bluuebunny/crossref_metadata_2025 huggingface dataset:
Velocity‐Porosity Relations in Carbonate and Siliciclastic Subduction Zone Input Materials
Authors: Jeppson Tamara N. , Kitajima Hiroko
Published: December 2021

The mechanical, physical, and frictional properties of incoming materials play an important role in subduction zone structure and slip behavior because these properties influence the strength of the accretionary wedge and megathrust plate boundary faults. Incoming sediment sections often show an increase in compressional wave speed (Vp) and a decrease in porosity with depth due to consolidation. These relations allow seismic‐velocity models to be used to elucidate properties and conditions at depth. However, variations in these properties are controlled by lithology and composition as well as cementation and diagenesis. We present an analysis of shipboard measurements of Vp and porosity on incoming sediment cores from International Ocean Discovery Program (IODP) expeditions at the Hikurangi Margin, Nankai Trough, Aleutian Trench, Middle America Trench, and Sunda Trench. Porosity for these samples ranges from 5% to 85% and Vp ranges from 1.5 to 6 km/s. Vp‐porosity relations developed by Erikson & Jarrad (1998), https://doi.org/10.1029/98JB02128 and Hoffman & Tobin (2004) https://10.2973/odp.proc.sr.190196.355.2004, with a critical porosity of ∼30%, can represent carbonate‐poor (<50 wt% CaCO3), mainly hemipelagic, incoming sediment regardless of the margin. But these relations tend to underestimate porosity in incoming sediments with carbonate content greater than 50 wt%, which appear to have a critical porosity of between 45% and 50%. This discrepancy will lead to inaccuracy in estimates of fluid budget and overpressure in subduction zones. The velocity‐porosity relation in carbonate sediments is non‐unique due to the complexity that results from the greater susceptibility of carbonate rocks to diagenetic processes.
Regional Heat Flow Analysis Reveals Frictionally Weak Dead Sea Fault
Authors: Oryan Bar , Savage Heather
Published: December 2021

The strength of faults was vigorously debated for years, but lately a growing number of studies suggest that faults are weaker than originally suggested. Nonetheless, only a handful of natural faults have been studied in detail, and only one, the San Andreas, is a strike‐slip fault. Here, we reanalyze 268 surface heat flow measurements taken in the proximity of the southern Dead Sea Transform fault to evaluate its friction. To account for large terrain relief, and the presence of salt diapirs, we apply 3‐D terrain and salt diapir corrections. Based on these corrected heat flow values we estimate that the long‐term frictional resistance of the Dead Sea fault is 0.28 ± 0.17. This low value is similar to friction estimates from the San Andreas fault and several subduction zones.
Weakly Constrained LETKF for Estimation of Hydrometeor Variables in Convective‐Scale Data Assimilation
Authors: Janjić Tijana , Zeng Yuefei
Published: December 2021

The ensemble Kalman filter algorithm can produce negative values for non‐negative variables. To mitigate this sign problem and to simultaneously maintain the mass conservation, a new concept of combining weak constraints on mass conservation and non‐negativity has been introduced in this work, with a focus on hydrometeor variables in convective‐scale data assimilation. We modify the local ensemble transform Kalman filter with weak constraints on mass conservation for each hydrometeor variable and adopt the assimilation of clear‐air reflectivity data as a weak constraint on non‐negativity. We examine the concept by a series of sensitivity experiments using an idealized setup. Results show that both weak constraints successfully improve the mass conservation property in analyses and both reduce the biased increase in integrated mass‐flux divergence and vorticity. Furthermore, the least biased increase is obtained by combining both constraints, and the best forecasts are also achieved by the combination.
Prolonged Marine Heatwaves in the Arctic: 1982−2020
Authors: Huang Boyin , Wang Zhaomin , Yin Xungang , Arguez Anthony , Graham Garrett , Liu Chunying , Smith Tom , Zhang Huai‐Min
Published: December 2021

Studies have indicated that marine heatwaves (MHWs) have had severe impacts on the marine ecosystem in the Pacific, Atlantic, and Indian Oceans, but there have been few studies focused on MHWs in the Arctic. On the other hand, amplified rapid warming in the Arctic region makes it a hotspot strategically and economically worldwide. In this study, we documented that the average intensity of MHWs in the Arctic was comparable with that in the other regions of the global oceans. The annual intensity, frequency, duration, and areal coverage of MHWs have increased significantly in recent decades. The increase of the annual duration is mainly owing to the postponed end time, thus the prolonged periods, of the MHW seasons. Our analysis indicates that the increasing trends of the annual intensity, frequency, duration, and areal coverage in the Arctic are closely associated with the increasing surface air temperature and decreasing sea‐ice concentration under the global warming environment. These features are robust across three different sea surface temperature (SST) products and using different MHW criteria.
How Does the High‐Latitude Thermal Forcing in One Hemisphere Affect the Other Hemisphere?
Authors: Shin Yechul , Kang Sarah M.
Published: December 2021

Significant progress has been made in our understanding of extratropical impacts on the tropical climate via energetics framework. It is of question whether the impact of extratropical thermal forcing in one hemisphere would extend far into high‐latitudes of the other hemisphere. We examine the possibility of the pole‐to‐pole linkage via atmospheric teleconnections by imposing a cyclic surface thermal forcing in the northern extratropics of an aquaplanet slab ocean model. We reveal a synchronous temperature response between the two poles mediated by zonal‐mean atmospheric dynamics. A warming in one polar region leads to a strengthened Hadley circulation of the unforced hemisphere, fluxing more momentum toward the subtropics, thereby pulling the eddy‐driven jet equatorward. A consequent anomalous descent over the polar region causes warming. The polar surface warming in the unforced hemisphere reaches 30% of that in the forced hemisphere, inferring a significance of the pole‐to‐pole connection.
Detailed 3D Seismic Velocity Structure of the Prague, Oklahoma Fault Zone and the Implications for Induced Seismicity
Authors: He Lipeng , Wu Qimin , Chen Xiaowei , Sun Xinlei , Guo Zhen , Chen Yongshun John
Published: December 2021

