bluuebunny/crossref_metadata_2025_split huggingface dataset:
On Dynamical Decomposition of Multiscale Oceanic Motions
Authors: Wang Chuanyin , Liu Zhiyu , Lin Hongyang 
Published: March 2023

AbstractThe ocean hosts a variety of fluid motions characterized by contrasting dynamical regimes and spatiotemporal scales. A practical decomposition of multiscale motions in realistic oceanic settings is crucial to advancing dynamical interpretation and prediction of oceanic processes, but remains a major challenge. To this end, methodology is developed in this study for decomposing multiscale oceanic motions based on their respective dynamical characteristics. Specifically, large‐scale currents and barotropic tides have the largest horizontal scales but contrasting frequencies; low‐mode internal gravity waves (IGWs) are well constrained by linear dispersion relations, whereas mesoscale flows are of relatively low frequency and with horizontal scales above the first baroclinic deformation radius; the intrinsic frequency of high‐mode IGWs (submesoscale flows) is above (well below) the inertial frequency. The validity and usefulness of the proposed methodology are demonstrated with a proof‐of‐concept application to simulated flows in the central basin of the South China Sea.
The Impact of Plant Oscillation on Dispersion in Emergent Aquatic Canopies
Authors: Sehat H. , Abdolahpour M. , Jamali M. , Ghisalberti M. 
Published: March 2023

AbstractFlexible canopies bend and oscillate in both the in‐line and cross‐flow directions due to periodic forcing associated with vortex shedding. The resultant plant motion impacts the vegetation wake structure and, thus, the rate of lateral dispersion in these environments. Despite significant improvements in our understanding of dispersion in rigid canopies, a reliable framework to predict mixing in oscillating canopies is still lacking. This research demonstrates how plant oscillation can profoundly impact rates of lateral mixing in steady flows. The lateral dispersion coefficients were evaluated experimentally, using photographs of injected dye plumes within two types of emergent flexible model vegetation. Results revealed a significant increase in the rates of lateral dispersion (by up to 45%) due to the plant oscillation. A predictive model, based on a redefined vegetation density that incorporates the impact of plant oscillation, was developed that can accurately predict dispersion in emergent canopies. A quantitative prediction of dispersion in oscillating flexible vegetation is a significant step toward a more accurate description of material transport in aquatic environments.
Novel multivalent S100A8 inhibitory peptides attenuate tumor progression and metastasis by inhibiting the TLR4-dependent pathway
Authors: Deguchi Atsuko , Watanabe-Takahashi Miho , Mishima Taishi , Omori Tsutomu , Ohto Umeharu , Arashiki Nobuto , Nakamura Fumio , Nishikawa Kiyotaka , Maru Yoshiro 
Published: March 2023

AbstractThe tumor-elicited inflammation is closely related to tumor microenvironment during tumor progression. S100A8, an endogenous ligand of Toll-like receptor 4 (TLR4), is known as a key molecule in the tumor microenvironment and premetastatic niche formation. We firstly generated a novel multivalent S100A8 competitive inhibitory peptide (divalent peptide3A5) against TLR4/MD-2, using the alanine scanning. Divalent peptide3A5 suppressed S100A8-mediated interleukin-8 and vascular endothelial growth factor production in human colorectal tumor SW480 cells. Using SW480-transplanted xenograft models, divalent peptide3A5 suppressed tumor progression in a dose-dependent manner. We demonstrated that combination therapy with divalent peptide3A5 and bevacizumab synergistically suppressed tumor growth in SW480 xenograft models. Using syngeneic mouse models, we found that divalent peptide3A5 improved the efficacy of anti-programmed death (PD)1 antibody, and lung metastasis. In addition, by using multivalent peptide library screening based on peptide3A5, we then isolated two more candidates; divalent ILVIK, and tetravalent ILVIK. Of note, multivalent ILVIK, but not monovalent ILVIK showed competitive inhibitory activity against TLR4/MD-2 complex, and anti-tumoral activity in SW480 xenograft models. As most tumor cells including SW480 cells also express TLR4, S100A8 inhibitory peptides would target both the tumor microenvironment and tumor cells. Thus, multivalent S100A8 inhibitory peptides would provide new pharmaceutical options for aggressive cancers.
HIF1α-BNIP3-mediated mitophagy protects against renal fibrosis by decreasing ROS and inhibiting activation of the NLRP3 inflammasome
Authors: Li Jialin , Lin Qisheng , Shao Xinghua , Li Shu , Zhu Xuying , Wu Jingkui , Mou Shan , Gu Leyi , Wang Qin , Zhang Minfang , Zhang Kaiqi , Lu Jiayue , Ni Zhaohui 
Published: March 2023

