a more diverse utilization of electron acceptors for anaerobic methane oxidation along the Atlantic and Pacific Margin.
Evidences for lipid involvement in SARS-CoV-2 cytopathogenesis
Authors: Nardacci Roberta , Colavita Francesca , Castilletti Concetta , Lapa Daniele , Matusali Giulia , Meschi Silvia , Del Nonno Franca , Colombo Daniele , Capobianchi Maria Rosaria , Zumla Alimuddin , Ippolito Giuseppe , Piacentini Mauro , Falasca Laura 
Published: March 2021

AbstractThe pathogenesis of SARS-CoV-2 remains to be completely understood, and detailed SARS-CoV-2 cellular cytopathic effects requires definition. We performed a comparative ultrastructural study of SARS-CoV-1 and SARS-CoV-2 infection in Vero E6 cells and in lungs from deceased COVID-19 patients. SARS-CoV-2 induces rapid death associated with profound ultrastructural changes in Vero cells. Type II pneumocytes in lung tissue showed prominent altered features with numerous vacuoles and swollen mitochondria with presence of abundant lipid droplets. The accumulation of lipids was the most striking finding we observed in SARS-CoV-2 infected cells, both in vitro and in the lungs of patients, suggesting that lipids can be involved in SARS-CoV-2 pathogenesis. Considering that in most cases, COVID-19 patients show alteration of blood cholesterol and lipoprotein homeostasis, our findings highlight a peculiar important topic that can suggest new approaches for pharmacological treatment to contrast the pathogenicity of SARS-CoV-2.
Autophagy, an accomplice or antagonist of drug resistance in HCC?
Authors: Wu Yafei , Zhang Jigang , Li Qin 
Published: March 2021

AbstractHepatocellular carcinoma (HCC) is a highly lethal malignancy characterized by poor prognosis and a low 5-year survival rate. Drug treatment is proving to be effective in anti-HCC. However, only a small number of HCC patients exhibit sensitive responses, and drug resistance occurs frequently in advanced patients. Autophagy, an evolutionary process responsible for the degradation of cellular substances, is closely associated with the acquisition and maintenance of drug resistance for HCC. This review focuses on autophagic proteins and explores the intricate relationship between autophagy and cancer stem cells, tumor-derived exosomes, and noncoding RNA. Clinical trials involved in autophagy inhibition combined with anticancer drugs are also concerned.
Cullin-5 neddylation-mediated NOXA degradation is enhanced by PRDX1 oligomers in colorectal cancer
Authors: Xu Shoufang , Ma Yilei , Tong Qingchao , Yang Jun , Liu Jia , Wang Yanzhong , Li Guoli , Zeng Jin , Fang Sining , Li Fengying , Xie Xinyou , Zhang Jun 
Published: March 2021

AbstractNOXA, a BH3-only proapoptotic protein involved in regulating cell death decisions, is highly expressed but short-lived in colorectal cancer (CRC). Neddylated cullin-5 (CUL5)-mediated ubiquitination and degradation of NOXA is crucial to prevent its overaccumulation and maintain an appropriate action time. However, how this process is manipulated by CRC cells commonly exposed to oxidative stress remain unknown. The peroxiredoxin PRDX1, a conceivable antioxidant overexpressed in CRC tissues, has been shown to inhibit apoptosis and TRAF6 ubiquitin-ligase activity. In this study, we found that PRDX1 inhibits CRC cell apoptosis by downregulating NOXA. Mechanistically, PRDX1 promotes NOXA ubiquitination and degradation, which completely depend on CUL5 neddylation. Further studies have demonstrated that PRDX1 oligomers bind with both the Nedd8-conjugating enzyme UBE2F and CUL5 and that this tricomplex is critical for CUL5 neddylation, since silencing PRDX1 or inhibiting PRDX1 oligomerization greatly dampens CUL5 neddylation and NOXA degradation. An increase in reactive oxygen species (ROS) is not only a hallmark of cancer cells but also the leading driving force for PRDX1 oligomerization. As shown in our study, although ROS play a role in upregulating NOXA mRNA transcription, ROS scavenging in CRC cells by N-acetyl-L-cysteine (NAC) can significantly reduce CUL5 neddylation and extend the NOXA protein half-life. Therefore, in CRC, PRDX1 plays a key role in maintaining intracellular homeostasis under conditions of high metabolic activity by reinforcing UBE2F-CUL5-mediated degradation of NOXA, which is also evidenced in the resistance of CRC cells to etoposide treatment. Based on these findings, targeting PRDX1 could be an effective strategy to overcome the resistance of CRC to DNA damage-inducing chemotherapeutics.
Ultrafast non-excitonic valley Hall effect in MoS2/WTe2 heterobilayers
Authors: Lee Jekwan , Heo Wonhyeok , Cha Myungjun , Watanabe Kenji , Taniguchi Takashi , Kim Jehyun , Cha Soonyoung , Kim Dohun , Jo Moon-Ho , Choi Hyunyong 
Published: March 2021