The 2011 Mw 5.7 Prague earthquake is the second largest induced earthquake in Oklahoma, and occurred after decades of wastewater disposal. The local geological structure that led to the triggering of this large earthquake is not well understood. In this study, tomographic inversion of seismic data recorded by a dense local seismic network resulted in a high‐resolution 3D velocity model with three major layers. The model clearly illuminates the geometry and characteristics of the Meeker‐Prague Fault that hosted the 2011 Prague sequence. A conceptual model is proposed to link the tomographic structure to the triggering process of the sequence. The low‐permeability second layer at ∼1.5–3.5 km may be the key that delays the occurrence of the first sizeable earthquake after decades of wastewater injection. However, a low‐shear‐velocity zone within this layer at the intersection of two major faults could have provided a fluid pathway to facilitate downward fluid propagation.
The Impact of Typhoon “Mangkhut” on Surface Water Nutrient and Chlorophyll Inventories of the South China Sea in September 2018
Authors: Kuss Joachim , Frazão Helena C. , Schulz‐Bull Detlef E. , Zhong Yisen , Gao Yonghui , Waniek Joanna J.
Published: December 2021

The influence of the exceptionally strong typhoon Mangkhut on the availability of nutrients and changes in primary production were studied in the northern South China Sea in September 2018. A tight station grid was sampled to analyze major nutrients, chlorophyll_a, particulate and dissolved organic carbon and nitrogen. Based on interpolated profiles, nutrients and organic matter budgets were determined for the upper 100 m of the water column prior to and after Mangkhut's passage. An upper layer of 100 m was found to reflect the important changes by the typhoon. Considerable differences between the on‐shelf, shelf edge and the deep‐sea stations were determined. Nitrate and phosphate increased by about 80% and 36% on the shelf, respectively, and both by almost 40% at the shelf edge. The open deep‐sea part of the study area reflects some deviating results that may be caused by just displacement of water or by mixing water of different origin. However, right on Mangkhut's track on the shelf even contact between surface waters and bottom waters was enabled, increasing phosphate and silicate, but declining nitrate. The inventory of organic carbon of the upper 100 m of the study area (138,000 km2) of 92 Gmol had increased within a few days after the typhoon's passage by 5 Gmol on the shelf and about 2 Gmol in the shelf edge area. Chlorophyll_a doubled during our stay and might have reached a factor of 3 increase in the subsequent time by nitrate supply and excess phosphate.
Applicability of the Long Chain Diol Index (LDI) as a Sea Surface Temperature Proxy in the Arabian Sea
Authors: Erdem Z. , Lattaud J. , van Erk M. R. , Mezger E. , Reichart G.‐J. , Lückge A. , Damsté J. S. Sinninghe , Schouten S.
Published: December 2021

The long‐chain diol index (LDI) is a relatively new proxy for sea surface temperature (SST) which has been rarely applied in upwelling regions. Here, we evaluated its application by comparison with other SST records obtained by commonly used proxies, that is, the Mg/Ca ratio of the planktonic foraminifera species Globigerinoides ruber and the alkenone paleothermometer UK´37. We focused on the last glacial–interglacial transition of four different sedimentary archives from the western and northern Arabian Sea, which are currently under the influence of monsoon‐induced upwelling and the associated development of an oxygen minimum zone. The and Mg/CaG.ruber SST records revealed an increase of 0.6–3.4°C from the Last Glacial Maximum to the late Holocene with somewhat higher amplitude in the northern part of the Arabian Sea than compared to the western part. In contrast, the LDI SSTs did not reveal major changes during the last glacial–interglacial transition which was followed by a decreasing trend during the Holocene. The LGM versus the Holocene LDI SSTs ranged between −0.2 and −2.7°C. Particularly at one record, offshore Oman, the SST decrease during the Holocene was high in amplitude, suggesting a potential cold bias, possibly related to changes in upwelling intensity. This indicates that care has to be taken when applying the LDI for annual mean SST reconstruction in upwelling regions.
Retreat and Regrowth of the Greenland Ice Sheet During the Last Interglacial as Simulated by the CESM2‐CISM2 Coupled Climate–Ice Sheet Model
Authors: Sommers Aleah N. , Otto‐Bliesner Bette L. , Lipscomb William H. , Lofverstrom Marcus , Shafer Sarah L. , Bartlein Patrick J. , Brady Esther C. , Kluzek Erik , Leguy Gunter , Thayer‐Calder Katherine , Tomas Robert A.
Published: December 2021

During the Last Interglacial, approximately 129 to 116 ka (thousand years ago), the Arctic summer climate was warmer than the present, and the Greenland Ice Sheet retreated to a smaller extent than its current state. Previous model‐derived and geological reconstruction estimates of the sea‐level contribution of the Greenland Ice Sheet during the Last Interglacial vary widely. Here, we conduct a transient climate simulation from 127 to 119 ka using the Community Earth System Model (CESM2), which includes a dynamic ice sheet component (the Community Ice Sheet Model, CISM2) that is interactively coupled to the atmosphere, land, ocean, and sea ice components. Vegetation distribution is updated every 500 years based on biomes simulated using a monthly climatology to force the BIOME4 equilibrium vegetation model. Results show a substantial retreat of the Greenland Ice Sheet, reaching a minimum extent at 121.9 ka, equivalent to a 3.0 m rise in sea level relative to the present day, followed by gradual regrowth. In contrast, a companion simulation employing static vegetation based on pre‐industrial conditions shows a much smaller ice‐sheet retreat, highlighting the importance of the changes in high‐latitude vegetation distribution for amplifying the ice‐sheet response.
TTK inhibition increases cisplatin sensitivity in high-grade serous ovarian carcinoma through the mTOR/autophagy pathway
Authors: Qi Gonghua , Ma Hanlin , Li Yingwei , Peng Jiali , Chen Jingying , Kong Beihua
Published: December 2021

