bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors Controlling O+ and H+ Outflow in the Cusp During a Geomagnetic Storm: FAST/TEAMS Observations
Authors: Zhao K. , Kistler L .M. , Lund E. J. , Nowrouzi N. , Kitamura N. , Strangeway R. J. 
Published: March 2020

AbstractFactors related to two sources of energy input to the ionosphere, the Poynting flux associated with both quasistatic fields (Sdc) and Alfvénic fluctuations (Sac), and the soft electron precipitation, are investigated to evaluate their correlations with the O+ and the H+ outflows in the dayside cusp region by using recalibrated FAST/Time‐of‐Flight Energy, Angle, and Mass Spectrograph (TEAMS) data during the 24–25 September 1998 geomagnetic storm studied by Strangeway et al. (2005, https://doi.org/10.1029/2004JA010829). The Poynting flux and the soft electron precipitation are well correlated with ion outflow flux in the dayside cusp region. Sdc shows the highest correlation with the O+ outflows, while it is the electron number flux that correlates best with the H+ outflows. The Alfvénic waves play an essential role in accelerating outflows. The averaged O+/H+ flux ratio is 3.0 and is positively correlated to the Poynting flux, suggesting that the O+ flux increases more strongly with the energy input.
Using physiologically-based pharmacokinetic modeling to assess the efficacy of glove materials in reducing internal doses and potential hazards of N-methylpyrrolidone during paint stripping
Authors: Kirman C. R. 
Published: March 2020

AbstractA refined risk assessment was conducted to evaluate the efficacy of different glove materials in reducing the potential hazards associated with using paint strippers containing N-methylpyrrolidone (NMP) under the scenarios defined by USEPA’s TSCA risk assessment. Three categories of gloves were identified based on measured permeation rates for NMP: (1) minimal protection; (2) moderate protection; and (3) maximal protection. Simulations for eight acute and chronic occupational exposure scenarios identified by USEPA as having a potential hazard (i.e., margins of exposure, MOE, <30) were reassessed for each glove category using PBPK modeling to predict peak (Cmax) and cumulative (AUC) internal doses of NMP. For the acute assessment, the refined MOE values were ≥30 for half of the scenarios for gloves from the moderate protection group category, and all of the scenarios for gloves from the maximal protection category. For the chronic assessment, the refined MOE values were ≥30 for all scenarios except one for gloves from the maximal protection category. The results of this assessment indicate that: (1) the degree of protection provided by gloves from NMP permeation can vary widely depending upon the glove material, NMP formulation, and internal dose measure (with calculated glove protection factors ranging from 1.1 to 1900); and (2) NMP-containing paint strippers can be used safely when appropriate PPE are used. As such, these results can be used to support risk-reduction methods (e.g., product labeling, MSDS instructions on use of appropriate glove materials) as alternatives to banning NMP use under TSCA.
Learning to synthesize: robust phase retrieval at low photon counts
Authors: Deng Mo , Li Shuai , Goy Alexandre , Kang Iksung , Barbastathis George 
Published: March 2020

AbstractThe quality of inverse problem solutions obtained through deep learning is limited by the nature of the priors learned from examples presented during the training phase. Particularly in the case of quantitative phase retrieval, spatial frequencies that are underrepresented in the training database, most often at the high band, tend to be suppressed in the reconstruction. Ad hoc solutions have been proposed, such as pre-amplifying the high spatial frequencies in the examples; however, while that strategy improves the resolution, it also leads to high-frequency artefacts, as well as low-frequency distortions in the reconstructions. Here, we present a new approach that learns separately how to handle the two frequency bands, low and high, and learns how to synthesize these two bands into full-band reconstructions. We show that this “learning to synthesize” (LS) method yields phase reconstructions of high spatial resolution and without artefacts and that it is resilient to high-noise conditions, e.g., in the case of very low photon flux. In addition to the problem of quantitative phase retrieval, the LS method is applicable, in principle, to any inverse problem where the forward operator treats different frequency bands unevenly, i.e., is ill-posed.
Detection and extraction of heavy metal ions using paper-based analytical devices fabricated via atom stamp printing
Authors: Guan Yanfang , Sun Baichuan 
Published: March 2020

