bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hölder‐Conditioned Hypsometry: A Refinement to a Classical Approach for the Characterization of Topography
Authors: Keylock Christopher J. , Singh Arvind , Passalacqua Paola , Foufoula‐Georgiou Efi 
Published: April 2020

AbstractThe effective characterization of topographic surfaces is a central tenet of geomorphology. Differences in land surface properties reveal variations in structural controls and the nature and efficacy of Earth‐shaping processes. In this paper, we employ the Hölder exponents, α, characterizing the local scaling behavior of topography and commonly used in the study of the (multi)fractal properties of landscapes and show that the joint probability distribution of the area of the terrain with a given elevation and α contains a wealth of information on topographic structure. The conditional distributions of the hypsometric integrals as a function of α, that is, Ihyp|α, are shown to capture this structure. A multivariate analysis reveals three metrics that summarize these conditional distributions: Strahler's original hypsometric integral, the standard deviation of the Ihyp|α, and the nature of any trend of the Ihyp|α against α. An analysis of five digital elevation models (DEMs) from different regions of the United States shows that only one is truly described by the hypsometric integral (Mettman Ridge from central Oregon). In the other cases, the new metrics clearly discriminate between instances where topographic roughness is more clearly a function of elevation, as captured by the conditional variables. In a final example, we artificially sharpen the ridges and valleys of one DEM to show that while the hypsometric integral and standard deviation of Ihyp|α are invariant to the change, the trend of Ihyp|α against α captures the changes in topography.
Can the GPM IMERG Hourly Products Replicate the Variation in Precipitation During the Wet Season Over the Sichuan Basin, China?
Authors: Wang H. , Wang L. , He J. , Ge F. , Chen Q. , Tang S. , Yao S. 
Published: April 2020

AbstractTwo near‐real‐time and one post‐processing products from the Integrated Multi‐satellite Retrievals for Global Precipitation Measurement Mission (GPM IMERG) were evaluated during the period from 2016 to 2018 in the wet seasons (June–November) over the Sichuan Basin, China. Results indicated the following: (1) The three products could generally replicate strong precipitation well; however, significantly large biases were observed when detecting weak precipitation. (2) All three products replicated summer precipitation more accurately than autumn precipitation. The IMERG “early run” product (IMERG‐E) largely underestimated precipitation in the wet season, while the “latter run” (IMERG‐L) and “final run” products (IMERG‐F) could counteract this to a certain degree. (3) IMERG‐F captured weak, moderate, and strong precipitation well during the wet season, and IMERG‐E showed excellent potential in detecting different precipitation intensities. All the three products could replicate the diurnal cycle of the wet season precipitation. The findings of this study can facilitate the application of IMERG products in regions with complex topography and have also highlighted the potential of IMERG‐E for rapid early warning and forecast systems.
Meteorological Change and Impacts on Air Pollution: Results From North China
Authors: Xu Ziping , Chen Song Xi , Wu Xiaoqing 
Published: April 2020

AbstractThere have been speculations that the severe air pollution experienced in North China was the act of meteorological change in general and a decreasing northerly wind in particular. We conduct a retrospective analysis on 1979–2016 reanalysis data from ERA‐Interim of European Centre for Medium‐Range Weather Forecasts over a region in North China to detect meteorological changes over the 38 years. No significant reduction in the northerly wind within the mixing layer is detected. Statistically significant increases are detected in the surface temperature, boundary layer height and dissipation, and significant decreases in relative humidity in the region between the first and second 19‐year periods from 1979 to 2016. We build regression models of PM2.5on the meteorological variables using data in 2014, 2015, and 2016 to quantify effects of the meteorological changes between the two 19‐year periods on PM2.5under the emission scenarios of 2014–2016. It is found that despite the warming, dew point temperature had been largely kept under control as the region had gotten dryer. This made the effects of temperature warming largely favorable to PM2.5reduction as it enhances boundary layer height and dissipation. It is found that the meteorological changes would lead to 1.29% to 2.76% reduction in annual PM2.5averages with January, March, and December having more than 4% reduction in the 3 years. Thus, the meteorological change in North China had helped alleviate PM2.5to certain extent and should not be held responsible for the regional air pollution problem.
Spi-C positively regulates RANKL-mediated osteoclast differentiation and function
Authors: Go Eun Mi , Oh Ju Hee , Park Jin Hee , Lee Soo Young , Lee Na Kyung 
Published: April 2020