High-grade serous ovarian cancer (HGSOC) is the most lethal gynecological malignancy. However, the molecular mechanisms underlying HGSOC development, progression, chemotherapy insensitivity and resistance remain unclear. Two independent GEO datasets, including the gene expression profile of primary ovarian carcinoma and normal controls, were analyzed to identify genes related to HGSOC development and progression. A KEGG pathway analysis of the differentially expressed genes (DEGs) revealed that the cell cycle pathway was the most enriched pathway, among which TTK protein kinase (TTK) was the only gene with a clinical-grade inhibitor that has been investigated in a clinical trial but had not been studied in HGSOC. TTK was also upregulated in cisplatin-resistant ovarian cancer cells from two other datasets. TTK is a regulator of spindle assembly checkpoint signaling, playing an important role in cell cycle control and tumorigenesis in various cancers. However, the function and regulatory mechanism of TTK in HGSOC remain to be determined. In this study, we observed TTK upregulation in patients with HGSOC. High TTK expression was related to a poor prognosis. Genetic and pharmacological inhibition of TTK impeded the proliferation of ovarian cancer cells by disturbing cell cycle progression and increasing apoptosis. TTK silencing increased cisplatin sensitivity by activating the mammalian target of rapamycin (mTOR) complex to further suppress cisplatin-induced autophagy in vitro. In addition, the enhanced sensitivity was partially diminished by rapamycin-mediated inhibition of mTOR in TTK knockdown cells. Furthermore, TTK knockdown increased the toxicity of cisplatin in vivo by decreasing autophagy. These findings suggest that the administration of TTK inhibitors in combination with cisplatin may lead to improved response rates to cisplatin in patients with HGSOC presenting high TTK expression. In summary, our study may provide a theoretical foundation for using the combination therapy of cisplatin and TTK inhibitors as a treatment for HGSOC in the future.
Corticotropin releasing hormone promotes inflammatory bowel disease via inducing intestinal macrophage autophagy
Authors: Zhao Sheng-Bing , Wu Jia-Yi , He Zi-Xuan , Song Yi-Hang , Chang Xin , Xia Tian , Fang Xue , Li Zhao-Shen , Xu Can , Wang Shu-Ling , Bai Yu
Published: December 2021

Psychosocial stress is a vital factor contributing to the pathogenesis and progression of inflammatory bowel disease (IBD). The contribution of intestinal macrophage autophagy to the onset and development of IBD has been widely studied. Herein, we investigated the underlying mechanism of psychosocial stress in an IBD mouse model pertaining to macrophage autophagy. Corticotropin releasing hormone (CRH) was peripherally administrated to induce psychosocial stress. For in vivo studies, dextran sulfate sodium (DSS) was used for the creation of our IBD mouse model. For in vitro studies, lipopolysaccharide (LPS) was applied on murine bone marrow-derived macrophages (BMDMs) as a cellular IBD-related challenge. Chloroquine was applied to inhibit autophagy. We found that CRH aggravated the severity of DSS-induced IBD, increasing overall and local inflammatory reactions and infiltration. The levels of autophagy in intestinal macrophages and murine BMDMs were increased under these IBD-related inflammatory challenges and CRH further enhanced these effects. Subsequent administration of chloroquine markedly attenuated the detrimental effects of CRH on IBD severity and inflammatory reactions via inhibition of autophagy. These findings illustrate the effects of peripheral administration of CRH on DSS-induced IBD via the enhancement of intestinal macrophage autophagy, thus providing a novel understanding as well as therapeutic target for the treatment of IBD.
LncRNA4930473A02Rik promotes cardiac hypertrophy by regulating TCF7 via sponging miR-135a in mice
Authors: Ren Jing , Qi Hanping , Song Chao , Ba Lina , Liu Renling , Feng Xiang , Wang Lixin , Zhang Meitian , Xie Yawen , Sun Hongli
Published: December 2021

Cardiac hypertrophy is a common pathological change accompanied by various cardiovascular diseases; however, its underlying mechanisms remain elusive. Mounting evidence indicates that long non-coding RNAs (lncRNAs) are novel transcripts involved in regulating multiple biological processes. However, little is known about their role in regulating cardiac hypertrophy. This study revealed a novel lncRNA4930473A02Rik (abbreviated as lncRNAA02Rik), which showed considerably increased expression in hypertrophic mouse hearts in vivo and angiotensin-II (Ang-II)-induced hypertrophic cardiomyocytes in vitro. Notably, lncRNAA02Rik knockdown partly ameliorated Ang-II induced hypertrophic cardiomyocytes in vitro and hypertrophic mouse heart function in vivo, whereas lncRNAA02Rik overexpression promoted cardiac hypertrophy in vitro. Furthermore, lncRNAA02Rik acted as a competing endogenous RNA by sponging miR-135a, while forced expression of lncRNAA02Rik could repress its activity and expression. Furthermore, forcing miR-135a overexpression exerted a significant protective effect against cardiac hypertrophy by inhibiting the activity of its downstream target TCF7, a critical member of Wnt signaling, and the protective effect could be reversed by AMO-135a. Luciferase assay showed direct interactions among lncRNAA02Rik, miR-135a, and TCF7. Altogether, our study demonstrated that lncRNAA02Rik upregulation could promote cardiac hypertrophy development via modulating miR-135a expression levels and TCF7 activity. Therefore, lncRNAA02Rik inhibition might be considered as a novel potential therapeutic strategy for cardiac hypertrophy.
Discovery of indole-modified aptamers for highly specific recognition of protein glycoforms
Authors: Yoshikawa Alex M. , Rangel Alexandra , Feagin Trevor , Chun Elizabeth M. , Wan Leighton , Li Anping , Moeckl Leonhard , Wu Diana , Eisenstein Michael , Pitteri Sharon , Soh H. Tom
Published: December 2021

