bluuebunny/crossref_metadata_2025_split huggingface dataset:
The HIF target MAFF promotes tumor invasion and metastasis through IL11 and STAT3 signaling
Authors: Moon Eui Jung , Mello Stephano S. , Li Caiyun G. , Chi Jen-Tsan , Thakkar Kaushik , Kirkland Jacob G. , Lagory Edward L. , Lee Ik Jae , Diep Anh N. , Miao Yu , Rafat Marjan , Vilalta Marta , Castellini Laura , Krieg Adam J. , Graves Edward E. , Attardi Laura D. , Giaccia Amato J. 
Published: July 2021

AbstractHypoxia plays a critical role in tumor progression including invasion and metastasis. To determine critical genes regulated by hypoxia that promote invasion and metastasis, we screen fifty hypoxia inducible genes for their effects on invasion. In this study, we identify v-maf musculoaponeurotic fibrosarcoma oncogene homolog F (MAFF) as a potent regulator of tumor invasion without affecting cell viability. MAFF expression is elevated in metastatic breast cancer patients and is specifically correlated with hypoxic tumors. Combined ChIP- and RNA-sequencing identifies IL11 as a direct transcriptional target of the heterodimer between MAFF and BACH1, which leads to activation of STAT3 signaling. Inhibition of IL11 results in similar levels of metastatic suppression as inhibition of MAFF. This study demonstrates the oncogenic role of MAFF as an activator of the IL11/STAT3 pathways in breast cancer.
Intracellular lipid droplet accumulation occurs early following viral infection and is required for an efficient interferon response
Authors: Monson E. A. , Crosse K. M. , Duan M. , Chen W. , O’Shea R. D. , Wakim L. M. , Carr J. M. , Whelan D. R. , Helbig K. J. 
Published: July 2021

AbstractLipid droplets (LDs) are increasingly recognized as critical organelles in signalling events, transient protein sequestration and inter-organelle interactions. However, the role LDs play in antiviral innate immune pathways remains unknown. Here we demonstrate that induction of LDs occurs as early as 2 h post-viral infection, is transient and returns to basal levels by 72 h. This phenomenon occurs following viral infections, both in vitro and in vivo. Virally driven in vitro LD induction is type-I interferon (IFN) independent, and dependent on Epidermal Growth Factor Receptor (EGFR) engagement, offering an alternate mechanism of LD induction in comparison to our traditional understanding of their biogenesis. Additionally, LD induction corresponds with enhanced cellular type-I and -III IFN production in infected cells, with enhanced LD accumulation decreasing viral replication of both Herpes Simplex virus 1 (HSV-1) and Zika virus (ZIKV). Here, we demonstrate, that LDs play vital roles in facilitating the magnitude of the early antiviral immune response specifically through the enhanced modulation of IFN following viral infection, and control of viral replication. By identifying LDs as a critical signalling organelle, this data represents a paradigm shift in our understanding of the molecular mechanisms which coordinate an effective antiviral response.
Ultrafast olivine-ringwoodite transformation during shock compression
Authors: Okuchi Takuo , Seto Yusuke , Tomioka Naotaka , Matsuoka Takeshi , Albertazzi Bruno , Hartley Nicholas J. , Inubushi Yuichi , Katagiri Kento , Kodama Ryosuke , Pikuz Tatiana A. , Purevjav Narangoo , Miyanishi Kohei , Sato Tomoko , Sekine Toshimori , Sueda Keiichi , Tanaka Kazuo A. , Tange Yoshinori , Togashi Tadashi , Umeda Yuhei , Yabuuchi Toshinori , Yabashi Makina , Ozaki Norimasa 
Published: July 2021

AbstractMeteorites from interplanetary space often include high-pressure polymorphs of their constituent minerals, which provide records of past hypervelocity collisions. These collisions were expected to occur between kilometre-sized asteroids, generating transient high-pressure states lasting for several seconds to facilitate mineral transformations across the relevant phase boundaries. However, their mechanisms in such a short timescale were never experimentally evaluated and remained speculative. Here, we show a nanosecond transformation mechanism yielding ringwoodite, which is the most typical high-pressure mineral in meteorites. An olivine crystal was shock-compressed by a focused high-power laser pulse, and the transformation was time-resolved by femtosecond diffractometry using an X-ray free electron laser. Our results show the formation of ringwoodite through a faster, diffusionless process, suggesting that ringwoodite can form from collisions between much smaller bodies, such as metre to submetre-sized asteroids, at common relative velocities. Even nominally unshocked meteorites could therefore contain signatures of high-pressure states from past collisions.
Autonomous reinforcement learning agent for chemical vapor deposition synthesis of quantum materials
Authors: Rajak Pankaj , Krishnamoorthy Aravind , Mishra Ankit , Kalia Rajiv , Nakano Aiichiro , Vashishta Priya 
Published: July 2021

