bluuebunny/crossref_metadata_2025_split huggingface dataset:
Source Estimate for the 1960 Chile Earthquake From Joint Inversion of Geodetic and Transoceanic Tsunami Data
Authors: Ho Tung‐Cheng , Satake Kenji , Watada Shingo , Fujii Yushiro 
Published: February 2019

AbstractThe slip distribution of the 1960 Chile earthquake was estimated using geodetic data, local tsunami data, and newly usable transoceanic tsunami data. The large slips triggered a significant tsunami which was recorded by the tide gauges around the Pacific Ocean. We performed a two‐step inversion to estimate the slip distribution. In the first step, we jointly inverted the tsunami waveforms and local geodetic data to recover the ground and seafloor vertical displacement. The transoceanic tsunami data could not be used for waveform inversions until the wave phase and arrival time discrepancies were recently reconciled by improving the long‐wave theory with the phase correction method. The random arrival time discrepancy due to inaccurate local bathymetry and/or instrumental problems was considered by the optimal time alignment. In the second step, we estimated the slip distribution on the plate interface by inverting the vertical displacement obtained in the first step. Checkerboard tests showed that our method and data can resolve displacement at a spatial resolution of at least ~100 km but cannot estimate the rupture velocity. The result for actual data shows a rupture extended about 800 km with a width of about 150 km and three asperities. The large slips are concentrated in the offshore shallow plate interface. Our results indicate that the central and south patches contribute to the large coastal elevation changes at southern source area and high tsunami waves at far field. The estimated moment ranges 1.3–1.9 × 1023 Nm (Mw 9.3–9.4) for rake angles of 90–140°.
Physical and Numerical Modeling of Infragravity Wave Generation and Transformation on Coral Reef Platforms
Authors: Masselink Gerd , Tuck Megan , McCall Robert , van Dongeren Ap , Ford Murray , Kench Paul 
Published: February 2019

AbstractWave transformation across reef platforms strongly controls sediment transport processes and coral reef island morphodynamics with infragravity (IG) waves playing an important contributing role. A small‐scale (1:50) laboratory experiment and prototype numerical modeling are used to explore the characteristics of IG wave motion on coral reefs. The slope of the fore reef is the key factor controlling the mechanism of IG wave generation. Steep slopes (>1/10) are dominated by landward and seaward propagating breakpoint‐forced long waves, whereas incoming and then released bound long waves become increasingly important for slopes <1/20. The breakpoint‐forced long wave mechanism is the more effective generator of IG energy, and the most energetic IG motion (normalized by incident wave motion) is generated on reef platforms with a fore reef slope > 1/6. The water level relative to the reef platform hreef is also a key factor, and the largest IG waves are generated for a ratio between hreef and offshore significant wave height Hs,o of −0.25 to 0.75, that is, when most waves break across the reef slope and a fully saturated surf zone extends across the reef platform. An island on the reef platform substantially increases the contribution of IG waves to the total wave spectrum, but increased reef surface roughness reduces IG importance. Under the most optimal conditions, the IG wave height averaged across the platform is 20–30% of the incident offshore wave height. The geomorphic influence of IG waves is considered most significant for reef platforms with energetic waves breaking on the steepest fore reefs.
Targeting the CALCB/RAMP1 axis inhibits growth of Ewing sarcoma
Authors: Dallmayer Marlene , Li Jing , Ohmura Shunya , Alba Rubio Rebeca , Baldauf Michaela C. , Hölting Tilman L. B. , Musa Julian , Knott Max M. L. , Stein Stefanie , Cidre-Aranaz Florencia , Wehweck Fabienne S. , Romero-Pérez Laura , Gerke Julia S. , Orth Martin F. , Marchetto Aruna , Kirchner Thomas , Bach Horacio , Sannino Giuseppina , Grünewald Thomas G. P. 
Published: February 2019