AbstractChronic kidney disease affects approximately 14.3% of people worldwide. Tubulointerstitial fibrosis is the final stage of almost all progressive CKD. To date, the pathogenesis of renal fibrosis remains unclear, and there is a lack of effective treatments, leading to renal replacement therapy. Mitophagy is a type of selective autophagy that has been recognized as an important way to remove dysfunctional mitochondria and abrogate the excessive accumulation of mitochondrial-derived reactive oxygen species (ROS) to balance the function of cells. However, the role of mitophagy and its regulation in renal fibrosis need further examination. In this study, we showed that mitophagy was induced in renal tubular epithelial cells in renal fibrosis. After silencing BNIP3, mitophagy was abolished in vivo and in vitro, indicating the important effect of the BNIP3-dependent pathway on mitophagy. Furthermore, in unilateral ureteral obstruction (UUO) models and hypoxic conditions, the production of mitochondrial ROS, mitochondrial damage, activation of the NLRP3 inflammasome, and the levels of αSMA and TGFβ1 increased significantly following BNIP3 gene deletion or silencing. Following silencing BNIP3 and pretreatment with mitoTEMPO or MCC950, the protein levels of αSMA and TGFβ1 decreased significantly in HK-2 cells under hypoxic conditions. These findings demonstrated that HIF1α-BNIP3-mediated mitophagy played a protective role against hypoxia-induced renal epithelial cell injury and renal fibrosis by reducing mitochondrial ROS and inhibiting activation of the NLRP3 inflammasome.
CRISPR-induced DNA reorganization for multiplexed nucleic acid detection
Authors: Karlikow Margot , Amalfitano Evan , Yang Xiaolong , Doucet Jennifer , Chapman Abigail , Mousavi Peivand Sadat , Homme Paige , Sutyrina Polina , Chan Winston , Lemak Sofia , Yakunin Alexander F. , Dolezal Adam G. , Kelley Shana , Foster Leonard J. , Harpur Brock A. , Pardee Keith 
Published: March 2023

AbstractNucleic acid sensing powered by the sequence recognition of CRIPSR technologies has enabled major advancement toward rapid, accurate and deployable diagnostics. While exciting, there are still many challenges facing their practical implementation, such as the widespread need for a PAM sequence in the targeted nucleic acid, labile RNA inputs, and limited multiplexing. Here we report FACT (Functionalized Amplification CRISPR Tracing), a CRISPR-based nucleic acid barcoding technology compatible with Cas12a and Cas13a, enabling diagnostic outputs based on cis- and trans-cleavage from any sequence. Furthermore, we link the activation of CRISPR-Cas12a to the expression of proteins through a Reprogrammable PAIRing system (RePAIR). We then combine FACT and RePAIR to create FACTOR (FACT on RePAIR), a CRISPR-based diagnostic, that we use to detect infectious disease in an agricultural use case: honey bee viral infection. With high specificity and accuracy, we demonstrate the potential of FACTOR to be applied to the sensing of any nucleic acid of interest.
Seasonality of downward carbon export in the Pacific Southern Ocean revealed by multi-year robotic observations
Authors: Lacour Léo , Llort Joan , Briggs Nathan , Strutton Peter G. , Boyd Philip W. 
Published: March 2023

