bluuebunny/crossref_metadata_2025_split huggingface dataset:
A River Channel Extraction Method for Urban Environments Based on Terrain Transition Lines
Authors: Qin Lianjie , Xu Wei , Tian Yugang , Chen Bo , Wang Siyue 
Published: June 2018

AbstractA river channel network is an important geomorphological feature in a catchment. A method to extract river channels in urban environments from a high‐resolution digital elevation model (DEM) is introduced in this paper. The method utilizes terrain transition lines to delineate channel networks. First, terrain transition lines are extracted from the DEM. Then, shallow road ditches are removed based on elevation from the terrain transition lines, and then, noise is removed using the region growing method. Subsequently, most of the road ditches are removed by pixel block expansion, and then, the nonchannel pixels are removed by fitting a quadratic surface. The computational efficiency and accurate localization of river channel extraction using the proposed method is demonstrated using light detection and ranging (LiDAR) data for an urban environment in Johnson County, Iowa. The proposed method is effective for extracting channels and removing road ditches in this urban environment. A potential application of this method is to provide the river channels required for riverine flood modeling and geomorphological studies.
Hydrogen sulfide maintains dental pulp stem cell function via TRPV1-mediated calcium influx
Authors: Yang Ruili , Liu Yi , Yu Tingting , Liu Dawei , Shi Songtao , Zhou Yongsheng , Zhou Yanheng 
Published: June 2018

AbstractHydrogen sulfide (H2S), an endogenous gasotransmitter, mediated a variety of biological processes through multiple signaling pathways, and aberrant H2S metabolism has been associated with mesenchymal stem cell (MSC) dysfunction. Here we employed the small interfering RNA treatment for cystathionine β-synthase (CBS), cystathionine γ-lyase, the main enzymes to synthesize H2S, and CBS-knockout mice to analyze the effect of H2S on dental pulp homeostasis. We showed that H2S deficiency attenuated dental pulp stem cell (DPSC) osteogenic/dentinogenic differentiation in vitro and in vivo with enhanced cell proliferation. Mechanically, H2S facilitated the transient receptor potential action channel subfamily V member 1-mediated calcium (Ca2+) influx, which subsequently activated the β-catenin pathway. While H2S deficiency decreased Ca2+, resulting in glycogen synthase kinase-3β-mediated β-catenin degradation, which controls proliferation and differentiation of DPSCs. Consistently, H2S-deficient mice displayed disturbed pattern of dental pulp and less dentin formation. In this study, we identified a previously unknown mechanism by which H2S regulates DPSC lineage determination and dental pulp homeostasis.
Postprandial FGF19-induced phosphorylation by Src is critical for FXR function in bile acid homeostasis
Authors: Byun Sangwon , Kim Dong-Hyun , Ryerson Daniel , Kim Young-Chae , Sun Hao , Kong Bo , Yau Peter , Guo Grace , Xu H. Eric , Kemper Byron , Kemper Jongsook Kim 
Published: June 2018

AbstractFarnesoid-X-Receptor (FXR) plays a central role in maintaining bile acid (BA) homeostasis by transcriptional control of numerous enterohepatic genes, including intestinal FGF19, a hormone that strongly represses hepatic BA synthesis. How activation of the FGF19 receptor at the membrane is transmitted to the nucleus for transcriptional regulation of BA levels and whether FGF19 signaling posttranslationally modulates FXR function remain largely unknown. Here we show that FXR is phosphorylated at Y67 by non-receptor tyrosine kinase, Src, in response to postprandial FGF19, which is critical for its nuclear localization and transcriptional regulation of BA levels. Liver-specific expression of phospho-defective Y67F-FXR or Src downregulation in mice results in impaired homeostatic responses to acute BA feeding, and exacerbates cholestatic pathologies upon drug-induced hepatobiliary insults. Also, the hepatic FGF19-Src-FXR pathway is defective in primary biliary cirrhosis (PBC) patients. This study identifies Src-mediated FXR phosphorylation as a potential therapeutic target and biomarker for BA-related enterohepatic diseases.
The role of momentum-dark excitons in the elementary optical response of bilayer WSe2
Authors: Lindlau Jessica , Selig Malte , Neumann Andre , Colombier Léo , Förste Jonathan , Funk Victor , Förg Michael , Kim Jonghwan , Berghäuser Gunnar , Taniguchi Takashi , Watanabe Kenji , Wang Feng , Malic Ermin , Högele Alexander 
Published: June 2018

