bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantification of the Uncertainty in Coastal Storm Hazard Predictions Due to Wave‐Current Interaction and Wind Forcing
Authors: Lyddon Charlotte E. , Brown Jennifer M. , Leonardi Nicoletta , Saulter Andrew , Plater Andrew J. 
Published: December 2019

AbstractCoastal flood warning and design of coastal protection schemes rely on accurate estimations of water level and waves during hurricanes and violent storms. These estimations frequently use numerical models, which, for computational reasons, neglect the interaction between the hydrodynamic and wave fields. Here, we show that neglecting such interactions, or local effects of atmospheric forcing, causes large uncertainties, which could have financial and operational consequences because flood warnings are potentially missed or protection schemes underdesigned. Using the Severn Estuary, SW England, we show that exclusion of locally generated winds underestimates high water significant wave height by up to 90.1%, high water level by 1.5%, and hazard proxy (water level + 1/2 significant wave height) by 9.1%. The uncertainty in water level and waves is quantified using a system to model tide‐surge‐wave conditions, Delft3D‐FLOW‐WAVE in a series of eight model simulations for four historic storm events.
Empirical Evidence Linking the Pacific Decadal Precession to Kuroshio Extension Variability
Authors: Anderson Bruce T. 
Published: December 2019

AbstractRecent research has revealed a new mode of quasi‐decadal climate variability—the Pacific Decadal Precession (PDP)—that has teleconnected impacts upon the state of the ocean and atmosphere across the North Pacific. Previous research has revealed similar decadal scale variability in the location, intensity, and stability of the North Pacific's western boundary current system and in particular the Kuroshio Extension (KE) current, suggesting potential links between the large‐scale (~1,000 km and larger) ocean/atmosphere variations associated with the PDP and mesoscale (~100 km) variations in the KE. Empirical analyses using self‐consistent historical state estimates of the ocean and atmosphere over the North Pacific—derived from the 20th Century Reanalysis Version 2c (20CRv2c) and Simple Ocean Data Assimilation – sparse input version 3 (SODAsi.3) data sets for the period 1851–2013—confirm these links exist. Further, these empirical analyses suggest that the PDP both forces and responds to KE variability on decadal time scales. Our synthesis of these empirical results with previously published empirical, theoretical, and numerical results argues for the presence of a self‐sustaining decadal oscillation of the ocean/atmosphere system across the extratropical North Pacific in which large‐scale ocean‐atmosphere coupling positively reinforces the atmospheric circulations that generate KE variability while mesoscale ocean‐atmosphere coupling allows the subsequent KE variability to reverse these atmospheric circulations.
Subauroral and Polar Traveling Ionospheric Disturbances During the 7–9 September 2017 Storms
Authors: Zhang Shun‐Rong , Erickson Philip J. , Coster Anthea J. , Rideout William , Vierinen Juha , Jonah Olusegun , Goncharenko Larisa P. 
Published: December 2019

AbstractThis study provides new scenarios for storm time traveling ionospheric disturbance excitation and subsequent propagation at subauroral and polar latitudes. We used ground‐based total electron content observations from Global Navigation Satellite System receivers combined with wide field, subauroral ionospheric plasma parameters measured with the Millstone Hill Incoherent Scatter Radar during strong September 2017 geospace storms. Observations provide the first evidence of significant influences on traveling ionospheric disturbance (TID) propagation and excitation caused by the presence of large subauroral polarization stream flow channels. Simultaneous large‐ and medium‐scale TIDs evolved during the event in a broad subauroral and midlatitude area near dusk. Similar concurrent TIDs occurred near dawn sectors as well during a period of sustained southward Bz. Medium‐scale TIDs at subauroral and midlatitudes had wave fronts aligned northwest‐southeast near dusk, and northeast‐southwest near dawn. These wave fronts were highly correlated with the direction of storm time large zonal plasma drift enhancements at these latitudes. At high latitudes, unexpected, predominant, and persistent storm time TIDs were identified with 2000+ km zonal wave fronts and 15% total electron content perturbation amplitudes, moving in transpolar propagation pathways from the dayside into the nightside. This propagation direction in the polar region was opposite to the normal assumption that TIDs originated in the nightside auroral region. Results suggest that significant dayside sources, such as cusp regions, can be efficient in generating transpolar TIDs during geospace storm intervals.
Multiplication and division of the orbital angular momentum of light with diffractive transformation optics
Authors: Ruffato Gianluca , Massari Michele , Romanato Filippo 
Published: December 2019