AbstractSpi-C is an SPI-group erythroblast transformation-specific domain transcription factor expressed during B-cell development. Here, we report that Spi-C is a novel receptor activator of nuclear factor-κB ligand (RANKL)-inducible protein that positively regulates RANKL-mediated osteoclast differentiation and function. Knockdown of Spi-C decreased the expression of RANKL-induced nuclear factor of activated T-cells, cytoplasmic 1, receptor activator of nuclear factor-κB (RANK), and tartrate-resistant acid phosphatase (TRAP), resulting in a marked decrease in the number of TRAP-positive multinucleated cells. Spi-C-transduced bone marrow-derived monocytes/macrophages (BMMs) displayed a significant increase in osteoclast formation in the presence of RANKL. In addition, Spi-C-depleted cells failed to show actin ring formation or bone resorption owing to a marked reduction in the expression of RANKL-mediated dendritic cell-specific transmembrane protein and the d2 isoform of vacuolar (H+) ATPase V0 domain, which are known osteoclast fusion-related genes. Interestingly, RANKL stimulation induced the translocation of Spi-C from the cytoplasm into the nucleus during osteoclastogenesis, which was specifically blocked by inhibitors of p38 mitogen-activated protein kinase (MAPK) or PI3 kinase. Moreover, Spi-C depletion prevented RANKL-induced MAPK activation and the degradation of inhibitor of κB-α (IκBα) in BMMs. Collectively, these results suggest that Spi-C is a novel positive regulator that promotes both osteoclast differentiation and function.
Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean
Authors: Han Qin , Ma Qun , Chen Yong , Tian Bing , Xu Lanxi , Bai Yang , Chen Wenfeng , Li Xia 
Published: April 2020

Abstract
Rhizobia–legume symbiosis is an important type of plant–microbe mutualism; however, the establishment of this association is complicated and can be affected by many factors. The soybean rhizosphere has a specific microbial community, yet whether these organisms affect rhizobial nodulation has not been well investigated. Here, we analyzed the compositions and relationships of soybean rhizocompartment microbiota in three types of soil. First, we found that the rhizosphere community composition of soybean varied significantly in different soils, and the association network between rhizobia and other rhizosphere bacteria was examined. Second, we found that some rhizosphere microbes were correlated with the composition of bradyrhizobia and sinorhizobia in nodules. We cultivated 278 candidate Bacillus isolates from alkaline soil. Finally, interaction and nodulation assays showed that the Bacillus cereus group specifically promotes and suppresses the growth of sinorhizobia and bradyrhizobia, respectively, and alleviates the effects of saline–alkali conditions on the nodulation of sinorhizobia as well as affecting its colonization in nodules. Our findings demonstrate a crucial role of the bacterial microbiota in shaping rhizobia–host interactions in soybean, and provide a framework for improving the symbiotic efficiency of this system of mutualism through the use of synthetic bacterial communities.
Island biogeography of soil bacteria and fungi: similar patterns, but different mechanisms
Authors: Li Shao-peng , Wang Pandeng , Chen Yongjian , Wilson Maxwell C , Yang Xian , Ma Chao , Lu Jianbo , Chen Xiao-yong , Wu Jianguo , Shu Wen-sheng , Jiang Lin 
Published: April 2020

Abstract
Microbes, similar to plants and animals, exhibit biogeographic patterns. However, in contrast with the considerable knowledge on the island biogeography of higher organisms, we know little about the distribution of microorganisms within and among islands. Here, we explored insular soil bacterial and fungal biogeography and underlying mechanisms, using soil microbiota from a group of land-bridge islands as a model system. Similar to island species-area relationships observed for many macroorganisms, both island-scale bacterial and fungal diversity increased with island area; neither diversity, however, was affected by island isolation. By contrast, bacterial and fungal communities exhibited strikingly different assembly patterns within islands. The loss of bacterial diversity on smaller islands was driven primarily by the systematic decline of diversity within samples, whereas the loss of fungal diversity on smaller islands was driven primarily by the homogenization of community composition among samples. Lower soil moisture limited within-sample bacterial diversity, whereas smaller spatial distances among samples restricted among-sample fungal diversity, on smaller islands. These results indicate that among-island differences in habitat quality generate the bacterial island species-area relationship, whereas within-island dispersal limitation generates the fungal island species-area relationship. Together, our study suggests that different mechanisms underlie similar island biogeography patterns of soil bacteria and fungi.
R-spondin2 signaling is required for oocyte-driven intercellular communication and follicular growth
Authors: De Cian Marie-Cécile , Gregoire Elodie P. , Le Rolle Morgane , Lachambre Simon , Mondin Magali , Bell Sheila , Guigon Céline J. , Chassot Anne-Amandine , Chaboissier Marie-Christine 
Published: April 2020

