bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local and Remote Influences on the Heat Content of Southern Ocean Mode Water Formation Regions
Authors: Boland Emma J. D. , Jones Daniel C. , Meijers Andrew J. S. , Forget Gael , Josey Simon A. 
Published: March 2021

AbstractThe Southern Ocean (SO) is a crucial region for the global ocean uptake of heat and carbon. There are large uncertainties in the observations of fluxes of heat and carbon between the atmosphere and the ocean mixed layer, which lead to large uncertainties in the amount entering into the global overturning circulation. In order to better understand where and when fluxes of heat and momentum have the largest impact on near‐surface heat content, we use an adjoint model to calculate the linear sensitivities of heat content in SO mode water formation regions (MWFRs) to surface fluxes. We find that the heat content of these regions is, in all three basins, most sensitive to same‐winter, local heat fluxes, and to local and remote wind one to eight years (the maximum lead‐time of our simulations) previously. This is supported by sensitivities to potential temperature changes, which reveal the sources of the MWFRs as well as dynamic links with boundary current regions and the Antarctic Circumpolar Current. We use the adjoint sensitivity fields to design a set of targeted perturbation experiments, allowing us to examine the linear and non‐linear responses of the heat content to changes in surface forcing. In these targeted experiments, the heat content is sensitive to both temperature changes and mixed layer volume changes in roughly equal magnitude.
Evidencing the Impact of Climate Change on the Phytoplankton Community of the Mediterranean Sea Through a Bioregionalization Approach
Authors: El Hourany Roy , Mejia Carlos , Faour Ghaleb , Crépon Michel , Thiria Sylvie 
Published: March 2021

AbstractWe revisited the partitioning of the Mediterranean Sea into bioregions by processing satellite Sea Surface Temperature (SST) and Chlorophyll‐a concentration (Chla) from ocean color observations combined with Argo mixed‐layer depth for a period ranging from 2003 up to 2020. This regionalization was performed using an innovative classification based on self‐organizing maps, the so‐called 2S‐SOM. We clustered the Mediterranean Sea waters into seven bioregions governed by specific physical and biogeochemical characteristics. We studied the interannual variability of these bioregions over the 18 years. We showed that the temperature is increasing with a mean rate of 0.4°C per decade. The chlorophyll‐a concentration is quasi constant, but we evidenced a noticeable change in satellite‐derived phytoplankton communities: Diatoms concentration is decreasing while cyanobacteria concentration is increasing. The bioregion trends could be related to global warming. The whole Mediterranean Sea is shifting to an eastern Mediterranean state.
Light People: Professor Donna Strickland
Authors: Wang Hui 
Published: March 2021

EditorialIt is rare for an associate professor to win the Nobel Prize for Physics, even more so when she was only the third woman in history to do so, but Dr. Donna Strickland did just that. A permanent smile on her face expressing her friendliness, the fast speaking speed showing her quick thinking, Dr. Strickland is not only a good tutor with strong hands-on ability and high working efficiency in the eyes of her students, but also an optimistic and diligent scholar in the eyes of her peers. Taking an active part in academic societies and the popularization of science, she regards scientific research as “fun”. The famous Canadian physicist Donna Strickland talks exclusively to Light: Science and Applications (light).
PUMA facilitates EMI1-promoted cytoplasmic Rad51 ubiquitination and inhibits DNA repair in stem and progenitor cells
Authors: Kang Jin Wook , Zhan Zhiyan , Ji Guangzhen , Sang Youzhou , Zhou Daohong , Li Yanxin , Feng Haizhong , Cheng Tao 
Published: March 2021