AbstractPredictive materials synthesis is the primary bottleneck in realizing functional and quantum materials. Strategies for synthesis of promising materials are currently identified by time-consuming trial and error and there are no known predictive schemes to design synthesis parameters for materials. We use offline reinforcement learning (RL) to predict optimal synthesis schedules, i.e., a time-sequence of reaction conditions like temperatures and concentrations, for the synthesis of semiconducting monolayer MoS2 using chemical vapor deposition. The RL agent, trained on 10,000 computational synthesis simulations, learned threshold temperatures and chemical potentials for onset of chemical reactions and predicted previously unknown synthesis schedules that produce well-sulfidized crystalline, phase-pure MoS2. The model can be extended to multi-task objectives such as predicting profiles for synthesis of complex structures including multi-phase heterostructures and can predict long-time behavior of reacting systems, far beyond the domain of molecular dynamics simulations, making these predictions directly relevant to experimental synthesis.
Predicting thermoelectric properties from chemical formula with explicitly identifying dopant effects
Authors: Na Gyoung S. , Jang Seunghun , Chang Hyunju 
Published: July 2021

AbstractDopants play an important role in synthesizing materials to improve target materials properties or stabilize the materials. In particular, the dopants are essential to improve thermoelectic performances of the materials. However, existing machine learning methods cannot accurately predict the materials properties of doped materials due to severely nonlinear relations with their materials properties. Here, we propose a unified architecture of neural networks, called DopNet, to accurately predict the materials properties of the doped materials. DopNet identifies the effects of the dopants by explicitly and independently embedding the host materials and the dopants. In our evaluations, DopNet outperformed existing machine learning methods in predicting experimentally measured thermoelectric properties, and the error of DopNet in predicting a figure of merit (ZT) was 0.06 in mean absolute error. In particular, DopNet was significantly effective in an extrapolation problem that predicts ZTs of unknown materials, which is a key task to discover novel thermoelectric materials.
A molecular roadmap towards organic donor-acceptor complexes with high-performance thermoelectric response
Authors: Shi Wen , Deng Tianqi , Wong Zicong Marvin , Wu Gang , Yang Shuo-Wang 
Published: July 2021

AbstractAs a unique class of molecular electronic materials, organic donor–acceptor complexes now exhibit tantalizing prospect for heat–electricity interconversion. Over the past decades, in design of these materials for thermoelectric applications, consistent efforts have been made to synthesize a wide variety of structures and to characterize their properties. However, hitherto, one of the paramount conundrums, namely lack of systematic molecular design principles, has not been addressed yet. Here, based on ab initio calculations, and by comprehensively examining the underlying correlation among thermoelectric power factors, non-intuitive transport processes, and fundamental chemical structures for 13 prototypical organic donor–acceptor complexes, we establish a unified roadmap for rational development of these materials with increased thermoelectric response. We corroborate that the energy levels of frontier molecular orbitals in the isolated donor and acceptor molecules control the charge transfer, electronic property, charge transport, and thermoelectric performance in the solid-state complexes. Our results demonstrate that tailoring a suitable energy-level difference between donor’s highest occupied molecular orbital and acceptor’s lowest unoccupied molecular orbital holds the key to achieving an outstanding power factor. Moreover, we reveal that the charge-transfer-caused Coulomb scattering governs the charge and thermoelectric transport in organic donor–acceptor complexes.
Riemann zeros from Floquet engineering a trapped-ion qubit
Authors: He Ran , Ai Ming-Zhong , Cui Jin-Ming , Huang Yun-Feng , Han Yong-Jian , Li Chuan-Feng , Guo Guang-Can , Sierra G. , Creffield C. E. 
Published: July 2021