AbstractR-spondin2 (RSPO2) is a member of the R-spondin family, which are secreted activators of the WNT/β-catenin (CTNNB1) signaling pathway. In the mouse postnatal ovary, WNT/CTNNB1 signaling is active in the oocyte and in the neighboring supporting cells, the granulosa cells. Although the role of Rspo2 has been previously studied using in vitro experiments, the results are conflicting and the in vivo ovarian function of Rspo2 remains unclear. In the present study, we found that RSPO2/Rspo2 expression is restricted to the oocyte of developing follicles in both human and mouse ovaries from the beginning of the follicular growth. In mice, genetic deletion of Rspo2 does not impair oocyte growth, but instead prevents cell cycle progression of neighboring granulosa cells, thus resulting in an arrest of follicular growth. We further show this cell cycle arrest to be independent of growth promoting GDF9 signaling, but rather associated with a downregulation of WNT/CTNNB1 signaling in granulosa cells. To confirm the contribution of WNT/CTNNB1 signaling in granulosa cell proliferation, we induced cell type specific deletion of Ctnnb1 postnatally. Strikingly, follicles lacking Ctnnb1 failed to develop beyond the primary stage. These results show that RSPO2 acts in a paracrine manner to sustain granulosa cell proliferation in early developing follicles. Taken together, our data demonstrate that the activation of WNT/CTNNB1 signaling by RSPO2 is essential for oocyte-granulosa cell interactions that drive maturation of the ovarian follicles and eventually female fertility.
The YY1/miR-548t-5p/CXCL11 signaling axis regulates cell proliferation and metastasis in human pancreatic cancer
Authors: Ge Wan-Li , Chen Qun , Meng Ling-Dong , Huang Xu-Min , Shi Guo-dong , Zong Qing-Qing , Shen Peng , Lu Yi-Chao , Zhang Yi-Han , Miao Yi , Zhang Jing-Jing , Jiang Kui-Rong 
Published: April 2020

AbstractPancreatic cancer (PC) is a malignant tumor with a poor prognosis and high mortality. However, the biological role of miR-548t-5p in PC has not been reported. In this study, we found that miR-548t-5p expression was significantly decreased in PC tissues compared with adjacent tissues, and that low miR-548t-5p expression was associated with malignant PC behavior. In addition, high miR-548t-5p expression inhibited the proliferation, migration, and invasion of PC cell lines. Regarding the molecular mechanism, the luciferase reporter gene, chromatin immunoprecipitation (ChIP), and functional recovery assays revealed that YY1 binds to the miR-548t-5p promoter and positively regulates the expression and function of miR-548t-5p. miR-548t-5p also directly regulates CXCL11 to inhibit its expression. A high level of CXCL11 was associated with worse Tumor Node Metastasis (TNM) staging in patients with PC, enhancing proliferation and metastasis in PC cells. Our study shows that the YY1/miR-548t-5p/CXCL11 axis plays an important role in PC and provides a new potential candidate for the treatment of PC.
The H2B ubiquitin-protein ligase RNF40 is required for somatic cell reprogramming
Authors: Xie Wanhua , Miehe Michaela , Laufer Sandra , Johnsen Steven A. 
Published: April 2020

AbstractDirect reprogramming of somatic cells to induced pluripotent stem cells (iPSCs) requires a resetting of the epigenome in order to facilitate a cell fate transition. Previous studies have shown that epigenetic modifying enzymes play a central role in controlling induced pluripotency and the generation of iPSC. Here we show that RNF40, a histone H2B lysine 120 E3 ubiquitin-protein ligase, is specifically required for early reprogramming during induced pluripotency. Loss of RNF40-mediated H2B monoubiquitination (H2Bub1) impaired early gene activation in reprogramming. We further show that RNF40 contributes to tissue-specific gene suppression via indirect effects by controlling the expression of the polycomb repressive complex-2 histone methyltransferase component EZH2, as well as through more direct effects by promoting the resolution of H3K4me3/H3K27me3 bivalency on H2Bub1-occupied pluripotency genes. Thus, we identify RNF40 as a central epigenetic mediator of cell state transition with distinct functions in resetting somatic cell state to pluripotency.
Mesenchymal stem cell-derived exosomal miR-223 regulates neuronal cell apoptosis
Authors: Wei Hong , Xu Yuhao , Chen Qi , Chen Hui , Zhu Xiaolan , Li Yuefeng 
Published: April 2020