AbstractMaintenance of genetic stability via proper DNA repair in stem and progenitor cells is essential for the tissue repair and regeneration, while preventing cell transformation after damage. Loss of PUMA dramatically increases the survival of mice after exposure to a lethal dose of ionizing radiation (IR), while without promoting tumorigenesis in the long-term survivors. This finding suggests that PUMA (p53 upregulated modulator of apoptosis) may have a function other than regulates apoptosis. Here, we identify a novel role of PUMA in regulation of DNA repair in embryonic or induced pluripotent stem cells (PSCs) and immortalized hematopoietic progenitor cells (HPCs) after IR. We found that PUMA-deficient PSCs and HPCs exhibited a significant higher double-strand break (DSB) DNA repair activity via Rad51-mediated homologous recombination (HR). This is because PUMA can be associated with early mitotic inhibitor 1 (EMI1) and Rad51 in the cytoplasm to facilitate EMI1-mediated cytoplasmic Rad51 ubiquitination and degradation, thereby inhibiting Rad51 nuclear translocation and HR DNA repair. Our data demonstrate that PUMA acts as a repressor for DSB DNA repair and thus offers a new rationale for therapeutic targeting of PUMA in regenerative cells in the context of DNA damage.
Bacterial cyclic diguanylate signaling networks sense temperature
Authors: Almblad Henrik , Randall Trevor E. , Liu Fanny , Leblanc Katherine , Groves Ryan A. , Kittichotirat Weerayuth , Winsor Geoffrey L. , Fournier Nicolas , Au Emily , Groizeleau Julie , Rich Jacquelyn D. , Lou Yuefei , Granton Elise , Jennings Laura K. , Singletary Larissa A. , Winstone Tara M. L. , Good Nathan M. , Bumgarner Roger E. , Hynes Michael F. , Singh Manu , Stietz Maria Silvina , Brinkman Fiona S. L. , Kumar Ayush , Brassinga Ann Karen Cornelia , Parsek Matthew R. , Tseng Boo Shan , Lewis Ian A. , Yipp Bryan G. , MacCallum Justin L. , Harrison Joe Jonathan 
Published: March 2021

AbstractMany bacteria use the second messenger cyclic diguanylate (c-di-GMP) to control motility, biofilm production and virulence. Here, we identify a thermosensory diguanylate cyclase (TdcA) that modulates temperature-dependent motility, biofilm development and virulence in the opportunistic pathogenPseudomonas aeruginosa. TdcA synthesizes c-di-GMP with catalytic rates that increase more than a hundred-fold over a ten-degree Celsius change. Analyses using protein chimeras indicate that heat-sensing is mediated by a thermosensitive Per-Arnt-SIM (PAS) domain. TdcA homologs are widespread in sequence databases, and a distantly related, heterologously expressed homolog from the Betaproteobacteria orderGallionellalesalso displayed thermosensitive diguanylate cyclase activity. We propose, therefore, that thermotransduction is a conserved function of c-di-GMP signaling networks, and that thermosensitive catalysis of a second messenger constitutes a mechanism for thermal sensing in bacteria.
Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing
Authors: Singleton Caitlin M. , Petriglieri Francesca , Kristensen Jannie M. , Kirkegaard Rasmus H. , Michaelsen Thomas Y. , Andersen Martin H. , Kondrotaite Zivile , Karst Søren M. , Dueholm Morten S. , Nielsen Per H. , Albertsen Mads 
Published: March 2021

AbstractMicroorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with >13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.
90% yield production of polymer nano-memristor for in-memory computing
Authors: Zhang Bin , Chen Weilin , Zeng Jianmin , Fan Fei , Gu Junwei , Chen Xinhui , Yan Lin , Xie Guangjun , Liu Shuzhi , Yan Qing , Baik Seung Jae , Zhang Zhi-Guo , Chen Weihua , Hou Jie , El-Khouly Mohamed E. , Zhang Zhang , Liu Gang , Chen Yu 
Published: March 2021

