bluuebunny/crossref_metadata_2025_split huggingface dataset:
NEXAFS imaging to characterize the physio-chemical composition of cuticle from African Flower Scarab Eudicella gralli
Authors: Baio Joe E. , Jaye Cherno , Sullivan Erin , Rasmussen Mette H. , Fischer Daniel A. , Gorb Stanislav , Weidner Tobias 
Published: October 2019

AbstractThe outermost surface of insect cuticle is a high-performance interface that provides wear protection, hydration, camouflage and sensing. The complex and inhomogeneous structure of insect cuticle imposes stringent requirements on approaches to elucidate its molecular structure and surface chemistry. Therefore, a molecular understanding and possible mimicry of the surface of insect cuticle has been a challenge. Conventional optical and electron microscopies as well as biochemical techniques provide information about morphology and chemistry but lack surface specificity. We here show that a near edge X-ray absorption fine structure microscope at the National Synchrotron Light Source can probe the surface chemistry of the curved and inhomogeneous cuticle of the African flower scarab. The analysis shows the distribution of organic and inorganic surface species while also hinting at the presence of aragonite at the dorsal protrusion region of the Eudicella gralli head, in line with its biological function.
The free energy landscape of retroviral integration
Authors: Vanderlinden Willem , Brouns Tine , Walker Philipp U. , Kolbeck Pauline J. , Milles Lukas F. , Ott Wolfgang , Nickels Philipp C. , Debyser Zeger , Lipfert Jan 
Published: October 2019

AbstractRetroviral integration, the process of covalently inserting viral DNA into the host genome, is a point of no return in the replication cycle. Yet, strand transfer is intrinsically iso-energetic and it is not clear how efficient integration can be achieved. Here we investigate the dynamics of strand transfer and demonstrate that consecutive nucleoprotein intermediates interacting with a supercoiled target are increasingly stable, resulting in a net forward rate. Multivalent target interactions at discrete auxiliary interfaces render target capture irreversible, while allowing dynamic site selection. Active site binding is transient but rapidly results in strand transfer, which in turn rearranges and stabilizes the intasome in an allosteric manner. We find the resulting strand transfer complex to be mechanically stable and extremely long-lived, suggesting that a resolving agent is required in vivo.
Optical mapping of biological water in single live cells by stimulated Raman excited fluorescence microscopy
Authors: Shi Lixue , Hu Fanghao , Min Wei 
Published: October 2019

AbstractWater is arguably the most common and yet least understood material on Earth. Indeed, the biophysical behavior of water in crowded intracellular milieu is a long-debated issue. Understanding of the spatial and compositional heterogeneity of water inside cells remains elusive, largely due to a lack of proper water-sensing tools with high sensitivity and spatial resolution. Recently, stimulated Raman excited fluorescence (SREF) microscopy was reported as the most sensitive vibrational imaging in the optical far field. Herein we develop SREF into a water-sensing tool by coupling it with vibrational solvatochromism. This technique allows us to directly visualize spatially-resolved distribution of water states inside single mammalian cells. Qualitatively, our result supports the concept of biological water and reveals intracellular water heterogeneity between nucleus and cytoplasm. Quantitatively, we unveil a compositional map of the water pool inside living cells. Hence we hope SREF will be a promising tool to study intracellular water and its relationship with cellular activities.
Towards symmetry driven and nature inspired UV filter design
Authors: Horbury Michael D. , Holt Emily L. , Mouterde Louis M. M. , Balaguer Patrick , Cebrián Juan , Blasco Laurent , Allais Florent , Stavros Vasilios G. 
Published: October 2019

AbstractIn plants, sinapate esters offer crucial protection from the deleterious effects of ultraviolet radiation exposure. These esters are a promising foundation for designing UV filters, particularly for the UVA region (400 – 315 nm), where adequate photoprotection is currently lacking. Whilst sinapate esters are highly photostable due to a cis-trans (and vice versa) photoisomerization, the cis-isomer can display increased genotoxicity; an alarming concern for current cinnamate ester-based human sunscreens. To eliminate this potentiality, here we synthesize a sinapate ester with equivalent cis- and trans-isomers. We investigate its photostability through innovative ultrafast spectroscopy on a skin mimic, thus modelling the as close to true environment of sunscreen formulas. These studies are complemented by assessing endocrine disruption activity and antioxidant potential. We contest, from our results, that symmetrically functionalized sinapate esters may show exceptional promise as nature-inspired UV filters in next generation sunscreen formulations.
Super-enhancer-guided mapping of regulatory networks controlling mouse trophoblast stem cells
Authors: Lee Bum-Kyu , Jang Yu jin , Kim Mijeong , LeBlanc Lucy , Rhee Catherine , Lee Jiwoon , Beck Samuel , Shen Wenwen , Kim Jonghwan 
Published: October 2019

