bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solar Irradiance Variability: Modeling the Measurements
Authors: Lean J. L. , Coddington O. , Marchenko S. V. , Machol J. , DeLand M. T. , Kopp G. 
Published: May 2020

AbstractNew models of the Sun's irradiance variability are developed from 15 years of direct observations made by the Solar Radiation and Climate Experiment (SORCE) spacecraft from 2003 to 2017 (inclusive). Multiple linear regression parameterizes the observations in terms of facular brightening and sunspot darkening, which are the primary sources of solar irradiance variability. The facular influence is specified as a combination of a linear and nonlinear solar ultraviolet (UV) index; the addition of the nonlinear term allows better reproduction of concurrent solar cycle and rotational variability. The sunspot darkening index is calculated using sunspot observations from both the Debrecen catalog and Air Force Solar Observing Optical Network (SOON) operational sites, the former providing superior model performance. The new model of total solar irradiance variability, NRLTSI3, with the Debrecen sunspot index reproduces the direct Total Irradiance Monitor (TIM) observations better than does the NRLTSI2 model that currently specifies irradiance for the NOAA Climate Data Record (CDR); the correlation of the model and observations increases from 0.956 to 0.971, and the standard deviation of the residuals decreases from 0.124 to 0.100 W m−2. The new model of solar spectral irradiance variability, NRLSSI3, which extends from 115 to 100,000 nm, reproduces rotational modulation in independent Ozone Monitoring Instrument (OMI) observations at near‐UV and visible wavelengths. The SATIRE model overestimates rotational modulation of near‐UV Fraunhofer spectral features because of excess facular brightness; the EMPIRE model overestimates rotational modulation at all near‐UV wavelengths.
Evaluation of the OPTRAM Model to Retrieve Soil Moisture in the Sanjiang Plain of Northeast China
Authors: Chen Mingxing , Zhang Yuhu , Yao Yunjun , Lu Jing , Pu Xiao , Hu Tao , Wang Peng 
Published: May 2020

AbstractSoil moisture is a key factor affecting crop growth and crop yield. Information on soil moisture is critical for crop growth monitoring and yield estimation. This study evaluated the OPtical TRApezoid Model (OPTRAM) on soil moisture estimates in the Sanjiang Plain, China, using Moderate Resolution Imaging Spectroradiometer (MODIS) data and in situ soil moisture data acquired from May to September in 2016 and 2017. This model was empirically calculated by parameterizing the relationship between the normalized difference vegetation index (NDVI) and shortwave infrared transformed reflectance (STR). In addition, the precipitation data were collected and used for verification of the results. According to the scatterplots of STR and NDVI, OPTRAM can estimate soil moisture from July to September, while it's inapplicable in May and June. Evaluation results indicated that OPTRAM‐based soil moisture estimates provide overall RMSE from 0.05 to 0.13 cm3/cm3, bias from −0.11 to 0.06 cm3/cm3, and R2 from 0.10 to 0.50, respectively, for all investigated sites. The performance of OPTRAM compared with the precipitation data showed good agreement. In conclusion, OPTRAM could be used to estimate soil moisture with reasonable accuracy in most areas from July to September in Sanjiang Plain.
Contribution of Secondary Particles to Wintertime PM2.5 During 2015–2018 in a Major Urban Area of the Sichuan Basin, Southwest China
Authors: Du X. X. , Shi G. M. , Zhao T. L. , Yang F. M. , Zheng X. B. , Zhang Y. J. , Tan Q. W. 
Published: May 2020

AbstractA novel method, noted as approximate envelope method (AEM), was developed to estimate the secondary PM2.5 concentrations based on the air quality monitoring data. This approach made it possible to obtain the long‐term characteristics of the secondary PM2.5 using only conventional observations. The secondary PM2.5 concentrations and their variation characteristics under different PM2.5 pollution levels during wintertime of 2015 to 2018 in Chengdu, a major urban area of Sichuan Basin over Southwest China, were analyzed. The results showed that the secondary PM2.5 concentrations ranged from 52.3 to 122.8 μg·m−3 and accounted for 56.3%, 63.6%, and 67.4% of the total PM2.5 in slight, moderate, and heavy pollution status, respectively. Additionally, the concentrations of secondary PM2.5 increased year by year, while the concentrations of primary PM2.5 performed significant decreasing trends from 2015 to 2018. The diurnal variations of primary and secondary PM2.5 presented a significantly unimodal patterns but with maximum at morning and noon, respectively. Specific meteorological conditions such as high (low) relative humidity and temperature (wind speed and air pressure) aggravated the secondary particulate pollution in wintertime of Chengdu, reflecting an influence of regional climate change over the Sichuan Basin of Southwest China on the urban air pollution.
Abundant Spontaneous and Dynamically Triggered Submarine Landslides in the Gulf of Mexico
Authors: Fan Wenyuan , McGuire Jeffrey J. , Shearer Peter M. 
Published: May 2020