AbstractEwing sarcoma (EwS) is an aggressive cancer characterized by chromosomal translocations generating fusions of the EWSR1 gene with ETS transcription factors (in 85% FLI1). EWSR1-FLI1 induces gene expression via binding to enhancer-like GGAA-microsatellites, whose activity correlates with the number of consecutive GGAA-repeats. Herein we investigate the role of the secretory neuropeptide CALCB (calcitonin-related polypeptide β) in EwS, which signals via the CGRP (calcitonin gene-related peptide) receptor complex, containing RAMP1 (receptor activity modifying protein 1) as crucial part for receptor specificity. Analysis of 2678 gene expression microarrays comprising 50 tumor entities and 71 normal tissue types revealed that CALCB is specifically and highly overexpressed in EwS. Time-course knockdown experiments showed that CALCB expression is tightly linked to that of EWSR1-FLI1. Consistently, gene set enrichment analyses of genes whose expression in primary EwS is correlated to that of CALCB indicated that it is co-expressed with other EWSR1-FLI1 target genes and associated with signatures involved in stemness and proliferation. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) data for FLI1 and histone marks from EwS cell lines demonstrated that EWSR1-FLI1 binds to a GGAA-microsatellite close to CALCB, which exhibits characteristics of an active enhancer. Reporter assays confirmed the strong EWSR1-FLI1- and length-dependent enhancer activity of this GGAA-microsatellite. Mass spectrometric analyses of EwS cell culture supernatants demonstrated that CALCB is secreted by EwS cells. While short-term RNA interference-mediated CALCB knockdown had no effect on proliferation and clonogenic growth of EwS cells in vitro, its long-term knockdown decreased EwS growth in vitro and in vivo. Similarly, knockdown of RAMP1 reduced clonogenic/spheroidal growth and tumorigenicity, and small-molecule inhibitors directed against the RAMP1-comprising CGRP receptor reduced growth of EwS. Collectively, our findings suggest that CALCB is a direct EWSR1-FLI1 target and that targeting the CALCB/RAMP1 axis may offer a new therapeutic strategy for inhibition of EwS growth.
Targeting KPNB1 overcomes TRAIL resistance by regulating DR5, Mcl-1 and FLIP in glioblastoma cells
Authors: Zhu Zhi-Chuan , Liu Ji-Wei , Yang Can , Li Ming-Jie , Wu Rong-Jie , Xiong Zhi-Qi 
Published: February 2019

AbstractTumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a cytokine with potential anticancer effect, but innate and adaptive TRAIL resistance in majority of cancers limit its clinical application. Karyopherin β1 (KPNB1) inhibition in cancer cells has been reported to abrogate the nuclear import of TRAIL receptor DR5 and facilitate its localization on the cell surface ready for TRAIL stimulation. However, our study reveals a more complicated mechanism. Genetic or pharmacological inhibition of KPNB1 potentiated TRAIL-induced apoptosis selectively in glioblastoma cells mainly by unfolded protein response (UPR). First, it augmented ATF4-mediated DR5 expression and promoted the assembly of death-inducing signaling complex (DISC). Second, it freed Bax and Bak from Mcl-1. Third, it downregulated FLIPLand FLIPS, inhibitors of caspase-8 cleavage, partly through upregulating ATF4–induced 4E-BP1 expression and disrupting the cap-dependent translation initiation. Meanwhile, KPNB1 inhibition-induced undesirable autophagy and accelerated cleaved caspase-8 clearance. Inhibition of autophagic flux maintained cleaved caspase-8 and aggravated apoptosis induced by KPNB1 inhibitor plus TRAIL, which were abolished by caspase-8 inhibitor. These results unveil new molecular mechanism for optimizing TRAIL-directed therapeutic efficacy against cancer.
Neurotrophins and their involvement in digestive cancers
Authors: Blondy Sabrina , Christou Niki , David Valentin , Verdier Mireille , Jauberteau Marie-Odile , Mathonnet Muriel , Perraud Aurélie 
Published: February 2019

AbstractCancers of the digestive system, including esophageal, gastric, pancreatic, hepatic, and colorectal cancers, have a high incidence and mortality worldwide. Efficient therapies have improved patient care; however, many challenges remain including late diagnosis, disease recurrence, and resistance to therapies. Mechanisms responsible for these aforementioned challenges are numerous. This review focuses on neurotrophins, including NGF, BDNF, and NT3, and their specific tyrosine kinase receptors called tropomyosin receptor kinase (Trk A, B, C, respectively), associated with sortilin and the p75 neurotrophin receptor (p75NTR), and their implication in digestive cancers. Globally, p75NTR is a frequently downregulated tumor suppressor. On the contrary, Trk and their ligands are considered oncogenic factors. New therapies which target NT and/or their receptors, or use them as diagnosis biomarkers could help us to combat digestive cancers.
Drosophila Pif1A is essential for spermatogenesis and is the homolog of human CCDC157, a gene associated with idiopathic NOA
Authors: Yuan Xin , Zheng Huimei , Su Yang , Guo Pengfei , Zhang Xiao , Zhao Qiang , Ge Wanzhong , Li Chen , Xi Yongmei , Yang Xiaohang 
Published: February 2019