Glycosylation is one of the most abundant forms of post-translational modification, and can have a profound impact on a wide range of biological processes and diseases. Unfortunately, efforts to characterize the biological function of such modifications have been greatly hampered by the lack of affinity reagents that can differentiate protein glycoforms with robust affinity and specificity. In this work, we use a fluorescence-activated cell sorting (FACS)-based approach to generate and screen aptamers with indole-modified bases, which are capable of recognizing and differentiating between specific protein glycoforms. Using this approach, we were able to select base-modified aptamers that exhibit strong selectivity for specific glycoforms of two different proteins. These aptamers can discriminate between molecules that differ only in their glycan modifications, and can also be used to label glycoproteins on the surface of cultured cells. We believe our strategy should offer a generally-applicable approach for developing useful reagents for glycobiology research.
Delayed induction of type I and III interferons mediates nasal epithelial cell permissiveness to SARS-CoV-2
Authors: Hatton Catherine F. , Botting Rachel A. , Dueñas Maria Emilia , Haq Iram J. , Verdon Bernard , Thompson Benjamin J. , Spegarova Jarmila Stremenova , Gothe Florian , Stephenson Emily , Gardner Aaron I. , Murphy Sandra , Scott Jonathan , Garnett James P. , Carrie Sean , Powell Jason , Khan C. M. Anjam , Huang Lei , Hussain Rafiqul , Coxhead Jonathan , Davey Tracey , Simpson A. John , Haniffa Muzlifah , Hambleton Sophie , Brodlie Malcolm , Ward Chris , Trost Matthias , Reynolds Gary , Duncan Christopher J. A.
Published: December 2021

The nasal epithelium is a plausible entry point for SARS-CoV-2, a site of pathogenesis and transmission, and may initiate the host response to SARS-CoV-2. Antiviral interferon (IFN) responses are critical to outcome of SARS-CoV-2. Yet little is known about the interaction between SARS-CoV-2 and innate immunity in this tissue. Here we apply single-cell RNA sequencing and proteomics to a primary cell model of human nasal epithelium differentiated at air-liquid interface. SARS-CoV-2 demonstrates widespread tropism for nasal epithelial cell types. The host response is dominated by type I and III IFNs and interferon-stimulated gene products. This response is notably delayed in onset relative to viral gene expression and compared to other respiratory viruses. Nevertheless, once established, the paracrine IFN response begins to impact on SARS-CoV-2 replication. When provided prior to infection, recombinant IFNβ or IFNλ1 induces an efficient antiviral state that potently restricts SARS-CoV-2 viral replication, preserving epithelial barrier integrity. These data imply that the IFN-I/III response to SARS-CoV-2 initiates in the nasal airway and suggest nasal delivery of recombinant IFNs to be a potential chemoprophylactic strategy.
A d-2-hydroxyglutarate biosensor based on specific transcriptional regulator DhdR
Authors: Xiao Dan , Zhang Wen , Guo Xiaoting , Liu Yidong , Hu Chunxia , Guo Shiting , Kang Zhaoqi , Xu Xianzhi , Ma Cuiqing , Gao Chao , Xu Ping
Published: December 2021

d-2-Hydroxyglutarate (d-2-HG) is a metabolite involved in many physiological metabolic processes. When d-2-HG is aberrantly accumulated due to mutations in isocitrate dehydrogenase or d-2-HG dehydrogenase, it functions in a pro-oncogenic manner and is thus considered a therapeutic target and biomarker in many cancers. In this study, DhdR from Achromobacter denitrificans NBRC 15125 is identified as an allosteric transcriptional factor that negatively regulates d-2-HG dehydrogenase expression and responds to the presence of d-2-HG. Based on the allosteric effect of DhdR, a d-2-HG biosensor is developed by combining DhdR with amplified luminescent proximity homogeneous assay (AlphaScreen) technology. The biosensor is able to detect d-2-HG in serum, urine, and cell culture medium with high specificity and sensitivity. Additionally, this biosensor is used to identify the role of d-2-HG metabolism in lipopolysaccharide biosynthesis of Pseudomonas aeruginosa, demonstrating its broad usages.
Nanosecond-resolution photothermal dynamic imaging via MHZ digitization and match filtering
Authors: Yin Jiaze , Lan Lu , Zhang Yi , Ni Hongli , Tan Yuying , Zhang Meng , Bai Yeran , Cheng Ji-Xin
Published: December 2021

Photothermal microscopy has enabled highly sensitive label-free imaging of absorbers, from metallic nanoparticles to chemical bonds. Photothermal signals are conventionally detected via modulation of excitation beam and demodulation of probe beam using lock-in amplifier. While convenient, the wealth of thermal dynamics is not revealed. Here, we present a lock-in free, mid-infrared photothermal dynamic imaging (PDI) system by MHz digitization and match filtering at harmonics of modulation frequency. Thermal-dynamic information is acquired at nanosecond resolution within single pulse excitation. Our method not only increases the imaging speed by two orders of magnitude but also obtains four-fold enhancement of signal-to-noise ratio over lock-in counterpart, enabling high-throughput metabolism analysis at single-cell level. Moreover, by harnessing the thermal decay difference between water and biomolecules, water background is effectively separated in mid-infrared PDI of living cells. This ability to nondestructively probe chemically specific photothermal dynamics offers a valuable tool to characterize biological and material specimens.
Plasmin activity promotes amyloid deposition in a transgenic model of human transthyretin amyloidosis
Authors: Slamova Ivana , Adib Rozita , Ellmerich Stephan , Golos Michal R. , Gilbertson Janet A. , Botcher Nicola , Canetti Diana , Taylor Graham W. , Rendell Nigel , Tennent Glenys A. , Verona Guglielmo , Porcari Riccardo , Mangione P. Patrizia , Gillmore Julian D. , Pepys Mark B. , Bellotti Vittorio , Hawkins Philip N. , Al-Shawi Raya , Simons J. Paul
Published: December 2021

