bluuebunny/crossref_metadata_2025_split huggingface dataset:
TAGAP instructs Th17 differentiation by bridging Dectin activation to EPHB2 signaling in innate antifungal response
Authors: Chen Jianwen , He Ruirui , Sun Wanwei , Gao Ru , Peng Qianwen , Zhu Liwen , Du Yanyun , Ma Xiaojian , Guo Xiaoli , Zhang Huazhi , Tan Chengcheng , Wang Junhan , Zhang Wei , Weng Xiufang , Man Jianghong , Bauer Hermann , Wang Qing K. , Martin Bradley N. , Zhang Cun-Jin , Li Xiaoxia , Wang Chenhui 
Published: April 2020

AbstractThe TAGAP gene locus has been linked to several infectious diseases or autoimmune diseases, including candidemia and multiple sclerosis. While previous studies have described a role of TAGAP in T cells, much less is known about its function in other cell types. Here we report that TAGAP is required for Dectin-induced anti-fungal signaling and proinflammatory cytokine production in myeloid cells. Following stimulation with Dectin ligands, TAGAP is phosphorylated by EPHB2 at tyrosine 310, which bridges proximal Dectin-induced EPHB2 activity to downstream CARD9-mediated signaling pathways. During Candida albicans infection, mice lacking TAGAP mount defective immune responses, impaired Th17 cell differentiation, and higher fungal burden. Similarly, in experimental autoimmune encephalomyelitis model of multiple sclerosis, TAGAP deficient mice develop significantly attenuated disease. In summary, we report that TAGAP plays an important role in linking Dectin-induced signaling to the promotion of effective T helper cell immune responses, during both anti-fungal host defense and autoimmunity.
Quantitative cellular-resolution map of the oxytocin receptor in postnatally developing mouse brains
Authors: Newmaster Kyra T. , Nolan Zachary T. , Chon Uree , Vanselow Daniel J. , Weit Abigael R. , Tabbaa Manal , Hidema Shizu , Nishimori Katsuhiko , Hammock Elizabeth A. D. , Kim Yongsoo 
Published: April 2020

AbstractThe oxytocin receptor (OTR) plays critical roles in social behavior development. Despite its significance, brain-wide quantitative understanding of OTR expression remains limited in postnatally developing brains. Here, we develop postnatal 3D template brains to register whole brain images with cellular resolution to systematically quantify OTR cell densities. We utilize fluorescent reporter mice (Otrvenus/+) and find that cortical regions show temporally and spatially heterogeneous patterns with transient postnatal OTR expression without cell death. Cortical OTR cells are largely glutamatergic neurons with the exception of cells in layer 6b. Subcortical regions show similar temporal regulation except the hypothalamus and two hypothalamic nuclei display sexually dimorphic OTR expression. Lack of OTR expression correlates with reduced dendritic spine densities in selected cortical regions of developing brains. Lastly, we create a website to visualize our high-resolution imaging data. In summary, our research provides a comprehensive resource for postnatal OTR expression in the mouse brain.
Complex k-uniform tilings by a simple bitopic precursor self-assembled on Ag(001) surface
Authors: Kormoš Lukáš , Procházka Pavel , Makoveev Anton O. , Čechal Jan 
Published: April 2020

AbstractThe realization of complex long-range ordered structures in a Euclidean plane presents a significant challenge en route to the utilization of their unique physical and chemical properties. Recent progress in on-surface supramolecular chemistry has enabled the engineering of regular and semi-regular tilings, expressing translation symmetric, quasicrystalline, and fractal geometries. However, the k-uniform tilings possessing several distinct vertices remain largely unexplored. Here, we show that these complex geometries can be prepared from a simple bitopic molecular precursor – 4,4’-biphenyl dicarboxylic acid (BDA) – by its controlled chemical transformation on the Ag(001) surface. The realization of 2- and 3-uniform tilings is enabled by partially carboxylated BDA mediating the seamless connection of two distinct binding motifs in a single long-range ordered molecular phase. These results define the basic self-assembly criteria, opening way to the utilization of complex supramolecular tilings.
Nitrogen limitation reveals large reserves in metabolic and translational capacities of yeast
Authors: Yu Rosemary , Campbell Kate , Pereira Rui , Björkeroth Johan , Qi Qi , Vorontsov Egor , Sihlbom Carina , Nielsen Jens 
Published: April 2020