AbstractHypoxia limits the survival and function of neurons in the development of Alzheimer’s diseases. Exosome-dependent intercellular communication is an emerging signaling mechanism involved in tissue repair and regeneration; however, the effect and underlying mechanism of mesenchymal stem cell-derived exosomes in regulating neuronal cell apoptosis have not been determined. Here, we showed that the establishment of an AD cell model was accompanied by increased HIF-1α expression and cell apoptosis, impaired cell migration, and decreased miR-223. MSC-derived exosomes were internalized by the AD cell coculture model in a time-dependent manner, resulting in reduced cell apoptosis, enhanced cell migration and increased miR-223, and these effects were reversed by KC7F2, a hypoxic inhibitor. Furthermore, MSC-derived exosomal miR-223 inhibited the apoptosis of neurons in vitro by targeting PTEN, thus activating the PI3K/Akt pathway. In addition, exosomes isolated from the serum of AD patients promoted cell apoptosis. In short, our study showed that MSC-derived exosomal miR-223 protected neuronal cells from apoptosis through the PTEN-PI3K/Akt pathway and provided a potential therapeutic approach for AD.
Cytokines regulate the antigen-presenting characteristics of human circulating and tissue-resident intestinal ILCs
Authors: Rao Anna , Strauss Otto , Kokkinou Efthymia , Bruchard Mélanie , Tripathi Kumar P. , Schlums Heinrich , Carrasco Anna , Mazzurana Luca , Konya Viktoria , Villablanca Eduardo J. , Björkström Niklas K. , Lindforss Ulrik , Spits Hergen , Mjösberg Jenny 
Published: April 2020

AbstractILCs and T helper cells have been shown to exert bi-directional regulation in mice. However, how crosstalk between ILCs and CD4+ T cells influences immune function in humans is unknown. Here we show that human intestinal ILCs co-localize with T cells in healthy and colorectal cancer tissue and display elevated HLA-DR expression in tumor and tumor-adjacent areas. Although mostly lacking co-stimulatory molecules ex vivo, intestinal and peripheral blood (PB) ILCs acquire antigen-presenting characteristics triggered by inflammasome-associated cytokines IL-1β and IL-18. IL-1β drives the expression of HLA-DR and co-stimulatory molecules on PB ILCs in an NF-κB-dependent manner, priming them as efficient inducers of cytomegalovirus-specific memory CD4+ T-cell responses. This effect is strongly inhibited by the anti-inflammatory cytokine TGF-β. Our results suggest that circulating and tissue-resident ILCs have the intrinsic capacity to respond to the immediate cytokine milieu and regulate local CD4+ T-cell responses, with potential implications for anti-tumor immunity and inflammation.
Optoplasmonic characterisation of reversible disulfide interactions at single thiol sites in the attomolar regime
Authors: Vincent Serge , Subramanian Sivaraman , Vollmer Frank 
Published: April 2020

AbstractProbing individual chemical reactions is key to mapping reaction pathways. Trace analysis of sub-kDa reactants and products is obfuscated by labels, however, as reaction kinetics are inevitably perturbed. The thiol-disulfide exchange reaction is of specific interest as it has many applications in nanotechnology and in nature. Redox cycling of single thiols and disulfides has been unresolvable due to a number of technological limitations, such as an inability to discriminate the leaving group. Here, we demonstrate detection of single-molecule thiol-disulfide exchange using a label-free optoplasmonic sensor. We quantify repeated reactions between sub-kDa thiolated species in real time and at concentrations down to 100’s of attomolar. A unique sensing modality is featured in our measurements, enabling the observation of single disulfide reaction kinetics and pathways on a plasmonic nanoparticle surface. Our technique paves the way towards characterising molecules in terms of their charge, oxidation state, and chirality via optoplasmonics.
Neutrophil swarming delays the growth of clusters of pathogenic fungi
Authors: Hopke Alex , Scherer Allison , Kreuzburg Samantha , Abers Michael S. , Zerbe Christa S. , Dinauer Mary C. , Mansour Michael K. , Irimia Daniel 
Published: April 2020