AbstractSubmarine landslides that occur offshore are common along the U.S. continental margins. These mass wasting events can trigger tsunamis and hence potentially devastate coastal communities and damage offshore infrastructure. However, the initiation and failure processes of submarine landslides are poorly understood. Here, we identify and locate 85 previously unknown submarine landslides in the Gulf of Mexico from 2008 to 2015. Ten of these landslides failed spontaneously while the remaining 75 were dynamically triggered by passing seismic surface waves from distant earthquakes with magnitudes as small as ∼5. Our observations demonstrate ongoing submarine landslide activity in the Gulf of Mexico where dense energy industry infrastructure is present and that the region is prone to secondary seismic hazard despite the low local seismicity rate. Our results should facilitate future investigations to identify unstable offshore slopes, to illuminate dynamic processes of landslides, and perhaps to apply remote detection technology in tsunami warning systems.
The Response in Air Quality to the Reduction of Chinese Economic Activities During the COVID‐19 Outbreak
Authors: Shi Xiaoqin , Brasseur Guy P. 
Published: May 2020

AbstractDuring the COVID‐19 outbreak that took place in early 2020, the economic activities in China were drastically reduced and accompanied by a strong reduction in the emission of primary air pollutants. On the basis of measurements made at the monitoring stations operated by the China National Environmental Monitoring Center, we quantify the reduction in surface PM2.5, NO2, CO, and SO2 concentrations in northern China during the lockdown, which started on 23 January 2020. We find that, on the average, the levels of surface PM2.5 and NO2 have decreased by approximately 35% and 60%, respectively, between the period 1 and 22 January 2020 and the period 23 January and 29 February 2020. At the same time, the mean ozone concentration has increased by a factor 1.5–2. In urban area of Wuhan, where drastic measures were adopted to limit the spread of the coronavirus, similar changes in the concentrations of PM2.5, NO2, and ozone are found.
Stress induces insertion of calcium-permeable AMPA receptors in the OFC–BLA synapse and modulates emotional behaviours in mice
Authors: Kuniishi Hiroshi , Yamada Daisuke , Wada Keiji , Yamada Mitsuhiko , Sekiguchi Masayuki 
Published: May 2020

AbstractStress increases the risk of neuropsychiatric disorders, such as major depression. Exposure to stress has been reported to induce various neuronal changes, such as alterations in synaptic transmission and structure. However, a causal link between stress-induced neural circuit alterations and changes in emotional behaviours is not well understood. In the present study, we focused on a projection pathway from the orbitofrontal cortex (OFC) to the basolateral nucleus of the amygdala (BLA) as a crucial circuit for negative emotions and examined the effect of stress on OFC–BLA excitatory synaptic transmission using optogenetic and whole-cell patch-clamp methods in mice. As a stress-inducing procedure, we used repeated tail-shock, which increased stress-related behaviours. We found greater α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA)/N-methyl-d-aspartate current ratios and insertion of calcium-permeable AMPA receptors (AMPARs) in the OFC–BLA synapse after stress. These stress-induced synaptic and behavioural changes were reduced by a blockade of protein kinase A, which plays a principal role in stress-induced targeting of AMPARs into the synaptic membrane. To examine a possible causal relationship between alterations in synaptic transmission in the OFC–BLA pathway and stress-related behaviour, we performed optogenetic activation or chemogenetic inactivation of OFC–BLA transmission in mice. We found that optogenetic activation and chemogenetic inactivation of OFC–BLA transmission increased and decreased stress-related behaviour, respectively. In conclusion, we have demonstrated that stress altered the postsynaptic properties of the OFC–BLA pathway. These synaptic changes might be one of the underlying mechanisms of stress-induced behavioural alterations.
The Pan-Immune-Inflammation Value is a new prognostic biomarker in metastatic colorectal cancer: results from a pooled-analysis of the Valentino and TRIBE first-line trials
Authors: Fucà Giovanni , Guarini Vincenzo , Antoniotti Carlotta , Morano Federica , Moretto Roberto , Corallo Salvatore , Marmorino Federica , Lonardi Sara , Rimassa Lorenza , Sartore-Bianchi Andrea , Borelli Beatrice , Tampellini Marco , Bustreo Sara , Claravezza Matteo , Boccaccino Alessandra , Murialdo Roberto , Zaniboni Alberto , Tomasello Gianluca , Loupakis Fotios , Adamo Vincenzo , Tonini Giuseppe , Cortesi Enrico , de Braud Filippo , Cremolini Chiara , Pietrantonio Filippo 
Published: May 2020

Abstract
Background
Immune-inflammatory biomarkers (IIBs) showed a prognostic relevance in patients with metastatic CRC (mCRC). We aimed at evaluating the prognostic power of a new comprehensive biomarker, the Pan-Immune-Inflammation Value (PIV), in patients with mCRC receiving first-line therapy.

