bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct observations of a surface eigenmode of the dayside magnetopause
Authors: Archer M. O. , Hietala H. , Hartinger M. D. , Plaschke F. , Angelopoulos V. 
Published: February 2019

AbstractThe abrupt boundary between a magnetosphere and the surrounding plasma, the magnetopause, has long been known to support surface waves. It was proposed that impulses acting on the boundary might lead to a trapping of these waves on the dayside by the ionosphere, resulting in a standing wave or eigenmode of the magnetopause surface. No direct observational evidence of this has been found to date and searches for indirect evidence have proved inconclusive, leading to speculation that this mechanism might not occur. By using fortuitous multipoint spacecraft observations during a rare isolated fast plasma jet impinging on the boundary, here we show that the resulting magnetopause motion and magnetospheric ultra-low frequency waves at well-defined frequencies are in agreement with and can only be explained by the magnetopause surface eigenmode. We therefore show through direct observations that this mechanism, which should impact upon the magnetospheric system globally, does in fact occur.
Structural basis of ECF-σ-factor-dependent transcription initiation
Authors: Lin Wei , Mandal Sukhendu , Degen David , Cho Min Sung , Feng Yu , Das Kalyan , Ebright Richard H. 
Published: February 2019

AbstractExtracytoplasmic (ECF) σ factors, the largest class of alternative σ factors, are related to primary σ factors, but have simpler structures, comprising only two of six conserved functional modules in primary σ factors: region 2 (σR2) and region 4 (σR4). Here, we report crystal structures of transcription initiation complexes containing Mycobacterium tuberculosis RNA polymerase (RNAP), M. tuberculosis ECF σ factor σL, and promoter DNA. The structures show that σR2 and σR4 of the ECF σ factor occupy the same sites on RNAP as in primary σ factors, show that the connector between σR2 and σR4 of the ECF σ factor–although shorter and unrelated in sequence–follows the same path through RNAP as in primary σ factors, and show that the ECF σ factor uses the same strategy to bind and unwind promoter DNA as primary σ factors. The results define protein-protein and protein-DNA interactions involved in ECF-σ-factor-dependent transcription initiation.
Costimulation of type-2 innate lymphoid cells by GITR promotes effector function and ameliorates type 2 diabetes
Authors: Galle-Treger Lauriane , Sankaranarayanan Ishwarya , Hurrell Benjamin P. , Howard Emily , Lo Richard , Maazi Hadi , Lewis Gavin , Banie Homayon , Epstein Alan L. , Hu Peisheng , Rehan Virender K. , Gilliland Frank D. , Allayee Hooman , Soroosh Pejman , Sharpe Arlene H. , Akbari Omid 
Published: February 2019

AbstractMetabolic syndrome is characterized by disturbances in glucose homeostasis and the development of low-grade systemic inflammation, which increase the risk to develop type 2 diabetes mellitus (T2DM). Type-2 innate lymphoid cells (ILC2s) are a recently discovered immune population secreting Th2 cytokines. While previous studies show how ILC2s can play a critical role in the regulation of metabolic homeostasis in the adipose tissue, a therapeutic target capable of modulating ILC2 activation has yet to be identified. Here, we show that GITR, a member of the TNF superfamily, is expressed on both murine and human ILC2s. Strikingly, we demonstrate that GITR engagement of activated, but not naïve, ILC2s improves glucose homeostasis, resulting in both protection against insulin resistance onset and amelioration of established insulin- resistance. Together, these results highlight the critical role of GITR as a novel therapeutic molecule against T2DM and its fundamental role as an immune checkpoint for activated ILC2s.
Inhibition of upper small intestinal mTOR lowers plasma glucose levels by inhibiting glucose production
Authors: Waise T. M. Zaved , Rasti Mozhgan , Duca Frank A. , Zhang Song-Yang , Bauer Paige V. , Rhodes Christopher J. , Lam Tony K. T. 
Published: February 2019