AbstractNeutrophils employ several mechanisms to restrict fungi, including the action of enzymes such as myeloperoxidase (MPO) or NADPH oxidase, and the release of neutrophil extracellular traps (NETs). Moreover, they cooperate, forming “swarms” to attack fungi that are larger than individual neutrophils. Here, we designed an assay for studying how these mechanisms work together and contribute to neutrophil's ability to contain clusters of live Candida. We find that neutrophil swarming over Candida clusters delays germination through the action of MPO and NADPH oxidase, and restricts fungal growth through NET release within the swarm. In comparison with neutrophils from healthy subjects, those from patients with chronic granulomatous disease produce larger swarms against Candida, but their release of NETs is delayed, resulting in impaired control of fungal growth. We also show that granulocyte colony-stimulating factors (GCSF and GM-CSF) enhance swarming and neutrophil ability to restrict fungal growth, even during treatment with chemical inhibitors that disrupt neutrophil function.
Immunoglobulin expression and the humoral immune response is regulated by the non-canonical poly(A) polymerase TENT5C
Authors: Bilska Aleksandra , Kusio-Kobiałka Monika , Krawczyk Paweł S. , Gewartowska Olga , Tarkowski Bartosz , Kobyłecki Kamil , Nowis Dominika , Golab Jakub , Gruchota Jakub , Borsuk Ewa , Dziembowski Andrzej , Mroczek Seweryn 
Published: April 2020

AbstractTENT5C is a non-canonical cytoplasmic poly(A) polymerase highly expressed by activated B cells to suppress their proliferation. Here we measure the global distribution of poly(A) tail lengths in responsive B cells using a Nanopore direct RNA-sequencing approach, showing that TENT5C polyadenylates immunoglobulin mRNAs regulating their half-life and consequently steady-state levels. TENT5C is upregulated in differentiating plasma cells by innate signaling. Compared with wild-type, Tent5c−/− mice produce fewer antibodies and have diminished T-cell-independent immune response despite having more CD138high plasma cells as a consequence of accelerated differentiation. B cells from Tent5c−/− mice also have impaired capacity of the secretory pathway, with reduced ER volume and unfolded protein response. Importantly, these functions of TENT5C are dependent on its enzymatic activity as catalytic mutation knock-in mice display the same defect as Tent5c−/−. These findings define the role of the TENT5C enzyme in the humoral immune response.
Versatile whole-organ/body staining and imaging based on electrolyte-gel properties of biological tissues
Authors: Susaki Etsuo A. , Shimizu Chika , Kuno Akihiro , Tainaka Kazuki , Li Xiang , Nishi Kengo , Morishima Ken , Ono Hiroaki , Ode Koji L. , Saeki Yuki , Miyamichi Kazunari , Isa Kaoru , Yokoyama Chihiro , Kitaura Hiroki , Ikemura Masako , Ushiku Tetsuo , Shimizu Yoshihiro , Saito Takashi , Saido Takaomi C. , Fukayama Masashi , Onoe Hirotaka , Touhara Kazushige , Isa Tadashi , Kakita Akiyoshi , Shibayama Mitsuhiro , Ueda Hiroki R. 
Published: April 2020

AbstractWhole-organ/body three-dimensional (3D) staining and imaging have been enduring challenges in histology. By dissecting the complex physicochemical environment of the staining system, we developed a highly optimized 3D staining imaging pipeline based on CUBIC. Based on our precise characterization of biological tissues as an electrolyte gel, we experimentally evaluated broad 3D staining conditions by using an artificial tissue-mimicking material. The combination of optimized conditions allows a bottom-up design of a superior 3D staining protocol that can uniformly label whole adult mouse brains, an adult marmoset brain hemisphere, an ~1 cm3 tissue block of a postmortem adult human cerebellum, and an entire infant marmoset body with dozens of antibodies and cell-impermeant nuclear stains. The whole-organ 3D images collected by light-sheet microscopy are used for computational analyses and whole-organ comparison analysis between species. This pipeline, named CUBIC-HistoVIsion, thus offers advanced opportunities for organ- and organism-scale histological analysis of multicellular systems.