AbstractPolymer memristors with light weight and mechanical flexibility are preeminent candidates for low-power edge computing paradigms. However, the structural inhomogeneity of most polymers usually leads to random resistive switching characteristics, which lowers the production yield and reliability of nanoscale devices. In this contribution, we report that by adopting the two-dimensional conjugation strategy, a record high 90% production yield of polymer memristors has been achieved with miniaturization and low power potentials. By constructing coplanar macromolecules with 2D conjugated thiophene derivatives to enhance the π–π stacking and crystallinity of the thin film, homogeneous switching takes place across the entire polymer layer, with fast responses in 32 ns, D2D variation down to 3.16% ~ 8.29%, production yield approaching 90%, and scalability into 100 nm scale with tiny power consumption of ~ 10−15 J/bit. The polymer memristor array is capable of acting as both the arithmetic-logic element and multiply-accumulate accelerator for neuromorphic computing tasks.
Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism
Authors: Horne Christopher R. , Venugopal Hariprasad , Panjikar Santosh , Wood David M. , Henrickson Amy , Brookes Emre , North Rachel A. , Murphy James M. , Friemann Rosmarie , Griffin Michael D. W. , Ramm Georg , Demeler Borries , Dobson Renwick C. J. 
Published: March 2021

AbstractBacteria respond to environmental changes by inducing transcription of some genes and repressing others. Sialic acids, which coat human cell surfaces, are a nutrient source for pathogenic and commensal bacteria. TheEscherichia coliGntR-type transcriptional repressor, NanR, regulates sialic acid metabolism, but the mechanism is unclear. Here, we demonstrate that three NanR dimers bind a (GGTATA)3-repeat operator cooperatively and with high affinity. Single-particle cryo-electron microscopy structures reveal the DNA-binding domain is reorganized to engage DNA, while three dimers assemble in close proximity across the (GGTATA)3-repeat operator. Such an interaction allows cooperative protein-protein interactions between NanR dimers via their N-terminal extensions. The effector,N-acetylneuraminate, binds NanR and attenuates the NanR-DNA interaction. The crystal structure of NanR in complex withN-acetylneuraminate reveals a domain rearrangement uponN-acetylneuraminate binding to lock NanR in a conformation that weakens DNA binding. Our data provide a molecular basis for the regulation of bacterial sialic acid metabolism.
Inactivating histone deacetylase HDA promotes longevity by mobilizing trehalose metabolism
Authors: Yu Ruofan , Cao Xiaohua , Sun Luyang , Zhu Jun-yi , Wasko Brian M , Liu Wei , Crutcher Emeline , Liu Haiying , Jo Myeong Chan , Qin Lidong , Kaeberlein Matt , Han Zhe , Dang Weiwei 
Published: March 2021

AbstractHistone acetylations are important epigenetic markers for transcriptional activation in response to metabolic changes and various stresses. Using the high-throughput SEquencing-Based Yeast replicative Lifespan screen method and the yeast knockout collection, we demonstrate that the HDA complex, a class-II histone deacetylase (HDAC), regulates aging through its target of acetylated H3K18 at storage carbohydrate genes. We find that, in addition to longer lifespan, disruption of HDA results in resistance to DNA damage and osmotic stresses. We show that these effects are due to increased promoter H3K18 acetylation and transcriptional activation in the trehalose metabolic pathway in the absence of HDA. Furthermore, we determine that the longevity effect of HDA is independent of the Cyc8-Tup1 repressor complex known to interact with HDA and coordinate transcriptional repression. Silencing the HDA homologs in C. elegans and Drosophila increases their lifespan and delays aging-associated physical declines in adult flies. Hence, we demonstrate that this HDAC controls an evolutionarily conserved longevity pathway.
Two-timescale response of a large Antarctic ice shelf to climate change
Authors: Naughten Kaitlin A. , De Rydt Jan , Rosier Sebastian H. R. , Jenkins Adrian , Holland Paul R. , Ridley Jeff K. 
Published: March 2021

AbstractA potentially irreversible threshold in Antarctic ice shelf melting would be crossed if the ocean cavity beneath the large Filchner–Ronne Ice Shelf were to become flooded with warm water from the deep ocean. Previous studies have identified this possibility, but there is great uncertainty as to how easily it could occur. Here, we show, using a coupled ice sheet-ocean model forced by climate change scenarios, that any increase in ice shelf melting is likely to be preceded by an extended period of reduced melting. Climate change weakens the circulation beneath the ice shelf, leading to colder water and reduced melting. Warm water begins to intrude into the cavity when global mean surface temperatures rise by approximately 7 °C above pre-industrial, which is unlikely to occur this century. However, this result should not be considered evidence that the region is unconditionally stable. Unless global temperatures plateau, increased melting will eventually prevail.
Heuristic machinery for thermodynamic studies of SU(N) fermions with neural networks
Authors: Zhao Entong , Lee Jeongwon , He Chengdong , Ren Zejian , Hajiyev Elnur , Liu Junwei , Jo Gyu-Boong 
Published: March 2021