AbstractGlucose homeostasis is partly controlled by the energy sensor mechanistic target of rapamycin (mTOR) in the muscle and liver. However, whether mTOR in the small intestine affects glucose homeostasis in vivo remains unknown. Here, we first report that delivery of rapamycin or an adenovirus encoding the dominant negative acting mTOR-mutated protein into the upper small intestine is sufficient to inhibit small intestinal mTOR signaling and lower glucose production in rodents with high fat diet-induced insulin resistance. Second, we found that molecular activation of small intestinal mTOR blunts the glucose-lowering effect of the oral anti-diabetic agent metformin, while inhibiting small intestinal mTOR alone lowers plasma glucose levels by inhibiting glucose production in rodents with diabetes as well. Thus, these findings illustrate that inhibiting upper small intestinal mTOR is sufficient and necessary to lower glucose production and enhance glucose homeostasis, and thereby unveil a previously unappreciated glucose-lowering effect of small intestinal mTOR.
Controlling light in complex media beyond the acoustic diffraction-limit using the acousto-optic transmission matrix
Authors: Katz Ori , Ramaz François , Gigan Sylvain , Fink Mathias 
Published: February 2019

AbstractStudying the internal structure of complex samples with light is an important task but a difficult challenge due to light scattering. While the complex optical distortions induced by scattering can be effectively undone if the medium’s scattering-matrix is known, this matrix generally cannot be retrieved without the presence of an invasive detector or guide-star at the target points of interest. To overcome this limitation, the current state-of-the-art approaches utilize focused ultrasound for generating acousto-optic guide-stars, in a variety of different techniques. Here, we introduce the acousto-optic transmission matrix (AOTM), which is an ultrasonically-encoded, spatially-resolved, optical scattering-matrix. The AOTM provides both a generalized framework to describe any acousto-optic based technique, and a tool for light control and focusing beyond the acoustic diffraction-limit inside complex samples. We experimentally demonstrate complex light control using the AOTM singular vectors, and utilize the AOTM framework to analyze the resolution limitation of acousto-optic guided focusing approaches.
Soil carbon sequestration accelerated by restoration of grassland biodiversity
Authors: Yang Yi , Tilman David , Furey George , Lehman Clarence 
Published: February 2019

AbstractAgriculturally degraded and abandoned lands can remove atmospheric CO2 and sequester it as soil organic matter during natural succession. However, this process may be slow, requiring a century or longer to re-attain pre-agricultural soil carbon levels. Here, we find that restoration of late-successional grassland plant diversity leads to accelerating annual carbon storage rates that, by the second period (years 13–22), are 200% greater in our highest diversity treatment than during succession at this site, and 70% greater than in monocultures. The higher soil carbon storage rates of the second period (years 13–22) are associated with the greater aboveground production and root biomass of this period, and with the presence of multiple species, especially C4 grasses and legumes. Our results suggest that restoration of high plant diversity may greatly increase carbon capture and storage rates on degraded and abandoned agricultural lands.
The (eg ⊗ eu) ⊗ Eg product Jahn–Teller effect in the neutral group-IV vacancy quantum bits in diamond
Authors: Thiering Gergő , Gali Adam 
Published: February 2019

AbstractThe product Jahn–Teller effect may occur for such coupled electron–phonon systems in solids where single electrons occupy double degenerate orbitals. We propose that the excited state of the neutral XV split-vacancy complex in diamond, where X and V labels a group-IV impurity atom of X = Si, Ge, Sn, Pb and the vacancy, respectively, is such a system with eg and eu double degenerate orbitals and Eg quasi-localized phonons. We develop and apply ab initio theory to quantify the strength of electron–phonon coupling for neutral XV complexes in diamond, and find a significant impact on the corresponding optical properties of these centers. Our results show good agreement with recent experimental data on the prospective SiV(0) quantum bit, and reveals the complex nature of the excited states of neutral XV color centers in diamond.
Both mass ratio effects and community diversity drive biomass production in a grassland experiment
Authors: Sonkoly Judit , Kelemen András , Valkó Orsolya , Deák Balázs , Kiss Réka , Tóth Katalin , Miglécz Tamás , Tóthmérész Béla , Török Péter 
Published: February 2019