AbstractThe non-trivial zeros of the Riemann zeta function are central objects in number theory. In particular, they enable one to reproduce the prime numbers. They have also attracted the attention of physicists working in random matrix theory and quantum chaos for decades. Here we present an experimental observation of the lowest non-trivial Riemann zeros by using a trapped-ion qubit in a Paul trap, periodically driven with microwave fields. The waveform of the driving is engineered such that the dynamics of the ion is frozen when the driving parameters coincide with a zero of the real component of the zeta function. Scanning over the driving amplitude thus enables the locations of the Riemann zeros to be measured experimentally to a high degree of accuracy, providing a physical embodiment of these fascinating mathematical objects in the quantum realm.
Immunologic mechanisms of seasonal influenza vaccination administered by microneedle patch from a randomized phase I trial
Authors: Rouphael Nadine G. , Lai Lilin , Tandon Sonia , McCullough Michele Paine , Kong Yunchuan , Kabbani Sarah , Natrajan Muktha S. , Xu Yongxian , Zhu Yerun , Wang Dongli , O’Shea Jesse , Sherman Amy , Yu Tianwei , Henry Sebastien , McAllister Devin , Stadlbauer Daniel , Khurana Surender , Golding Hana , Krammer Florian , Mulligan Mark J. , Prausnitz Mark R. 
Published: July 2021

AbstractIn a phase 1 randomized, single-center clinical trial, inactivated influenza virus vaccine delivered through dissolvable microneedle patches (MNPs) was found to be safe and immunogenic. Here, we compare the humoral and cellular immunologic responses in a subset of participants receiving influenza vaccination by MNP to the intramuscular (IM) route of administration. We collected serum, plasma, and peripheral blood mononuclear cells in 22 participants up to 180 days post-vaccination. Hemagglutination inhibition (HAI) titers and antibody avidity were similar after MNP and IM vaccination, even though MNP vaccination used a lower antigen dose. MNPs generated higher neuraminidase inhibition (NAI) titers for all three influenza virus vaccine strains tested and triggered a larger percentage of circulating T follicular helper cells (CD4 + CXCR5 + CXCR3 + ICOS + PD-1+) compared to the IM route. Our study indicates that inactivated influenza virus vaccination by MNP produces humoral and cellular immune response that are similar or greater than IM vaccination.
Tetramethylguanidine-functionalized melamine as a multifunctional organocatalyst for the expeditious synthesis of 1,2,4-triazoloquinazolinones
Authors: Keshavarz Mahnoush , Dekamin Mohammad G. , Mamaghani Manouchehr , Nikpassand Mohammad 
Published: July 2021

AbstractNovel nano-ordered 1,1,3,3-tetramethylguanidine-functionalized melamine (Melamine@TMG) organocatalyst was prepared and adequately identified by various techniques including FTIR, EDX, XRD and SEM spectroscopic or microscopic methods as well as TGA and DTG analytical methods. The Melamine@TMG, as an effective multifunctional organocatalyst, was found to promote smoothly the three-component synthesis of 1,2,4-triazoloquinazolinone derivatives using cyclic dimedone, 3-amino-1,2,4-triazole and different benzaldehyde derivatives in EtOH at 40 °C. This practical method afforded the desired products in high to excellent yields (86–99%) and short reaction times (10–25 min). The main advantages of this new method are the use of heterogeneous multifunctional nanocatalyst, simple work-up procedure with no need for chromatographic purification, highly selective conversion of substrates and recyclability of the catalyst, which could be used in five consecutive runs with only a small decrease in its activity.
Clubroot resistance derived from the European Brassica napus cv. ‘Tosca’ is not effective against virulent Plasmodiophora brassicae isolates from Alberta, Canada
Authors: Fredua-Agyeman Rudolph , Hwang Sheau-Fang , Zhang Hui , Falak Igor , Huang Xiuqiang , Strelkov Stephen E. 
Published: July 2021