AbstractThe valley Hall effect (VHE) in two-dimensional (2D) van der Waals (vdW) crystals is a promising approach to study the valley pseudospin. Most experiments so far have used bound electron-hole pairs (excitons) through local photoexcitation. However, the valley depolarization of such excitons is fast, so that several challenges remain to be resolved. We address this issue by exploiting a unipolar VHE using a heterobilayer made of monolayer MoS2/WTe2 to exhibit a long valley-polarized lifetime due to the absence of electron-hole exchange interaction. The unipolar VHE is manifested by reduced photoluminescence at the MoS2 A exciton energy. Furthermore, we provide quantitative information on the time-dependent valley Hall dynamics by performing the spatially-resolved ultrafast Kerr-rotation microscopy; we find that the valley-polarized electrons persist for more than 4 nanoseconds and the valley Hall mobility exceeds 4.49 × 103 cm2/Vs, which is orders of magnitude larger than previous reports.
Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions
Authors: Butler Daniel , Mozsary Christopher , Meydan Cem , Foox Jonathan , Rosiene Joel , Shaiber Alon , Danko David , Afshinnekoo Ebrahim , MacKay Matthew , Sedlazeck Fritz J. , Ivanov Nikolay A. , Sierra Maria , Pohle Diana , Zietz Michael , Gisladottir Undina , Ramlall Vijendra , Sholle Evan T. , Schenck Edward J. , Westover Craig D. , Hassan Ciaran , Ryon Krista , Young Benjamin , Bhattacharya Chandrima , Ng Dianna L. , Granados Andrea C. , Santos Yale A. , Servellita Venice , Federman Scot , Ruggiero Phyllis , Fungtammasan Arkarachai , Chin Chen-Shan , Pearson Nathaniel M. , Langhorst Bradley W. , Tanner Nathan A. , Kim Youngmi , Reeves Jason W. , Hether Tyler D. , Warren Sarah E. , Bailey Michael , Gawrys Justyna , Meleshko Dmitry , Xu Dong , Couto-Rodriguez Mara , Nagy-Szakal Dorottya , Barrows Joseph , Wells Heather , O’Hara Niamh B. , Rosenfeld Jeffrey A. , Chen Ying , Steel Peter A. D. , Shemesh Amos J. , Xiang Jenny , Thierry-Mieg Jean , Thierry-Mieg Danielle , Iftner Angelika , Bezdan Daniela , Sanchez Elizabeth , Campion Thomas R. , Sipley John , Cong Lin , Craney Arryn , Velu Priya , Melnick Ari M. , Shapira Sagi , Hajirasouliha Iman , Borczuk Alain , Iftner Thomas , Salvatore Mirella , Loda Massimo , Westblade Lars F. , Cushing Melissa , Wu Shixiu , Levy Shawn , Chiu Charles , Schwartz Robert E. , Tatonetti Nicholas , Rennert Hanna , Imielinski Marcin , Mason Christopher E. 
Published: March 2021