AbstractThe maintenance of biodiversity is crucial for ecosystem processes such as plant biomass production, as higher species richness is associated with increased biomass production in plant communities. However, the effects of evenness and functional diversity on biomass production are understudied. We manipulated the composition of an experimental grassland by sowing various seed mixtures and examined the effects of diversity and evenness on biomass production after three years. We found that biomass production increased with greater species and functional richness but decreased with greater species and functional evenness. Standing biomass increased but species number and functional richness decreased with increasing proportion of perennial grasses. Our findings emphasise the importance of productive dominant species, as the proportion of perennial grasses had a positive effect on standing biomass, while species and functional evenness had a negative effect on it. Thus, our findings support the theory that, besides diversity, dominance effects and the so-called mass ratio hypothesis may also play a key role in explaining primary biomass production.
Novel function of PiT1/SLC20A1 in LPS-related inflammation and wound healing
Authors: Koumakis Eugénie , Millet-Botti Joëlle , Benna Jamel El , Leroy Christine , Boitez Valérie , Codogno Patrice , Friedlander Gérard , Forand Anne 
Published: February 2019

AbstractPiT1/SLC20A1 is an inorganic phosphate transporter with additional functions including the regulation of TNFα-induced apoptosis, erythropoiesis, cell proliferation and insulin signaling. Recent data suggest a relationship between PiT1 and NF-κB-dependent inflammation: (i)Pit1mRNA is up-regulated in the context of NF-κB pathway activation; (ii) NF-κB target gene transcription is decreased in PiT1-deficient conditions. This led us to investigate the role of PiT1 in lipopolysaccharide (LPS)-induced inflammation. MCP-1 and IL-6 concentrations were impaired in PiT1-deficient bone marrow derived macrophages (BMDMs) upon LPS stimulation. Lower MCP-1 and IL-6 serum levels were observed inMx1-Cre;Pit1lox/loxmice dosed intraperitoneally with LPS. Lower PiT1 expression correlated with decreasedin vitrowound healing and lower reactive oxygen species levels. Reduced IκB degradation and lower p65 nuclear translocation were observed in PiT1-deficient cells stimulated with LPS. Conversely, PiT1 expression was inducedin vitroupon LPS stimulation. Addition of an NF-κB inhibitor abolished LPS-induced PiT1 expression. Furthermore, we showed that p65 expression activatedPit1promoter activity. Finally, ChIP assays demonstrated that p65 directly binds to themPit1promoter in response to LPS. These data demonstrate a completely novel function of PiT1 in the response to LPS and provide mechanistic insights into the regulation of PiT1 expression by NF-κB.
NKT Cells in Mice Originate from Cytoplasmic CD3-Positive, CD4−CD8− Double-Negative Thymocytes that Express CD44 and IL-7Rα
Authors: Hu Zhansheng , Gu Wen , Wei Yang , Liu Gang , Wu Shengli , Liu Tie 
Published: February 2019

AbstractAlthough natural killer T cells (NKT cells) are thought to be generated from CD4+CD8+ (DP) thymocytes, the developmental origin of CD4−CD8− (DN) NKT cells has remained unclear. In this study, we found the level of NK1.1 expression was highest in DN cells, followed by CD4 and CD8 (SP) and DP cells. The level of NK1.1 expression was highest in CD44+CD25− (DN1) cells, after that CD44+CD25+ (DN2), finally, CD44−CD25− (DN3) and CD44− CD25+ (DN4) cells. Unexpectedly, cytoplasmic CD3 was not only expressed in SP and DP thymocytes but also in most DN thymocytes at various stages. The mean fluorescence of cytoplasmic and surface CD3 in DN cells was significantly lower than in mature (SP) T and NKT cells in the thymus and spleen. Interestingly, there were more NKT cells in DN-cytoplasmic CD3 expression cells was higher than in DN-surface CD3 expression cells. There were more CD3-NKT cells in DN1 thymocytes than in TCR-β-NKT cells. NKT cells expressed higher levels of IL-7Rα which was correlated with CD44 expression in the thymus. Our data suggest that T cells and NKT cells follow similar patterns of expression with respect to cytoplasmic and surface CD3. Cytoplasmic CD3 could be used as a marker for early stage T cells. Both cytoplasmic CD3 and surface CD3 were expressed in mature T cells and immature T cells, including the immature cytoplasmic CD3+ surface CD3− and surface CD3+TCR-β− cells in DN1-NKT thymocytes. CD44 could be used as an additional marker of NKT cells which may originate from cytoplasmic CD3-positive DN thymocytes that express CD44 and IL-7Rα in mice.
Clinical evaluation of tissue stops on 3D-printed custom trays
Authors: Deng Kehui , Chen Hu , Li Rong , Li Linlin , Wang Yong , Zhou Yongsheng , Sun Yuchun 
Published: February 2019

