bluuebunny/crossref_metadata_2025_split huggingface dataset:
Storm Surge and Tidal Dissipation in Deltaic Wetlands Bordering a Main Channel
Authors: Nordio Giovanna , Fagherazzi Sergio 
Published: February 2022

AbstractDeltas are complex systems where tidal and riverine signals interact with each other. In river‐dominated deltas, where river discharge is sufficiently high, tidal amplitude is attenuated and distorted. Here we use wavelet analysis to examine the water level signal in stations located in wetlands adjacent to the main river outlet in the Wax Lake system, part of the Mississippi River Delta in Louisiana, USA. We study the signal attenuation in lateral wetlands at different frequency bands, following the propagation of the water level signal from the Gulf of Mexico to the innermost stations. During high river discharge, the astronomical tide measured inside the wetlands is reduced of 90%–98% in comparison to the tide in Atchafalaya Bay. Storm surge events, largely occurring at lower temporal frequencies, propagate conserving their energy once the signal enters the delta mouth. The river discharge signal, mostly present at frequencies lower than 1.59 μHz, is felt depending on river discharge conditions and the station position within the wetlands. Our results suggest that lateral wetlands in the Wax Lake system act as a low pass filter, attenuating tidal components but not the low frequency components of storm surges.
3D Numerical Simulation of Secondary Wave Generation From Mountain Wave Breaking Over Europe
Authors: Heale Christopher J. , Bossert Katrina , Vadas Sharon L. 
Published: February 2022

AbstractIn this paper, we simulate an observed mountain wave event over central Europe and investigate the subsequent generation, propagation, phase speeds and spatial scales, and momentum deposition of secondary waves under three different tidal wind conditions. We find the mountain wave breaks just below the lowest critical level in the mesosphere. As the mountain wave breaks, it extends outwards along the phases and fluid associated with the breaking flows downstream of its original location by 500–1,000 km. The breaking generates a broad range of secondary waves with horizontal scales ranging from the mountain wave instability scales (20–300 km), to multiples of the mountain wave packet scale (420 km+) and phase speeds from 40 to 150 m/s in the lower thermosphere. The secondary wave morphology consists of semi‐concentric patterns with wave propagation generally opposing the local tidal winds in the mesosphere. Shears in the tidal winds cause breaking of the secondary waves and local wave forcing which generates even more secondary waves. The tidal winds also influence the dominant wavelengths and phase speeds of secondary waves that reach the thermosphere. The secondary waves that reach the thermosphere deposit their energy and momentum over a broad area of the thermosphere, mostly eastward of the source and concentrated between 110 and 130 km altitude. The secondary wave forcing is significant and will likely be very important for the dynamics of the thermosphere. A large portion of this forcing comes from nonlinearly generated secondary waves at relatively small‐scales which arise from the wave breaking processes.
The Role of Snow in Controlling Halogen Chemistry and Boundary Layer Oxidation During Arctic Spring: A 1D Modeling Case Study
Authors: Ahmed Shaddy , Thomas Jennie L. , Tuite Katie , Stutz Jochen , Flocke Frank , Orlando John J. , Hornbrook Rebecca S. , Apel Eric C. , Emmons Louisa K. , Helmig Detlev , Boylan Patrick , Huey L. Gregory , Hall Samuel R. , Ullmann Kirk , Cantrell Christopher A. , Fried Alan 
Published: February 2022

AbstractReactive chlorine and bromine species emitted from snow and aerosols can significantly alter the oxidative capacity of the polar boundary layer. However, halogen production mechanisms from snow remain highly uncertain, making it difficult for most models to include descriptions of halogen snow emissions and to understand the impact on atmospheric chemistry. We investigate the influence of Arctic halogen emissions from snow on boundary layer oxidation processes using a one‐dimensional atmospheric chemistry and transport model (PACT‐1D). To understand the combined impact of snow emissions and boundary layer dynamics on atmospheric chemistry, we model Cl2 and Br2 primary emissions from snow and include heterogeneous recycling of halogens on both snow and aerosols. We focus on a 2‐day case study from the 2009 Ocean‐Atmosphere‐Sea Ice‐Snowpack campaign at Utqiaġvik, Alaska. The model reproduces both the diurnal cycle and high quantity of Cl2 observed, along with the measured concentrations of Br2, BrO, and HOBr. Due to the combined effects of emissions, recycling, vertical mixing, and atmospheric chemistry, reactive chlorine is typically confined to the lowest 15 m of the atmosphere, while bromine can impact chemistry up to and above the surface inversion height. Upon including halogen emissions and recycling, the concentration of HOx (HOx = OH + HO2) at the surface increases by as much as a factor of 30 at mid‐day. The change in HOx due to halogen chemistry, as well as chlorine atoms derived from snow emissions, significantly reduce volatile organic compound lifetimes within a shallow layer near the surface.
Activating α7nAChR ameliorates abdominal aortic aneurysm through inhibiting pyroptosis mediated by NLRP3 inflammasome
Authors: Fu Hui , Shen Qi-rui , Zhao Yi , Ni Min , Zhou Can-can , Chen Ji-kuai , Chi Chen , Li Dong-jie , Liang Guang , Shen Fu-ming 
Published: February 2022