AbstractIn less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, we use 50,821 patient records to find that renin–angiotensin–aldosterone system inhibitors have a protective effect for severe COVID-19 outcomes, unlike similar drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinctACE2expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive SARS-CoV-2 diagnostic, prevention, and treatment strategies.
Structural and functional characterization of a putative de novo gene in Drosophila
Authors: Lange Andreas , Patel Prajal H. , Heames Brennen , Damry Adam M. , Saenger Thorsten , Jackson Colin J. , Findlay Geoffrey D. , Bornberg-Bauer Erich 
Published: March 2021

AbstractComparative genomic studies have repeatedly shown that new protein-coding genes can emerge de novo from noncoding DNA. Still unknown is how and when the structures of encoded de novo proteins emerge and evolve. Combining biochemical, genetic and evolutionary analyses, we elucidate the function and structure of goddard, a gene which appears to have evolved de novo at least 50 million years ago within the Drosophila genus. Previous studies found that goddard is required for male fertility. Here, we show that Goddard protein localizes to elongating sperm axonemes and that in its absence, elongated spermatids fail to undergo individualization. Combining modelling, NMR and circular dichroism (CD) data, we show that Goddard protein contains a large central α-helix, but is otherwise partially disordered. We find similar results for Goddard’s orthologs from divergent fly species and their reconstructed ancestral sequences. Accordingly, Goddard’s structure appears to have been maintained with only minor changes over millions of years.
Predicting gastric cancer outcome from resected lymph node histopathology images using deep learning
Authors: Wang Xiaodong , Chen Ying , Gao Yunshu , Zhang Huiqing , Guan Zehui , Dong Zhou , Zheng Yuxuan , Jiang Jiarui , Yang Haoqing , Wang Liming , Huang Xianming , Ai Lirong , Yu Wenlong , Li Hongwei , Dong Changsheng , Zhou Zhou , Liu Xiyang , Yu Guanzhen 
Published: March 2021

AbstractN-staging is a determining factor for prognostic assessment and decision-making for stage-based cancer therapeutic strategies. Visual inspection of whole-slides of intact lymph nodes is currently the main method used by pathologists to calculate the number of metastatic lymph nodes (MLNs). Moreover, even at the same N stage, the outcome of patients varies dramatically. Here, we propose a deep-learning framework for analyzing lymph node whole-slide images (WSIs) to identify lymph nodes and tumor regions, and then to uncover tumor-area-to-MLN-area ratio (T/MLN). After training, our model’s tumor detection performance was comparable to that of experienced pathologists and achieved similar performance on two independent gastric cancer validation cohorts. Further, we demonstrate that T/MLN is an interpretable independent prognostic factor. These findings indicate that deep-learning models could assist not only pathologists in detecting lymph nodes with metastases but also oncologists in exploring new prognostic factors, especially those that are difficult to calculate manually.
Impacts of long-term temperature change and variability on electricity investments
Authors: Khan Zarrar , Iyer Gokul , Patel Pralit , Kim Son , Hejazi Mohamad , Burleyson Casey , Wise Marshall 
Published: March 2021

AbstractLong-term temperature change and variability are expected to have significant impacts on future electric capacity and investments. This study improves upon past studies by accounting for hourly and monthly dynamics of electricity use, long-term socioeconomic drivers, and interactions of the electric sector with rest of the economy for a comprehensive analysis of temperature change impacts on cooling and heating services and their corresponding impact on electric capacity and investments. Using the United States as an example, here we show that under a scenario consistent with a socioeconomic pathway 2 (SSP2) and representative concentration pathway 8.5 (RCP 8.5), mean temperature changes drive increases in annual electricity demands by 0.5-8% across states in 2100. But more importantly, peak temperature changes drive increases in capital investments by 3-22%. Moreover, temperature-induced capital investments are highly sensitive to both long-term socioeconomic assumptions and spatial heterogeneity of fuel prices and capital stock characteristics, which underscores the importance of a comprehensive approach to inform long-term electric sector planning.
Digital logic gates in soft, conductive mechanical metamaterials
Authors: El Helou Charles , Buskohl Philip R. , Tabor Christopher E. , Harne Ryan L. 
Published: March 2021