AbstractAs a promising concept, microfluidic paper-based analytical devices (μPADs) have seen rapid development in recent years. In this study, a new method of fabricating μPADs by atom stamp printing (ASP) is proposed and studied. The advantages of this new method compared to other methods include its low cost, ease of operation, high production efficiency, and high resolution (the minimum widths of the hydrophilic channels and hydrophobic barriers are 328 and 312 μm, respectively). As a proof of concept, μPADs fabricated with the ASP method were used to detect different concentrations of Cu2+via a colorimetric method. Moreover, combined with a distance-based detection method, these devices achieved a Cu2+detection limit of down to 1 mg/L. In addition, a new paper-based solid–liquid extraction device (PSED) based on a three-dimensional (3D) μPAD with a “3 + 2” structure and a recyclable extraction mode was developed. Specifically, using the characteristics of paper filtration and capillary force, the device completed multiple extraction and filtration steps from traditional solid–liquid extraction processes with high efficiency. The developed PSED platform allows the detection of heavy metal ions much more cheaply and simply and with a faster response time at the point of care, and it has great promise for applications in food safety and environmental pollution in resource-limited areas.
Bacterial vitamin B12 production enhances nematode predatory behavior
Authors: Akduman Nermin , Lightfoot James W , Röseler Waltraud , Witte Hanh , Lo Wen-Sui , Rödelsperger Christian , Sommer Ralf J 
Published: March 2020

Abstract
Although the microbiota is known to affect host development, metabolism, and immunity, its impact on host behavior is only beginning to be understood. In order to better characterize behavior modulation by host-associated microorganisms, we investigated how bacteria modulate complex behaviors in the nematode model organism Pristionchus pacificus. This nematode is a predator that feeds on the larvae of other nematodes, including Caenorhabditis elegans. By growing P. pacificus on different bacteria and testing their ability to kill C. elegans, we reveal large differences in killing efficiencies, with a Novosphingobium species showing the strongest enhancement. This enhanced killing was not accompanied by an increase in feeding, which is a phenomenon known as surplus killing, whereby predators kill more prey than necessary for sustenance. Our RNA-seq data demonstrate widespread metabolic rewiring upon exposure to Novosphingobium, which facilitated screening of bacterial mutants with altered transcriptional responses. We identified bacterial production of vitamin B12 as an important cause of such enhanced predatory behavior. Although vitamin B12 is an essential cofactor for detoxification and metabolite biosynthesis, shown previously to accelerate development in C. elegans, supplementation with this enzyme cofactor amplified surplus killing in P. pacificus, whereas mutants in vitamin B12-dependent pathways reduced surplus killing. By demonstrating that production of vitamin B12 by host-associated microbiota can affect complex host behaviors, we reveal new connections between animal diet, microbiota, and nervous system.
Mitochondrial division inhibitor (mdivi-1) decreases oxidative metabolism in cancer
Authors: Dai Wenting , Wang Guan , Chwa Jason , Oh Myung Eun , Abeywardana Tharindumala , Yang Yanzhong , Wang Qiong A. , Jiang Lei 
Published: March 2020

Abstract
Background
Previous studies suggested that mdivi-1 (mitochondrial division inhibitor), a putative inhibitor of dynamin-related protein (DRP1), decreased cancer cell proliferation through inducing mitochondrial fusion and altering oxygen consumption. However, the metabolic reprogramming underlying the DRP1 inhibition is still unclear in cancer cells.

Methods
To better understand the metabolic effect of DRP1 inhibition, [U-13C]glucose isotope tracing was employed to assess mdivi-1 effects in several cancer cell lines, DRP1-WT (wild-type) and DRP1-KO (knockout) H460 lung cancer cells and mouse embryonic fibroblasts (MEFs).

Results
Mitochondrial staining confirmed that mdivi-1 treatment and DRP1 deficiency induced mitochondrial fusion. Surprisingly, metabolic isotope tracing found that mdivi-1 decreased mitochondrial oxidative metabolism in the lung cancer cell lines H460, A549 and the colon cancer cell line HCT116. [U-13C]glucose tracing studies also showed that the TCA cycle intermediates had significantly lower enrichment in mdivi-1-treated cells. In comparison, DRP1-WT and DRP1-KO H460 cells had similar oxidative metabolism, which was decreased by mdivi-1 treatment. Furthermore, mdivi-1-mediated effects on oxidative metabolism were independent of mitochondrial fusion.