AbstractWe present a method to efficiently multiply or divide the orbital angular momentum (OAM) of light beams using a sequence of two optical elements. The key element is represented by an optical transformation mapping the azimuthal phase gradient of the input OAM beam onto a circular sector. By combining multiple circular-sector transformations into a single optical element, it is possible to multiply the value of the input OAM state by splitting and mapping the phase onto complementary circular sectors. Conversely, by combining multiple inverse transformations, the division of the initial OAM value is achievable by mapping distinct complementary circular sectors of the input beam into an equal number of circular phase gradients. Optical elements have been fabricated in the form of phase-only diffractive optics with high-resolution electron-beam lithography. Optical tests confirm the capability of the multiplier optics to perform integer multiplication of the input OAM, whereas the designed dividers are demonstrated to correctly split up the input beam into a complementary set of OAM beams. These elements can find applications for the multiplicative generation of higher-order OAM modes, optical information processing based on OAM beam transmission, and optical routing/switching in telecom.
PDGFB-expressing mesenchymal stem cells improve human hematopoietic stem cell engraftment in immunodeficient mice
Authors: Yin Xiuxiu , Hu Linping , Zhang Yawen , Zhu Caiying , Cheng Hui , Xie Xiaowei , Shi Ming , Zhu Ping , Zhao Xueying , Chen Wanqiu , Zhang Lu , Arakaki Cameron , Hao Sha , Wang Mei , Cao Wenbin , Ma Shihui , Zhang Xiao-Bing , Cheng Tao 
Published: December 2019

AbstractThe bone marrow (BM) niche regulates multiple hematopoietic stem cell (HSC) processes. Clinical treatment for hematological malignancies by HSC transplantation often requires preconditioning via total body irradiation, which severely and irreversibly impairs the BM niche and HSC regeneration. Novel strategies are needed to enhance HSC regeneration in irradiated BM. We compared the effects of EGF, FGF2, and PDGFB on HSC regeneration using human mesenchymal stem cells (MSCs) that were transduced with these factors via lentiviral vectors. Among the above niche factors tested, MSCs transduced with PDGFB (PDGFB-MSCs) most significantly improved human HSC engraftment in immunodeficient mice. PDGFB-MSC-treated BM enhanced transplanted human HSC self-renewal in secondary transplantations more efficiently than GFP-transduced MSCs (GFP-MSCs). Gene set enrichment analysis showed increased antiapoptotic signaling in PDGFB-MSCs compared with GFP-MSCs. PDGFB-MSCs exhibited enhanced survival and expansion after transplantation, resulting in an enlarged humanized niche cell pool that provide a better humanized microenvironment to facilitate superior engraftment and proliferation of human hematopoietic cells. Our studies demonstrate the efficacy of PDGFB-MSCs in supporting human HSC engraftment.
Pyroptosis is a critical inflammatory pathway in the placenta from early onset preeclampsia and in human trophoblasts exposed to hypoxia and endoplasmic reticulum stressors
Authors: Cheng Shi-Bin , Nakashima Akitoshi , Huber Warren J. , Davis Sarah , Banerjee Sayani , Huang Zheping , Saito Shigeru , Sadovsky Yoel , Sharma Surendra 
Published: December 2019