AbstractAbdominal aortic aneurysm (AAA) is defined as a dilated aorta in diameter at least 1.5 times of a normal aorta. Our previous studies found that activating α7 nicotinic acetylcholine receptor (α7nAChR) had a protective effect on vascular injury. This work was to investigate whether activating α7nAChR could influence AAA formation and explore its mechanisms. AAA models were established by angiotensin II (Ang II) infusion in ApoE−/−mice or in wild type and α7nAChR−/−mice. In vitro mouse aortic smooth muscle (MOVAS) cells were treated with tumor necrosis factor-α (TNF-α). PNU-282987 was chosen to activate α7nAChR. We found that cell pyroptosis effector GSDMD and NLRP3 inflammasome were activated in abdominal aorta, and inflammatory cytokines in serum were elevated in AAA models of ApoE−/−mice. Activating α7nAChR reduced maximal aortic diameters, preserved elastin integrity and decreased inflammatory responses in ApoE−/−mice with Ang II infusion. While α7nAChR−/−mice led to aggravated aortic injury and increased inflammatory cytokines with Ang II infusion when compared with wild type. Moreover, activating α7nAChR inhibited NLRP3/caspase-1/GSDMD pathway in AAA model of ApoE−/−mice, while α7nAChR deficiency promoted this pathway. In vitro, N-acetylcysteine (NAC) inhibited NLRP3 inflammasome activation and NLRP3 knockdown reduced GSDMD expression, in MOVAS cells treated with TNF-α. Furthermore, activating α7nAChR inhibited oxidative stress, reduced NLRP3/GSDMD expression, and decreased cell pyroptosis in MOVAS cells with TNF-α. In conclusion, our study found that activating α7nAChR retarded AAA through inhibiting pyroptosis mediated by NLRP3 inflammasome. These suggested that α7nAChR would be a potential pharmacological target for AAA.
Trimetazidine enhances myocardial angiogenesis in pressure overload-induced cardiac hypertrophy mice through directly activating Akt and promoting the binding of HSF1 to VEGF-A promoter
Authors: Shu Hong-yang , Peng Yi-zhong , Hang Wei-jian , Zhang Min , Shen Lan , Wang Dao-wen , Zhou Ning 
Published: February 2022

AbstractLatest clinical research shows that trimetazidine therapy during the perioperative period relieves endothelial dysfunction in patients with unstable angina induced by percutaneous coronary intervention. In this study we investigated the effects of TMZ on myocardial angiogenesis in pressure overload-induced cardiac hypertrophy mice. Cardiac hypertrophy was induced in mice by transverse aortic constriction (TAC) surgery. TAC mice were administered trimetazidine (2.8 mg/100 µL, i.g.) for 28 consecutive days. We showed that trimetazidine administration significantly increased blood vessel density in the left ventricular myocardium and abrogated cardiac dysfunction in TAC mice. Co-administration of a specific HSF1 inhibitor KRIBB11 (1.25 mg/100 µL, i.h.) abrogated the angiogenesis-promoting effects of trimetazidine in TAC mice. Using luciferase reporter and electrophoretic mobility shift assays we demonstrated that the transcription factor HSF1 bound to the promoter region of VEGF-A, and the transcriptional activity of HSF1 was enhanced upon trimetazidine treatment. In molecular docking analysis we found that trimetazidine directly bound to Akt via a hydrogen bond with Asp292 and a pi–pi bond with Trp80. In norepinephrine-treated HUVECs, we showed that trimetazidine significantly increased the phosphorylation of Akt and the synergistic nuclear translocation of Akt and HSF1, as well as the binding of Akt and HSF1 in the nucleus. These results suggest that trimetazidine enhances myocardial angiogenesis through a direct interaction with Akt and promotion of nuclear translocation of HSF1, and that trimetazidine may be used for the treatment of myocardial angiogenic disorders in hypertensive patients.
Computer vision-aided bioprinting for bone research
Authors: Liu Changxi , Wang Liqiang , Lu Weijie , Liu Jia , Yang Chengliang , Fan Chunhai , Li Qian , Tang Yujin 
Published: February 2022

