bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global thermal spring distribution and relationship to endogenous and exogenous factors
Authors: Tamburello G. , Chiodini G. , Ciotoli G. , Procesi M. , Rouwet D. , Sandri L. , Carbonara N. , Masciantonio C. 
Published: October 2022

AbstractHere we present digitization and analysis of the thermal springs of the world dataset compiled by Gerald Ashley Waring in 1965 into a collection of analog maps. We obtain the geographic coordinates of ~6,000 geothermal spring areas, including complementary data (e.g., temperature, total dissolved solids, flow rate), making them available in electronic format. Using temperature and flow rate, we derive the heat discharged from 1483 thermal spring areas (between ~10−5 and ~103 MW, with a median value of ~0.5 MW and ~8300 MW in total). We integrate this data set with other global data sets to study the relationship between thermalism and endogenous and exogenous factors with a supervised machine learning algorithm. This analysis confirms a dominant role of the terrestrial heat flow, topography, volcanism and extensional tectonics. This data set offers new insights and will boost future studies in geothermal energy exploration.
Crystal structure of the Na+/H+ antiporter NhaA at active pH reveals the mechanistic basis for pH sensing
Authors: Winkelmann Iven , Uzdavinys Povilas , Kenney Ian M. , Brock Joseph , Meier Pascal F. , Wagner Lina-Marie , Gabriel Florian , Jung Sukkyeong , Matsuoka Rei , von Ballmoos Christoph , Beckstein Oliver , Drew David 
Published: October 2022

AbstractThe strict exchange of protons for sodium ions across cell membranes by Na+/H+exchangers is a fundamental mechanism for cell homeostasis. At active pH, Na+/H+exchange can be modelled as competition between H+and Na+to an ion-binding site, harbouring either one or two aspartic-acid residues. Nevertheless, extensive analysis on the model Na+/H+antiporter NhaA fromEscherichia coli, has shown that residues on the cytoplasmic surface, termed the pH sensor, shifts the pH at which NhaA becomes active. It was unclear how to incorporate the pH senor model into an alternating-access mechanism based on the NhaA structure at inactive pH 4. Here, we report the crystal structure of NhaA at active pH 6.5, and to an improved resolution of 2.2 Å. We show that at pH 6.5, residues in the pH sensor rearrange to form new salt-bridge interactions involving key histidine residues that widen the inward-facing cavity. What we now refer to as a pH gate, triggers a conformational change that enables water and Na+to access the ion-binding site, as supported by molecular dynamics (MD) simulations. Our work highlights a unique, channel-like switch prior to substrate translocation in a secondary-active transporter.
Dual interfacial engineering of a Chevrel phase electrode material for stable hydrogen evolution at 2500 mA cm−2
Authors: Liu Heming , Xie Ruikuan , Luo Yuting , Cui Zhicheng , Yu Qiangmin , Gao Zhiqiang , Zhang Zhiyuan , Yang Fengning , Kang Xin , Ge Shiyu , Li Shaohai , Gao Xuefeng , Chai Guoliang , Liu Le , Liu Bilu 
Published: October 2022

AbstractConstructing stable electrodes which function over long timescales at large current density is essential for the industrial realization and implementation of water electrolysis. However, rapid gas bubble detachment at large current density usually results in peeling-off of electrocatalysts and performance degradation, especially for long term operations. Here we construct a mechanically-stable, all-metal, and highly active CuMo6S8/Cu electrode by in-situ reaction between MoS2 and Cu. The Chevrel phase electrode exhibits strong binding at the electrocatalyst-support interface with weak adhesion at electrocatalyst-bubble interface, in addition to fast hydrogen evolution and charge transfer kinetics. These features facilitate the achievement of large current density of 2500 mA cm−2 at a small overpotential of 334 mV which operate stably at 2500 mA cm−2 for over 100 h. In-situ total internal reflection imaging at micrometer level and mechanical tests disclose the relationships of two interfacial forces and performance of electrocatalysts. This dual interfacial engineering strategy can be extended to construct stable and high-performance electrodes for other gas-involving reactions.
Electrically regulating nonlinear optical limiting of metal-organic framework film
Authors: Ma Zhi-Zhou , Li Qiao-Hong , Wang Zirui , Gu Zhi-Gang , Zhang Jian 
Published: October 2022