AbstractCells maintain reserves in their metabolic and translational capacities as a strategy to quickly respond to changing environments. Here we quantify these reserves by stepwise reducing nitrogen availability in yeast steady-state chemostat cultures, imposing severe restrictions on total cellular protein and transcript content. Combining multi-omics analysis with metabolic modeling, we find that seven metabolic superpathways maintain >50% metabolic capacity in reserve, with glucose metabolism maintaining >80% reserve capacity. Cells maintain >50% reserve in translational capacity for 2490 out of 3361 expressed genes (74%), with a disproportionately large reserve dedicated to translating metabolic proteins. Finally, ribosome reserves contain up to 30% sub-stoichiometric ribosomal proteins, with activation of reserve translational capacity associated with selective upregulation of 17 ribosomal proteins. Together, our dataset provides a quantitative link between yeast physiology and cellular economics, which could be leveraged in future cell engineering through targeted proteome streamlining.
Stepwise internal potential jumps caused by multiple-domain polarization flips in metal/ferroelectric/metal/paraelectric/metal stack
Authors: Li Xiuyan , Toriumi Akira 
Published: April 2020

AbstractNegative capacitance (NC) effects in ferroelectric/paraelectric (FE/PE) stacks have been recently discussed intensively in terms of the steep subthreshold swing (SS) in field-effect transistors (FETs). It is, however, still disputable to stabilize quasi-static-NC effects. In this work, stepwise internal potential jumps in a metal/FE/metal/PE/metal system observed near the coercive voltage of the FE layer are reported through carefully designed DC measurements. The relationship of the internal potential jumps with the steep SS in FETs is also experimentally confirmed by connecting a FE capacitor to a simple metal-oxide-semiconductor FET. On the basis of the experimental results, the observed internal potential jumps are analytically modelled from the viewpoint of bound charge emission associated with each domain flip in a multiple-domain FE layer in a FE/PE stack. This view is different from the original NC concept and should be employed for characterizing FE/PE gate stack FETs.
All-dielectric metasurface for high-performance structural color
Authors: Yang Wenhong , Xiao Shumin , Song Qinghai , Liu Yilin , Wu Yunkai , Wang Shuai , Yu Jie , Han Jiecai , Tsai Din-Ping 
Published: April 2020

AbstractThe achievement of structural color has shown advantages in large-gamut, high-saturation, high-brightness, and high-resolution. While a large number of plasmonic/dielectric nanostructures have been developed for structural color, the previous approaches fail to match all the above criterion simultaneously. Herein we utilize the Si metasurface to demonstrate an all-in-one solution for structural color. Due to the intrinsic material loss, the conventional Si metasurfaces only have a broadband reflection and a small gamut of 78% of sRGB. Once they are combined with a refractive index matching layer, the reflection bandwidth and the background reflection are both reduced, improving the brightness and the color purity significantly. Consequently, the experimentally demonstrated gamut has been increased to around 181.8% of sRGB, 135.6% of Adobe RGB, and 97.2% of Rec.2020. Meanwhile, high refractive index of silicon preserves the distinct color in a pixel with 2 × 2 array of nanodisks, giving a diffraction-limit resolution.
Perturbing proteomes at single residue resolution using base editing
Authors: Després Philippe C. , Dubé Alexandre K. , Seki Motoaki , Yachie Nozomu , Landry Christian R. 
Published: April 2020

AbstractBase editors derived from CRISPR-Cas9 systems and DNA editing enzymes offer an unprecedented opportunity for the precise modification of genes, but have yet to be used at a genome-scale throughput. Here, we test the ability of the Target-AID base editor to systematically modify genes genome-wide by targeting yeast essential genes. We mutate around 17,000 individual sites in parallel across more than 1500 genes. We identify over 700 sites at which mutations have a significant impact on fitness. Using previously determined and preferred Target-AID mutational outcomes, we find that gRNAs with significant effects on fitness are enriched in variants predicted to be deleterious based on residue conservation and predicted protein destabilization. We identify key features influencing effective gRNAs in the context of base editing. Our results show that base editing is a powerful tool to identify key amino acid residues at the scale of proteomes.
Optogenetic manipulation of a value-coding pathway from the primate caudate tail facilitates saccadic gaze shift
Authors: Amita Hidetoshi , Kim Hyoung F. , Inoue Ken-ichi , Takada Masahiko , Hikosaka Okihide 
Published: April 2020