AbstractMonolayer transition metal dichalcogenides (TMDs) undergo substantial changes in the single-particle band structure and excitonic optical response upon the addition of just one layer. As opposed to the single-layer limit, the bandgap of bilayer (BL) TMD semiconductors is indirect which results in reduced photoluminescence with richly structured spectra that have eluded a detailed understanding to date. Here, we provide a closed interpretation of cryogenic emission from BL WSe2 as a representative material for the wider class of TMD semiconductors. By combining theoretical calculations with comprehensive spectroscopy experiments, we identify the crucial role of momentum-indirect excitons for the understanding of BL TMD emission. Our results shed light on the origin of quantum dot formation in BL crystals and will facilitate further advances directed at opto-electronic applications of layered TMD semiconductors in van der Waals heterostructures and devices.
High energy flexible supercapacitors formed via bottom-up infilling of gel electrolytes into thick porous electrodes
Authors: Li Xiangming , Shao Jinyou , Kim Sung-Kon , Yao Chaochao , Wang Junjie , Miao Yu-Run , Zheng Qiye , Sun Pengcheng , Zhang Runyu , Braun Paul V. 
Published: June 2018

AbstractFormation of thick, high energy density, flexible solid supercapacitors is challenging because of difficulties infilling gel electrolytes into porous electrodes. Incomplete infilling results in a low capacitance and poor mechanical properties. Here we report a bottom-up infilling method to overcome these challenges. Electrodes up to 500 μm thick, formed from multi-walled carbon nanotubes and a composite of poly(3,4-ethylenedioxythiophene), polystyrene sulfonate and multi-walled carbon nanotubes are successfully infilled with a polyvinyl alcohol/phosphoric acid gel electrolyte. The exceptional mechanical properties of the multi-walled carbon nanotube-based electrode enable it to be rolled into a radius of curvature as small as 0.5 mm without cracking and retain 95% of its initial capacitance after 5000 bending cycles. The areal capacitance of our 500 μm thick poly(3,4-ethylenedioxythiophene), polystyrene sulfonate, multi-walled carbon nanotube-based flexible solid supercapacitor is 2662 mF cm–2 at 2 mV s–1, at least five times greater than current flexible supercapacitors.
Embryos and embryonic stem cells from the white rhinoceros
Authors: Hildebrandt Thomas B. , Hermes Robert , Colleoni Silvia , Diecke Sebastian , Holtze Susanne , Renfree Marilyn B. , Stejskal Jan , Hayashi Katsuhiko , Drukker Micha , Loi Pasqualino , Göritz Frank , Lazzari Giovanna , Galli Cesare 
Published: June 2018

AbstractThe northern white rhinoceros (NWR, Ceratotherium simum cottoni) is the most endangered mammal in the world with only two females surviving. Here we adapt existing assisted reproduction techniques (ART) to fertilize Southern White Rhinoceros (SWR) oocytes with NWR spermatozoa. We show that rhinoceros oocytes can be repeatedly recovered from live SWR females by transrectal ovum pick-up, matured, fertilized by intracytoplasmic sperm injection and developed to the blastocyst stage in vitro. Next, we generate hybrid rhinoceros embryos in vitro using gametes of NWR and SWR. We also establish embryonic stem cell lines from the SWR blastocysts. Blastocysts are cryopreserved for later embryo transfer. Our results indicate that ART could be a viable strategy to rescue genes from the iconic, almost extinct, northern white rhinoceros and may also have broader impact if applied with similar success to other endangered large mammalian species.
Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics
Authors: Auburn Sarah , Benavente Ernest D. , Miotto Olivo , Pearson Richard D. , Amato Roberto , Grigg Matthew J. , Barber Bridget E. , William Timothy , Handayuni Irene , Marfurt Jutta , Trimarsanto Hidayat , Noviyanti Rintis , Sriprawat Kanlaya , Nosten Francois , Campino Susana , Clark Taane G. , Anstey Nicholas M. , Kwiatkowski Dominic P. , Price Ric N. 
Published: June 2018