Methods
In the present pooled-analysis, we included patients enrolled in the Valentino and TRIBE trials. PIV was calculated as: (neutrophil count × platelet count × monocyte count)/lymphocyte count. A cut-off was determined using the maximally selected rank statistics method. Generalised boosted regression (GBR), the Kaplan–Meier method and Cox hazards regression models were used for survival analyses.

Results
A total of 438 patients were included. Overall, 208 patients (47%) had a low-baseline PIV and 230 (53%) had a high-baseline PIV. Patients with high PIV experienced a worse PFS (HR, 1.66; 95% CI, 1.36–2.03, P < 0.001) and worse OS (HR, 2.01; 95% CI, 1.57–2.57; P < 0.001) compared to patients with low PIV. PIV outperformed the other IIBs in the GBR model and in the multivariable models.

Conclusion
PIV is a strong predictor of survival outcomes with better performance than other well-known IIBs in patients with mCRC treated with first-line therapy. PIV should be prospectively validated to better stratify mCRC patients undergoing first-line therapy.
LOXL1 confers antiapoptosis and promotes gliomagenesis through stabilizing BAG2
Authors: Yu Hua , Ding Jun , Zhu Hongwen , Jing Yao , Zhou Hu , Tian Hengli , Tang Ke , Wang Gang , Wang Xiongjun 
Published: May 2020

AbstractThe lysyl oxidase (LOX) family is closely related to the progression of glioma. To ensure the clinical significance of LOX family in glioma, The Cancer Genome Atlas (TCGA) database was mined and the analysis indicated that higher LOXL1 expression was correlated with more malignant glioma progression. The functions of LOXL1 in promoting glioma cell survival and inhibiting apoptosis were studied by gain- and loss-of-function experiments in cells and animals. LOXL1 was found to exhibit antiapoptotic activity by interacting with multiple antiapoptosis modulators, especially BAG family molecular chaperone regulator 2 (BAG2). LOXL1-D515 interacted with BAG2-K186 through a hydrogen bond, and its lysyl oxidase activity prevented BAG2 degradation by competing with K186 ubiquitylation. Then, we discovered that LOXL1 expression was specifically upregulated through the VEGFR-Src-CEBPA axis. Clinically, the patients with higher LOXL1 levels in their blood had much more abundant BAG2 protein levels in glioma tissues. Conclusively, LOXL1 functions as an important mediator that increases the antiapoptotic capacity of tumor cells, and approaches targeting LOXL1 represent a potential strategy for treating glioma. In addition, blood LOXL1 levels can be used as a biomarker to monitor glioma progression.
Determinants of transcription factor regulatory range
Authors: Chen Chen-Hao , Zheng Rongbin , Tokheim Collin , Dong Xin , Fan Jingyu , Wan Changxin , Tang Qin , Brown Myles , Liu Jun S. , Meyer Clifford A. , Liu X. Shirley 
Published: May 2020

AbstractCharacterization of the genomic distances over which transcription factor (TF) binding influences gene expression is important for inferring target genes from TF chromatin immunoprecipitation followed by sequencing (ChIP-seq) data. Here we systematically examine the relationship between thousands of TF and histone modification ChIP-seq data sets with thousands of gene expression profiles. We develop a model for integrating these data, which reveals two classes of TFs with distinct ranges of regulatory influence, chromatin-binding preferences, and auto-regulatory properties. We find that the regulatory range of the same TF bound within different topologically associating domains (TADs) depend on intrinsic TAD properties such as local gene density and G/C content, but also on the TAD chromatin states. Our results suggest that considering TF type, binding distance to gene locus, as well as chromatin context is important in identifying implicated TFs from GWAS SNPs.
A Cas9 with PAM recognition for adenine dinucleotides
Authors: Chatterjee Pranam , Lee Jooyoung , Nip Lisa , Koseki Sabrina R. T. , Tysinger Emma , Sontheimer Erik J. , Jacobson Joseph M. , Jakimo Noah 
Published: May 2020