AbstractIn the primate basal ganglia, the caudate tail (CDt) encodes the historical values (good or bad) of visual objects (i.e., stable values), and electrical stimulation of CDt evokes saccadic eye movements. However, it is still unknown how output from CDt conveys stable value signals to govern behavior. Here, we apply a pathway-selective optogenetic manipulation to elucidate how such value information modulates saccades. We express channelrhodopsin-2 in CDt delivered by viral vector injections. Selective optical activation of CDt-derived terminals in the substantia nigra pars reticulata (SNr) inhibits SNr neurons. Notably, these SNr neurons show inhibitory responses to good objects. Furthermore, the optical stimulation causes prolonged excitation of visual-saccadic neurons in the superior colliculus (SC), and induces contralateral saccades. These SC neurons respond more strongly to good than to bad objects in the contralateral hemifield. The present results demonstrate that CDt facilitates saccades toward good objects by serial inhibitory pathways through SNr.
Heat stress-induced transposon activation correlates with 3D chromatin organization rearrangement in Arabidopsis
Authors: Sun Linhua , Jing Yuqing , Liu Xinyu , Li Qi , Xue Zhihui , Cheng Zhukuan , Wang Daowen , He Hang , Qian Weiqiang 
Published: April 2020

AbstractIn higher eukaryotes, heterochromatin is mainly composed of transposable elements (TEs) silenced by epigenetic mechanisms. But, the silencing of certain heterochromatin-associated TEs is disrupted by heat stress. By comparing genome-wide high-resolution chromatin packing patterns under normal or heat conditions obtained through Hi-C analysis, we show here that heat stress causes global rearrangement of the 3D genome inArabidopsis thaliana. Contacts between pericentromeric regions and distal chromosome arms, as well as proximal intra-chromosomal interactions along the chromosomes, are enhanced. However, interactions within pericentromeres and those between distal intra-chromosomal regions are decreased. Many inter-chromosomal interactions, including those within theKNOT, are also reduced. Furthermore, heat activation of TEs exhibits a high correlation with the reduction of chromosomal interactions involving pericentromeres, theKNOT, the knob, and the upstream and downstream flanking regions of the activated TEs. Together, our results provide insights into the relationship between TE activation and 3D genome reorganization.
Cable bacteria reduce methane emissions from rice-vegetated soils
Authors: Scholz Vincent V. , Meckenstock Rainer U. , Nielsen Lars Peter , Risgaard-Petersen Nils 
Published: April 2020

AbstractMethane is the second most important greenhouse gas after carbon dioxide and approximately 11% of the global anthropogenic methane emissions originate from rice fields. Sulfate amendment is a mitigation strategy to reduce methane emissions from rice fields because sulfate reducers and methanogens compete for the same substrates. Cable bacteria are filamentous bacteria known to increase sulfate levels via electrogenic sulfide oxidation. Here we show that one-time inoculation of rice-vegetated soil pots with cable bacteria increases the sulfate inventory 5-fold, which leads to the reduction of methane emissions by 93%, compared to control pots lacking cable bacteria. Promoting cable bacteria in rice fields by enrichment or sensible management may thus become a strategy to reduce anthropogenic methane emissions.
CO oxidation activity of non-reducible oxide-supported mass-selected few-atom Pt single-clusters
Authors: Beniya Atsushi , Higashi Shougo , Ohba Nobuko , Jinnouchi Ryosuke , Hirata Hirohito , Watanabe Yoshihide 
Published: April 2020

AbstractPlatinum nanocatalysts play critical roles in CO oxidation, an important catalytic conversion process. As the catalyst size decreases, the influence of the support material on catalysis increases which can alter the chemical states of Pt atoms in contact with the support. Herein, we demonstrate that under-coordinated Pt atoms at the edges of the first cluster layer are rendered cationic by direct contact with the Al2O3 support, which affects the overall CO oxidation activity. The ratio of neutral to cationic Pt atoms in the Pt nanocluster is strongly correlated with the CO oxidation activity, but no correlation exists with the total surface area of surface-exposed Pt atoms. The low oxygen affinity of cationic Pt atoms explains this counterintuitive result. Using this relationship and our modified bond-additivity method, which only requires the catalyst–support bond energy as input, we successfully predict the CO oxidation activities of various sized Pt clusters on TiO2.
Effects of xylem embolism on the winter survival of Abies veitchii shoots in an upper subalpine region of central Japan
Authors: Maruta Emiko , Kubota Mitsumasa , Ikeda Takefumi 
Published: April 2020