AbstractThe dynamic process of spermatogenesis shows little variation between invertebrate models such as Drosophila, and vertebrate models such as mice and rats. In each case, germ stem cells undergo mitotic division to proliferate and then continue, via meiosis, through various stages of elongation and individualization from spermatogonia to spermatid to finally to form mature sperm. Mature sperm are then stored in the seminal vesicles for fertilization. Errors in any of these stages can lead to male infertility. Here, we identify that Drosophila Pif1A acts as a key regulator for sperm individualization. Loss of Pif1A leads to male sterility associated with irregular individualization complex and empty seminal vesicles without mature sperm. Pif1A is highly expressed in the testes of mated male adult flies and the Pif1A protein is expressed at a higher level in male than in female flies. Pif1A is homologous to mammalian coiled-coil domain-containing protein 157 (CCDC157), which is also enriched in the testes of humans and mice. Human CCDC157, with unknown function, was identified to be downregulated in men with idiopathic non-obstructive azoospermia (NOA). We map the function of Drosophila Pif1A during spermatogenesis, showing that Pif1A is essential for spermatide individualization and involved in the regulation of the lipid metabolism genes. Our findings might be applicable for studying the function of CCDC157 in spermatogenesis and other aspects of human male fertility.
Oxidation induced strain and defects in magnetite crystals
Authors: Yuan Ke , Lee Sang Soo , Cha Wonsuk , Ulvestad Andrew , Kim Hyunjung , Abdilla Bektur , Sturchio Neil C. , Fenter Paul 
Published: February 2019

AbstractOxidation of magnetite (Fe3O4) has broad implications in geochemistry, environmental science and materials science. Spatially resolving strain fields and defect evolution during oxidation of magnetite provides further insight into its reaction mechanisms. Here we show that the morphology and internal strain distributions within individual nano-sized (~400 nm) magnetite crystals can be visualized using Bragg coherent diffractive imaging (BCDI). Oxidative dissolution in acidic solutions leads to increases in the magnitude and heterogeneity of internal strains. This heterogeneous strain likely results from lattice distortion caused by Fe(II) diffusion that leads to the observed domains of increasing compressive and tensile strains. In contrast, strain evolution is less pronounced during magnetite oxidation at elevated temperature in air. These results demonstrate that oxidative dissolution of magnetite can induce a rich array of strain and defect structures, which could be an important factor that contributes to the high reactivity observed on magnetite particles in aqueous environment.
Clothianidin seed-treatment has no detectable negative impact on honeybee colonies and their pathogens
Authors: Osterman Julia , Wintermantel Dimitry , Locke Barbara , Jonsson Ove , Semberg Emilia , Onorati Piero , Forsgren Eva , Rosenkranz Peter , Rahbek-Pedersen Thorsten , Bommarco Riccardo , Smith Henrik G. , Rundlöf Maj , de Miranda Joachim R. 
Published: February 2019

AbstractInteractions between multiple stressors have been implicated in elevated honeybee colony losses. Here, we extend our landscape-scale study on the effects of placement at clothianidin seed-treated oilseed rape fields on honeybees with an additional year and new data on honeybee colony development, swarming, mortality, pathogens and immune gene expression. Clothianidin residues in pollen, nectar and honeybees were consistently higher at clothianidin-treated fields, with large differences between fields and years. We found large variations in colony development and microbial composition and no observable negative impact of placement at clothianidin-treated fields. Clothianidin treatment was associated with an increase in brood, adult bees and Gilliamella apicola (beneficial gut symbiont) and a decrease in Aphid lethal paralysis virus and Black queen cell virus - particularly in the second year. The results suggest that at colony level, honeybees are relatively robust to the effects of clothianidin in real-world agricultural landscapes, with moderate, natural disease pressure.
A phenome-wide association study to discover pleiotropic effects of PCSK9, APOB, and LDLR
Authors: Safarova Maya S. , Satterfield Benjamin A. , Fan Xiao , Austin Erin E. , Ye Zhan , Bastarache Lisa , Zheng Neil , Ritchie Marylyn D. , Borthwick Kenneth M. , Williams Marc S. , Larson Eric B. , Scrol Aaron , Jarvik Gail P. , Crosslin David R. , Leppig Kathleen , Rasmussen-Torvik Laura J. , Pendergrass Sarah A. , Sturm Amy C. , Namjou Bahram , Shah Amy Sanghavi , Carroll Robert J. , Chung Wendy K. , Wei Wei-Qi , Feng QiPing , Stein C. Michael , Roden Dan M. , Manolio Teri A. , Schaid Daniel J. , Denny Joshua C. , Hebbring Scott J. , de Andrade Mariza , Kullo Iftikhar J. 
Published: February 2019