AbstractThe power of machine learning (ML) provides the possibility of analyzing experimental measurements with a high sensitivity. However, it still remains challenging to probe the subtle effects directly related to physical observables and to understand physics behind from ordinary experimental data using ML. Here, we introduce a heuristic machinery by using machine learning analysis. We use our machinery to guide the thermodynamic studies in the density profile of ultracold fermions interacting within SU(N) spin symmetry prepared in a quantum simulator. Although such spin symmetry should manifest itself in a many-body wavefunction, it is elusive how the momentum distribution of fermions, the most ordinary measurement, reveals the effect of spin symmetry. Using a fully trained convolutional neural network (NN) with a remarkably high accuracy of ~94% for detection of the spin multiplicity, we investigate how the accuracy depends on various less-pronounced effects with filtered experimental images. Guided by our machinery, we directly measure a thermodynamic compressibility from density fluctuations within the single image. Our machine learning framework shows a potential to validate theoretical descriptions of SU(N) Fermi liquids, and to identify less-pronounced effects even for highly complex quantum matter with minimal prior understanding.
Long-range optofluidic control with plasmon heating
Authors: Ciraulo B. , Garcia-Guirado J. , de Miguel I. , Ortega Arroyo J. , Quidant R. 
Published: March 2021

AbstractUsing light to manipulate fluids has been a long-sought-after goal for lab-on-a-chip applications to address the size mismatch between bulky external fluid controllers and microfluidic devices. Yet, this goal has remained elusive due to the complexity of thermally driven fluid dynamic phenomena, and the lack of approaches that allow comprehensive multiscale and multiparameter studies. Here, we report an innovative optofluidic platform that fulfills this need by combining digital holographic microscopy with state-of-the-art thermoplasmonics, allowing us to identify the different contributions from thermophoresis, thermo-osmosis, convection, and radiation pressure. In our experiments, we demonstrate that a local thermal perturbation at the microscale can lead to mm-scale changes in both the particle and fluid dynamics, thus achieving long-range transport. Furthermore, thanks to a comprehensive parameter study involving sample geometry, temperature increase, light fluence, and size of the heat source, we showcase an integrated and reconfigurable all-optical control strategy for microfluidic devices, thereby opening new frontiers in fluid actuation technology.
A designer FG-Nup that reconstitutes the selective transport barrier of the nuclear pore complex
Authors: Fragasso Alessio , de Vries Hendrik W. , Andersson John , van der Sluis Eli O. , van der Giessen Erik , Dahlin Andreas , Onck Patrick R. , Dekker Cees 
Published: March 2021

AbstractNuclear Pore Complexes (NPCs) regulate bidirectional transport between the nucleus and the cytoplasm. Intrinsically disordered FG-Nups line the NPC lumen and form a selective barrier, where transport of most proteins is inhibited whereas specific transporter proteins freely pass. The mechanism underlying selective transport through the NPC is still debated. Here, we reconstitute the selective behaviour of the NPC bottom-up by introducing a rationally designed artificial FG-Nup that mimics natural Nups. Using QCM-D, we measure selective binding of the artificial FG-Nup brushes to the transport receptor Kap95 over cytosolic proteins such as BSA. Solid-state nanopores with the artificial FG-Nups lining their inner walls support fast translocation of Kap95 while blocking BSA, thus demonstrating selectivity. Coarse-grained molecular dynamics simulations highlight the formation of a selective meshwork with densities comparable to native NPCs. Our findings show that simple design rules can recapitulate the selective behaviour of native FG-Nups and demonstrate that no specific spacer sequence nor a spatial segregation of different FG-motif types are needed to create selective NPCs.
A continuum of invariant sensory and behavioral-context perceptual coding in secondary somatosensory cortex
Authors: Rossi-Pool Román , Zainos Antonio , Alvarez Manuel , Diaz-deLeon Gabriel , Romo Ranulfo 
Published: March 2021