AbstractRegulating nonlinear optical (NLO) property of metal−organic frameworks (MOFs) is of pronounced significance for their scientific research and practical application, but the regulation through external stimuli is still a challenging task. Here we prepare and electrically control the nonlinear optical regulation of conductive MOFs Cu-HHTP films with [001]- (Cu-HHTP[001]) and [100]-orientations (Cu-HHTP[100]). Z-scan results show that the nonlinear absorption coefficient (β) of Cu-HHTP[001] film (7.60 × 10−6 m/W) is much higher than that of Cu-HHTP[100] film (0.84 × 10−6 m/W) at 0 V and the β of Cu-HHTP[001] and Cu-HHTP[100] films gradually increase to 3.84 × 10−5 and 1.71 × 10−6 m/W at 10 V by increasing the applied voltage, respectively. Due to 2D Cu-HHTP having anisotropy of charge transfer in different orientations, the NLO of MOFs film can be dependent on their growth orientations and improved by tuning the electrical field. This study provides more avenues for the regulation and NLO applications of MOFs.
HiFi metagenomic sequencing enables assembly of accurate and complete genomes from human gut microbiota
Authors: Kim Chan Yeong , Ma Junyeong , Lee Insuk 
Published: October 2022

AbstractAdvances in metagenomic assembly have led to the discovery of genomes belonging to uncultured microorganisms. Metagenome-assembled genomes (MAGs) often suffer from fragmentation and chimerism. Recently, 20 complete MAGs (cMAGs) have been assembled from Oxford Nanopore long-read sequencing of 13 human fecal samples, but with low nucleotide accuracy. Here, we report 102 cMAGs obtained by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing of five human fecal samples, whose initial circular contigs were selected for complete prokaryotic genomes using our bioinformatics workflow. Nucleotide accuracy of the final cMAGs was as high as that of Illumina sequencing. The cMAGs could exceed 6 Mbp and included complete genomes of diverse taxa, including entirely uncultured RF39 and TANB77 orders. Moreover, cMAGs revealed that regions hard to assemble by short-read sequencing comprised mostly genomic islands and rRNAs. HiFi metagenomic sequencing will facilitate cataloging accurate and complete genomes from complex microbial communities, including uncultured species.
Rescue of deficits by Brwd1 copy number restoration in the Ts65Dn mouse model of Down syndrome
Authors: Fulton Sasha L. , Wenderski Wendy , Lepack Ashley E. , Eagle Andrew L. , Fanutza Tomas , Bastle Ryan M. , Ramakrishnan Aarthi , Hays Emma C. , Neal Arianna , Bendl Jaroslav , Farrelly Lorna A. , Al-Kachak Amni , Lyu Yang , Cetin Bulent , Chan Jennifer C. , Tran Tina N. , Neve Rachael L. , Roper Randall J. , Brennand Kristen J. , Roussos Panos , Schimenti John C. , Friedman Allyson K. , Shen Li , Blitzer Robert D. , Robison Alfred J. , Crabtree Gerald R. , Maze Ian 
Published: October 2022

AbstractWith an incidence of ~1 in 800 births, Down syndrome (DS) is the most common chromosomal condition linked to intellectual disability worldwide. While the genetic basis of DS has been identified as a triplication of chromosome 21 (HSA21), the genes encoded from HSA21 that directly contribute to cognitive deficits remain incompletely understood. Here, we found that the HSA21-encoded chromatin effector, BRWD1, was upregulated in neurons derived from iPS cells from an individual with Down syndrome and brain of trisomic mice. We showed that selective copy number restoration of Brwd1 in trisomic animals rescued deficits in hippocampal LTP, cognition and gene expression. We demonstrated that Brwd1 tightly binds the BAF chromatin remodeling complex, and that increased Brwd1 expression promotes BAF genomic mistargeting. Importantly, Brwd1 renormalization rescued aberrant BAF localization, along with associated changes in chromatin accessibility and gene expression. These findings establish BRWD1 as a key epigenomic mediator of normal neurodevelopment and an important contributor to DS-related phenotypes.
METTL3 acetylation impedes cancer metastasis via fine-tuning its nuclear and cytosolic functions
Authors: Li Yuanpei , He Xiaoniu , Lu Xiao , Gong Zhicheng , Li Qing , Zhang Lei , Yang Ronghui , Wu Chengyi , Huang Jialiang , Ding Jiancheng , He Yaohui , Liu Wen , Chen Ceshi , Cao Bin , Zhou Dawang , Shi Yufeng , Chen Juxiang , Wang Chuangui , Zhang Shengping , Zhang Jian , Ye Jing , You Han 
Published: October 2022