AbstractWe conducted an electronic health record (EHR)-based phenome-wide association study (PheWAS) to discover pleiotropic effects of variants in three lipoprotein metabolism genesPCSK9,APOB, andLDLR. Using high-density genotype data, we tested the associations of variants in the three genes with 1232 EHR-derived binary phecodes in 51,700 European-ancestry (EA) individuals and 585 phecodes in 10,276 African-ancestry (AA) individuals; 457PCSK9, 730APOB, and 720LDLRvariants were filtered by imputation quality (r2 > 0.4), minor allele frequency (>1%), linkage disequilibrium (r2 < 0.3), and association with LDL-C levels, yielding a set of twoPCSK9, threeAPOB, and fiveLDLRvariants in EA but no variants in AA. Cases and controls were defined for each phecode using the PheWAS package in R. Logistic regression assuming an additive genetic model was used with adjustment for age, sex, and the first two principal components. Significant associations were tested in additional cohorts from Vanderbilt University (n = 29,713), the Marshfield Clinic Personalized Medicine Research Project (n = 9562), and UK Biobank (n = 408,455). We identified onePCSK9, twoAPOB, and twoLDLRvariants significantly associated with an examined phecode. Only one of the variants was associated with a non-lipid disease phecode, (“myopia”) but this association was not significant in the replication cohorts. In this large-scale PheWAS we did not find LDL-C-related variants inPCSK9,APOB, andLDLRto be associated with non-lipid-related phenotypes including diabetes, neurocognitive disorders, or cataracts.
The effects of Co on the enhancement of magnetic properties by modifying the intergranular phase in Nd-Fe-B alloys
Authors: Liang Y. , Deng Q. , Tan X. H. , Li H. , Xu H. 
Published: February 2019

AbstractIn Nd2Fe14B-based permanent materials, the intergranular phase has a strong influence on magnetic properties. Here, we study the effect of partial substitution of Fe by Co on the microstructure to gain insight into the mechanism of enhancing magnetic properties of (Nd0.8Pr0.2)2.2Fe14−xCoxB (x = 0, 1.75, 2, 2.25) alloys. Our results show that the substitution Co for Fe changes the magnetic properties obviously by tuning the chemistry and distribution of the intergranular phase between hard magnetic grains. In particular, for (Nd0.8Pr0.2)2.2Fe12Co2B (x = 2) alloy, no obvious intergranular phase is observed. And the through-thickness homogeneity and ultrafine microstructure with an average size of ~25 nm is obtained, which produces maximum product ((BH)max) of 141 kJ/m3, 29% higher than that of quaternary alloy. Our findings provide a new idea to design prospective permanent alloys with increased magnetic properties by tuning the distribution and chemical composition of the intergranular phase.
Metabolomics Approach Based on Multivariate Techniques for Blood Transfusion Reactions
Authors: Lee Seul Ji , Wang Haiping , Ahn Soo Hyun , Son Mi Kwon , Hyun Gyu Hwan , Yoon Sang Jun , Lee Jeongmi , Park Jeong Hill , Lim Johan , Hong Soon-Sun , Kwon Sung Won 
Published: February 2019

AbstractBlood transfusions temporarily improve the physical state of the patient but exert widespread effects on immune and non-immune systems. Perioperative allogeneic blood transfusions (ABT) are associated with various risks, including coagulopathy, incompatibility, transmission of infectious agents, and allergic reactions. Nevertheless, little is known about the global metabolic alterations that reflect the possible reactions of blood transfusions. In this study, we investigated metabolite changes generated by ABT in a rat model using metabolomics technology. To further profile the “metabolome” after blood transfusions, we used both liquid chromatography-quadrupole time-of-flight high-definition mass spectrometry and gas chromatography-mass spectrometry. ABT promoted a stimulatory microenvironment associated with a relative increase in glucose transporter 1/4 (GLUT1/GLUT4) expression. Supporting this result, glucose metabolism-related enzyme IRS1 and interleukin-6 (IL-6) were abnormally expressed, and levels of lysophosphatidylcholine (LysoPC) and its related enzyme phospholipase A2 (PLA2) were significantly altered in allogeneic groups compared to those in autologous groups. Finally, amino acid metabolism was also altered following ABT. Taken together, our results show a difference between autologous and allogeneic blood transfusions and demonstrate correlations with cancer-associated metabolic changes. Our data provide endogenous information for a better understanding of blood transfusion reactions.
A comparative in vitro study of the osteogenic and adipogenic potential of human dental pulp stem cells, gingival fibroblasts and foreskin fibroblasts
Authors: Monterubbianesi Riccardo , Bencun Mladen , Pagella Pierfrancesco , Woloszyk Anna , Orsini Giovanna , Mitsiadis Thimios A. 
Published: February 2019

