bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effects of Light Intensity and Flow Speed on Biogeochemical Variability Within a Fringing Coral Reef in Onna‐Son, Okinawa, Japan
Authors: Rintoul M. S. , Courtney T. A. , Dohner J. L. , Giddings S. N. , Kekuewa S. A. H. , Mitarai S. , Monismith S. G. , Pezner A. K. , Andersson A. J. 
Published: November 2022

AbstractGlobal warming and ocean acidification are driving declines in seawater dissolved oxygen (DO) concentrations and pH. Predicting how these changes will affect shallow, near‐shore environments such as coral reefs is challenging due to their high natural biogeochemical variability present over both spatial (m to km) and temporal (diel to seasonal) scales. To make predictions, we must understand the drivers of this variability. The impact of metabolic processes on coral reef biogeochemical variability has been the subject of significant research effort, however, physical factors, including flow speed and light intensity, have received less attention. Here, we measured seawater flow, photosynthetically active radiation (PAR), pH, and DO at three reef habitats (reef flat, lagoon, and outflow channel) in a fringing coral reef system in Okinawa, Japan for 3 weeks in October 2019. During the study, pH ranged from 7.86 to 8.37 units while DO varied from 127 to 369 μmol/kg. Circulation was primarily wave‐driven with mean flow speeds ranging from 14 to 26 cm/s. Flow direction became increasingly consistent at higher flow speeds and traced benthic striations visible in satellite imagery. Multiple linear regression models of daytime changes in pH and DO versus daily mean flow speed and PAR described 25%–74% of the observed variability across all sites while at night, flow speed alone accounted for 7%–75% of the observed variability. These results demonstrate PAR, water flow speed, and the path water takes play important roles in controlling biogeochemical variability within coral reefs and must be considered when assessing their vulnerability to both local and global environmental change.
Violent Groundwater Eruption Triggered by a Distant Earthquake
Authors: Yan Xin , Shi Zheming , Wang Chi‐Yuen , Ingebritsen Steve E. , Manga Michael 
Published: November 2022

AbstractIt is now well established that earthquakes cause various hydrogeological responses at distances thousands of kilometers from the epicenter. What remains unexplained is the large amplitude and intensity of some responses. Following the 2004 Mw 9.1 Sumatra earthquake, groundwater 3,200 km from the epicenter erupted violently from a well and formed a water fountain reaching a height exceeding 60 m. We model the relevant processes by combining tidal analysis of groundwater level with numerical simulations using a two‐dimensional finite‐element model. We suggest that the eruption resulted from a combination of factors, including a rapid increase of crustal permeability and runaway CO2 exsolution and bubble nucleation induced by the passage of seismic waves. Our results may have implications for some engineering applications such as oil production and CO2 sequestration, and the eruption of hydrothermal features such as geysers.
Wind‐Driven Seasonal Intrusion of Modified Circumpolar Deep Water Onto the Continental Shelf in Prydz Bay, East Antarctica
Authors: Guo Guijun , Gao Libao , Shi Jiuxin , Zu Yongcan 
Published: November 2022

AbstractIntrusion of warm modified Circumpolar Deep Water (mCDW) is critical to heat transport onto the continental shelf around Antarctica, with substantial impacts on basal melting of ice shelves and sea ice production. We use hydrographic data collected in Prydz Bay, East Antarctica, and atmospheric and ocean reanalyses to investigate the seasonality of mCDW intrusions onto the East Antarctic continental shelf. Mooring measurements confirm that there is significant intrusion of mCDW over the inner continental shelf of Prydz Bay in March–July (austral autumn and early winter). The warming signal of intruded mCDW over the inner shelf is correlated with wind changes north of the shelf break, with a significant lag. This suggests that the autumn‐winter mCDW intrusions over the inner shelf are significantly affected by the wind regime north of the shelf break in January–May, when a southward displacement of the westerly winds occurs. The southward shift of westerly winds drives the shallowest depth of upwelled mCDW to move poleward and contributes more warm water to the shelf break. This results in the shoaling of mCDW near the shelf break in January–May and promotes mCDW intrusions onto the continental shelf. The dynamic barrier imposed on mCDW intrusions by the strong Antarctic Slope Front in January–May is offset by this shoaling of mCDW. This study indicates the strong sensitivity of continental shelves in East Antarctica to atmospheric forcing changes over the Southern Ocean.
SMARCC2 mediates the regulation of DKK1 by the transcription factor EGR1 through chromatin remodeling to reduce the proliferative capacity of glioblastoma
Authors: Li Chiyang , Wang Tong , Gu Junwei , Qi Songtao , Li Junjie , Chen Lei , Wu Hang , Shi Linyong , Song Chong , Li Hong , Zhu Liwen , Lu Yuntao , Zhou Qiang 
Published: November 2022