AbstractThis study evaluated the quality of impressions taken using three-dimensional (3D)-printed custom trays with different tissue stops to optimize the custom tray designs. Different custom trays were designed and printed based on six edentulous patients. These trays were divided into four groups based on the tissue-stop designs: 3DP trays (3D-printed trays without tissue stops), 3DPS trays (3D-printed trays with saddle-shaped tissue stops), 3DPM trays (3D-printed trays with marginal-band tissue stops) and 3DPIM trays (3D-printed trays with inner marginal-band tissue stops). Final impressions were taken using these trays, of which, the 3DP and 3DPIM trays were preborder-moulded. The finished complete dentures were used to take impressions that were set as the reference group to analyse the accuracy of the final impressions. The impressions taken using the 3DP custom trays (preborder-moulded) were used as a reference to analyse the extensions of the impressions taken using the other three custom trays. Randomized block or Friedman tests were used to evaluate each group’s statistical significance. The results revealed that the 3DPIM custom trays with the inner marginal-band tissue stop facilitated the preborder-moulding process and improved the accuracy and extension of the impression.
Experimental Evidence of Rainbow Trapping and Bloch Oscillations of Torsional Waves in Chirped Metallic Beams
Authors: Arreola-Lucas A. , Báez G. , Cervera F. , Climente A. , Méndez-Sánchez R. A. , Sánchez-Dehesa J. 
Published: February 2019

AbstractThe Bloch oscillations (BO) and the rainbow trapping (RT) are two apparently unrelated phenomena, the former arising in solid state physics and the latter in metamaterials. A Bloch oscillation, on the one hand, is a counter-intuitive effect in which electrons start to oscillate in a crystalline structure when a static electric field is applied. This effect has been observed not only in solid state physics but also in optical and acoustical structured systems since a static electric field can be mimicked by a chirped structure. The RT, on the other hand, is a phenomenon in which the speed of a wave packet is slowed down in a dielectric structure; different colors then arrive to different depths within the structure thus separating the colors also in time. Here we show experimentally the emergence of both phenomena studying the propagation of torsional waves in chirped metallic beams. Experiments are performed in three aluminum beams in which different structures were machined: one periodic and two chirped. For the smaller value of the chirping parameter the wave packets, with different central frequencies, are back-scattered at different positions inside the corrugated beam; the packets with higher central frequencies being the ones with larger penetration depths. This behavior represents the mechanical analogue of the rainbow trapping effect. This phenomenon is the precursor of the mechanical Bloch oscillations, which are here demonstrated for a larger value of the chirping parameter. It is observed that the oscillatory behavior observed at small values of the chirp parameter is rectified according to the penetration length of the wave packet.
Multilayer fabrication of unobtrusive poly(dimethylsiloxane) nanobrush for tunable cell adhesion
Authors: Chae Soo Sang , Jung Joo Hyun , Choi Won Jin , Park Joung Kyu , Baik Hong Koo , Jung Jongjin , Ko Hyuk Wan 
Published: February 2019

AbstractPrecise modulation of polymer brush in its thickness and grafting density can cause unexpected cell behaviors and regulated bioactivities. Herein, a nanoscale poly(dimethylsiloxane) (PDMS) brush was employed to use as a controllable material for cell adhesion. Facile fabrication of ultrathin monolayer PDMS nanobrush on an underlying substrate facilitated regaining cell adhesion through long-range cell attractive forces such as the van der Waals forces. We showed that cell adhesion is diminished by increasing the number of nanobrush layers, causing a gradual decrease of the effectiveness of the long-range force. The result demonstrates that ultrathin PDMS nanobrush can either promote or inhibit cell adhesion, which is required for various biomedical fields such as tissue-engineering, anti-fouling coating, and implantable biomaterials and sensors.
Gene silencing based on RNA-guided catalytically inactive Cas9 (dCas9): a new tool for genetic engineering in Leptospira
Authors: Fernandes L. G. V. , Guaman L. P. , Vasconcellos S. A. , Heinemann Marcos B. , Picardeau M. , Nascimento A. L. T. O. 
Published: February 2019