AbstractIntegrated circuits utilize networked logic gates to compute Boolean logic operations that are the foundation of modern computation and electronics. With the emergence of flexible electronic materials and devices, an opportunity exists to formulate digital logic from compliant, conductive materials. Here, we introduce a general method of leveraging cellular, mechanical metamaterials composed of conductive polymers to realize all digital logic gates and gate assemblies. We establish a method for applying conductive polymer networks to metamaterial constituents and correlate mechanical buckling modes with network connectivity. With this foundation, each of the conventional logic gates is realized in an equivalent mechanical metamaterial, leading to soft, conductive matter that thinks about applied mechanical stress. These findings may advance the growing fields of soft robotics and smart mechanical matter, and may be leveraged across length scales and physics.
In-situ observation of trapped carriers in organic metal halide perovskite films with ultra-fast temporal and ultra-high energetic resolutions
Authors: Kobbekaduwa Kanishka , Shrestha Shreetu , Adhikari Pan , Liu Exian , Coleman Lawrence , Zhang Jianbing , Shi Ying , Zhou Yuanyuan , Bekenstein Yehonadav , Yan Feng , Rao Apparao M. , Tsai Hsinhan , Beard Matthew C. , Nie Wanyi , Gao Jianbo 
Published: March 2021

AbstractWe in-situ observe the ultrafast dynamics of trapped carriers in organic methyl ammonium lead halide perovskite thin films by ultrafast photocurrent spectroscopy with a sub-25 picosecond time resolution. Upon ultrafast laser excitation, trapped carriers follow a phonon assisted tunneling mechanism and a hopping transport mechanism along ultra-shallow to shallow trap states ranging from 1.72–11.51 millielectronvolts and is demonstrated by time-dependent and independent activation energies. Using temperature as an energetic ruler, we map trap states with ultra-high energy resolution down to < 0.01 millielectronvolt. In addition to carrier mobility of ~4 cm2V−1s−1 and lifetime of ~1 nanosecond, we validate the above transport mechanisms by highlighting trap state dynamics, including trapping rates, de-trapping rates and trap properties, such as trap density, trap levels, and capture-cross sections. In this work we establish a foundation for trap dynamics in high defect-tolerant perovskites with ultra-fast temporal and ultra-high energetic resolution.
PGC1/PPAR drive cardiomyocyte maturation at single cell level via YAP1 and SF3B2
Authors: Murphy Sean A. , Miyamoto Matthew , Kervadec Anaïs , Kannan Suraj , Tampakakis Emmanouil , Kambhampati Sandeep , Lin Brian Leei , Paek Sam , Andersen Peter , Lee Dong-Ik , Zhu Renjun , An Steven S. , Kass David A. , Uosaki Hideki , Colas Alexandre R. , Kwon Chulan 
Published: March 2021

AbstractCardiomyocytes undergo significant structural and functional changes after birth, and these fundamental processes are essential for the heart to pump blood to the growing body. However, due to the challenges of isolating single postnatal/adult myocytes, how individual newborn cardiomyocytes acquire multiple aspects of the mature phenotype remains poorly understood. Here we implement large-particle sorting and analyze single myocytes from neonatal to adult hearts. Early myocytes exhibit wide-ranging transcriptomic and size heterogeneity that is maintained until adulthood with a continuous transcriptomic shift. Gene regulatory network analysis followed by mosaic gene deletion reveals that peroxisome proliferator-activated receptor coactivator-1 signaling, which is active in vivo but inactive in pluripotent stem cell-derived cardiomyocytes, mediates the shift. This signaling simultaneously regulates key aspects of cardiomyocyte maturation through previously unrecognized proteins, including YAP1 and SF3B2. Our study provides a single-cell roadmap of heterogeneous transitions coupled to cellular features and identifies a multifaceted regulator controlling cardiomyocyte maturation.