AbstractAt high latitudes, the biological carbon pump, which exports organic matter from the surface ocean to the interior, has been attributed to the gravitational sinking of particulate organic carbon. Conspicuous deficits in ocean carbon budgets challenge this as a sole particle export pathway. Recent model estimates revealed that particle injection pumps have a comparable downward flux of particulate organic carbon to the biological gravitational pump, but with different seasonality. To date, logistical constraints have prevented concomitant and extensive observations of these mechanisms. Here, using year-round robotic observations and recent advances in bio-optical signal analysis, we concurrently investigated the functioning of two particle injection pumps, the mixed layer and eddy subduction pumps, and the gravitational pump in Southern Ocean waters. By comparing three annual cycles in contrasting physical and biogeochemical environments, we show how physical forcing, phytoplankton phenology and particle characteristics influence the magnitude and seasonality of these export pathways, with implications for carbon sequestration efficiency over the annual cycle.
A melanopsin ganglion cell subtype forms a dorsal retinal mosaic projecting to the supraoptic nucleus
Authors: Berry Michael H. , Moldavan Michael , Garrett Tavita , Meadows Marc , Cravetchi Olga , White Elizabeth , Leffler Joseph , von Gersdorff Henrique , Wright Kevin M. , Allen Charles N. , Sivyer Benjamin 
Published: March 2023

AbstractVisual input to the hypothalamus from intrinsically photosensitive retinal ganglion cells (ipRGCs) influences several functions including circadian entrainment, body temperature, and sleep. ipRGCs also project to nuclei such as the supraoptic nucleus (SON), which is involved in systemic fluid homeostasis, maternal behavior, social behaviors, and appetite. However, little is known about the SON-projecting ipRGCs or their relationship to well-characterized ipRGC subtypes. Using aGlyT2Cremouse line, we show a subtype of ipRGCs restricted to the dorsal retina that selectively projects to the SON. These ipRGCs tile a dorsal region of the retina, forming a substrate for encoding ground luminance. Optogenetic activation of their axons demonstrates they release the neurotransmitter glutamate in multiple regions, including the suprachiasmatic nucleus (SCN) and SON. Our results challenge the idea that ipRGC dendrites overlap to optimize photon capture and suggests non-image forming vision operates to sample local regions of the visual field to influence diverse behaviors.
Synergy of cations in high entropy oxide lithium ion battery anode
Authors: Wang Kai , Hua Weibo , Huang Xiaohui , Stenzel David , Wang Junbo , Ding Ziming , Cui Yanyan , Wang Qingsong , Ehrenberg Helmut , Breitung Ben , Kübel Christian , Mu Xiaoke 
Published: March 2023

AbstractHigh entropy oxides (HEOs) with chemically disordered multi-cation structure attract intensive interest as negative electrode materials for battery applications. The outstanding electrochemical performance has been attributed to the high-entropy stabilization and the so-called ‘cocktail effect’. However, the configurational entropy of the HEO, which is thermodynamically only metastable at room-temperature, is insufficient to drive the structural reversibility during conversion-type battery reaction, and the ‘cocktail effect’ has not been explained thus far. This work unveils the multi-cations synergy of the HEO Mg0.2Co0.2Ni0.2Cu0.2Zn0.2O at atomic and nanoscale during electrochemical reaction and explains the ‘cocktail effect’. The more electronegative elements form an electrochemically inert 3-dimensional metallic nano-network enabling electron transport. The electrochemical inactive cation stabilizes an oxide nanophase, which is semi-coherent with the metallic phase and accommodates Li+ ions. This self-assembled nanostructure enables stable cycling of micron-sized particles, which bypasses the need for nanoscale pre-modification required for conventional metal oxides in battery applications. This demonstrates elemental diversity is the key for optimizing multi-cation electrode materials.
The protective role of conjunctival goblet cell mucin sialylation
Authors: Matsuzawa Moe , Ando Tomoaki , Fukase Saaya , Kimura Meiko , Kume Yasuharu , Ide Takuma , Izawa Kumi , Kaitani Ayako , Hara Mutsuko , Nakamura Eri , Kamei Anna , Matsuda Akira , Nakano Nobuhiro , Maeda Keiko , Tada Norihiro , Ogawa Hideoki , Okumura Ko , Murakami Akira , Ebihara Nobuyuki , Kitaura Jiro 
Published: March 2023