AbstractAt high elevations, winter climatic conditions frequently cause excessive drought stress, which can induce embolism in conifer trees. We investigated the formation and repair of winter embolism in subalpine fir (Abies veitchii) growing near the timberline. We found a complete loss in xylem conductivity [100% percent loss of conductivity (PLC)] at the wind-exposed site (W+) and 40% PLC at the wind-protected site (W−). A PLC of 100% was far above the embolism rate expected from the drought-induced vulnerability analysis in the laboratory. At the W+ site, a PLC of 100% was maintained until May; this suddenly decreased to a negligible value in June, whereas the recovery at the W− site started in late winter and proceeded stepwise. The contrast between the two sites may have occurred because of the different underlying mechanisms of winter embolism. If most tracheids in the xylem of 100% PLC are air-filled, it will be difficult to refill quickly. However, embolism caused by pit aspiration could be restored rapidly, because aspirated pits isolate tracheids from each other and prevent the spread of cavitation. Although severe embolism may cause frost damage of needles, it may have a role in holding water within the stem.
Incorporating chemical sub-structures and protein evolutionary information for inferring drug-target interactions
Authors: Wang Lei , You Zhu-Hong , Li Li-Ping , Yan Xin , Zhang Wei 
Published: April 2020

AbstractAccumulating evidence has shown that drug-target interactions (DTIs) play a crucial role in the process of genomic drug discovery. Although biological experimental technology has made great progress, the identification of DTIs is still very time-consuming and expensive nowadays. Hence it is urgent to develop in silico model as a supplement to the biological experiments to predict the potential DTIs. In this work, a new model is designed to predict DTIs by incorporating chemical sub-structures and protein evolutionary information. Specifically, we first use Position-Specific Scoring Matrix (PSSM) to convert the protein sequence into the numerical descriptor containing biological evolutionary information, then use Discrete Cosine Transform (DCT) algorithm to extract the hidden features and integrate them with the chemical sub-structures descriptor, and finally utilize Rotation Forest (RF) classifier to accurately predict whether there is interaction between the drug and the target protein. In the 5-fold cross-validation (CV) experiment, the average accuracy of the proposed model on the benchmark datasets of Enzymes, Ion Channels, GPCRs and Nuclear Receptors reached 0.9140, 0.8919, 0.8724 and 0.8111, respectively. In order to fully evaluate the performance of the proposed model, we compare it with different feature extraction model, classifier model, and other state-of-the-art models. Furthermore, we also implemented case studies. As a result, 8 of the top 10 drug-target pairs with the highest prediction score were confirmed by related databases. These excellent results indicate that the proposed model has outstanding ability in predicting DTIs and can provide reliable candidates for biological experiments.
A cross-sectional study on selected child health outcomes in India: Quantifying the spatial variations and identification of the parental risk factors
Authors: Puri Parul , Khan Junaid , Shil Apurba , Ali Mohammad 
Published: April 2020

AbstractThis study examined association between selected child health indicators- anaemia, stunting and no/incomplete immunization by inter-linking maternal characteristics at district level and parental characteristics at individual level. A spatial analysis and a binary logit model estimation were employed to draw inferences using the data from the fourth round of National Family Health Survey, 2015–16 of India. Significant spatial clustering of the selected child health outcomes was observed in the country. Mother’s educational attainment explained significant district level differential in the selected child health outcomes. At the individual level, parents who are very young, not-educated, socially excluded, belong to poor class were found to be significantly associated with the poor child health outcomes. This study indicates that parental characteristics, such as age, educational attainment and employment substantially determine child health in India, suggesting that an intervention by targeting the households where children are vulnerable is important to improve child health in the country.
Dysregulated miRNA in a cancer-prone environment: A study of gastric non-neoplastic mucosa
Authors: Kim Binnari , Jang Jiryeon , Heo You Jeong , Kang So Young , Yoo Heejin , Sohn Insuk , Min Byung-Hoon , Kim Kyoung-Mee 
Published: April 2020