AbstractThe incidence of Plasmodium vivax infection has declined markedly in Malaysia over the past decade despite evidence of high-grade chloroquine resistance. Here we investigate the genetic changes in a P. vivax population approaching elimination in 51 isolates from Sabah, Malaysia and compare these with data from 104 isolates from Thailand and 104 isolates from Indonesia. Sabah displays extensive population structure, mirroring that previously seen with the emergence of artemisinin-resistant P. falciparum founder populations in Cambodia. Fifty-four percent of the Sabah isolates have identical genomes, consistent with a rapid clonal expansion. Across Sabah, there is a high prevalence of loci known to be associated with antimalarial drug resistance. Measures of differentiation between the three countries reveal several gene regions under putative selection in Sabah. Our findings highlight important factors pertinent to parasite resurgence and molecular cues that can be used to monitor low-endemic populations at the end stages of P. vivax elimination.
Coupling of ocean redox and animal evolution during the Ediacaran-Cambrian transition
Authors: Wang Dan , Ling Hong-Fei , Struck Ulrich , Zhu Xiang-Kun , Zhu Maoyan , He Tianchen , Yang Ben , Gamper Antonia , Shields Graham A. 
Published: June 2018

AbstractThe late Ediacaran to early Cambrian interval witnessed extraordinary radiations of metazoan life. The role of the physical environment in this biological revolution, such as changes to oxygen levels and nutrient availability, has been the focus of longstanding debate. Seemingly contradictory data from geochemical redox proxies help to fuel this controversy. As an essential nutrient, nitrogen can help to resolve this impasse by establishing linkages between nutrient supply, ocean redox, and biological changes. Here we present a comprehensive N-isotope dataset from the Yangtze Basin that reveals remarkable coupling between δ15N, δ13C, and evolutionary events from circa 551 to 515 Ma. The results indicate that increased fixed nitrogen supply may have facilitated episodic animal radiations by reinforcing ocean oxygenation, and restricting anoxia to near, or even at the sediment–water interface. Conversely, sporadic ocean anoxic events interrupted ocean oxygenation, and may have led to extinctions of the Ediacaran biota and small shelly animals.
Evidence for line width and carrier screening effects on excitonic valley relaxation in 2D semiconductors
Authors: Miyauchi Yuhei , Konabe Satoru , Wang Feijiu , Zhang Wenjin , Hwang Alexander , Hasegawa Yusuke , Zhou Lizhong , Mouri Shinichiro , Toh Minglin , Eda Goki , Matsuda Kazunari 
Published: June 2018

AbstractMonolayers of transition metal dichalcogenides (TMDC) have recently emerged as excellent platforms for exploiting new physics and applications relying on electronic valley degrees of freedom in two-dimensional (2D) systems. Here, we demonstrate that Coulomb screening by 2D carriers plays a critical role in excitonic valley pseudospin relaxation processes in naturally carrier-doped WSe2 monolayers (1L-WSe2). The exciton valley relaxation times were examined using polarization- and time-resolved photoluminescence spectroscopy at temperatures ranging from 10 to 160 K. We show that the temperature-dependent exciton valley relaxation times in 1L-WSe2 under various exciton and carrier densities can be understood using a unified framework of intervalley exciton scattering via momentum-dependent long-range electron–hole exchange interactions screened by 2D carriers that depend on the carrier density and the exciton linewidth. Moreover, the developed framework was successfully applied to engineer the valley polarization of excitons in 1L-WSe2. These findings may facilitate the development of TMDC-based opto-valleytronic devices.
Monoacylglycerol lipase regulates cannabinoid receptor 2-dependent macrophage activation and cancer progression
Authors: Xiang Wei , Shi Rongchen , Kang Xia , Zhang Xuan , Chen Peng , Zhang Lili , Hou Along , Wang Rui , Zhao Yuanyin , Zhao Kun , Liu Yingzhe , Ma Yue , Luo Huan , Shang Shenglan , Zhang Jinyu , He Fengtian , Yu Songtao , Gan Lixia , Shi Chunmeng , Li Yongsheng , Yang Wei , Liang Houjie , Miao Hongming 
Published: June 2018