AbstractTrophectoderm (TE) lineage development is pivotal for proper implantation, placentation, and healthy pregnancy. However, only a few TE-specific transcription factors (TFs) have been systematically characterized, hindering our understanding of the process. To elucidate regulatory mechanisms underlying TE development, here we map super-enhancers (SEs) in trophoblast stem cells (TSCs) as a model. We find both prominent TE-specific master TFs (Cdx2, Gata3, and Tead4), and >150 TFs that had not been previously implicated in TE lineage, that are SE-associated. Mapping targets of 27 SE-predicted TFs reveals a highly intertwined transcriptional regulatory circuitry. Intriguingly, SE-predicted TFs show 4 distinct expression patterns with dynamic alterations of their targets during TSC differentiation. Furthermore, depletion of a subset of TFs results in dysregulation of the markers for specialized cell types in placenta, suggesting a role during TE differentiation. Collectively, we characterize an expanded TE-specific regulatory network, providing a framework for understanding TE lineage development and placentation.
Identification of atrial fibrillation associated genes and functional non-coding variants
Authors: van Ouwerkerk Antoinette F. , Bosada Fernanda M. , van Duijvenboden Karel , Hill Matthew C. , Montefiori Lindsey E. , Scholman Koen T. , Liu Jia , de Vries Antoine A. F. , Boukens Bastiaan J. , Ellinor Patrick T. , Goumans Marie José T. H. , Efimov Igor R. , Nobrega Marcelo A. , Barnett Phil , Martin James F. , Christoffels Vincent M. 
Published: October 2019

AbstractDisease-associated genetic variants that lie in non-coding regions found by genome-wide association studies are thought to alter the functionality of transcription regulatory elements and target gene expression. To uncover causal genetic variants, variant regulatory elements and their target genes, here we cross-reference human transcriptomic, epigenomic and chromatin conformation datasets. Of 104 genetic variant regions associated with atrial fibrillation candidate target genes are prioritized. We optimize EMERGE enhancer prediction and use accessible chromatin profiles of human atrial cardiomyocytes to more accurately predict cardiac regulatory elements and identify hundreds of sub-threshold variants that co-localize with regulatory elements. Removal of mouse homologues of atrial fibrillation-associated regions in vivo uncovers a distal regulatory region involved in Gja1 (Cx43) expression. Our analyses provide a shortlist of genes likely affected by atrial fibrillation-associated variants and provide variant regulatory elements in each region that link genetic variation and target gene regulation, helping to focus future investigations.
Energy transformation cost for the Japanese mid-century strategy
Authors: Fujimori Shinichiro , Oshiro Ken , Shiraki Hiroto , Hasegawa Tomoko 
Published: October 2019

AbstractThe costs of climate change mitigation policy are one of the main concerns in decarbonizing the economy. The macroeconomic and sectoral implications of policy interventions are typically estimated by economic models, which tend be higher than the additional energy system costs projected by energy system models. Here, we show the extent to which policy costs can be lower than those from conventional economic models by integrating an energy system and an economic model, applying Japan’s mid-century climate mitigation target. The GDP losses estimated with the integrated model were significantly lower than those in the conventional economic model by more than 50% in 2050. The representation of industry and service sector energy consumption is the main factor causing these differences. Our findings suggest that this type of integrated approach would contribute new insights by providing improved estimates of GDP losses, which can be critical information for setting national climate policies.
Radar vision in the mapping of forest biodiversity from space
Authors: Bae Soyeon , Levick Shaun R. , Heidrich Lea , Magdon Paul , Leutner Benjamin F. , Wöllauer Stephan , Serebryanyk Alla , Nauss Thomas , Krzystek Peter , Gossner Martin M. , Schall Peter , Heibl Christoph , Bässler Claus , Doerfler Inken , Schulze Ernst-Detlef , Krah Franz-Sebastian , Culmsee Heike , Jung Kirsten , Heurich Marco , Fischer Markus , Seibold Sebastian , Thorn Simon , Gerlach Tobias , Hothorn Torsten , Weisser Wolfgang W. , Müller Jörg 
Published: October 2019