AbstractA crucial role of cortical networks is the conversion of sensory inputs into perception. In the cortical somatosensory network, neurons of the primary somatosensory cortex (S1) show invariant sensory responses, while frontal lobe neuronal activity correlates with the animal’s perceptual behavior. Here, we report that in the secondary somatosensory cortex (S2), neurons with invariant sensory responses coexist with neurons whose responses correlate with perceptual behavior. Importantly, the vast majority of the neurons fall along a continuum of combined sensory and categorical dynamics. Furthermore, during a non-demanding control task, the sensory responses remain unaltered while the sensory information exhibits an increase. However, perceptual responses and the associated categorical information decrease, implicating a task context-dependent processing mechanism. Conclusively, S2 neurons exhibit intriguing dynamics that are intermediate between those of S1 and frontal lobe. Our results contribute relevant evidence about the role that S2 plays in the conversion of touch into perception.
Emitting long-distance spiral airborne sound using low-profile planar acoustic antenna
Authors: Gao Shuxiang , Li Yunbo , Ma Chengrong , Cheng Ying , Liu Xiaojun 
Published: March 2021

AbstractRecent years have witnessed a rapidly growing interest in exploring the use of spiral sound carrying artificial orbital angular momentum (OAM), toward establishing a spiral-wave-based technology that is significantly more efficient in energy or information delivering than the ordinary plane wave technology. A major bottleneck of advancing this technology is the efficient excitation of far-field spiral waves in free space, which is a must in exploring the use of spiral waves for long-distance information transmission and particle manipulation. Here, we report a low-profile planar acoustic antenna to modulate wavefronts emitted from a near-field point source and achieve far-field spiral airborne sound carrying OAM. Using the holographic interferogram as a 2D modulated artificial acoustic impedance metasurface, we show the efficient conversion from the surface wave into the propagating spiral shape beam both numerically and experimentally. The vortex fields with spiral phases originate from the complex inter-modal interactions between cylindrical surface waves and a spatially-modulated impedance boundary condition. This antenna can open new routes to highly integrated spiral sound emitters that are critical for practical acoustic functional devices.
RETRACTED ARTICLE: Safety and efficacy of favipiravir versus hydroxychloroquine in management of COVID-19: A randomised controlled trial
Authors: Dabbous Hany M. , El-Sayed Manal H. , El Assal Gihan , Elghazaly Hesham , Ebeid Fatma F. S. , Sherief Ahmed F. , Elgaafary Maha , Fawzy Ehab , Hassany Sahar M. , Riad Ahmed R. , TagelDin Mohamed A. 
Published: March 2021

AbstractFavipiravir is considered a potential treatment for COVID-19 due its efficacy against different viral infections. We aimed to explore the safety and efficacy of favipiravir in treatment of COVID-19 mild and moderate cases. It was randomized-controlled open-label interventional phase 3 clinical trial [NCT04349241]. 100 patients were recruited from 18th April till 18th May. 50 patients received favipiravir 3200 mg at day 1 followed by 600 mg twice (day 2–day 10). 50 patients received hydroxychloroquine 800 mg at day 1 followed by 200 mg twice (day 2–10) and oral oseltamivir 75 mg/12 h/day for 10 days. Patients were enrolled from Ain Shams University Hospital and Assiut University Hospital. Both arms were comparable as regards demographic characteristics and comorbidities. The average onset of SARS-CoV-2 PCR negativity was 8.1 and 8.3 days in HCQ-arm and favipiravir-arm respectively. 55.1% of those on HCQ-arm turned PCR negative at/or before 7th day from diagnosis compared to 48% in favipiravir-arm (p = 0.7). 4 patients in FVP arm developed transient transaminitis on the other hand heartburn and nausea were reported in about 20 patients in HCQ-arm. Only one patient in HCQ-arm died after developing acute myocarditis resulted in acute heart failure. Favipiravir is a safe effective alternative for hydroxychloroquine in mild or moderate COVID-19 infected patients.