AbstractMetabolic reprogramming greatly contributes to the regulation of macrophage activation. However, the mechanism of lipid accumulation and the corresponding function in tumor-associated macrophages (TAMs) remain unclear. With primary investigation in colon cancer and confirmation in other cancer models, here we determine that deficiency of monoacylglycerol lipase (MGLL) results in lipid overload in TAMs. Functionally, macrophage MGLL inhibits CB2 cannabinoid receptor-dependent tumor progression in inoculated and genetic cancer models. Mechanistically, MGLL deficiency promotes CB2/TLR4-dependent macrophage activation, which further suppresses the function of tumor-associated CD8+ T cells. Treatment with CB2 antagonists delays tumor progression in inoculated and genetic cancer models. Finally, we verify that expression of macrophage MGLL is decreased in cancer tissues and positively correlated with the survival of cancer patients. Taken together, our findings identify MGLL as a switch for CB2/TLR4-dependent macrophage activation and provide potential targets for cancer therapy.
Task-dependent representations of stimulus and choice in mouse parietal cortex
Authors: Pho Gerald N. , Goard Michael J. , Woodson Jonathan , Crawford Benjamin , Sur Mriganka 
Published: June 2018

AbstractThe posterior parietal cortex (PPC) has been implicated in perceptual decisions, but whether its role is specific to sensory processing or sensorimotor transformation is not well understood. Here, we trained mice to perform a go/no-go visual discrimination task and imaged the activity of neurons in primary visual cortex (V1) and PPC during engaged behavior and passive viewing. Unlike V1 neurons, which respond robustly to stimuli in both conditions, most PPC neurons respond exclusively during task engagement. To test whether signals in PPC primarily encoded the stimulus or the animal’s impending choice, we image the same neurons before and after re-training mice with a reversed sensorimotor contingency. Unlike V1 neurons, most PPC neurons reflect the animal’s choice of the new target stimulus after re-training. Mouse PPC is therefore strongly task-dependent, reflects choice more than stimulus, and may play a role in the transformation of visual inputs into motor commands.
Transcriptional synergy as an emergent property defining cell subpopulation identity enables population shift
Authors: Okawa Satoshi , Saltó Carmen , Ravichandran Srikanth , Yang Shanzheng , Toledo Enrique M. , Arenas Ernest , del Sol Antonio 
Published: June 2018

AbstractSingle-cell RNA sequencing allows defining molecularly distinct cell subpopulations. However, the identification of specific sets of transcription factors (TFs) that define the identity of these subpopulations remains a challenge. Here we propose that subpopulation identity emerges from the synergistic activity of multiple TFs. Based on this concept, we develop a computational platform (TransSyn) for identifying synergistic transcriptional cores that determine cell subpopulation identities. TransSyn leverages single-cell RNA-seq data, and performs a dynamic search for an optimal synergistic transcriptional core using an information theoretic measure of synergy. A large-scale TransSyn analysis identifies transcriptional cores for 186 subpopulations, and predicts identity conversion TFs between 3786 pairs of cell subpopulations. Finally, TransSyn predictions enable experimental conversion of human hindbrain neuroepithelial cells into medial floor plate midbrain progenitors, capable of rapidly differentiating into dopaminergic neurons. Thus, TransSyn can facilitate designing strategies for conversion of cell subpopulation identities with potential applications in regenerative medicine.
Tunable and switchable magnetic dipole patterns in nanostructured superconductors
Authors: Ge Jun-Yi , Gladilin Vladimir N. , Tempere Jacques , Devreese Jozef T. , Moshchalkov Victor V. 
Published: June 2018

AbstractDesign and manipulation of magnetic moment arrays have been at the focus of studying the interesting cooperative physical phenomena in various magnetic systems. However, long-range ordered magnetic moments are rather difficult to achieve due to the excited states arising from the relatively weak exchange interactions between the localized moments. Here, using a nanostructured superconductor, we investigate a perfectly ordered magnetic dipole pattern with the magnetic poles having the same distribution as the magnetic charges in an artificial spin ice. The magnetic states can simply be switched on/off by applying a current flowing through nanopatterned area. Moreover, by coupling magnetic dipoles with the pinned vortex lattice, we are able to erase the positive/negative poles, resulting in a magnetic dipole pattern of only one polarity, analogous to the recently predicted vortex ice. These switchable and tunable magnetic dipole patterns open pathways for the study of exotic ordering phenomena in magnetic systems.
Comparison of intestinal bacterial and fungal communities across various xylophagous beetle larvae (Coleoptera: Cerambycidae)
Authors: Mohammed Waleed S. , Ziganshina Elvira E. , Shagimardanova Elena I. , Gogoleva Natalia E. , Ziganshin Ayrat M. 
Published: June 2018