AbstractCRISPR-associated (Cas) DNA-endonucleases are remarkably effective tools for genome engineering, but have limited target ranges due to their protospacer adjacent motif (PAM) requirements. We demonstrate a critical expansion of the targetable sequence space for a type II-A CRISPR-associated enzyme through identification of the natural 5$$^{\prime}$$′-NAAN-3$$^{\prime}$$′ PAM preference of Streptococcus macacae Cas9 (SmacCas9). To achieve efficient editing activity, we graft the PAM-interacting domain of SmacCas9 to its well-established ortholog from Streptococcus pyogenes (SpyCas9), and further engineer an increased efficiency variant (iSpyMac) for robust genome editing activity. We establish that our hybrids can target all adenine dinucleotide PAM sequences and possess robust and accurate editing capabilities in human cells.
Adaptation of the master antioxidant response connects metabolism, lifespan and feather development pathways in birds
Authors: Castiglione Gianni M. , Xu Zhenhua , Zhou Lingli , Duh Elia J. 
Published: May 2020

AbstractBirds (Aves) display high metabolic rates and oxygen consumption relative to mammals, increasing reactive oxygen species (ROS) formation. Although excess ROS reduces lifespan by causing extensive cellular dysfunction and damage, birds are remarkably long-lived. We address this paradox by identifying the constitutive activation of the NRF2 master antioxidant response in Neoaves (~95% of bird species), providing an adaptive mechanism capable of counterbalancing high ROS levels. We demonstrate that a KEAP1 mutation in the Neoavian ancestor disrupted the repression of NRF2 by KEAP1, leading to constitutive NRF2 activity and decreased oxidative stress in wild Neoaves tissues and cells. Our evidence suggests this ancient mutation induced a compensatory program in NRF2-target genes with functions beyond redox regulation—including feather development—while enabling significant metabolic rate increases that avoid trade-offs with lifespan. The strategy of NRF2 activation sought by intense clinical investigation therefore appears to have also unlocked a massively successful evolutionary trajectory.
Mottness versus unit-cell doubling as the driver of the insulating state in 1T-TaS2
Authors: Butler C. J. , Yoshida M. , Hanaguri T. , Iwasa Y. 
Published: May 2020

AbstractIf a material with an odd number of electrons per unit-cell is insulating, Mott localisation may be invoked as an explanation. This is widely accepted for the layered compound 1T-TaS2, which has a low-temperature insulating phase comprising charge order clusters with 13 unpaired orbitals each. But if the stacking of layers doubles the unit-cell to include an even number of orbitals, the nature of the insulating state is ambiguous. Here, scanning tunnelling microscopy reveals two distinct terminations of the charge order in 1T-TaS2, the sign of such a double-layer stacking pattern. However, spectroscopy at both terminations allows us to disentangle unit-cell doubling effects and determine that Mott localisation alone can drive gap formation. We also observe the collapse of Mottness at an extrinsically re-stacked termination, demonstrating that the microscopic mechanism of insulator-metal transitions lies in degrees of freedom of inter-layer stacking.
Experimental violation of n-locality in a star quantum network
Authors: Poderini Davide , Agresti Iris , Marchese Guglielmo , Polino Emanuele , Giordani Taira , Suprano Alessia , Valeri Mauro , Milani Giorgio , Spagnolo Nicolò , Carvacho Gonzalo , Chaves Rafael , Sciarrino Fabio 
Published: May 2020

AbstractThe launch of a satellite capable of distributing entanglement through long distances and the first loophole-free violation of Bell inequalities are milestones indicating a clear path for the establishment of quantum networks. However, nonlocality in networks with independent entanglement sources has only been experimentally verified in simple tripartite networks, via the violation of bilocality inequalities. Here, by using a scalable photonic platform, we implement star-shaped quantum networks consisting of up to five distant nodes and four independent entanglement sources. We exploit this platform to violate the chained n-locality inequality and thus witness, in a device-independent way, the emergence of nonlocal correlations among the nodes of the implemented networks. These results open new perspectives for quantum information processing applications in the relevant regime where the observed correlations are compatible with standard local hidden variable models but are non-classical if the independence of the sources is taken into account.
Histone H2A variants alpha1-extension helix directs RNF168-mediated ubiquitination
Authors: Kelliher Jessica L. , West Kirk L. , Gong Qingguo , Leung Justin W. C. 
Published: May 2020