Cardiac ATTR amyloidosis, a serious but much under-diagnosed form of cardiomyopathy, is caused by deposition of amyloid fibrils derived from the plasma protein transthyretin (TTR), but its pathogenesis is poorly understood and informative in vivo models have proved elusive. Here we report the generation of a mouse model of cardiac ATTR amyloidosis with transgenic expression of human TTRS52P. The model is characterised by substantial ATTR amyloid deposits in the heart and tongue. The amyloid fibrils contain both full-length human TTR protomers and the residue 49-127 cleavage fragment which are present in ATTR amyloidosis patients. Urokinase-type plasminogen activator (uPA) and plasmin are abundant within the cardiac and lingual amyloid deposits, which contain marked serine protease activity; knockout of α2-antiplasmin, the physiological inhibitor of plasmin, enhances amyloid formation. Together, these findings indicate that cardiac ATTR amyloid deposition involves local uPA-mediated generation of plasmin and cleavage of TTR, consistent with the previously described mechano-enzymatic hypothesis for cardiac ATTR amyloid formation. This experimental model of ATTR cardiomyopathy has potential to allow further investigations of the factors that influence human ATTR amyloid deposition and the development of new treatments.
An injury-induced serotonergic neuron subpopulation contributes to axon regrowth and function restoration after spinal cord injury in zebrafish
Authors: Huang Chun-Xiao , Zhao Yacong , Mao Jie , Wang Zhen , Xu Lulu , Cheng Jianwei , Guan Na N. , Song Jianren
Published: December 2021

Spinal cord injury (SCI) interrupts long-projecting descending spinal neurons and disrupts the spinal central pattern generator (CPG) that controls locomotion. The intrinsic mechanisms underlying re-wiring of spinal neural circuits and recovery of locomotion after SCI are unclear. Zebrafish shows axonal regeneration and functional recovery after SCI making it a robust model to study mechanisms of regeneration. Here, we use a two-cut SCI model to investigate whether recovery of locomotion can occur independently of supraspinal connections. Using this injury model, we show that injury induces the localization of a specialized group of intraspinal serotonergic neurons (ISNs), with distinctive molecular and cellular properties, at the injury site. This subpopulation of ISNs have hyperactive terminal varicosities constantly releasing serotonin activating 5-HT1B receptors, resulting in axonal regrowth of spinal interneurons. Axon regrowth of excitatory interneurons is more pronounced compared to inhibitory interneurons. Knock-out of htr1b prevents axon regrowth of spinal excitatory interneurons, negatively affecting coordination of rostral-caudal body movements and restoration of locomotor function. On the other hand, treatment with 5-HT1B receptor agonizts promotes functional recovery following SCI. In summary, our data show an intraspinal mechanism where a subpopulation of ISNs stimulates axonal regrowth resulting in improved recovery of locomotor functions following SCI in zebrafish.
Oxidative stress-induced FABP5 S-glutathionylation protects against acute lung injury by suppressing inflammation in macrophages
Authors: Guo Yuxian , Liu Yaru , Zhao Shihao , Xu Wangting , Li Yiqing , Zhao Pengwei , Wang Di , Cheng Hongqiang , Ke Yuehai , Zhang Xue
Published: December 2021

Oxidative stress contributes to the pathogenesis of acute lung injury. Protein S-glutathionylation plays an important role in cellular antioxidant defense. Here we report that the expression of deglutathionylation enzyme Grx1 is decreased in the lungs of acute lung injury mice. The acute lung injury induced by hyperoxia or LPS is significantly relieved in Grx1 KO and Grx1fl/flLysMcremice, confirming the protective role of Grx1-regulated S-glutathionylation in macrophages. Using a quantitative redox proteomics approach, we show that FABP5 is susceptible to S-glutathionylation under oxidative conditions. S-glutathionylation of Cys127 in FABP5 promotes its fatty acid binding ability and nuclear translocation. Further results indicate S-glutathionylation promotes the interaction of FABP5 and PPARβ/δ, activates PPARβ/δ target genes and suppresses the LPS-induced inflammation in macrophages. Our study reveals a molecular mechanism through which FABP5 S-glutathionylation regulates macrophage inflammation in the pathogenesis of acute lung injury.
Electric-field control of field-free spin-orbit torque switching via laterally modulated Rashba effect in Pt/Co/AlOx structures
Authors: Kang Min-Gu , Choi Jong-Guk , Jeong Jimin , Park Jae Yeol , Park Hyeon-Jong , Kim Taehwan , Lee Taekhyeon , Kim Kab-Jin , Kim Kyoung-Whan , Oh Jung Hyun , Viet Duc Duong , Jeong Jong-Ryul , Yuk Jong Min , Park Jongsun , Lee Kyung-Jin , Park Byong-Guk
Published: December 2021

Spin-orbit coupling effect in structures with broken inversion symmetry, known as the Rashba effect, facilitates spin-orbit torques (SOTs) in heavy metal/ferromagnet/oxide structures, along with the spin Hall effect. Electric-field control of the Rashba effect is established for semiconductor interfaces, but it is challenging in structures involving metals owing to the screening effect. Here, we report that the Rashba effect in Pt/Co/AlOx structures is laterally modulated by electric voltages, generating out-of-plane SOTs. This enables field-free switching of the perpendicular magnetization and electrical control of the switching polarity. Changing the gate oxide reverses the sign of out-of-plane SOT while maintaining the same sign of voltage-controlled magnetic anisotropy, which confirms the Rashba effect at the Co/oxide interface is a key ingredient of the electric-field modulation. The electrical control of SOT switching polarity in a reversible and non-volatile manner can be utilized for programmable logic operations in spintronic logic-in-memory devices.
Observation of the ponderomotive effect in non-valence bound states of polyatomic molecular anions
Authors: Kang Do Hyung , Kim Jinwoo , Noh Heung-Ryoul , Kim Sang Kyu
Published: December 2021