AbstractSwitch/sucrose-nonfermenting (SWI/SNF) complexes play a key role in chromatin remodeling. Recent studies have found that SMARCC2, as the core subunit of the fundamental module of the complex, plays a key role in its early assembly. In this study, we found a unique function of SMARCC2 in inhibiting the progression of glioblastoma by targeting the DKK1 signaling axis. Low expression of SMARCC2 is found in malignant glioblastoma (GBM) compared with low-grade gliomas. SMARCC2 knockout promoted the proliferation of glioblastoma cells, while its overexpression showed the opposite effect. Mechanistically, SMARCC2 negatively regulates transcription by dynamically regulating the chromatin structure and closing the promoter region of the target gene DKK1, which can be bound by the transcription factor EGR1. DKK1 knockdown significantly reduced the proliferation of glioblastoma cell lines by inhibiting the PI3K–AKT pathway. We also studied the functions of the SWIRM and SANT domains of SMARCC2 and found that the SWIRM domain plays a more important role in the complete chromatin remodeling function of SMARCC2. In addition, in vivo studies confirmed that overexpression of SMARCC2 could significantly inhibit the size of intracranial gliomas in situ in nude mice. Overall, this study shows that SMARCC2, as a tumor suppressor, inhibits the proliferation of glioblastoma by targeting the transcription of the oncogene DKK1 through chromatin remodeling, indicating that SMARCC2 is a potentially attractive therapeutic target in glioblastoma.
Reversion mutations in germline BRCA1/2-mutant tumors reveal a BRCA-mediated phenotype in non-canonical histologies
Authors: Murciano-Goroff Yonina R. , Schram Alison M. , Rosen Ezra Y. , Won Helen , Gong Yixiao , Noronha Anne Marie , Janjigian Yelena Y. , Stadler Zsofia K. , Chang Jason C. , Yang Soo-Ryum , Mandelker Diana , Offit Kenneth , Berger Michael F. , Donoghue Mark T. A. , Bandlamudi Chaitanya , Drilon Alexander 
Published: November 2022

AbstractThe association between loss of BRCA1/2 and a homologous recombination deficiency phenotype is lineage dependent. In BRCA-associated cancers such as breast, ovarian, pancreas and prostate, this phenotype confers sensitivity to PARP inhibitors and platinum-therapies. Somatic reversion mutations restoring BRCA1/2 function mediate resistance, and have exclusively been reported in BRCA-associated tumors. In this study, we analyze matched tumor and normal sequencing from 31,927 patients and identify 846 (2.7%) patients with germline BRCA1/2 variants across 43 different cancer types, including 11 with somatic reversion mutations. While nine are in BRCA-associated tumors, we find two reversion mutations in non-BRCA-associated histologies, namely lung and esophagogastric adenocarcinomas. Both were detected following platinum therapy. Whole exome sequencing confirms the homologous recombination deficiency phenotype of these tumors. While reversion mutations arise in all BRCA-associated cancer types, here we show that reversion mutations arising post-platinum in non-BRCA associated histologies, while rare, may indicate BRCA1/2 mediated tumorigenesis.
RNA-controlled nucleocytoplasmic shuttling of mRNA decay factors regulates mRNA synthesis and a novel mRNA decay pathway
Authors: Chattopadhyay Shiladitya , Garcia-Martinez Jose , Haimovich Gal , Fischer Jonathan , Khwaja Aya , Barkai Oren , Chuartzman Silvia Gabriela , Schuldiner Maya , Elran Ron , Rosenberg Miriam I. , Urim Shira , Deshmukh Shubham , Bohnsack Katherine E. , Bohnsack Markus T. , Perez-Ortin Jose E. , Choder Mordechai 
Published: November 2022