AbstractSystemic manifestation of preeclampsia (PE) is associated with circulating factors, including inflammatory cytokines and damage-associated molecular patterns (DAMPs), or alarmins. However, it is unclear whether the placenta directly contributes to the increased levels of these inflammatory triggers. Here, we demonstrate that pyroptosis, a unique inflammatory cell death pathway, occurs in the placenta predominantly from early onset PE, as evidenced by elevated levels of active caspase-1 and its substrate or cleaved products, gasdermin D (GSDMD), IL-1β, and IL-18. Using cellular models mimicking pathophysiological conditions (e.g., autophagy deficiency, hypoxia, and endoplasmic reticulum (ER) stress), we observed that pyroptosis could be induced in autophagy-deficient human trophoblasts treated with sera from PE patients as well as in primary human trophoblasts exposed to hypoxia. Exposure to hypoxia elicits excessive unfolded protein response (UPR) and ER stress and activation of the NOD-like receptor pyrin-containing 3 (NLRP3) inflammasome in primary human trophoblasts. Thioredoxin-interacting protein (TXNIP), a marker for hyperactivated UPR and a crucial signaling molecule linked to NLRP3 inflammasome activation, is significantly increased in hypoxia-treated trophoblasts. No evidence was observed for necroptosis-associated events. Importantly, these molecular events in hypoxia-treated human trophoblasts are significantly observed in placental tissue from women with early onset PE. Taken together, we propose that placental pyroptosis is a key event that induces the release of factors into maternal circulation that possibly contribute to severe sterile inflammation and early onset PE pathology.
Origin of the mixed alkali effect in silicate glass
Authors: Onodera Yohei , Takimoto Yasuyuki , Hijiya Hiroyuki , Taniguchi Taketoshi , Urata Shingo , Inaba Seiji , Fujita Sanae , Obayashi Ippei , Hiraoka Yasuaki , Kohara Shinji 
Published: December 2019

Abstract
Silicate glasses have evolved from basic structural materials to enabling materials for advanced applications. In this article, we unravel the origin of the mixed alkali effect for alkali silicate 22.7R2O–77.3SiO2 glasses (R = Na and/or K) by identifying the variation in the alkali ion location around the non-bridging oxygen atoms. To do so, we constructed a state-of-the art structural model, which reproduces both diffraction and NMR data with a particular focus on the behavior of the alkali ions. A novel topological analysis using persistent homology found that sodium-potassium silicate glass shows a significant reduction in large cavities as a result of the mixed alkali effect. Furthermore, a highly correlated pair arrangement between sodium and potassium ions around non-bridging oxygen atoms was identified. The potassium ions can be trapped in K–O polyhedra due to the increased bridging oxygen coordination; therefore, the correlated pair arrangement is likely the intrinsic origin of the mixed alkali effect.
Determination of the Faraday rotation perpendicular to the optical axis in uniaxial CeF3 crystal by using the Generalized-High Accuracy Universal Polarimeter
Authors: Nakagawa Kenta , Asahi Toru 
Published: December 2019

AbstractMany single crystals have been developed and commercialized for optical isolators. However, optical isolator materials have been limited to isotropic crystals or to the isotropic direction (optic axis) of anisotropic crystals. This study investigates the wavelength dependences of linear birefringence, linear dichroism, Faraday rotation and magnetic-circular dichroism in a single crystal rare-earth fluoride, namely CeF3. Measurements were made in the direction parallel and perpendicular to the optic axis under an applied magnetic field. The magnetic field was generated by Nd-Fe-B magnets installed in the generalized-high accuracy universal polarimeter (G-HAUP). The first application of G-HAUP to a magneto-optical material is presented. In the CeF3 crystal, the Verdet constants along directions parallel and perpendicular to the optic axis were positive over the measured wavelength region (300–680 nm), and their magnitudes were nearly equal. The success in the accurate measurement on Faraday rotation along anisotropic directions has opened the way to study on optical isolators along the direction other than optic axis.
Impact of aging on transition of acute kidney injury to chronic kidney disease
Authors: Kim Myung-Gyu , Yang Jihyun , Ko Yoon Sook , Lee Hee Young , Oh Se Won , Cho Won Yong , Jo Sang-Kyung 
Published: December 2019