AbstractHistone ubiquitination plays an important role in the DNA damage response (DDR) pathway. RNF168 catalyzes H2A and H2AX ubiquitination on lysine 13/15 (K13/K15) upon DNA damage and promotes the accrual of downstream repair factors at damaged chromatin. Here, we report that RNF168 ubiquitinates the non-canonical H2A variants H2AZ and macroH2A1/2 at the divergent N-terminal tail lysine residue. In addition to their evolutionarily conserved nucleosome acidic patch, we identify the positively charged alpha1-extension helix as essential for RNF168-mediated ubiquitination of H2A variants. Moreover, mutation of the RNF168 UMI (UIM- and MIU-related UBD) hydrophilic acidic residues abolishes RNF168-mediated ubiquitination as well as 53BP1 and BRCA1 ionizing radiation-induced foci formation. Our results reveal a juxtaposed bipartite electrostatic interaction utilized by the nucleosome to direct RNF168 orientation towards the target lysine residues in proximity to the H2A alpha1-extension helix, which plays an important role in the DDR pathway.
Structural basis for assembly and function of a diatom photosystem I-light-harvesting supercomplex
Authors: Nagao Ryo , Kato Koji , Ifuku Kentaro , Suzuki Takehiro , Kumazawa Minoru , Uchiyama Ikuo , Kashino Yasuhiro , Dohmae Naoshi , Akimoto Seiji , Shen Jian-Ren , Miyazaki Naoyuki , Akita Fusamichi 
Published: May 2020

AbstractPhotosynthetic light-harvesting complexes (LHCs) play a pivotal role in collecting solar energy for photochemical reactions in photosynthesis. One of the major LHCs are fucoxanthin chlorophyll a/c-binding proteins (FCPs) present in diatoms, a group of organisms having important contribution to the global carbon cycle. Here, we report a 2.40-Å resolution structure of the diatom photosystem I (PSI)-FCPI supercomplex by cryo-electron microscopy. The supercomplex is composed of 16 different FCPI subunits surrounding a monomeric PSI core. Each FCPI subunit showed different protein structures with different pigment contents and binding sites, and they form a complicated pigment–protein network together with the PSI core to harvest and transfer the light energy efficiently. In addition, two unique, previously unidentified subunits were found in the PSI core. The structure provides numerous insights into not only the light-harvesting strategy in diatom PSI-FCPI but also evolutionary dynamics of light harvesters among oxyphototrophs.
Direct observation of dual-step twinning nucleation in hexagonal close-packed crystals
Authors: He Yang , Li Bin , Wang Chongmin , Mao Scott X. 
Published: May 2020

AbstractDesign and processing of advanced lightweight structural alloys based on magnesium and titanium rely critically on a control over twinning that remains elusive to date and is dependent on an explicit understanding on the twinning nucleation mechanism in hexagonal close-packed (HCP) crystals. Here, by using in-situ high resolution transmission electron microscopy, we directly show a dual-step twinning nucleation mechanism in HCP rhenium nanocrystals. We find that nucleation of the predominant {1 0 −1 2} twinning is initiated by disconnections on the Prismatic│Basal interfaces which establish the lattice correspondence of the twin with a minor deviation from the ideal orientation. Subsequently, the minor deviation is corrected by the formation of coherent twin boundaries through rearrangement of the disconnections on the Prismatic│Basal interface; thereafter, the coherent twin boundaries propagate by twinning dislocations. The findings provide high-resolution direct evidence of the twinning nucleation mechanism in HCP crystals.
Stepwise PathNet: a layer-by-layer knowledge-selection-based transfer learning algorithm
Authors: Imai Shunsuke , Kawai Shin , Nobuhara Hajime 
Published: May 2020

AbstractSome neural network can be trained by transfer learning, which uses a pre-trained neural network as the source task, for a small target task’s dataset. The performance of the transfer learning depends on the knowledge (i.e., layers) selected from the pre-trained network. At present, this knowledge is usually chosen by humans. The transfer learning method PathNet automatically selects pre-trained modules or adjustable modules in a modular neural network. However, PathNet requires modular neural networks as the pre-trained networks, therefore non-modular pre-trained neural networks are currently unavailable. Consequently, PathNet limits the versatility of the network structure. To address this limitation, we propose Stepwise PathNet, which regards the layers of a non-modular pre-trained neural network as the module in PathNet and selects the layers automatically through training. In an experimental validation of transfer learning from InceptionV3 pre-trained on the ImageNet dataset to networks trained on three other datasets (CIFAR-100, SVHN and Food-101), Stepwise PathNet was up to 8% and 10% more accurate than finely tuned and from-scratch approaches, respectively. Also, some of the selected layers were not supported by the layer functions assumed in PathNet.