Conclusions
Our data suggest that, in cancer cells, mdivi-1, a putative inhibitor of DRP1, decreases oxidative metabolism to impair cell proliferation.
Perinatal inflammation influences but does not arrest rapid immune development in preterm babies
Authors: Kamdar S. , Hutchinson R. , Laing A. , Stacey F. , Ansbro K. , Millar M. R. , Costeloe K. , Wade W. G. , Fleming P. , Gibbons D. L. 
Published: March 2020

AbstractInfection and infection-related complications are important causes of death and morbidity following preterm birth. Despite this risk, there is limited understanding of the development of the immune system in those born prematurely, and of how this development is influenced by perinatal factors. Here we prospectively and longitudinally follow a cohort of babies born before 32 weeks of gestation. We demonstrate that preterm babies, including those born extremely prematurely (<28 weeks), are capable of rapidly acquiring some adult levels of immune functionality, in which immune maturation occurs independently of the developing heterogeneous microbiome. By contrast, we observe a reduced percentage of CXCL8-producing T cells, but comparable levels of TNF-producing T cells, from babies exposed to in utero or postnatal infection, which precedes an unstable post-natal clinical course. These data show that rapid immune development is possible in preterm babies, but distinct identifiable differences in functionality may predict subsequent infection mediated outcomes.
Full-length human GLP-1 receptor structure without orthosteric ligands
Authors: Wu Fan , Yang Linlin , Hang Kaini , Laursen Mette , Wu Lijie , Han Gye Won , Ren Qiansheng , Roed Nikolaj Kulahin , Lin Guangyao , Hanson Michael A. , Jiang Hualiang , Wang Ming-Wei , Reedtz-Runge Steffen , Song Gaojie , Stevens Raymond C. 
Published: March 2020

AbstractGlucagon-like peptide-1 receptor (GLP-1R) is a class B G protein-coupled receptor that plays an important role in glucose homeostasis and treatment of type 2 diabetes. Structures of full-length class B receptors were determined in complex with their orthosteric agonist peptides, however, little is known about their extracellular domain (ECD) conformations in the absence of orthosteric ligands, which has limited our understanding of their activation mechanism. Here, we report the 3.2 Å resolution, peptide-free crystal structure of the full-length human GLP-1R in an inactive state, which reveals a unique closed conformation of the ECD. Disulfide cross-linking validates the physiological relevance of the closed conformation, while electron microscopy (EM) and molecular dynamic (MD) simulations suggest a large degree of conformational dynamics of ECD that is necessary for binding GLP-1. Our inactive structure represents a snapshot of the peptide-free GLP-1R and provides insights into the activation pathway of this receptor family.
Strong metal-support interaction promoted scalable production of thermally stable single-atom catalysts
Authors: Liu Kaipeng , Zhao Xintian , Ren Guoqing , Yang Tao , Ren Yujing , Lee Adam Fraser , Su Yang , Pan Xiaoli , Zhang Jingcai , Chen Zhiqiang , Yang Jingyi , Liu Xiaoyan , Zhou Tong , Xi Wei , Luo Jun , Zeng Chaobin , Matsumoto Hiroaki , Liu Wei , Jiang Qike , Wilson Karen , Wang Aiqin , Qiao Botao , Li Weizhen , Zhang Tao 
Published: March 2020

AbstractSingle-atom catalysts (SACs) have demonstrated superior catalytic performance in numerous heterogeneous reactions. However, producing thermally stable SACs, especially in a simple and scalable way, remains a formidable challenge. Here, we report the synthesis of Ru SACs from commercial RuO2 powders by physical mixing of sub-micron RuO2 aggregates with a MgAl1.2Fe0.8O4 spinel. Atomically dispersed Ru is confirmed by aberration-corrected scanning transmission electron microscopy and X-ray absorption spectroscopy. Detailed studies reveal that the dispersion process does not arise from a gas atom trapping mechanism, but rather from anti-Ostwald ripening promoted by a strong covalent metal-support interaction. This synthetic strategy is simple and amenable to the large-scale manufacture of thermally stable SACs for industrial applications.
Complexation-induced resolution enhancement of 3D-printed hydrogel constructs
Authors: Gong Jiaxing , Schuurmans Carl C. L. , Genderen Anne Metje van , Cao Xia , Li Wanlu , Cheng Feng , He Jacqueline Jialu , López Arturo , Huerta Valentin , Manríquez Jennifer , Li Ruiquan , Li Hongbin , Delavaux Clément , Sebastian Shikha , Capendale Pamela E. , Wang Huiming , Xie Jingwei , Yu Mengfei , Masereeuw Rosalinde , Vermonden Tina , Zhang Yu Shrike 
Published: March 2020