AbstractRecent progress in remote sensing provides much-needed, large-scale spatio-temporal information on habitat structures important for biodiversity conservation. Here we examine the potential of a newly launched satellite-borne radar system (Sentinel-1) to map the biodiversity of twelve taxa across five temperate forest regions in central Europe. We show that the sensitivity of radar to habitat structure is similar to that of airborne laser scanning (ALS), the current gold standard in the measurement of forest structure. Our models of different facets of biodiversity reveal that radar performs as well as ALS; medianR²over twelve taxa by ALS and radar are 0.51 and 0.57 respectively for the first non-metric multidimensional scaling axes representing assemblage composition. We further demonstrate the promising predictive ability of radar-derived data with external validation based on the species composition of birds and saproxylic beetles. Establishing new area-wide biodiversity monitoring by remote sensing will require the coupling of radar data to stratified and standardized collected local species data.
Phagocytosis is mediated by two-dimensional assemblies of the F-BAR protein GAS7
Authors: Hanawa-Suetsugu Kyoko , Itoh Yuzuru , Ab Fatah Maisarah , Nishimura Tamako , Takemura Kazuhiro , Takeshita Kohei , Kubota Satoru , Miyazaki Naoyuki , Wan Mohamad Noor Wan Nurul Izzati , Inaba Takehiko , Nguyen Nhung Thi Hong , Hamada-Nakahara Sayaka , Oono-Yakura Kayoko , Tachikawa Masashi , Iwasaki Kenji , Kohda Daisuke , Yamamoto Masaki , Kitao Akio , Shimada Atsushi , Suetsugu Shiro 
Published: October 2019

AbstractPhagocytosis is a cellular process for internalization of micron-sized large particles including pathogens. The Bin-Amphiphysin-Rvs167 (BAR) domain proteins, including the FCH-BAR (F-BAR) domain proteins, impose specific morphologies on lipid membranes. Most BAR domain proteins are thought to form membrane invaginations or protrusions by assembling into helical submicron-diameter filaments, such as on clathrin-coated pits, caveolae, and filopodia. However, the mechanism by which BAR domain proteins assemble into micron-scale phagocytic cups was unclear. Here, we show that the two-dimensional sheet-like assembly of Growth Arrest-Specific 7 (GAS7) plays a critical role in phagocytic cup formation in macrophages. GAS7 has the F-BAR domain that possesses unique hydrophilic loops for two-dimensional sheet formation on flat membranes. Super-resolution microscopy reveals the similar assemblies of GAS7 on phagocytic cups and liposomes. The mutations of the loops abolishes both the membrane localization of GAS7 and phagocytosis. Thus, the sheet-like assembly of GAS7 plays a significant role in phagocytosis.
Hydrogen bonding structure of confined water templated by a metal-organic framework with open metal sites
Authors: Rieth Adam J. , Hunter Kelly M. , Dincă Mircea , Paesani Francesco 
Published: October 2019

AbstractWater in confinement exhibits properties significantly different from bulk water due to frustration in the hydrogen-bond network induced by interactions with the substrate. Here, we combine infrared spectroscopy and many-body molecular dynamics simulations to probe the structure and dynamics of confined water as a function of relative humidity within a metal-organic framework containing cylindrical pores lined with ordered cobalt open coordination sites. Building upon the agreement between experimental and theoretical spectra, we demonstrate that water at low relative humidity binds initially to open metal sites and subsequently forms disconnected one-dimensional chains of hydrogen-bonded water molecules bridging between cobalt atoms. With increasing relative humidity, these water chains nucleate pore filling, and water molecules occupy the entire pore interior before the relative humidity reaches 30%. Systematic analysis of rotational and translational dynamics indicates heterogeneity in this pore-confined water, with water molecules displaying variable mobility as a function of distance from the interface.
Rashba-like spin splitting along three momentum directions in trigonal layered PtBi2
Authors: Feng Ya , Jiang Qi , Feng Baojie , Yang Meng , Xu Tao , Liu Wenjing , Yang Xiufu , Arita Masashi , Schwier Eike F. , Shimada Kenya , Jeschke Harald O. , Thomale Ronny , Shi Youguo , Wu Xianxin , Xiao Shaozhu , Qiao Shan , He Shaolong 
Published: October 2019