The ponderomotive force on molecular systems has rarely been observed hitherto, despite potentially being extremely useful for the manipulation of the molecular properties. Here, the ponderomotive effect in the non-valence bound states has been experimentally demonstrated, for the first time to the best of our knowledge, giving great promise for the manipulation of polyatomic molecules by the dynamic Stark effect. Entire quantum levels of the dipole-bound state (DBS) and quadrupole-bound state (QBS) of the phenoxide (or 4-bromophenoxide) and 4-cyanophenoxide anions, respectively, show clear-cut ponderomotive blue-shifts in the presence of the spatiotemporally overlapped non-resonant picosecond control laser pulse. The quasi-free electron in the QBS is found to be more vulnerable to the external oscillating electromagnetic field compared to that in the DBS, suggesting that the non-valence orbital of the former is more diffusive and thus more polarizable compared to that of the latter.
Dynamic restructuring of supported metal nanoparticles and its implications for structure insensitive catalysis
Authors: Vogt Charlotte , Meirer Florian , Monai Matteo , Groeneveld Esther , Ferri Davide , van Santen Rutger A. , Nachtegaal Maarten , Unocic Raymond R. , Frenkel Anatoly I. , Weckhuysen Bert M.
Published: December 2021

Some fundamental concepts of catalysis are not fully explained but are of paramount importance for the development of improved catalysts. An example is the concept of structure insensitive reactions, where surface-normalized activity does not change with catalyst metal particle size. Here we explore this concept and its relation to surface reconstruction on a set of silica-supported Ni metal nanoparticles (mean particle sizes 1–6 nm) by spectroscopically discerning a structure sensitive (CO2hydrogenation) from a structure insensitive (ethene hydrogenation) reaction. Using state-of-the-art techniques,inter aliain-situ STEM, and quick-X-ray absorption spectroscopy with sub-second time resolution, we have observed particle-size-dependent effects like restructuring which increases with increasing particle size, and faster restructuring for larger particle sizes during ethene hydrogenation while for CO2no such restructuring effects were observed. Furthermore, a degree of restructuring is irreversible, and we also show that the rate of carbon diffusion on, and into nanoparticles increases with particle size. We finally show that these particle size-dependent effects induced by ethene hydrogenation, can make a structure sensitive reaction (CO2hydrogenation), structure insensitive. We thus postulate that structure insensitive reactions are actuallyapparentlystructure insensitive, which changes our fundamental understanding of the empirical observation of structure insensitivity.
Aberrant chromatin landscape following loss of the H3.3 chaperone Daxx in haematopoietic precursors leads to Pu.1-mediated neutrophilia and inflammation
Authors: Gerber Julia P. , Russ Jenny , Chandrasekar Vijay , Offermann Nina , Lee Hang-Mao , Spear Sarah , Guzzi Nicola , Maida Simona , Pattabiraman Sundararaghavan , Zhang Ruoyu , Kayvanjoo Amir H. , Datta Preeta , Kasturiarachchi Jagath , Sposito Teresa , Izotova Natalia , Händler Kristian , Adams Peter D. , Marafioti Teresa , Enver Tariq , Wenzel Jörg , Beyer Marc , Mass Elvira , Bellodi Cristian , Schultze Joachim L. , Capasso Melania , Nimmo Rachael , Salomoni Paolo
Published: December 2021

Defective silencing of retrotransposable elements has been linked to inflammageing, cancer and autoimmune diseases. However, the underlying mechanisms are only partially understood. Here we implicate the histone H3.3 chaperone Daxx, a retrotransposable element repressor inactivated in myeloid leukaemia and other neoplasms, in protection from inflammatory disease. Loss of Daxx alters the chromatin landscape, H3.3 distribution and histone marks of haematopoietic progenitors, leading to engagement of a Pu.1-dependent transcriptional programme for myelopoiesis at the expense of B-cell differentiation. This causes neutrophilia and inflammation, predisposing mice to develop an autoinflammatory skin disease. While these molecular and phenotypic perturbations are in part reverted in animals lacking both Pu.1 and Daxx, haematopoietic progenitors in these mice show unique chromatin and transcriptome alterations, suggesting an interaction between these two pathways. Overall, our findings implicate retrotransposable element silencing in haematopoiesis and suggest a cross-talk between the H3.3 loading machinery and the pioneer transcription factor Pu.1.
Search for topological defect dark matter with a global network of optical magnetometers
Authors: Afach Samer , Buchler Ben C. , Budker Dmitry , Dailey Conner , Derevianko Andrei , Dumont Vincent , Figueroa Nataniel L. , Gerhardt Ilja , Grujić Zoran D. , Guo Hong , Hao Chuanpeng , Hamilton Paul S. , Hedges Morgan , Jackson Kimball Derek F. , Kim Dongok , Khamis Sami , Kornack Thomas , Lebedev Victor , Lu Zheng-Tian , Masia-Roig Hector , Monroy Madeline , Padniuk Mikhail , Palm Christopher A. , Park Sun Yool , Paul Karun V. , Penaflor Alexander , Peng Xiang , Pospelov Maxim , Preston Rayshaun , Pustelny Szymon , Scholtes Theo , Segura Perrin C. , Semertzidis Yannis K. , Sheng Dong , Shin Yun Chang , Smiga Joseph A. , Stalnaker Jason E. , Sulai Ibrahim , Tandon Dhruv , Wang Tao , Weis Antoine , Wickenbrock Arne , Wilson Tatum , Wu Teng , Wurm David , Xiao Wei , Yang Yucheng , Yu Dongrui , Zhang Jianwei
Published: December 2021