AbstractIn this study, clubroot resistance in the resynthesized European winter Brassica napus cv. ‘Tosca’ was introgressed into a Canadian spring canola line ‘11SR0099’, which was then crossed with the clubroot susceptible spring line ‘12DH0001’ to produce F1 seeds. The F1 plants were used to develop a doubled haploid (DH) mapping population. The parents and the DH lines were screened against ‘old’ pathotypes 2F, 3H, 5I, 6M and 8N of the clubroot pathogen, Plasmodiophora brassicae, as well as against the ‘new’ pathotypes 5X, 5L, 2B, 3A, 3D, 5G, 8E, 5C, 8J, 5K, 3O and 8P. Genotyping was conducted using a Brassica 15K SNP array. The clubroot screening showed that ‘Tosca, ‘11SR0099’ and the resistant DH lines were resistant to three (2F, 3H and 5I) of the five ‘old’ pathotypes and four (2B, 3O, 8E and 8P) of the 12 ‘new’ pathotypes, while being moderately resistant to the ‘old’ pathotype 8N and the ‘new’ pathotypes 3D and 5G. ‘Tosca’ was susceptible to isolates representing pathotype 3A (the most common among the ‘new’ pathotypes) as well as pathotypes 6M, 5X, 5L, 5K and 8J. Linkage analysis and QTL mapping identified a ca. 0.88–0.95 Mb genomic region on the A03 chromosome of ‘Tosca’ as conferring resistance to pathotypes 2F, 3H, 5I, 2B, 3D, 5G, 8E, 3O and 8P. The identified QTL genomic region housed the CRk, Crr3 and CRd gene(s). However, the susceptibility of ‘Tosca’ to most of the common virulent pathotypes makes it unattractive as a sole CR donor in the breeding of commercial canola varieties in western Canada.
Iodine containing porous organosilica nanoparticles trigger tumor spheroids destruction upon monochromatic X-ray irradiation: DNA breaks and K-edge energy X-ray
Authors: Higashi Yuya , Matsumoto Kotaro , Saitoh Hiroyuki , Shiro Ayumi , Ma Yue , Laird Mathilde , Chinnathambi Shanmugavel , Birault Albane , Doan Tan Le Hoang , Yasuda Ryo , Tajima Toshiki , Kawachi Tetsuya , Tamanoi Fuyuhiko 
Published: July 2021

AbstractX-ray irradiation of high Z elements causes photoelectric effects that include the release of Auger electrons that can induce localized DNA breaks. We have previously established a tumor spheroid-based assay that used gadolinium containing mesoporous silica nanoparticles and synchrotron-generated monochromatic X-rays. In this work, we focused on iodine and synthesized iodine-containing porous organosilica (IPO) nanoparticles. IPO were loaded onto tumor spheroids and the spheroids were irradiated with 33.2 keV monochromatic X-ray. After incubation in CO2 incubator, destruction of tumor spheroids was observed which was accompanied by apoptosis induction, as determined by the TUNEL assay. By employing the γH2AX assay, we detected double strand DNA cleavages immediately after the irradiation. These results suggest that IPO first generate double strand DNA breaks upon X-ray irradiation followed by apoptosis induction of cancer cells. Use of three different monochromatic X-rays having energy levels of 33.0, 33.2 and 33.4 keV as well as X-rays with 0.1 keV energy intervals showed that the optimum effect of all three events (spheroid destruction, apoptosis induction and generation of double strand DNA breaks) occurred with a 33.2 keV monochromatic X-ray. These results uncover the preferential effect of K-edge energy X-ray for tumor spheroid destruction mediated by iodine containing nanoparticles.
Quantitative observation of monochromatic X-rays emitted from implosion hotspot in high spatial resolution in inertial confinement fusion
Authors: Ren Kuan , Wu Junfeng , Dong Jianjun , Li Yaran , Huang Tianxuan , Zhao Hang , Liu Yaoyuan , Cao Zhurong , Zhang Jiyan , Mu Baozhong , Yan Ji , Jiang Wei , Pu Yudong , Li Yulong , Peng Xiaoshi , Xu Tao , Yang Jiamin , Lan Ke , Ding Yongkun , Jiang Shaoen , Wang Feng 
Published: July 2021

AbstractIn inertial confinement fusion, quantitative and high-spatial resolution ($$< 10\,\upmu $$

<
10

μ

m) measurements of the X-rays self-emitted by the hotspot are critical for studying the physical processes of the implosion stagnation stage. Herein, the 8 ± 0.39-keV monochromatic X-ray distribution from the entire hotspot is quantitatively observed in 5-$$\upmu $$
μ
m spatial resolution using a Kirkpatrick–Baez microscope, with impacts from the responses of the diagnosis system removed, for the first time, in implosion experiments at the 100 kJ laser facility in China. Two-dimensional calculations along with 2.5% P2 drive asymmetry and 0.3 ablator self-emission are congruent with the experimental results, especially for the photon number distribution, hotspot profile, and neutron yield. Theoretical calculations enabled a better understanding of the experimental results. Furthermore, the origins of the 17.81% contour profile of the deuterium-deuterium hotspot and the accurate Gaussian source approximation of the core emission area in the implosion capsule are clarified in detail. This work is significant for quantitatively exploring the physical conditions of the hotspot and updating the theoretical model of capsule implosion.
Unveiling the third dimension in morphometry with automated quantitative volumetric computations
Authors: Frank Lawrence R. , Rowe Timothy B. , Boyer Doug M. , Witmer Lawrence M. , Galinsky Vitaly L. 
Published: July 2021