AbstractThree-dimensional (3D) hydrogel printing enables production of volumetric architectures containing desired structures using programmed automation processes. Our study reports a unique method of resolution enhancement purely relying on post-printing treatment of hydrogel constructs. By immersing a 3D-printed patterned hydrogel consisting of a hydrophilic polyionic polymer network in a solution of polyions of the opposite net charge, shrinking can rapidly occur resulting in various degrees of reduced dimensions comparing to the original pattern. This phenomenon, caused by complex coacervation and water expulsion, enables us to reduce linear dimensions of printed constructs while maintaining cytocompatible conditions in a cell type-dependent manner. We anticipate our shrinking printing technology to find widespread applications in promoting the current 3D printing capacities for generating higher-resolution hydrogel-based structures without necessarily having to involve complex hardware upgrades or other printing parameter alterations.
Food sources for the Ediacara biota communities
Authors: Bobrovskiy Ilya , Hope Janet M. , Golubkova Elena , Brocks Jochen J. 
Published: March 2020

AbstractThe Ediacara biota represents the first complex macroscopic organisms in the geological record, foreshadowing the radiation of eumetazoan animals in the Cambrian explosion. However, little is known about the contingencies that lead to their emergence, including the possible roles of nutrient availability and the quality of food sources. Here we present information on primary producers in the Ediacaran based on biomarker molecules that were extracted from sediments hosting Ediacaran macrofossils. High relative abundances of algal steranes over bacterial hopanes suggest that the Ediacara biota inhabited nutrient replete environments with an abundance of algal food sources comparable to Phanerozoic ecosystems. Thus, organisms of the Ediacara biota inhabited nutrient-rich environments akin to those that later fuelled the Cambrian explosion.
Histone variant H3.3 residue S31 is essential for Xenopus gastrulation regardless of the deposition pathway
Authors: Sitbon David , Boyarchuk Ekaterina , Dingli Florent , Loew Damarys , Almouzni Geneviève 
Published: March 2020

AbstractVertebrates exhibit specific requirements for replicative H3 and non-replicative H3.3 variants during development. To disentangle whether this involves distinct modes of deposition or unique functions once incorporated into chromatin, we combined studies inXenopusearly development with chromatin assays. Here we investigate the extent to which H3.3 mutated at residues that differ from H3.2 rescue developmental defects caused by H3.3 depletion. Regardless of the deposition pathway, only variants at residue 31—a serine that can become phosphorylated—failed to rescue endogenous H3.3 depletion. Although an alanine substitution fails to rescue H3.3 depletion, a phospho-mimic aspartate residue at position 31 rescues H3.3 function. To explore mechanisms involving H3.3 S31 phosphorylation, we identified factors attracted or repulsed by the presence of aspartate at position 31, along with modifications on neighboring residues. We propose that serine 31-phosphorylated H3.3 acts as a signaling module that stimulates the acetylation of K27, providing a chromatin state permissive to the embryonic development program.
Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps
Authors: Si Dong , Moritz Spencer A. , Pfab Jonas , Hou Jie , Cao Renzhi , Wang Liguo , Wu Tianqi , Cheng Jianlin 
Published: March 2020