AbstractThe methyltransferase like 3 (METTL3) has been generally recognized as a nuclear protein bearing oncogenic properties. We find predominantly cytoplasmic METTL3 expression inversely correlates with node metastasis in human cancers. It remains unclear if nuclear METTL3 is functionally distinct from cytosolic METTL3 in driving tumorigenesis and, if any, how tumor cells sense oncogenic insults to coordinate METTL3 functions within these intracellular compartments. Here, we report an acetylation-dependent regulation of METTL3 localization that impacts on metastatic dissemination. We identify an IL-6-dependent positive feedback axis to facilitate nuclear METTL3 functions, eliciting breast cancer metastasis. IL-6, whose mRNA transcript is subjected to METTL3-mediated m6A modification, promotes METTL3 deacetylation and nuclear translocation, thereby inducing global m6A abundance. This deacetylation-mediated nuclear shift of METTL3 can be counterbalanced by SIRT1 inhibition, a process that is further enforced by aspirin treatment, leading to ablated lung metastasis via impaired m6A methylation. Intriguingly, acetylation-mimetic METTL3 mutant reconstitution results in enhanced translation and compromised metastatic potential. Our study identifies an acetylation-dependent regulatory mechanism determining the subcellular localization of METTL3, which may provide mechanistic clues for developing therapeutic strategies to combat breast cancer metastasis.
Comparison of COPD primary care in England, Scotland, Wales, and Northern Ireland
Authors: Stone Philip W. , Hickman Katherine , Holmes Steve , Feary Johanna R. , Quint Jennifer K. 
Published: October 2022

AbstractCurrently the National Asthma and COPD audit programme (NACAP) only undertakes audit of COPD primary care in Wales due to its near complete data coverage. We aimed to determine if the quality of COPD primary care in the other UK nations is comparable with Wales. We found that English, Scottish, and Northern Irish practices were significantly worse than Welsh practices at recording coded lung function parameters used in COPD diagnosis (ORs: 0.51 [0.43–0.59], 0.29 [0.23–0.36], 0.42 [0.31–0.58], respectively) and referring appropriate patients for pulmonary rehabilitation (ORs: 0.10 [0.09–0.11], 0.12 [0.11–0.14], 0.22 [0.19–0.25], respectively). Completing national audits of primary care in Wales only may have led to improvements in care, or at least improvements in the recording of care in Wales that are not occurring elsewhere in the UK. This highlights the potential importance of audit in improving care quality and accurate recording of that care.
Evasion of cGAS and TRIM5 defines pandemic HIV
Authors: Zuliani-Alvarez Lorena , Govasli Morten L. , Rasaiyaah Jane , Monit Chris , Perry Stephen O. , Sumner Rebecca P. , McAlpine-Scott Simon , Dickson Claire , Rifat Faysal K. M. , Hilditch Laura , Miles Richard J. , Bibollet-Ruche Frederic , Hahn Beatrice H. , Boecking Till , Pinotsis Nikos , James Leo C. , Jacques David A. , Towers Greg J. 
Published: October 2022

AbstractOf the 13 known independent zoonoses of simian immunodeficiency viruses to humans, only one, leading to human immunodeficiency virus (HIV) type 1(M) has become pandemic, causing over 80 million human infections. To understand the specific features associated with pandemic human-to-human HIV spread, we compared replication of HIV-1(M) with non-pandemic HIV-(O) and HIV-2 strains in myeloid cell models. We found that non-pandemic HIV lineages replicate less well than HIV-1(M) owing to activation of cGAS and TRIM5-mediated antiviral responses. We applied phylogenetic and X-ray crystallography structural analyses to identify differences between pandemic and non-pandemic HIV capsids. We found that genetic reversal of two specific amino acid adaptations in HIV-1(M) enables activation of TRIM5, cGAS and innate immune responses. We propose a model in which the parental lineage of pandemic HIV-1(M) evolved a capsid that prevents cGAS and TRIM5 triggering, thereby allowing silent replication in myeloid cells. We hypothesize that this capsid adaptation promotes human-to-human spread through avoidance of innate immune response activation.
Freshwater microbial metagenomes sampled across different water body characteristics, space and time in Israel
Authors: Al-Ashhab Ashraf , Marmen Sophi , Schweitzer-Natan Orna , Bolotin Evgeni , Patil Hemant , Viner-Mozzini Diti , Aharonovich Dikla , Hershberg Ruth , Minz Dror , Carmeli Shmuel , Cytryn Eddie , Sukenik Assaf , Sher Daniel 
Published: October 2022