AbstractBioprinting is an emerging additive manufacturing technology that has enormous potential in bone implantation and repair. The insufficient accuracy of the shape of bioprinted parts is a primary clinical barrier that prevents widespread utilization of bioprinting, especially for bone design with high-resolution requirements. During the last five years, the use of computer vision for process control has been widely practiced in the manufacturing field. Computer vision can improve the performance of bioprinting for bone research with respect to various aspects, including accuracy, resolution, and cell survival rate. Hence, computer vision plays a substantial role in addressing the current defect problem in bioprinting for bone research. In this review, recent advances in the application of computer vision in bioprinting for bone research are summarized and categorized into three groups based on different defect types: bone scaffold process control, deep learning, and cell viability models. The collection of printing parameters, data processing, and feedback of bioprinting information, which ultimately improves printing capabilities, are further discussed. We envision that computer vision may offer opportunities to accelerate bioprinting development and provide a new perception for bone research.
Asparaginyl endopeptidase protects against podocyte injury in diabetic nephropathy through cleaving cofilin-1
Authors: Lei Chuntao , Li Mengran , Qiu Yang , Xie Yaru , Hao Zhe , Yin Xingjie , Zhang Zhentao , Su Hua , Yang Linlin , Lin Jihong , Hammes Hans-Peter , Zhang Chun 
Published: February 2022

AbstractPodocyte injury and loss are critical events in diabetic nephropathy (DN); however, the underlying molecular mechanisms remain unclear. Here, we demonstrate that asparaginyl endopeptidase (AEP) protects against podocyte injury through modulating the dynamics of the cytoskeleton. AEP was highly upregulated in diabetic glomeruli and hyperglycemic stimuli treated-podocytes; however, AEP gene knockout and its compound inhibitor treatment accelerated DN in streptozotocin-induced diabetic mice, whereas specific induction of AEP in glomerular cells attenuated podocyte injury and renal function deterioration. In vitro, elevated AEP was involved in actin cytoskeleton maintenance and anti-apoptosis effects. Mechanistically, we found that AEP directly cleaved the actin-binding protein cofilin-1 after the asparagine 138 (N138) site. The protein levels of endogenous cofilin-1 1-138 fragments were upregulated in diabetic podocytes, consistent with the changes in AEP levels. Importantly, we found that cofilin-1 1-138 fragments were remarkably unphosphorylated than full-length cofilin-1, indicating the enhanced cytoskeleton maintenance activity of cofilin-1 1-138. Then we validated cofilin-1 1-138 could rescue podocytes from cytoskeleton disarrangement and injury in diabetic conditions. Taken together, our data suggest a protective role of elevated AEP in podocyte injury during DN progression through cleaving cofilin-1 to maintain podocyte cytoskeleton dynamics and defend damage.
Structure and assembly of the S-layer in C. difficile
Authors: Lanzoni-Mangutchi Paola , Banerji Oishik , Wilson Jason , Barwinska-Sendra Anna , Kirk Joseph A. , Vaz Filipa , O’Beirne Shauna , Baslé Arnaud , El Omari Kamel , Wagner Armin , Fairweather Neil F. , Douce Gillian R. , Bullough Per A. , Fagan Robert P. , Salgado Paula S. 
Published: February 2022

AbstractMany bacteria and archaea possess a two-dimensional protein array, or S-layer, that covers the cell surface and plays crucial roles in cell physiology. Here, we report the crystal structure of SlpA, the main S-layer protein of the bacterial pathogen Clostridioides difficile, and use electron microscopy to study S-layer organisation and assembly. The SlpA crystal lattice mimics S-layer assembly in the cell, through tiling of triangular prisms above the cell wall, interlocked by distinct ridges facing the environment. Strikingly, the array is very compact, with pores of only ~10 Å in diameter, compared to other S-layers (30–100 Å). The surface-exposed flexible ridges are partially dispensable for overall structure and assembly, although a mutant lacking this region becomes susceptible to lysozyme, an important molecule in host defence. Thus, our work gives insights into S-layer organisation and provides a basis for development of C. difficile-specific therapeutics.
Increased fMRI connectivity upon chemogenetic inhibition of the mouse prefrontal cortex
Authors: Rocchi Federico , Canella Carola , Noei Shahryar , Gutierrez-Barragan Daniel , Coletta Ludovico , Galbusera Alberto , Stuefer Alexia , Vassanelli Stefano , Pasqualetti Massimo , Iurilli Giuliano , Panzeri Stefano , Gozzi Alessandro 
Published: February 2022