AbstractCryo-electron microscopy (cryo-EM) has become a leading technology for determining protein structures. Recent advances in this field have allowed for atomic resolution. However, predicting the backbone trace of a protein has remained a challenge on all but the most pristine density maps (<2.5 Å resolution). Here we introduce a deep learning model that uses a set of cascaded convolutional neural networks (CNNs) to predict Cα atoms along a protein’s backbone structure. The cascaded-CNN (C-CNN) is a novel deep learning architecture comprised of multiple CNNs, each predicting a specific aspect of a protein’s structure. This model predicts secondary structure elements (SSEs), backbone structure, and Cα atoms, combining the results of each to produce a complete prediction map. The cascaded-CNN is a semantic segmentation image classifier and was trained using thousands of simulated density maps. This method is largely automatic and only requires a recommended threshold value for each protein density map. A specialized tabu-search path walking algorithm was used to produce an initial backbone trace with Cα placements. A helix-refinement algorithm made further improvements to the α-helix SSEs of the backbone trace. Finally, a novel quality assessment-based combinatorial algorithm was used to effectively map protein sequences onto Cα traces to obtain full-atom protein structures. This method was tested on 50 experimental maps between 2.6 Å and 4.4 Å resolution. It outperformed several state-of-the-art prediction methods including Rosetta de-novo, MAINMAST, and a Phenix based method by producing the most complete predicted protein structures, as measured by percentage of found Cα atoms. This method accurately predicted 88.9% (mean) of the Cα atoms within 3 Å of a protein’s backbone structure surpassing the 66.8% mark achieved by the leading alternate method (Phenix based fully automatic method) on the same set of density maps. The C-CNN also achieved an average root-mean-square deviation (RMSD) of 1.24 Å on a set of 50 experimental density maps which was tested by the Phenix based fully automatic method. The source code and demo of this research has been published at https://github.com/DrDongSi/Ca-Backbone-Prediction.
Reconstruction of composite oral and maxillofacial defects by free flaps based on a new classification
Authors: Yao Xi Yu , Liu Hui , Liu Wei Wei 
Published: March 2020

AbstractReconstruction of composite oral and maxillofacial defects using free flaps is challenging. The key to such delicate reconstruction lies in the evaluation of the defect. However, few reports have described the clinical classification of these difficult defects. In this study, we proposed a classification method and developed different reconstructive solutions using free flap techniques according to this classification. This classification method was established based on two parameters (the elements and distribution of the missing tissues). Among the 17 patients with composite oral and maxillofacial defects included in this study, 8 patients presented with type A defects, one patient presented with a type B defect, and the other 8 patients presented with type C defects. No type D defects were observed in this study. Three types of free flaps were used to reconstruct the respective types of composite defects. Perforator-based ALT flaps were used to reconstruct Type A defects. Branch-based ALT flaps were used to reconstruct Type B defects. For Type C defects, two reconstructive solutions were used, including a well-designed fibular flap and a perforator-based ALT flap with or without a metal plate for bony reconstruction. All flaps survived after surgery. This classification system may help select and design specific free flaps for reconstructing composite oral and maxillofacial defects.
The role of necroptosis and apoptosis through the oxidative stress pathway in the liver of selenium-deficient swine
Authors: Zhang Yuan , Yu Dahai , Zhang Jiuli , Bao Jun , Tang Chaohua , Zhang Ziwei 
Published: March 2020

Abstract
Necroptosis is regarded as a new paradigm of cell death that plays a key role in the liver damage observed with selenium (Se) deficiency. Se deficiency has a significant impact on the livestock and poultry industries. Previous studies have confirmed that Se deficiency causes serious injury to the swine liver; however, it is unclear whether this liver damage is the result of necroptosis and apoptosis. To understand the damage induced by Se deficiency, swine were divided into a control group and Se-deficient group. The results showed that in the liver of swine, Se deficiency initiated apoptosis by increasing the expression of cysteinyl aspartate specific proteinase 3 (caspase-3), cysteinyl aspartate specific proteinase 9 (caspase-9) and BCL-2 antagonist/killer (BAK) at both the mRNA and protein levels and by decreasing the B cell lymphoma/leukemia 2 (BCL-2) levels compared with the levels in the control group. Meanwhile, compared with the control group, necroptosis was confirmed in the liver of Se-deficient swine through increased the expression of mixed lineage kinase domain like pseudokinase (MLKL) and receptor interacting serine/threonine kinase 1 (RIPK1) at both the mRNA and protein levels. In addition, the activities of catalase (CAT), nitric oxide (NO), and total antioxidative capacity (T-AOC) were clearly increased (P &lt; 0.05), and the activities of OH- and total nitric oxide synthase (TNOS) were obviously decreased (P &lt; 0.05), whereas in the Se-deficient group, the hydrogen peroxide (H2O2) and malondialdehyde (MDA) levels were obviously increased (P &lt; 0.05) compared with those in the control group. Moreover, the number of apoptotic cells was increased significantly in the Se-deficient group, and the liver tissues showed obvious necroptosis damage. These results show that Se deficiency induces apoptosis and necroptosis through the oxidative stress pathway in the swine liver.