AbstractAcute kidney injury (AKI) increases the risk of end stage renal disease among the elderly, but the precise underlying mechanism is unknown. We investigated the effects of aging on AKI-to-chronic kidney disease (CKD) transition, focusing on renal inflammation. Aged and young C57BL/6 mice were subjected to bilateral ischemia-reperfusion injury (IRI). Baseline proinflammatory cytokine levels of kidneys were elevated in aged mice. After IRI, aged mice also showed persistent M1 dominant inflammation, with increased proinflammatory cytokines during the recovery phase. Persistent M1 inflammation was associated with blunted activation of CSF-1/IRF4 signal for M1/M2 polarization, but in vitro macrophage polarization with cytokine stimulation was not different between young and aged mononuclear cells. The tubular expressions of cell cycle arrest markers increased in aged mice during recovery phase, and in vitro transwell experiments showed that mononuclear cells or M1 macrophages co-cultured with arrested proximal tubular cells at G1 phase significantly impaired M2 polarization, suggesting that prolonged G1 arrest might be involved in persistent M1 inflammation in aged mice. Finally, M1 dominant inflammation in aged mice resulted in fibrosis progression. Our data show that impaired M2 polarization partially driven by senescent tubule cells with cell-cycle arrest may lead to an accelerated progression to CKD in the elderly.
Seven-day Green Tea Supplementation Revamps Gut Microbiome and Caecum/Skin Metabolome in Mice from Stress
Authors: Jung Eun Sung , Park Jong il , Park Hyunjoon , Holzapfel Wilhelm , Hwang Jae Sung , Lee Choong Hwan 
Published: December 2019

AbstractGreen tea supplementation has beneficial health effects. However, its underlying mechanisms, such as effects on modulating the intestinal microbiome and endogenous metabolome, particularly following short-term supplementation, are largely unclear. We conducted an integrative metabolomics study to evaluate the effects of short-term (7-day) supplementation of green tea extract (GTE) or its components, epigallocatechin gallate, caffeine, and theanine, on the caecum microbiota and caecum/skin metabolome in mice. Further, we established an integrative metabolome-microbiome model for correlating gut and skin findings. The effects of short-term supplementation with dietary compounds were evaluated with respect to UV stress response, with GTE showing the most remarkable effects. Biplot analysis revealed that Bifidobacteria and Lactobacillus spp. were considerably influenced by short-term GTE supplementation, while Clostridium butyricum was significantly increased by UV stress without supplementation. GTE supplementation helped the skin metabolome defend against UV stress. Interestingly, a significant positive correlation was observed between caecum bacteria (Bifidobacteria, Lactobacillus spp.) and metabolites including skin barrier function-related skin metabolites, caecal fatty acids, and caecal amino acids. Overall, 7-day GTE supplementation was sufficient to alter the gut microbiota and endogenous caecum/skin metabolome, with positive effects on UV stress response, providing insight into the mechanism of the prebiotic effects of GTE supplementation.
Comparative analysis of corrected tiger genome provides clues to its neuronal evolution
Authors: Mittal Parul , Jaiswal Shubham K. , Vijay Nagarjun , Saxena Rituja , Sharma Vineet K. 
Published: December 2019

AbstractThe availability of completed and draft genome assemblies of tiger, leopard, and other felids provides an opportunity to gain comparative insights on their unique evolutionary adaptations. However, genome-wide comparative analyses are susceptible to errors in genome sequences and thus require accurate genome assemblies for reliable evolutionary insights. In this study, while analyzing the tiger genome, we found almost one million erroneous substitutions in the coding and non-coding region of the genome affecting 4,472 genes, hence, biasing the current understanding of tiger evolution. Moreover, these errors produced several misleading observations in previous studies. Thus, to gain insights into the tiger evolution, we corrected the erroneous bases in the genome assembly and gene set of tiger using ‘SeqBug’ approach developed in this study. We sequenced the first Bengal tiger genome and transcriptome from India to validate these corrections. A comprehensive evolutionary analysis was performed using 10,920 orthologs from nine mammalian species including the corrected gene sets of tiger and leopard and using five different methods at three hierarchical levels, i.e. felids,Panthera, and tiger. The unique genetic changes in tiger revealed that the genes showing signatures of adaptation in tiger were enriched in development and neuronal functioning. Specifically, the genes belonging to the Notch signalling pathway, which is among the most conserved pathways involved in embryonic and neuronal development, were found to have significantly diverged in tiger in comparison to the other mammals. Our findings suggest the role of adaptive evolution in neuronal functions and development processes, which correlates well with the presence of exceptional traits such as sensory perception, strong neuro-muscular coordination, and hypercarnivorous behaviour in tiger.
Associations between echocardiographic findings and prospective changes in residual renal function in patients new to peritoneal dialysis
Authors: Mahdavi Sara , Yared Kibar , Wu George , Omar Billy , Savundra Dinesh , Nagai Gordon , Hockmann Edgar , Svendrovski Anton , Bellasi Antonio , Tam Paul , Sikaneta Tabo 
Published: December 2019