AbstractAs computed tomography and related technologies have become mainstream tools across a broad range of scientific applications, each new generation of instrumentation produces larger volumes of more-complex 3D data. Lagging behind are step-wise improvements in computational methods to rapidly analyze these new large, complex datasets. Here we describe novel computational methods to capture and quantify volumetric information, and to efficiently characterize and compare shape volumes. It is based on innovative theoretical and computational reformulation of volumetric computing. It consists of two theoretical constructs and their numerical implementation: the spherical wave decomposition (SWD), that provides fast, accurate automated characterization of shapes embedded within complex 3D datasets; and symplectomorphic registration with phase space regularization by entropy spectrum pathways (SYMREG), that is a non-linear volumetric registration method that allows homologous structures to be correctly warped to each other or a common template for comparison. Together, these constitute the Shape Analysis for Phenomics from Imaging Data (SAPID) method. We demonstrate its ability to automatically provide rapid quantitative segmentation and characterization of single unique datasets, and both inter-and intra-specific comparative analyses. We go beyond pairwise comparisons and analyze collections of samples from 3D data repositories, highlighting the magnified potential our method has when applied to data collections. We discuss the potential of SAPID in the broader context of generating normative morphologies required for meaningfully quantifying and comparing variations in complex 3D anatomical structures and systems.
Intrauterine﻿ growth restriction weakens anticontractile influence of NO in coronary arteries of adult rats
Authors: Selivanova Ekaterina K. , Shvetsova Anastasia A. , Shilova Lyubov D. , Tarasova Olga S. , Gaynullina Dina K. 
Published: July 2021

AbstractIntrauterine growth restriction (IUGR) is one of the most common pathologies of pregnancy. The cardiovascular consequences of IUGR do not disappear in adulthood and can manifest themselves in pathological alterations of vasomotor control. The hypothesis was tested that IUGR weakens anticontractile influence of NO and augments procontractile influence of Rho-kinase in arteries of adult offspring. To model IUGR in the rat, dams were 50% food restricted starting from the gestational day 11 till delivery. Mesenteric and coronary arteries of male offspring were studied at the age of 3 months using wire myography, qPCR, and Western blotting. Contractile responses of mesenteric arteries to α1-adrenoceptor agonist methoxamine as well as influences of NO and Rho-kinase did not differ between control and IUGR rats. However, coronary arteries of IUGR rats demonstrated elevated contraction to thromboxane A2 receptor agonist U46619 due to weakened anticontractile influence of NO and enhanced role of Rho-kinase in the endothelium. This was accompanied by reduced abundance of SODI protein and elevated content of RhoA protein in coronary arteries of IUGR rats. IUGR considerably changes the regulation of coronary vascular tone in adulthood and, therefore, can serve as a risk factor for the development of cardiac disorders.
Integrated whole transcriptome and small RNA analysis revealed multiple regulatory networks in colorectal cancer
Authors: Shaath Hibah , Toor Salman M. , Nada Mohamed Abu , Elkord Eyad , Alajez Nehad M. 
Published: July 2021

AbstractColorectal cancer (CRC) remains a global disease burden and a leading cause of cancer related deaths worldwide. The identification of aberrantly expressed messenger RNA (mRNA), long non-coding RNA (lncRNA), and microRNA (miRNA), and the resulting molecular interactions and signaling networks is essential for better understanding of CRC, identification of novel diagnostic biomarkers and potential development of therapeutic interventions. Herein, we performed microRNA (miRNA) sequencing on fifteen CRC and their non-tumor adjacent tissues and whole transcriptome RNA-Seq on six paired samples from the same cohort and identified alterations in miRNA, mRNA, and lncRNA expression. Computational analyses using Ingenuity Pathway Analysis (IPA) identified multiple activated signaling networks in CRC, including ERBB2, RABL6, FOXM1, and NFKB networks, while functional annotation highlighted activation of cell proliferation and migration as the hallmark of CRC. IPA in combination with in silico prediction algorithms and experimentally validated databases gave insight into the complex associations and interactions between downregulated miRNAs and upregulated mRNAs in CRC and vice versa. Additionally, potential interaction between differentially expressed lncRNAs such as H19, SNHG5, and GATA2-AS1 with multiple miRNAs has been revealed. Taken together, our data provides thorough analysis of dysregulated protein-coding and non-coding RNAs in CRC highlighting numerous associations and regulatory networks thus providing better understanding of CRC.