AbstractFreshwater bodies are critical components of terrestrial ecosystems. The microbial communities of freshwater ecosystems are intimately linked water quality. These microbes interact with, utilize and recycle inorganic elements and organic matter. Here, we present three metagenomic sequence datasets (total of 182.9 Gbp) from different freshwater environments in Israel. The first dataset is from diverse freshwater bodies intended for different usages – a nature reserve, irrigation and aquaculture facilities, a tertiary wastewater treatment plant and a desert rainfall reservoir. The second represents a two-year time-series, collected during 2013–2014 at roughly monthly intervals, from a water reservoir connected to an aquaculture facility. The third is from several time-points during the winter and spring of 2015 in Lake Kinneret, including a bloom of the cyanobacterium Microcystis sp. These datasets are accompanied by physical, chemical, and biological measurements at each sampling point. We expect that these metagenomes will facilitate a wide range of comparative studies that seek to illuminate new aspects of freshwater microbial ecosystems and inform future water quality management approaches.
Assessing the impact of COVID-19 mass testing in South Tyrol using a semi-parametric growth model
Authors: Ferrari Davide , Stillman Steven , Tonin Mirco 
Published: October 2022

AbstractMass antigen testing has been proposed as a possible cost-effective tool to contain the COVID-19 pandemic. We test the impact of a voluntary mass testing campaign implemented in the Italian region of South Tyrol on the spread of the virus in the following months. We do so by using an innovative empirical approach which embeds a semi-parametric growth model—where COVID-19 transmission dynamics are allowed to vary across regions and to be impacted by the implementation of the mass testing campaign—into a synthetic control framework which creates an appropriate control group of other Italian regions. Our results suggest that mass testing campaigns are useful instruments for mitigating the pandemic.
Intronic primers reveal unexpectedly high major histocompatibility complex diversity in Antarctic fur seals
Authors: Tebbe Jonas , Ottensmann Meinolf , Havenstein Katja , Efstratiou Artemis , Lenz Tobias L. , Caspers Barbara A. , Forcada Jaume , Tiedemann Ralph , Hoffman Joseph I. 
Published: October 2022

AbstractThe major histocompatibility complex (MHC) is a group of genes comprising one of the most important components of the vertebrate immune system. Consequently, there has been much interest in characterising MHC variation and its relationship with fitness in a variety of species. Due to the exceptional polymorphism of MHC genes, careful PCR primer design is crucial for capturing all of the allelic variation present in a given species. We therefore developed intronic primers to amplify the full-length 267 bp protein-coding sequence of the MHC class II DQB exon 2 in the Antarctic fur seal. We then characterised patterns of MHC variation among mother–offspring pairs from two breeding colonies and detected 19 alleles among 771 clone sequences from 56 individuals. The distribution of alleles within and among individuals was consistent with a single-copy, classical DQB locus showing Mendelian inheritance. Amino acid similarity at the MHC was significantly associated with genome-wide relatedness, but no relationship was found between MHC heterozygosity and genome-wide heterozygosity. Finally, allelic diversity was several times higher than reported by a previous study based on partial exon sequences. This difference appears to be related to allele-specific amplification bias, implying that primer design can strongly impact the inference of MHC diversity.
Detection of the 40 Hz auditory steady-state response with optically pumped magnetometers
Authors: An Kyung-min , Shim Jeong Hyun , Kwon Hyukchan , Lee Yong-Ho , Yu Kwon-Kyu , Kwon Moonyoung , Chun Woo Young , Hirosawa Tetsu , Hasegawa Chiaki , Iwasaki Sumie , Kikuchi Mitsuru , Kim Kiwoong 
Published: October 2022

AbstractMagnetoencephalography (MEG) is a functional neuroimaging technique that noninvasively detects the brain magnetic field from neuronal activations. Conventional MEG measures brain signals using superconducting quantum interference devices (SQUIDs). SQUID-MEG requires a cryogenic environment involving a bulky non-magnetic Dewar flask and the consumption of liquid helium, which restricts the variability of the sensor array and the gap between the cortical sources and sensors. Recently, miniature optically pumped magnetometers (OPMs) have been developed and commercialized. OPMs do not require cryogenic cooling and can be placed within millimeters from the scalp. In the present study, we arranged six OPM sensors on the temporal area to detect auditory-related brain responses in a two-layer magnetically shielded room. We presented the auditory stimuli of 1 kHz pure-tone bursts with 200 ms duration and obtained the M50 and M100 components of auditory-evoked fields. We delivered the periodic stimuli with a 40 Hz repetition rate and observed the gamma-band power changes and inter-trial phase coherence of auditory steady-state responses at 40 Hz. We found that the OPM sensors have a performance comparable to that of conventional SQUID-MEG sensors, and our results suggest the feasibility of using OPM sensors for functional neuroimaging and brain–computer interface applications.
Radiative heat transfer between two carbon nanotubes
Authors: Nefedov Igor S. , Davidovich Michael V. , Glukhova Olga E. , Slepchenkov Michael M. , Rubi J. Miguel 
Published: October 2022