AbstractmRNA level is controlled by factors that mediate both mRNA synthesis and decay, including the 5’ to 3’ exonuclease Xrn1. Here we show that nucleocytoplasmic shuttling of several yeast mRNA decay factors plays a key role in determining both mRNA synthesis and decay. Shuttling is regulated by RNA-controlled binding of the karyopherin Kap120 to two nuclear localization sequences (NLSs) in Xrn1, location of one of which is conserved from yeast to human. The decaying RNA binds and masks NLS1, establishing a link between mRNA decay and Xrn1 shuttling. Preventing Xrn1 import, either by deleting KAP120 or mutating the two Xrn1 NLSs, compromises transcription and, unexpectedly, also cytoplasmic decay, uncovering a cytoplasmic decay pathway that initiates in the nucleus. Most mRNAs are degraded by both pathways - the ratio between them represents a full spectrum. Importantly, Xrn1 shuttling is required for proper responses to environmental changes, e.g., fluctuating temperatures, involving proper changes in mRNA abundance and in cell proliferation rate.
Optically trapped room temperature polariton condensate in an organic semiconductor
Authors: Wei Mengjie , Verstraelen Wouter , Orfanakis Konstantinos , Ruseckas Arvydas , Liew Timothy C. H. , Samuel Ifor D. W. , Turnbull Graham A. , Ohadi Hamid 
Published: November 2022

AbstractThe strong nonlinearities of exciton-polariton condensates in lattices make them suitable candidates for neuromorphic computing and physical simulations of complex problems. So far, all room temperature polariton condensate lattices have been achieved by nanoimprinting microcavities, which by nature lacks the crucial tunability required for realistic reconfigurable simulators. Here, we report the observation of a quantised oscillating nonlinear quantum fluid in 1D and 2D potentials in an organic microcavity at room temperature, achieved by an on-the-fly fully tuneable optical approach. Remarkably, the condensate is delocalised from the excitation region by macroscopic distances, leading both to longer coherence and a threshold one order of magnitude lower than that with a conventional Gaussian excitation profile. We observe different mode selection behaviour compared to inorganic materials, which highlights the anomalous scaling of blueshift with pump intensity and the presence of sizeable energy-relaxation mechanisms. Our work is a major step towards a fully tuneable polariton simulator at room temperature.
A charged diatomic triple-bonded U≡N species trapped in C82 fullerene cages
Authors: Meng Qingyu , Abella Laura , Yao Yang-Rong , Sergentu Dumitru-Claudiu , Yang Wei , Liu Xinye , Zhuang Jiaxin , Echegoyen Luis , Autschbach Jochen , Chen Ning 
Published: November 2022

AbstractActinide diatomic molecules are ideal models to study elusive actinide multiple bonds, but most of these diatomic molecules have so far only been studied in solid inert gas matrices. Herein, we report a charged U≡N diatomic species captured in fullerene cages and stabilized by the U-fullerene coordination interaction. Two diatomic clusterfullerenes, viz. UN@Cs(6)-C82 and UN@C2(5)-C82, were successfully synthesized and characterized. Crystallographic analysis reveals U-N bond lengths of 1.760(7) and 1.760(20) Å in UN@Cs(6)-C82 and UN@C2(5)-C82. Moreover, U≡N was found to be immobilized and coordinated to the fullerene cages at 100 K but it rotates inside the cage at 273 K. Quantum-chemical calculations show a (UN)2+@(C82)2− electronic structure with formal +5 oxidation state (f1) of U and unambiguously demonstrate the presence of a U≡N bond in the clusterfullerenes. This study constitutes an approach to stabilize fundamentally important actinide multiply bonded species.
Enhanced activity of Alzheimer disease-associated variant of protein kinase Cα drives cognitive decline in a mouse model
Authors: Lordén Gema , Wozniak Jacob M. , Doré Kim , Dozier Lara E. , Cates-Gatto Chelsea , Patrick Gentry N. , Gonzalez David J. , Roberts Amanda J. , Tanzi Rudolph E. , Newton Alexandra C. 
Published: November 2022