AbstractWhile shaped and constrained by axonal connections, fMRI-based functional connectivity reorganizes in response to varying interareal input or pathological perturbations. However, the causal contribution of regional brain activity to whole-brain fMRI network organization remains unclear. Here we combine neural manipulations, resting-state fMRI and in vivo electrophysiology to probe how inactivation of a cortical node causally affects brain-wide fMRI coupling in the mouse. We find that chronic inhibition of the medial prefrontal cortex (PFC) via overexpression of a potassium channel increases fMRI connectivity between the inhibited area and its direct thalamo-cortical targets. Acute chemogenetic inhibition of the PFC produces analogous patterns of fMRI overconnectivity. Using in vivo electrophysiology, we find that chemogenetic inhibition of the PFC enhances low frequency (0.1–4 Hz) oscillatory power via suppression of neural firing not phase-locked to slow rhythms, resulting in increased slow and δ band coherence between areas that exhibit fMRI overconnectivity. These results provide causal evidence that cortical inactivation can counterintuitively increase fMRI connectivity via enhanced, less-localized slow oscillatory processes.
Different gut microbial communities correlate with efficacy of albendazole-ivermectin against soil-transmitted helminthiases
Authors: Schneeberger Pierre H. H. , Gueuning Morgan , Welsche Sophie , Hürlimann Eveline , Dommann Julian , Häberli Cécile , Frey Jürg E. , Sayasone Somphou , Keiser Jennifer 
Published: February 2022

AbstractSoil-transmitted helminth infections represent a large burden with over a quarter of the world’s population at risk. Low cure rates are observed with standard of care (albendazole); therefore, a more effective combination therapy (albendazole and ivermectin) is being investigated but showed variable treatment efficacies without evidence of intrinsic parasite resistance. Here, we analyzed the microbiome ofTrichuris trichiuraand hookworm-infected patients and found an association of different enterotypes with treatment efficacy. 80 T. trichiura-infected patients with hookworm co-infections from Pak-Khan, Laos, received either albendazole (n = 41) or albendazole and ivermectin combination therapy (n = 39). Pre-/post-treatment stool samples were collected to monitor treatment efficacy and microbial communities were profiled using 16S rRNA gene sequencing, qPCR, and shotgun sequencing. We identified three bacterial enterotypes and show that pre-treatment enterotype is associated with efficacy of the combination treatment for bothT. trichiura(CRET1 = 5.8%; CRET2 = 16.6%; CRET3 = 68.8%) and hookworm (CRET1 = 31.3%; CRET2 = 16.6%; CRET3 = 78.6%). This study shows that pre-treatment enterotype enables predicting treatment outcome of combination therapy forT. trichiuraand hookworm infections.Trial registration: ClinicalTrials.gov, NCT03527732. Registered 17 May 2018,https://clinicaltrials.gov/ct2/show/NCT03527732.
Natural variation in Glume Coverage 1 causes naked grains in sorghum
Authors: Xie Peng , Tang Sanyuan , Chen Chengxuan , Zhang Huili , Yu Feifei , Li Chao , Wei Huimin , Sui Yi , Wu Chuanyin , Diao Xianmin , Wu Yaorong , Xie Qi 
Published: February 2022

AbstractOne of the most critical steps in cereal threshing is the ease with which seeds are detached from sticky glumes. Naked grains with low glume coverage have dramatically increased threshing efficiency and seed quality. Here, we demonstrate that GC1 (Glume Coverage 1), encoding an atypical G protein γ subunit, negatively regulates sorghum glume coverage. Naturally truncated variations of GC1 C-terminus accumulate at higher protein levels and affect the stability of a patatin-related phospholipase SbpPLAII-1. A strong positive selection signature around the GC1 genic region is found in the naked sorghum cultivars. Our findings reveal a crucial event during sorghum domestication through a subtle regulation of glume development by GC1 C-terminus variation, and establish a strategy for future breeding of naked grains.
Phosphoproteomic profiling of T cell acute lymphoblastic leukemia reveals targetable kinases and combination treatment strategies
Authors: Cordo’ Valentina , Meijer Mariska T. , Hagelaar Rico , de Goeij-de Haas Richard R. , Poort Vera M. , Henneman Alex A. , Piersma Sander R. , Pham Thang V. , Oshima Koichi , Ferrando Adolfo A. , Zaman Guido J. R. , Jimenez Connie R. , Meijerink Jules P. P. 
Published: February 2022