AbstractUnderstanding cancer-prone environments is important to efficiently detect and prevent cancers. The associations between miRNA and cancer-prone environments are still largely unknown in gastric cancer (GC). Six miRNAs that are differentially expressed during gastric carcinogenesis were selected, and quantitative real-time PCR was performed in an independent training set (fresh non-tumor and tumor samples from 18 GC patients) and validation sets (set 1 with formalin-fixed paraffin-embedded non-tumor and tumor samples from 19 solitary GC and set 2 with 37 multiple GC patients). The results were compared with those of 37 gastric mucosa from 20 healthy volunteers. The expression levels of miR-26a, miR-375, and miR-1260 in gastric mucosa from healthy volunteers were statistically higher than that of non-tumorous gastric mucosa located 3 cm apart from the GC in the training set (miR-26a,P < 0.0001; miR-375,P = 0.0049; miR-1260,P = 0.0172), validation set 1 (miR-26a and miR-375,P < 0.0001; miR-1260,P = 0.0008), and validation set 2 (miR-26a, miR-375, and miR-1260,P < 0.0001). And a combination of miR-26a and miR-1260 showed the highest area under the curve value of 0.89. miRNAs are differentially expressed in non-neoplastic gastric mucosa and can be used as a biomarker to predict cancer-prone environments.
High browsing skeletal adaptations in Spinophorosaurus reveal an evolutionary innovation in sauropod dinosaurs
Authors: Vidal D. , Mocho P. , Aberasturi A. , Sanz J. L. , Ortega F. 
Published: April 2020

AbstractSauropods were among the most diverse lineages of dinosaurs, with an ample geographic distribution throughout the Mesozoic. This evolutionary success is largely attributed to neck elongation and its impact on feeding efficiency. However, how neck elongation influenced exactly on feeding strategies is subject of debate. The process of mounting a nearly complete virtual skeleton of Spinophorosaurus nigerensis, from the Middle (?) Jurassic of Niger, has revealed several previously unknown osteological adaptations in this taxon. Wedged sacral and posterior dorsal vertebrae cause the presacral column to deflect antero-dorsally. This, together with elongated scapulae and humeri make the anterior region of the skeleton vertically lengthened. Also, elongated prezygapophyseal facets on the cervical vertebrae and a specialized first dorsal vertebra greatly increase the vertical range of motion of the neck. These characters support this early eusauropod as a more capable high browser than more basally branching sauropods. While limb proportions and zygapophyseal facets vary among Eusauropoda, the sacrum retained more than 10° of wedging in all Eusauropoda. This implied a functional constraint for sauropod species which evolved lower browsing feeding strategies: the antero-dorsal sloping caused by the sacrum had to be counteracted with further skeletal modifications, e.g. a ventrally curved mid to anterior presacral spine to hinder the dorsal slope of the whole presacral series caused by the wedged sacrum. This suggests that at least the last common ancestor of Eusauropoda developed high browsing capabilities, partially due to the modified wedged sacrum, likely a potential synapomorphy of the clade and key in the evolutionary history of the group.
Self-Assembled Electret for Vibration-Based Power Generator
Authors: Tanaka Yuya , Matsuura Noritaka , Ishii Hisao 
Published: April 2020

AbstractThe vibration-based electret generators (EGs) for energy harvesting have been extensively studied because they can obtain electrical energy from ambient vibrations. EGs exhibit a sandwich structure of electrodes surrounding an air gap and an electret, which is a dielectric material with a quasi-permanent electrical charge or dipole polarisation. Various charging processes have been developed because the surface charge density (σ) of the electret determines the output power of the device. However, such processes are considered to constitute a key productivity-limiting factor from the mass production viewpoint, making their simplification or elimination a highly desired objective. Herein, a model EG that does not require any charging process by utilising the spontaneous orientation polarisation of 1,3,5-tris(1-phenyl-1H-benzimidazole-2-yl)benzene (TPBi) is demonstrated. The surface potential (Vsp) of an evaporated TPBi film has reached 30.2 V at a film thickness of 500 nm without using a charging process. The estimated σ of 1.7 mC m−2 is comparable with that obtained using a conventional polymer-based electret after charging. Furthermore, Vsp is considerably stable in environmental conditions; thus, TPBi can be considered to be “self-assembled” electret (SAE). Application of SAE leads to developing an EG without requiring the charging process.