AbstractExquisitely tuned activity of protein kinase C (PKC) isozymes is essential to maintaining cellular homeostasis. Whereas loss-of-function mutations are generally associated with cancer, gain-of-function variants in one isozyme, PKCα, are associated with Alzheimer’s disease (AD). Here we show that the enhanced activity of one variant, PKCα M489V, is sufficient to rewire the brain phosphoproteome, drive synaptic degeneration, and impair cognition in a mouse model. This variant causes a modest 30% increase in catalytic activity without altering on/off activation dynamics or stability, underscoring that enhanced catalytic activity is sufficient to drive the biochemical, cellular, and ultimately cognitive effects observed. Analysis of hippocampal neurons from PKCα M489V mice reveals enhanced amyloid-β-induced synaptic depression and reduced spine density compared to wild-type mice. Behavioral studies reveal that this mutation alone is sufficient to impair cognition, and, when coupled to a mouse model of AD, further accelerates cognitive decline. The druggability of protein kinases positions PKCα as a promising therapeutic target in AD.
Multi-omics analysis identifies osteosarcoma subtypes with distinct prognosis indicating stratified treatment
Authors: Jiang Yafei , Wang Jinzeng , Sun Mengxiong , Zuo Dongqing , Wang Hongsheng , Shen Jiakang , Jiang Wenyan , Mu Haoran , Ma Xiaojun , Yin Fei , Lin Jun , Wang Chongren , Yu Shuting , Jiang Lu , Lv Gang , Liu Feng , Xue Linghang , Tian Kai , Wang Gangyang , Zhou Zifei , Lv Yu , Wang Zhuoying , Zhang Tao , Xu Jing , Yang Liu , Zhao Kewen , Sun Wei , Tang Yujie , Cai Zhengdong , Wang Shengyue , Hua Yingqi 
Published: November 2022

AbstractOsteosarcoma (OS) is a primary malignant bone tumor that most commonly affects children, adolescents, and young adults. Here, we comprehensively analyze genomic, epigenomic and transcriptomic data from 121 OS patients. Somatic mutations are diverse within the cohort, and only TP53 is significantly mutated. Through unsupervised integrative clustering of the multi-omics data, we classify OS into four subtypes with distinct molecular features and clinical prognosis: (1) Immune activated (S-IA), (2) Immune suppressed (S-IS), (3) Homologous recombination deficiency dominant (S-HRD), and (4) MYC driven (S-MD). MYC amplification with HR proficiency tumors is identified with a high oxidative phosphorylation signature resulting in resistance to neoadjuvant chemotherapy. Potential therapeutic targets are identified for each subtype, including platinum-based chemotherapy, immune checkpoint inhibitors, anti-VEGFR, anti-MYC and PARPi-based synthetic lethal strategies. Our comprehensive integrated characterization provides a valuable resource that deepens our understanding of the disease, and may guide future clinical strategies for the precision treatment of OS.
Differential compartmentalization of myeloid cell phenotypes and responses towards the CNS in Alzheimer’s disease
Authors: Fernández Zapata Camila , Giacomello Ginevra , Spruth Eike J. , Middeldorp Jinte , Gallaccio Gerardina , Dehlinger Adeline , Dames Claudia , Leman Julia K. H. , van Dijk Roland E. , Meisel Andreas , Schlickeiser Stephan , Kunkel Desiree , Hol Elly M. , Paul Friedemann , Parr Maria Kristina , Priller Josef , Böttcher Chotima 
Published: November 2022

AbstractMyeloid cells are suggested as an important player in Alzheimer´s disease (AD). However, its continuum of phenotypic and functional changes across different body compartments and their use as a biomarker in AD remains elusive. Here, we perform multiple state-of-the-art analyses to phenotypically and metabolically characterize immune cells between peripheral blood (n = 117), cerebrospinal fluid (CSF, n = 117), choroid plexus (CP, n = 13) and brain parenchyma (n = 13). We find that CSF cells increase expression of markers involved in inflammation, phagocytosis, and metabolism. Changes in phenotype of myeloid cells from AD patients are more pronounced in CP and brain parenchyma and upon in vitro stimulation, suggesting that AD-myeloid cells are more vulnerable to environmental changes. Our findings underscore the importance of myeloid cells in AD and the detailed characterization across body compartments may serve as a resource for future studies focusing on the assessment of these cells as biomarkers in AD.
Engineering superconducting qubits to reduce quasiparticles and charge noise
Authors: Pan Xianchuang , Zhou Yuxuan , Yuan Haolan , Nie Lifu , Wei Weiwei , Zhang Libo , Li Jian , Liu Song , Jiang Zhi Hao , Catelani Gianluigi , Hu Ling , Yan Fei , Yu Dapeng 
Published: November 2022