AbstractProtein kinase inhibitors are amongst the most successful cancer treatments, but targetable kinases activated by genomic abnormalities are rare in T cell acute lymphoblastic leukemia. Nevertheless, kinases can be activated in the absence of genetic defects. Thus, phosphoproteomics can provide information on pathway activation and signaling networks that offer opportunities for targeted therapy. Here, we describe a mass spectrometry-based global phosphoproteomic profiling of 11 T cell acute lymphoblastic leukemia cell lines to identify targetable kinases. We report a comprehensive dataset consisting of 21,000 phosphosites on 4,896 phosphoproteins, including 217 kinases. We identify active Src-family kinases signaling as well as active cyclin-dependent kinases. We validate putative targets for therapy ex vivo and identify potential combination treatments, such as the inhibition of the INSR/IGF-1R axis to increase the sensitivity to dasatinib treatment. Ex vivo validation of selected drug combinations using patient-derived xenografts provides a proof-of-concept for phosphoproteomics-guided design of personalized treatments.
Ultrafast visualization of incipient plasticity in dynamically compressed matter
Authors: Mo Mianzhen , Tang Minxue , Chen Zhijiang , Peterson J. Ryan , Shen Xiaozhe , Baldwin John Kevin , Frost Mungo , Kozina Mike , Reid Alexander , Wang Yongqiang , E Juncheng , Descamps Adrien , Ofori-Okai Benjamin K. , Li Renkai , Luo Sheng-Nian , Wang Xijie , Glenzer Siegfried 
Published: February 2022

AbstractPlasticity is ubiquitous and plays a critical role in material deformation and damage; it inherently involves the atomistic length scale and picosecond time scale. A fundamental understanding of the elastic-plastic deformation transition, in particular, incipient plasticity, has been a grand challenge in high-pressure and high-strain-rate environments, impeded largely by experimental limitations on spatial and temporal resolution. Here, we report femtosecond MeV electron diffraction measurements visualizing the three-dimensional (3D) response of single-crystal aluminum to the ultrafast laser-induced compression. We capture lattice transitioning from a purely elastic to a plastically relaxed state within 5 ps, after reaching an elastic limit of ~25 GPa. Our results allow the direct determination of dislocation nucleation and transport that constitute the underlying defect kinetics of incipient plasticity. Large-scale molecular dynamics simulations show good agreement with the experiment and provide an atomic-level description of the dislocation-mediated plasticity.
Bamboo-inspired cell-scale assembly for energy device applications
Authors: Lin Qiuqin , Gao Runan , Li Daohao , Lu Yun , Liu Shiqin , Yu Yanglun , Huang Yuxiang , Yu Wenji 
Published: February 2022

AbstractRapid advances in flexible and wearable smart textiles demand low-cost, high-energy/power-density fiber-shaped supercapacitors (FSCs). The performance of FSCs is determined by the fabrication and assembly of fiber-shaped electrodes (FSEs), where an active charge-storage material is always clad around flexible charge transmission current collectors. Inspired by the tissue structure of natural bamboo, wherein parenchyma cells (PCs) that store nutrients are clad around bamboo fibers (BFs), we propose a strategy for converting bamboo cells into FSEs using conductive BFs and activated PCs as current collectors and active materials, respectively. The assembled electrode has a high specific capacitance of 1454 mF cm−2 at 0.64 mA cm−2. A solid-state FSC with a pair of bamboo-structured electrodes exhibited a substantially high energy density. Its mechanical flexibility enabled the knitting of wearable wristbands to drive ultra-small voltmeter indicators. This lightweight, low cost, and high-energy-density bamboo-structured FSC could enable numerous smart textile applications.
Chemical and molecular structure transformations in atomistic conformation of cellulose nanofibers under thermal environment
Authors: Pakharenko Viktoriya , Dias Otavio Augusto Titton , Mukherjee Sankha , Konar Samir , Singh Chandra Veer , Oksman Kristiina , Sain Mohini 
Published: February 2022

AbstractThe structural changes of the glucopyranose chain and the chemical compositional response of cellulose nanofibers (CNFs) under thermal exposure (at 190 °C for 5 h) have remained a significant gap in the understanding of the long-term performance of nanocellulose. Herein, CNF films with different chemical compositions were investigated to confirm the structural transformation of glucopyranose (coupling constant of OH groups changed up to 50%) by nuclear magnetic resonance (NMR) analysis. Remarkably, the glucopyranose rings underwent partial dehydration during the thermal exposure resulting in enol formation. This study confirms the chain mobility that could lead to the conformational and dimensional changes of the CNFs during thermal exposure. The broad range of conformations was defined by the dihedral angles that varied from ±27° to ±139° after thermal exposure. Investigation into the mechanism involving chemical transformation of the substrates during heating is important for the fabrication of the next generation of flexible electrical materials.