AbstractSpin-orbit coupling (SOC) has gained much attention for its rich physical phenomena and highly promising applications in spintronic devices. The Rashba-type SOC in systems with inversion symmetry breaking is particularly attractive for spintronics applications since it allows for flexible manipulation of spin current by external electric fields. Here, we report the discovery of a giant anisotropic Rashba-like spin splitting along three momentum directions (3D Rashba-like spin splitting) with a helical spin polarization around the M points in the Brillouin zone of trigonal layered PtBi2. Due to its inversion asymmetry and reduced symmetry at the M point, Rashba-type as well as Dresselhaus-type SOC cooperatively yield a 3D spin splitting with αR ≈ 4.36 eV Å in PtBi2. The experimental realization of 3D Rashba-like spin splitting not only has fundamental interests but also paves the way to the future exploration of a new class of material with unprecedented functionalities for spintronics applications.
B-1a cells acquire their unique characteristics by bypassing the pre-BCR selection stage
Authors: Wong Jason B. , Hewitt Susannah L. , Heltemes-Harris Lynn M. , Mandal Malay , Johnson Kristen , Rajewsky Klaus , Koralov Sergei B. , Clark Marcus R. , Farrar Michael A. , Skok Jane A. 
Published: October 2019

AbstractB-1a cells are long-lived, self-renewing innate-like B cells that predominantly inhabit the peritoneal and pleural cavities. In contrast to conventional B-2 cells, B-1a cells have a receptor repertoire that is biased towards bacterial and self-antigens, promoting a rapid response to infection and clearing of apoptotic cells. Although B-1a cells are known to primarily originate from fetal tissues, the mechanisms by which they arise has been a topic of debate for many years. Here we show that in the fetal liver versus bone marrow environment, reduced IL-7R/STAT5 levels promoteimmunoglobulin kappagene recombination at the early pro-B cell stage. As a result, differentiating B cells can directly generate a mature B cell receptor (BCR) and bypass the requirement for a pre-BCR and pairing with surrogate light chain. This ‘alternate pathway’ of development enables the production of B cells with self-reactive, skewed specificity receptors that are peculiar to the B-1a compartment. Together our findings connect seemingly opposing lineage and selection models of B-1a cell development and explain how these cells acquire their unique properties.
Cobalt(II)-coordination polymers containing glutarates and bipyridyl ligands and their antifungal potential
Authors: Kim Hyun-Chul , Mitra Sarmistha , Veerana Mayura , Lim Jun-Sup , Jeong Hye-Ryeon , Park Gyungsoon , Huh Seong , Kim Sung-Jin , Kim Youngmee 
Published: October 2019

AbstractThree new CoII-coordination polymers (Co-CPs) containing glutarates and bipyridyl ligands, formulated as [Co2(Glu)2(µ-bpa)2]·(H2O)4 (1), [Co4(Glu)4(µ-bpp)2] (2), and [Co2(Glu)2(µ-bpe)2]·(H2O)0.5 (3), were prepared, and their structures were determined by X-ray crystallography. Glutarates bridge CoII ions to form 2D sheets, and the sheets are connected either by bpa or by bpp ligands to form 3D networks 1 and 2, respectively. Both frameworks 1 and 2 are two-fold interpenetrated, and there is no significant void volume in either network. Four glutarates bridge two CoII ions to form chains, and these chains are connected by bpe ligands to form the 2D sheet 3. The antifungal properties of these new Co-CPs were tested against two model fungal pathogens, Candida albicans and Aspergillus niger. Under the maximum concentration of Co-CPs, 2.0 mg mL−1, the inhibition rates of Co-CPs against A. niger were much lower (44–62%) than those (90–99.98%) observed in C. albicans. The results indicate that 1–3 can inactivate C. albicans cells more efficiently than A. niger spores in the same treatment time, and the greater inactivation of C. albicans can be explained by dramatic changes in the morphology of C. albicans cells. We also found that Co-CPs could generate the reactive species NO and H2O2, and these species might play a role in inactivating fungal cells. Additionally, degradation tests confirmed that the leaching of CoII ions from Co-CPs was not significant. The small amount of leached CoII ions and the robust Co-CPs themselves as well as the reactive species generated by Co-CPs can actively participate in fungal inactivation.
Higher temporal evapotranspiration estimation with improved SEBS model from geostationary meteorological satellite data
Authors: Zhao Jing , Chen Xuelong , Zhang Jing , Zhao Honggang , Song Yongyu 
Published: October 2019