AbstractHuman teeth contain a variety of mesenchymal stem cell populations that could be used for cell-based regenerative therapies. However, the isolation and potential use of these cells in the clinics require the extraction of functional teeth, a process that may represent a significant barrier to such treatments. Fibroblasts are highly accessible and might represent a viable alternative to dental stem cells. We thus investigated and compared the in vitro differentiation potential of human dental pulp stem cells (hDPSCs), gingival fibroblasts (hGFs) and foreskin fibroblasts (hFFs). These cell populations were cultured in osteogenic and adipogenic differentiation media, followed by Alizarin Red S and Oil Red O staining to visualize cytodifferentiation. Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) was performed to assess the expression of markers specific for stem cells (NANOG, OCT-4), osteogenic (RUNX2, ALP, SP7/OSX) and adipogenic (PPAR-γ2, LPL) differentiation. While fibroblasts are more prone towards adipogenic differentiation, hDPSCs exhibit a higher osteogenic potential. These results indicate that although fibroblasts possess a certain mineralization capability, hDPSCs represent the most appropriate cell population for regenerative purposes involving bone and dental tissues.
Cytotoxicity of apo bovine α-lactalbumin complexed with La3+ on cancer cells supported by its high resolution crystal structure
Authors: Yarramala Deepthi S. , Prakash Prem , Ranade Dnyanesh S. , Doshi Sejal , Kulkarni Prasad P. , Bhaumik Prasenjit , Rao Chebrolu Pulla 
Published: February 2019

AbstractCancer remains one of the biggest threats to human society. There are massive demands for compounds to selectively kill cancerous cells. Earlier studies have shown that bovine α -lactalbumin made lethal to tumor cells (BAMLET) becomes cytotoxic against cancer cells in complex with oleic acid {Hoque, M. et. al., PLoSOne8, e68390 (2013)}. In our study, we obtained bovine α-lactalbumin complexed with lanthanum ion (La3+-B-α-LA) and determined its high resolution crystal structure. The natural calcium binding site of bovine α-lactalbumin is replaced by lanthanum. The La3+ complex formation by B-α-apo-LA was also supported by various biophysical methods. Interestingly, our complex, La3+-B-α-LA exhibits much greater anticancer activity against breast cancer cells as compared to the reported BAMLET-oleic acid complex. This study shows that La3+-B-α-LA complex is preferentially more toxic to MCF-7 cells as compared to KB (oral cancer) and HeLa (cervical) cells, while almost non-toxic to the healthy cells that we studied. Our data indicates that the cytotoxicity of La3+-B-α-LA against cancer cells is through apoptotic path way. The higher anticancer activity of La3+-B-α-LA is attributable to the requisite structural changes induced in the protein by La3+ binding as supported by the crystal structure of the complex.
Ultra-Short Pulse Generation in a Three Section Tapered Passively Mode-Locked Quantum-Dot Semiconductor Laser
Authors: Meinecke Stefan , Drzewietzki Lukas , Weber Christoph , Lingnau Benjamin , Breuer Stefan , Lüdge Kathy 
Published: February 2019

AbstractWe experimentally and theoretically investigate the pulsed emission dynamics of a three section tapered semiconductor quantum dot laser. The laser output is characterized in terms of peak power, pulse width, timing jitter and amplitude stability and a range of outstanding pulse performance is found. A cascade of dynamic operating regimes is identified and comprehensively investigated. We propose a microscopically motivated traveling-wave model, which optimizes the computation time and naturally allows insights into the internal carrier dynamics. The model excellently reproduces the measured results and is further used to study the pulse-generation mechanism as well as the influence of the geometric design on the pulsed emission. We identify a pulse shortening mechanism responsible for the device performance, that is unique to the device geometry and configuration. The results may serve as future guidelines for the design of monolithic high-power passively mode-locked quantum dot semiconductor lasers.