AbstractThe microbial gut communities associated with various xylophagous beetles offer great potential for different biotechnologies and elaboration of novel pest management strategies. In this research, the intestinal bacterial and fungal communities of various cerambycid larvae, including Acmaeops septentrionis, Acanthocinus aedilis, Callidium coriaceum, Trichoferus campestris and Chlorophorus herbstii, were investigated. The intestinal microbial communities of these Cerambycidae species were mostly represented by members of the bacterial phyla Proteobacteria and Actinobacteria and the fungal phylum Ascomycota. However, the bacterial and fungal communities varied by beetle species and between individual organisms. Furthermore, bacterial communities’ metagenomes reconstruction indicated the genes that encode enzymes involved in the lignocellulose degradation (such as peroxidases, alpha-L-fucosidases, beta-xylosidases, beta-mannosidases, endoglucanases, beta-glucosidases and others) and nitrogen fixation (nitrogenases). Most of the predicted genes potentially related to lignocellulose degradation were enriched in the T. campestris,A. aedilis and A. septentrionis larval gut consortia, whereas predicted genes affiliated with the nitrogenase component proteins were enriched in the T. campestris, A. septentrionis and C. herbstii larval gut consortia. Several bacteria and fungi detected in the current work could be involved in the nutrition of beetle larvae.
Fiber density of collagen grafts impacts rabbit urethral regeneration
Authors: Larsson H. M. , Vythilingam G. , Pinnagoda K. , Vardar E. , Engelhardt E. M. , Sothilingam S. , Thambidorai R. C. , Kamarul T. , Hubbell J. A. , Frey P. 
Published: June 2018

AbstractThere is a need for efficient and “off-the-shelf” grafts in urethral reconstructive surgery. Currently available surgical techniques require harvesting of grafts from autologous sites, with increased risk of surgical complications and added patient discomfort. Therefore, a cost-effective and cell-free graft with adequate regenerative potential has a great chance to be translated into clinical practice. Tubular cell-free collagen grafts were prepared by varying the collagen density and fiber distribution, thereby creating a polarized low fiber density collagen graft (LD-graft). A uniform, high fiber density collagen graft (HD-graft) was engineered as a control. These two grafts were implanted to bridge a 2 cm long iatrogenic urethral defect in a rabbit model. Histology revealed that rabbits implanted with the LD-graft had a better smooth muscle regeneration compared to the HD-graft. The overall functional outcome assessed by contrast voiding cystourethrography showed patency of the urethra in 90% for the LD-graft and in 66.6% for the HD-graft. Functional regeneration of the rabbit implanted with the LD-graft could further be demonstrated by successful mating, resulting in healthy offspring. In conclusion, cell-free low-density polarized collagen grafts show better urethral regeneration than high-density collagen grafts.
Complex spectrum of phenobarbital effects in a mouse model of neonatal hypoxia-induced seizures
Authors: Quinlan Sean M. M. , Rodriguez-Alvarez Natalia , Molloy Eleanor J. , Madden Stephen F. , Boylan Geraldine B. , Henshall David C. , Jimenez-Mateos Eva M. 
Published: June 2018

AbstractSeizures in neonates, mainly caused by hypoxic-ischemic encephalopathy, are thought to be harmful to the brain. Phenobarbital remains the first line drug therapy for the treatment of suspected neonatal seizures but concerns remain with efficacy and safety. Here we explored the short- and long-term outcomes of phenobarbital treatment in a mouse model of hypoxia-induced neonatal seizures. Seizures were induced in P7 mice by exposure to 5% O2 for 15 minutes. Immediately after hypoxia, pups received a single dose of phenobarbital (25 mg.kg−1) or saline. We observed that after administration of phenobarbital seizure burden and number of seizures were reduced compared to the hypoxic period; however, PhB did not suppress acute histopathology. Behavioural analysis of mice at 5 weeks of age previously subjected to hypoxia-seizures revealed an increase in anxiety-like behaviour and impaired memory function compared to control littermates, and these effects were not normalized by phenobarbital. In a seizure susceptibility test, pups previously exposed to hypoxia, with or without phenobarbital, developed longer and more severe seizures in response to kainic acid injection compared to control mice. Unexpectedly, mice treated with phenobarbital developed less hippocampal damage after kainic acid than untreated counterparts. The present study suggests phenobarbital treatment in immature mice does not improve the long lasting functional deficits induces by hypoxia-induced seizures but, unexpectedly, may reduce neuronal death caused by exposure to a second seizure event in later life.