Ultralight bosons such as axion-like particles are viable candidates for dark matter. They can form stable, macroscopic field configurations in the form of topological defects that could concentrate the dark matter density into many distinct, compact spatial regions that are small compared with the Galaxy but much larger than the Earth. Here we report the results of the search for transient signals from the domain walls of axion-like particles by using the global network of optical magnetometers for exotic (GNOME) physics searches. We search the data, consisting of correlated measurements from optical atomic magnetometers located in laboratories all over the world, for patterns of signals propagating through the network consistent with domain walls. The analysis of these data from a continuous month-long operation of GNOME finds no statistically significant signals, thus placing experimental constraints on such dark matter scenarios.
Signature of long-lived memory CD8+ T cells in acute SARS-CoV-2 infection
Authors: Adamo Sarah , Michler Jan , Zurbuchen Yves , Cervia Carlo , Taeschler Patrick , Raeber Miro E. , Baghai Sain Simona , Nilsson Jakob , Moor Andreas E. , Boyman Onur
Published: December 2021

Immunological memory is a hallmark of adaptive immunity and facilitates an accelerated and enhanced immune response upon re-infection with the same pathogen1,2. Since the outbreak of the ongoing COVID-19 pandemic, a key question has focused on which SARS-CoV-2-specific T cells stimulated during acute infection give rise to long-lived memory T cells3. Here, using spectral flow cytometry combined with cellular indexing of transcriptomes and T cell receptor sequencing, we longitudinally characterized individual SARS-CoV-2-specific CD8+ T cells of patients with COVID-19 from acute infection to 1 year into recovery and found a distinct signature identifying long-lived memory CD8+ T cells. SARS-CoV-2-specific memory CD8+ T cells persisting 1 year after acute infection express CD45RA, IL-7 receptor-α and T cell factor 1, but they maintain low expression of CCR7, thus resembling CD45RA+ effector memory T cells. Tracking individual clones of SARS-CoV-2-specific CD8+ T cells, we reveal that an interferon signature marks clones that give rise to long-lived cells, whereas prolonged proliferation and mechanistic target of rapamycin signalling are associated with clonal disappearance from the blood. Collectively, we describe a transcriptional signature that marks long-lived, circulating human memory CD8+ T cells following an acute viral infection.
An auditory-visual tradeoff in susceptibility to clutter
Authors: Zhang Min , Denison Rachel N , Pelli Denis G , Le Thuy Tien C , Ihlefeld Antje
Published: December 2021

Sensory cortical mechanisms combine auditory or visual features into perceived objects. This is difficult in noisy or cluttered environments. Knowing that individuals vary greatly in their susceptibility to clutter, we wondered whether there might be a relation between an individual’s auditory and visual susceptibilities to clutter. In auditory masking, background sound makes spoken words unrecognizable. When masking arises due to interference at central auditory processing stages, beyond the cochlea, it is called informational masking. A strikingly similar phenomenon in vision, called visual crowding, occurs when nearby clutter makes a target object unrecognizable, despite being resolved at the retina. We here compare susceptibilities to auditory informational masking and visual crowding in the same participants. Surprisingly, across participants, we find a negative correlation (R = –0.7) between susceptibility to informational masking and crowding: Participants who have low susceptibility to auditory clutter tend to have high susceptibility to visual clutter, and vice versa. This reveals a tradeoff in the brain between auditory and visual processing.
Preparation and evaluation of crocin loaded in nanoniosomes and their effects on ischemia–reperfusion injuries in rat kidney
Authors: Naderi Reyhaneh , Pardakhty Abbas , Abbasi Mohammad Farajli , Ranjbar Mehdi , Iranpour Maryam
Published: December 2021

As a powerful antioxidant compound, crocin can partially protect against renal ischemia/reperfusion (I/R) injuries. The encapsulation of components in niosomes (non-ionic surfactant-based vesicle) as nano-sized carrier systems has been proposed as they improve the solubility, stability, and bioavailability of drugs. Herein, the encapsulation of crocin in nano-niosomes and the effects of crocin-loaded nano-niosomes on renal ischemia/reperfusion-induced damages were evaluated. Nano-niosomes containing crocin were formulated by a modified heating method and were characterized for their physicochemical characteristics. Ischemia was induced by clamping the renal artery for 30 min followed by 1 or 24 h of reperfusion. Rats received an intra-arterial injection of nano-niosome-loaded crocin at the outset of reperfusion. Blood samples were taken after reperfusion to measure urea, creatinine (Cr), malondialdehyde (MDA), and superoxide dismutase (SOD) activity. The right kidney was removed for histological examination. The results showed that crocin-contain nano-niosomes have appropriate size and morphology, acceptable encapsulation efficiency, and a proper release pattern of crocin. I/R enhanced creatinine (Cr), urea, and malondialdehyde (MDA) serum levels and reduced SOD activity and histological damages in the renal tissue.
Ketogenic Diet as a potential treatment for traumatic brain injury in mice
Authors: Har-Even Meirav , Rubovitch Vardit , Ratliff Whitney A. , Richmond-Hacham Bar , Citron Bruce A. , Pick Chaim G.
Published: December 2021