AbstractGel-forming mucins secreted by conjunctival goblet cells have been implicated in the clearance of allergens, pathogens, and debris. However, their roles remain incompletely understood. Here we show that human and mouse conjunctival goblet cell mucins have Alcian blue-detectable sialic acids, but not sulfates in the steady state. Interestingly, Balb/c mouse strain lacks this sialylation due to a point mutation in a sialyltransferase gene, St6galnac1, which is responsible for sialyl-Tn synthesis. Introduction of intact St6galnac1 to Balb/c restores the sialylation of conjunctival goblet cell mucus. Sialylated mucus efficiently captures and encapsulates the allergen particles in an impenetrable layer, leading to the protection of mice from the development of allergic conjunctivitis. Expression of ST6GALNAC1 and sialyl-Tn is upregulated in humans under conditions with chronic stimuli. These results indicate that the sialylated glycans on the ocular mucins play an essential role in maintaining the conjunctival mucosa by protecting from the incoming foreign bodies such as allergen particles.
Wavelength engineerable porous organic polymer photosensitizers with protonation triggered ROS generation
Authors: Shin Jinwoo , Kang Dong Won , Lim Jong Hyeon , An Jong Min , Kim Youngseo , Kim Ji Hyeon , Ji Myung Sun , Park Sungnam , Kim Dokyoung , Lee Jin Yong , Kim Jong Seung , Hong Chang Seop 
Published: March 2023

AbstractEngineering excitation wavelength of photosensitizers (PSs) for enhanced reactive oxygen species (ROS) generation has inspired new windows for opportunities, enabling investigation of previously impracticable biomedical and photocatalytic applications. However, controlling the wavelength corresponding to operating conditions remains challenging while maintaining high ROS generation. To address this challenge, we implement a wavelength-engineerable imidazolium-based porous organic photocatalytic ROS generation system (KUP system) via a cost-effective one-pot reaction. Remarkably, the optimal wavelength for maximum performance can be tuned by modifying the linker, generating ROS despite the absence of metal ions and covalently attached heavy atoms. We demonstrate that protonated polymerization exclusively enables photosensitization and closely interacts with oxygen related to the efficiency of photosensitizing. Furthermore, superior tumor eradication and biocompatibility of the KUP system were confirmed through bioassays. Overall, the results document an unprecedented polymerization method capable of engineering wavelength, providing a potential basis for designing nanoscale photosensitizers in various ROS-utilizing applications.
Telomere length associates with chronological age and mortality across racially diverse pulmonary fibrosis cohorts
Authors: Adegunsoye Ayodeji , Newton Chad A. , Oldham Justin M. , Ley Brett , Lee Cathryn T. , Linderholm Angela L. , Chung Jonathan H. , Garcia Nicole , Zhang Da , Vij Rekha , Guzy Robert , Jablonski Renea , Bag Remzi , Voogt Rebecca S. , Ma Shwu-Fan , Sperling Anne I. , Raghu Ganesh , Martinez Fernando J. , Strek Mary E. , Wolters Paul J. , Garcia Christine Kim , Pierce Brandon L. , Noth Imre 
Published: March 2023