AbstractLeptospirosis is a worldwide zoonosis caused by pathogenic bacteria of the genus Leptospira, which also includes free-living saprophyte strains. Many aspects of leptospiral basic biology and virulence mechanisms remain unexplored mainly due to the lack of effective genetic tools available for these bacteria. Recently, the type II CRISPR/Cas system from Streptococcus pyogenes has been widely used as an efficient genome engineering tool in bacteria by inducing double-strand breaks (DSBs) in the desired genomic targets caused by an RNA-guided DNA endonuclease called Cas9, and the DSB repair associated machinery. In the present work, plasmids expressing heterologous S. pyogenes Cas9 in L. biflexa cells were generated, and the enzyme could be expressed with no apparent toxicity to leptospiral cells. However, L. biflexa cells were unable to repair RNA-guided Cas9-induced DSBs. Thus, we used a catalytically dead Cas9 (dCas9) to obtain gene silencing rather than disruption, in a strategy called CRISPR interference (CRISPRi). We demonstrated complete gene silencing in L. biflexa cells when both dCas9 and single-guide RNA (sgRNA) targeting the coding strand of the β-galactosidase gene were expressed simultaneously. Furthermore, when the system was applied for silencing the dnaK gene, no colonies were recovered, indicating that DnaK protein is essential in Leptospira. In addition, flagellar motor switch FliG gene silencing resulted in reduced bacterial motility. To the best of our knowledge, this is the first work applying the CRISPRi system in Leptospira and spirochetes in general, expanding the tools available for understanding leptospiral biology.
Analysis of SMALP co-extracted phospholipids shows distinct membrane environments for three classes of bacterial membrane protein
Authors: Teo Alvin C. K. , Lee Sarah C. , Pollock Naomi L. , Stroud Zoe , Hall Stephen , Thakker Alpesh , Pitt Andrew R. , Dafforn Timothy R. , Spickett Corinne M. , Roper David I. 
Published: February 2019

AbstractBiological characterisation of membrane proteins lags behind that of soluble proteins. This reflects issues with the traditional use of detergents for extraction, as the surrounding lipids are generally lost, with adverse structural and functional consequences. In contrast, styrene maleic acid (SMA) copolymers offer a detergent-free method for biological membrane solubilisation to produce SMA-lipid particles (SMALPs) containing membrane proteins together with their surrounding lipid environment. We report the development of a reverse-phase LC-MS/MS method for bacterial phospholipids and the first comparison of the profiles of SMALP co-extracted phospholipids from three exemplar bacterial membrane proteins with different topographies: FtsA (associated membrane protein), ZipA (single transmembrane helix), and PgpB (integral membrane protein). The data showed that while SMA treatment per se did not preferentially extract specific phospholipids from the membrane, SMALP-extracted ZipA showed an enrichment in phosphatidylethanolamines and depletion in cardiolipins compared to the bulk membrane lipid. Comparison of the phospholipid profiles of the 3 SMALP-extracted proteins revealed distinct lipid compositions for each protein: ZipA and PgpB were similar, but in FtsA samples longer chain phosphatidylglycerols and phosphatidylethanolamines were more abundant. This method offers novel information on the phospholipid interactions of these membrane proteins.
Synergic effects of oxygen supply and antioxidants on pancreatic β-cell spheroids
Authors: Myasnikova Dina , Osaki Tatsuya , Onishi Kisaki , Kageyama Tatsuto , Zhang Molino Binbin , Fukuda Junji 
Published: February 2019

AbstractDiabetes is one of the most common metabolic disorders, and is characterized by the inability to secrete/sense insulin and abnormal blood glucose concentration. Many researchers have concentrated their efforts on improving islet transplantation, in particular by fabricating bioartificial pancreatic islets in vitro. One of the critical points for the success of this research direction is the improvement of culture conditions, such as oxygen supply, in the engineering of bioartificial pancreatic islets to ensure their viability and functionality after transplantation. In this work, we fabricated microwell spheroid culture devices made of oxygen-permeable polydimethylsiloxane (PDMS), with which hypoxia in the core of bioartificial islets was alleviated and glucose-stimulated insulin secretion was increased ~2.5-fold compared to a device with the same configuration but made of non-oxygen-permeable plastic. We also demonstrated that antioxidants, such as ascorbic acid-2-phosphate (AA2P), could neutralize islet damage caused by increased reactive oxygen species (ROS) in the cell culture environment. These results suggest that supply of oxygen together with removal of ROS may lead to a better approach to prepare highly viable and functional bioartificial pancreatic islets.