AbstractAlthough echocardiograms are often performed when peritoneal dialysis is started, associations between commonly reported findings and prospective changes in renal function remain understudied. Ninety-nine of 101 patients in the Trio Trial had transthoracic echocardiograms within 6 months of dialysis initiation, and measurements of residual renal function every six weeks for up to two years. Generalized mixed modelling linear regression in STATA was used to examine associations between left atrial size, left ventricular hypertrophy, left ventricular ejection fraction, right ventricular systolic pressure, and left valvular calcification with subsequent slopes in renal function. After echocardiography (performed a median of 16 days following peritoneal dialysis initiation) right ventricular systolic pressure was associated with faster, while declining left ventricular ejection fraction and valvular calcification were associated with slower declines in residual renal function. Future studies could be conducted to confirm these findings, and identify pathophysiological mechanisms.
Common genetic variants associated with Parkinson’s disease display widespread signature of epigenetic plasticity
Authors: Sharma Amit , Osato Naoki , Liu Hongde , Asthana Shailendra , Dakal Tikam Chand , Ambrosini Giovanna , Bucher Philipp , Schmitt Ina , Wüllner Ullrich 
Published: December 2019

AbstractParkinson disease (PD) is characterized by a pivotal progressive loss of substantia nigra dopaminergic neurons and aggregation of α-synuclein protein encoded by the SNCA gene. Genome-wide association studies identified almost 100 sequence variants linked to PD in SNCA. However, the consequences of this genetic variability are rather unclear. Herein, our analysis on selective single nucleotide polymorphisms (SNPs) which are highly associated with the PD susceptibility revealed that several SNP sites attribute to the nucleosomes and overlay with bivalent regions poised to adopt either active or repressed chromatin states. We also identified large number of transcription factor (TF) binding sites associated with these variants. In addition, we located two docking sites in the intron-1 methylation prone region of SNCA which are required for the putative interactions with DNMT1. Taken together, our analysis reflects an additional layer of epigenomic contribution for the regulation of the SNCA gene in PD.
A new antiviral scaffold for human norovirus identified with computer-aided approaches on the viral polymerase
Authors: Giancotti Gilda , Rigo Ilaria , Pasqualetto Gaia , Young Mark T. , Neyts Johan , Rocha-Pereira Joana , Brancale Andrea , Ferla Salvatore , Bassetto Marcella 
Published: December 2019

AbstractHuman norovirus is the leading cause of acute gastroenteritis worldwide, affecting every year 685 million people. In about one third of cases, this virus affects children under five years of age, causing each year up to 200,000 child deaths, mainly in the developing countries. Norovirus outbreaks are associated with very significant economic losses, with an estimated societal cost of 60 billion dollars per year. Despite the marked socio-economic consequences associated, no therapeutic options or vaccines are currently available to treat or prevent this infection. One promising target to identify new antiviral agents for norovirus is the viral polymerase, which has a pivotal role for the viral replication and lacks closely homologous structures in the host. Starting from the scaffold of a novel class of norovirus polymerase inhibitors recently discovered in our research group with a computer-aided method, different new chemical modifications were designed and carried out, with the aim to identify improved agents effective against norovirus replication in cell-based assays. While different new inhibitors of the viral polymerase were found, a further computer-aided ligand optimisation approach led to the identification of a new antiviral scaffold for norovirus, which inhibits human norovirus replication at low-micromolar concentrations.