AbstractWe analyze the radiative heat transfer between two parallel and infinitely long carbon nanotubes (CNTs). The radiative heat exchange is due to the difference between the Poynting vectors generated by the fluctuating currents when the CNTs are at different temperatures. The radiated and absorbed Poynting vectors are expressed in terms of the correlations of the electromagnetic fields obtained from the Green’s function and the fluctuation-dissipation theorem for the current density. The analysis takes into account the scattering of the fields by the nanotubes. We show that the radiative heat transfer depends not only on the distance between nanotubes, but also on their chiralities and thus on their semiconducting or metallic nature, which would allow the design of nanostructures for optimal radiative heat exchange.
Vortex-electromagnetic-wave-based ISAR imaging for high-speed maneuvering targets
Authors: Bu Lijun , Zhu Yongzhong , Chen Yijun , Yang Yufei , Zang Yadan 
Published: October 2022

AbstractVortex electromagnetic wave (VEMW) carrying orbital angular momentum (OAM), which is expected to introduce additional degrees of freedom in inverse synthetic aperture radar(ISAR) imaging. However, the current research about maneuvering targets is based on the "stop go" hypothesis, which does not apply to high-speed motion scenarios due to the intrapulse movement of the target. To improve the imaging quality, this letter proposes a VEMW-based high-speed maneuvering targets imaging method. Firstly, the ISAR imaging scenario of high-speed target is established. According to the spatial geometric relationship between radar and maneuvering target, the vortex echo is deduced and its characteristics are analyzed. Subsequently, a frequency modulation rate estimation method considering both calculation efficiency and high precision is proposed to realize the accurate estimation of target speed. Then, an adaptive azimuth image compensation method based on minimum entropy is proposed. Through the setting of threshold, the number of component signals in linear frequency modulation (LFM) signal is determined and compensated successively. Finally, the range profile and azimuth profile are combined to reconstruct the three-dimensional information. The simulation results demonstrate that this work can effectively eliminate the influence of high-speed motion on range and azimuth profile, also benefit the development of ISAR imaging technique of high-speed maneuvering targets.
Intercellular interaction mechanisms promote diversity in intracellular ATP concentration in Escherichia coli populations
Authors: Nakatani Ryo J. , Itabashi Masahiro , Yamada Takahiro G. , Hiroi Noriko F. , Funahashi Akira 
Published: October 2022

AbstractIn fluctuating environments, many microorganisms acquire phenotypic heterogeneity as a survival tactic to increase the likelihood of survival of the overall population. One example of this interindividual heterogeneity is the diversity of ATP concentration among members ofEscherichia colipopulations under glucose deprivation. Despite the importance of such environmentally driven phenotypic heterogeneity, how the differences in intracellular ATP concentration emerge among individualE. coliorganisms is unknown. In this study, we focused on the mechanism through which individualE. coliachieve high intracellular ATP concentrations. First, we measured the ATP retained byE. coliover time when cultured at low (0.1 mM) and control (22.2 mM) concentrations of glucose and obtained the chronological change in ATP concentrations. Then, by comparing these chronological change of ATP concentrations and analyzing whether stochastic state transitions, periodic oscillations, cellular age, and intercellular communication—which have been reported as molecular biological mechanisms for generating interindividual heterogeneity—are involved, we showed that the appearance of high ATP-holding individuals observed amongE. colican be explained only by intercellular transmission. By performing metabolomic analysis of post-culture medium, we revealed a significant increase in the ATP, especially at low glucose, and that the number ofE. colithat retain significantly higher ATP can be controlled by adding large amounts of ATP to the medium, even in populations cultured under control glucose concentrations. These results reveal for the first time that ATP-mediated intercellular transmission enables some individuals inE. colipopulations grown at low glucose to retain large amounts of ATP.