AbstractPulmonary fibrosis (PF) is characterized by profound scarring and poor survival. We investigated the association of leukocyte telomere length (LTL) with chronological age and mortality across racially diverse PF cohorts. LTL measurements among participants with PF stratified by race/ethnicity were assessed in relation to age and all-cause mortality, and compared to controls. Generalized linear models were used to evaluate the age-LTL relationship, Cox proportional hazards models were used for hazard ratio estimation, and the Cochran–Armitage test was used to assess quartiles of LTL. Standardized LTL shortened with increasing chronological age; this association in controls was strengthened in PF (R = −0.28; P < 0.0001). In PF, age- and sex-adjusted LTL below the median consistently predicted worse mortality across all racial groups (White, HR = 2.21, 95% CI = 1.79–2.72; Black, HR = 2.22, 95% CI = 1.05–4.66; Hispanic, HR = 3.40, 95% CI = 1.88–6.14; and Asian, HR = 2.11, 95% CI = 0.55–8.23). LTL associates uniformly with chronological age and is a biomarker predictive of mortality in PF across racial groups.
Insights into membrane association of the SMP domain of extended synaptotagmin
Authors: Wang Yunyun , Li Zhenni , Wang Xinyu , Zhao Ziyuan , Jiao Li , Liu Ruming , Wang Keying , Ma Rui , Yang Yang , Chen Guo , Wang Yong , Bian Xin 
Published: March 2023

AbstractThe Synaptotagmin-like Mitochondrial-lipid-binding Protein (SMP) domain is a newly identified lipid transfer module present in proteins that regulate lipid homeostasis at membrane contact sites (MCSs). However, how the SMP domain associates with the membrane to extract and unload lipids is unclear. Here, we performed in vitro DNA brick-assisted lipid transfer assays and in silico molecular dynamics simulations to investigate the molecular basis of the membrane association by the SMP domain of extended synaptotagmin (E-Syt), which tethers the tubular endoplasmic reticulum (ER) to the plasma membrane (PM). We demonstrate that the SMP domain uses its tip region to recognize the extremely curved subdomain of tubular ER and the acidic-lipid-enriched PM for highly efficient lipid transfer. Supporting these findings, disruption of these mechanisms results in a defect in autophagosome biogenesis contributed by E-Syt. Our results suggest a model that provides a coherent picture of the action of the SMP domain at MCSs.
Clinically important alterations in pharmacogene expression in histologically severe nonalcoholic fatty liver disease
Authors: Powell Nicholas R. , Liang Tiebing , Ipe Joseph , Cao Sha , Skaar Todd C. , Desta Zeruesenay , Qian Hui-Rong , Ebert Philip J. , Chen Yu , Thomas Melissa K. , Chalasani Naga 
Published: March 2023

AbstractPolypharmacy is common in patients with nonalcoholic fatty liver disease (NAFLD) and previous reports suggest that NAFLD is associated with altered drug disposition. This study aims to determine if patients with NAFLD are at risk for altered drug response by characterizing changes in hepatic mRNA expression of genes mediating drug disposition (pharmacogenes) across the histological NAFLD severity spectrum. We utilize RNA-seq for 93 liver biopsies with histologically staged NAFLD Activity Score (NAS), fibrosis stage, and steatohepatitis (NASH). We identify 37 significant pharmacogene-NAFLD severity associations including CYP2C19 downregulation. We chose to validate CYP2C19 due to its actionability in drug prescribing. Meta-analysis of 16 independent studies demonstrate that CYP2C19 is significantly downregulated to 46% in NASH, to 58% in high NAS, and to 43% in severe fibrosis. Our data demonstrate the downregulation of CYP2C19 in NAFLD which supports developing personalized medicine approaches for drugs sensitive to metabolism by the CYP2C19 enzyme.
Blocking Dectin-1 prevents colorectal tumorigenesis by suppressing prostaglandin E2 production in myeloid-derived suppressor cells and enhancing IL-22 binding protein expression
Authors: Tang Ce , Sun Haiyang , Kadoki Motohiko , Han Wei , Ye Xiaoqi , Makusheva Yulia , Deng Jianping , Feng Bingbing , Qiu Ding , Tan Ying , Wang Xinying , Guo Zehao , Huang Chanyan , Peng Sui , Chen Minhu , Adachi Yoshiyuki , Ohno Naohito , Trombetta Sergio , Iwakura Yoichiro 
Published: March 2023