Traumatic brain injury (TBI) is a brain dysfunction without present treatment. Previous studies have shown that animals fed ketogenic diet (KD) perform better in learning tasks than those fed standard diet (SD) following brain injury. The goal of this study was to examine whether KD is a neuroprotective in TBI mouse model. We utilized a closed head injury model to induce TBI in mice, followed by up to 30 days of KD/SD. Elevated levels of ketone bodies were confirmed in the blood following KD. Cognitive and behavioral performance was assessed post injury and molecular and cellular changes were assessed within the temporal cortex and hippocampus. Y-maze and Novel Object Recognition tasks indicated that mTBI mice maintained on KD displayed better cognitive abilities than mTBI mice maintained on SD. Mice maintained on SD post-injury demonstrated SIRT1 reduction when compared with uninjured and KD groups. In addition, KD management attenuated mTBI-induced astrocyte reactivity in the dentate gyrus and decreased degeneration of neurons in the dentate gyrus and in the cortex. These results support accumulating evidence that KD may be an effective approach to increase the brain’s resistance to damage and suggest a potential new therapeutic strategy for treating TBI.
Butyrate producing microbiota are reduced in chronic kidney diseases
Authors: Gao Bei , Jose Adarsh , Alonzo-Palma Norma , Malik Taimur , Shankaranarayanan Divya , Regunathan-Shenk Renu , Raj Dominic S.
Published: December 2021

Chronic kidney disease is a major public health concern that affects millions of people globally. Alterations in gut microbiota composition have been observed in patients with chronic kidney disease. Nevertheless, the correlation between the gut microbiota and disease severity has not been investigated. In this study, we performed shot-gun metagenomics sequencing and identified several taxonomic and functional signatures associated with disease severity in patients with chronic kidney disease. We noted that 19 microbial genera were significantly associated with the severity of chronic kidney disease. The butyrate-producing bacteria were reduced in patients with advanced stages of chronic kidney diseases. In addition, functional metagenomics showed that two-component systems, metabolic activity and regulation of co-factor were significantly associated with the disease severity. Our study provides valuable information for the development of microbiota-oriented therapeutic strategies for chronic kidney disease.
Rapid IRMPD (InfraRed multiple photon dissociation) analysis for glycomics
Authors: Yeni Oznur , Schindler Baptiste , Moge Baptiste , Compagnon Isabelle
Published: December 2021

Infrared ion spectroscopy has emerged as a powerful addition to mass spectrometry-based analytical tools.
Determining a wide range of antibiotics and pesticides in poultry feathers using selective accelerated solvent extraction-liquid chromatography-mass spectrometry
Authors: Wu Huizhen , Zhou Min , Xu Jie , Wang Jianmei , Tong Jianying , Sun Nabo , Qian Mingrong
Published: December 2021

This study established a detection method based on accelerated solvent extraction-liquid chromatography-mass spectrometry for determining residues of 3 chloramphenicols, 8 macrolides, 18 sulfonamides, 4 nitroimidazoles, 15 insecticides, and 22 fungicides in poultry feathers.
Morphology library of nanosilica based on a thermally induced deformable template
Authors: Yuan Yukun , Zhang Kangmin , Li Xiaofei , Wu Mingyuan , Wu Qingyun , Liu Jiuyi , Yang Jianjun , Zhang Jianan
Published: December 2021

We report a versatile platform for the synthesis of shape-tunable nanosilica based on a thermally induced deformable template with diverse morphologies ranging from spheres, horns, ultrathin nanosheets, and rings to belts.
Stimuli-responsive nanomaterials for cancer treatment: boundaries, opportunities and applications
Authors: Lafuente-Gómez Nuria , Latorre Ana , Milán-Rois Paula , Rodriguez Diaz Ciro , Somoza Álvaro
Published: December 2021

This comprehensive feature article summarizes the recent progress of controlled release systems based on nanostructures for cancer treatment.
A self-assembled subphthalocyanine-based nanophotosensitiser for photodynamic therapy
Authors: Casellas Nicolás M. , Dai Gaole , Xue Evelyn Y. , Fonseca Alba , Ng Dennis K. P. , García-Iglesias Miguel , Torres Tomás
Published: December 2021

A novel amphiphilic subphthalocyanine can self-assemble into spherical nanoparticles in water, which can be internalized by cancer cells and activated upon disassembly causing high photocytotoxicity.
Silver nanoparticles modified by water-soluble leaning tower[6]arenes for sensing and catalysis
Authors: Zhang Yinan , Li Zheng , Meng Suriguga , Dong Alideertu , Yang Ying-Wei
Published: December 2021

A hybrid nanoplatform was fabricated using a tower[6]arene sodium salt as a stabiliser on the surface of silver nanoparticles, showing good performance in catalysis and detection.
Ion migration mechanism in all-inorganic Ruddlesden–Popper lead halide perovskites by first-principles calculations
Authors: Zhao Shuai , Xiao Li
Published: December 2021

The diffusion mechanisms of halide ions in all-inorganic Ruddlesden–Popper halide perovskites are investigated by first-principles calculations.
The effects of glycine to alanine mutations on the structure of GPO collagen model peptides
Authors: Röder Konstantin
Published: December 2021

Gly to Ala mutations in GPO collagen leads to significant changes in hydrogen bonding and Pro ring puckering, with a single mutation sufficient to introduce significant local structural changes.
pH-Dependent formation of three porous In(iii)-MOFs: framework diversity and selective gas adsorption
Authors: Zhang Chengcheng , Qin Yuanyuan , Duan Lijuan , Wang Lu , Wu Yuewei , Guo Yan , Song Weiming , Liu Xiangyu
Published: December 2021

pH has a significant effect on the architectures of resulting In(iii)-MOFs, one of which exhibits highly selective uptake of CO2 over CH4.
Lanthanide–uranyl phosphonates constructed from diethyl ((phenylsulfonyl)methyl)phosphonate
Authors: Hou Xiaomin , Tang Si-Fu
Published: December 2021

Lanthanide–uranyl sulfonylphosphonates with intriguing crystal structures and photophysical properties can be assembled from a heterofunctional diethyl phosphonate precursor ligand.