AbstractIdentifying, quantifying, and suppressing decoherence mechanisms in qubits are important steps towards the goal of engineering a quantum computer or simulator. Superconducting circuits offer flexibility in qubit design; however, their performance is adversely affected by quasiparticles (broken Cooper pairs). Developing a quasiparticle mitigation strategy compatible with scalable, high-coherence devices is therefore highly desirable. Here we experimentally demonstrate how to control quasiparticle generation by downsizing the qubit, capping it with a metallic cover, and equipping it with suitable quasiparticle traps. Using a flip-chip design, we shape the electromagnetic environment of the qubit above the superconducting gap, inhibiting quasiparticle poisoning. Our findings support the hypothesis that quasiparticle generation is dominated by the breaking of Cooper pairs at the junction, as a result of photon absorption by the antenna-like qubit structure. We achieve record low charge-parity switching rate (<1 Hz). Our aluminium devices also display improved stability with respect to discrete charging events.
A class-mismatched TCR bypasses MHC restriction via an unorthodox but fully functional binding geometry
Authors: Singh Nishant K. , Alonso Jesus A. , Devlin Jason R. , Keller Grant L. J. , Gray George I. , Chiranjivi Adarsh K. , Foote Sara G. , Landau Lauren M. , Arbuiso Alyssa G. , Weiss Laura I. , Rosenberg Aaron M. , Hellman Lance M. , Nishimura Michael I. , Baker Brian M. 
Published: November 2022

AbstractMHC restriction, which describes the binding of TCRs from CD4+T cells to class II MHC proteins and TCRs from CD8+T cells to class I MHC proteins, is a hallmark of immunology. Seemingly rare TCRs that break this paradigm exist, but mechanistic insight into their behavior is lacking. TIL1383I is a prototypical class-mismatched TCR, cloned from a CD4+T cell but recognizing the tyrosinase tumor antigen presented by the class I MHC HLA-A2 in a fully functional manner. Here we find that TIL1383I binds this class I target with a highly atypical geometry. Despite unorthodox binding, TCR signaling, antigen specificity, and the ability to use CD8 are maintained. Structurally, a key feature of TIL1383I is an exceptionally long CDR3β loop that mediates functions that are traditionally performed separately by hypervariable and germline loops in canonical TCR structures. Our findings thus expand the range of known TCR binding geometries compatible with normal function and specificity, provide insight into the determinants of MHC restriction, and may help guide TCR selection and engineering for immunotherapy.
Fundamentals and future applications of electrochemical energy conversion in space
Authors: Brinkert Katharina , Mandin Philippe 
Published: November 2022

AbstractLong-term space missions require power sources and energy storage possibilities, capable at storing and releasing energy efficiently and continuously or upon demand at a wide operating temperature range, an ultra-high vacuum environment and a significantly reduced buoyant force. Electrochemical energy conversion systems play already a major role e.g., during launch and on the International Space Station, and it is evident from these applications that future human space missions - particularly to Moon and Mars - will not be possible without them. Here, we will provide an overview of currently existing electrochemical conversion technologies for space applications such as battery systems and fuel cells and outline their role in materials design and fabrication as well as fuel production. The focus lies on the current operation of these energy conversion systems in space as well as the challenges posed on them by this special environment. Future experiment designs which could help elucidating and optimizing their key operating parameters for an efficient and long-term operation are discussed.
Dose-response meta-analysis on urate, gout, and the risk for Parkinson’s disease
Authors: Chang Hongtao , Wang Benqiao , Shi Yue , Zhu Ruixia 
Published: November 2022

AbstractThe relationship between Parkinson’s disease (PD) and urate or gout has attracted significant interest in recent years, but the results were conflicting. This dose-response meta-analysis aimed to estimate the correlation between urate levels or gout and the risk for PD. The Embase, PubMed, and Medline databases were searched for studies that investigated the relationship between the risk for PD and urate levels or gout. Random-effects or fixed-effects models were used to obtain pooled relative risks (RRs) and corresponding 95% confidence intervals (CIs). Fifteen studies, involving 449,816 participants and 14,687 cases in total, were included in the meta-analysis. High serum urate levels were associated with decreased risk for PD (RR 0.44 [95% CI 0.32–0.55]). Subgroup analysis according to sex revealed a neuroprotective effect of high urate levels against PD among females (0.68 [95% CI 0.43–0.93]) and males (0.49 [95% CI 0.34–0.64]). The risk for PD was lowered by 6% (0.94 [95% CI 0.90–0.98]) for each 1 mg/dl increase in serum urate level and reduced by 13% (0.87 [95% CI 0.80–0.95]) with each 2 mg/dl increase in serum urate level. However, gout was not closely correlated with the risk for PD (0.97 [95% CI 0.85–1.09]). Higher serum urate levels reduced the risk for PD, which was decreased by 6% (relative risk reduction) for each 1 mg/dl increase in serum urate levels. And the results indicated that urate may exert protective effects against the development of PD.