AbstractDectin-1 (gene Clec7a), a receptor for β-glucans, plays important roles in the host defense against fungi and immune homeostasis of the intestine. Although this molecule is also suggested to be involved in the regulation of tumorigenesis, the role in intestinal tumor development remains to be elucidated. In this study, we find that azoxymethane-dextran-sodium-sulfate-induced and ApcMin-induced intestinal tumorigenesis are suppressed in Clec7a−/− mice independently from commensal microbiota. Dectin-1 is preferentially expressed on myeloid-derived suppressor cells (MDSCs). In the Clec7a−/− mouse colon, the proportion of MDSCs and MDSC-derived prostaglandin E2 (PGE2) levels are reduced, while the expression of IL-22 binding protein (IL-22BP; gene Il22ra2) is upregulated. Dectin-1 signaling induces PGE2-synthesizing enzymes and PGE2 suppresses Il22ra2 expression in vitro and in vivo. Administration of short chain β-glucan laminarin, an antagonist of Dectin-1, suppresses the development of mouse colorectal tumors. Furthermore, in patients with colorectal cancer (CRC), the expression of CLEC7A is also observed in MDSCs and correlated with the death rate and tumor severity. Dectin-1 signaling upregulates PGE2-synthesizing enzyme expression and PGE2 suppresses IL22RA2 expression in human CRC-infiltrating cells. These observations indicate a role of the Dectin-1-PGE2-IL-22BP axis in regulating intestinal tumorigenesis, suggesting Dectin-1 as a potential target for CRC therapy.
Brain-wide and cell-specific transcriptomic insights into MRI-derived cortical morphology in macaque monkeys
Authors: Bo Tingting , Li Jie , Hu Ganlu , Zhang Ge , Wang Wei , Lv Qian , Zhao Shaoling , Ma Junjie , Qin Meng , Yao Xiaohui , Wang Meiyun , Wang Guang-Zhong , Wang Zheng 
Published: March 2023

AbstractIntegrative analyses of transcriptomic and neuroimaging data have generated a wealth of information about biological pathways underlying regional variability in imaging-derived brain phenotypes in humans, but rarely in nonhuman primates due to the lack of a comprehensive anatomically-defined atlas of brain transcriptomics. Here we generate complementary bulk RNA-sequencing dataset of 819 samples from 110 brain regions and single-nucleus RNA-sequencing dataset, and neuroimaging data from 162 cynomolgus macaques, to examine the link between brain-wide gene expression and regional variation in morphometry. We not only observe global/regional expression profiles of macaque brain comparable to human but unravel a dorsolateral-ventromedial gradient of gene assemblies within the primate frontal lobe. Furthermore, we identify a set of 971 protein-coding and 34 non-coding genes consistently associated with cortical thickness, specially enriched for neurons and oligodendrocytes. These data provide a unique resource to investigate nonhuman primate models of human diseases and probe cross-species evolutionary mechanisms.
Fabrication of phosphor in glass using waste glass for automotive lighting application
Authors: Choi Seung Hee , Kwon Seok Bin , Yoo Jung Hyeon , Na MinYoung , Kim Bo Young , Yoon HoShin , Park Seoung Hyok , Kinski Isabel , Kang Bong Kyun , Yoon Dae Ho , Song Young Hyun 
Published: March 2023

AbstractWith advancement of technology, requirements for light-emitting devices are increasing. Various types of packaging technologies have been suggested to improve the performance of light-emitting diode (LED). Among them, phosphor in glass (PiG) is attracting attention due to its manufactural facility and easily tunable characteristics. As PiG draws increasing attention, research on glass materials is also being actively conducted. However, studies about glass in the field of phosphor are mainly conducted on fabrication. Only a few studies about recycling have been reported. Thus, the objective of this study was to recycle waste glass discarded in other fields due to breakage and failure and use it to fabricate phosphor in glass. Cylindrical waste glass was pulverized into powder with an average size of 12 μm, mixed with a phosphor and sintered to be reborn as a phosphor in glass to broaden the recycling route for waste glass.