AbstractEvapotranspiration (ET) is a key variable in hydrologic cycle that directly affects the redistribution of precipitation and surface balance. ET measurements with high temporal resolution are required for coupling with models of highly dynamic processes, e.g., hydrological and land surface processes. The Haihe River Basin is the focus of China’s industrial base and it is one of the three major grain-producing regions within the country. However, this area is facing serious water resource shortages and water pollution problems. The present study used geostationary satellite remote sensing data, in situ meteorological observations, and the surface energy balance system (SEBS) model with a new kB−1 parameterization to estimate 3-hourly and daily energy and water fluxes in the Haihe River Basin. The results of the SEBS model were validated with point-scale data from five observation flux towers. Validation showed that 3-hourly and daily ET derived from the SEBS model performed well (R2 = 0.67, mean bias = 0.027 mm/h, RMSE = 0.1 mm/h). Moreover, factors influencing ET were also identified based on the results of this study. ET varies with land cover type and physical and chemical properties of the underlying surface. Furthermore, ET is also controlled by water availability, radiation, and other atmospheric conditions. It was found that ET had strong correlation with the normalized difference vegetation index (NDVI). Specifically, daily ET fluctuated with the NDVI when the NDVI was <0.29, and ET increased rapidly as the NDVI increased from 0.29 to 0.81. For NDVI values >0.81, indicating a state of saturation, the rate of increase of ET slowed. This research produced reliable information that could assist in sustainable management of the water resources and in improved understanding of the hydrologic cycle of the Haihe River Basin.
Specific effects of antitumor active norspermidine on the structure and function of DNA
Authors: Nishio Takashi , Yoshikawa Yuko , Shew Chwen-Yang , Umezawa Naoki , Higuchi Tsunehiko , Yoshikawa Kenichi 
Published: October 2019

AbstractWe compared the effects of trivalent polyamines, spermidine (SPD) and norspermidine (NSPD), a chemical homologue of SPD, on the structure of DNA and gene expression. The chemical structures of SPD and NSPD are different only with the number of methylene groups between amine groups, [N-3-N-4-N] and [N-3-N-3-N], respectively. SPD plays vital roles in cell function and survival, including in mammals. On the other hand, NSPD has antitumor activity and is found in some species of plants, bacteria and algae, but not in humans. We found that both polyamines exhibit biphasic effect; enhancement and inhibition on in vitro gene expression, where SPD shows definitely higher potency in enhancement but NSPD causes stronger inhibition. Based on the results of AFM (atomic force microscopy) observations together with single DNA measurements with fluorescence microscopy, it becomes clear that SPD tends to align DNA orientation, whereas NSPD induces shrinkage with a greater potency. The measurement of binding equilibrium by NMR indicates that NSPD shows 4–5 times higher affinity to DNA than SPD. Our theoretical study with Monte Carlo simulation provides the insights into the underlying mechanism of the specific effect of NSPD on DNA.
Extensive vegetation browning and drying in forests of India’s Tiger Reserves
Authors: Koulgi Pradeep S. , Clinton Nicholas , Karanth Krithi K. 
Published: October 2019

AbstractForest conservation includes stemming deforestation as well as preserving its vegetation condition. Traditional Protected Area (PA) effectiveness evaluations have assessed changes in forest extent but have mostly ignored vegetation condition. Tiger Reserves (TRs) are India’s PAs with highest protection and management resources. We used a before-after-control-impact-style design with long-term Landsat 5 TM data to evaluate the effects of protection elevation on vegetation condition (greenness and moisture) in 25 TRs. After declaration as TRs, vegetation condition in 13 TRs (52%) declined in more than 50% of their areas, with 12 TRs (48%) being overall better than their matched Wildlife Sanctuaries (WLSs; PAs with lower protection). In 8 of these TRs analysed for change from before to after declaration, vegetation condition in 5 TRs was harmed over more than 25% of their areas, with 3 TRs being overall better than their matched WLSs. Our results indicate extensive vegetation browning and drying in about half of the study TRs, with these trends often being similar or worse than in matched WLSs. These results suggest that TRs’ elevated protection alone may be insufficient to preserve vegetation condition and cast doubt on the effectiveness of protection elevation alone in safeguarding long-term viability of tiger habitats.