bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene-metabolite profile integration to understand the cause of spaceflight induced immunodeficiency
Authors: Chakraborty Nabarun , Cheema Amrita , Gautam Aarti , Donohue Duncan , Hoke Allison , Conley Carolynn , Jett Marti , Hammamieh Rasha 
Published: January 2018

AbstractSpaceflight presents a spectrum of stresses very different from those associated with terrestrial conditions. Our previous study (BMC Genom. 15: 659, 2014) integrated the expressions of mRNAs, microRNAs, and proteins and results indicated that microgravity induces an immunosuppressive state that can facilitate opportunistic pathogenic attack. However, the existing data are not sufficient for elucidating the molecular drivers of the given immunosuppressed state. To meet this knowledge gap, we focused on the metabolite profile of spaceflown human cells. Independent studies have attributed cellular energy deficiency as a major cause of compromised immunity of the host, and metabolites that are closely associated with energy production could be a robust signature of atypical energy fluctuation. Our protocol involved inoculation of human endothelial cells in cell culture modules in spaceflight and on the ground concurrently. Ten days later, the cells in space and on the ground were exposed to lipopolysaccharide (LPS), a ubiquitous membrane endotoxin of Gram-negative bacteria. Nucleic acids, proteins, and metabolites were collected 4 and 8 h post-LPS exposure. Untargeted profiling of metabolites was followed by targeted identification of amino acids and knowledge integration with gene expression profiles. Consistent with the past reports associating microgravity with increased energy expenditure, we identified several markers linked to energy deficiency, including various amino acids such as tryptophan, creatinine, dopamine, and glycine, and cofactors such as lactate and pyruvate. The present study revealed a molecular architecture linking energy metabolism and immunodeficiency in microgravity. The energy-deficient condition potentially cascaded into dysregulation of protein metabolism and impairment of host immunity. This project is limited by a small sample size. Although a strict statistical screening was carefully implemented, the present results further emphasize the need for additional studies with larger sample sizes. Validating this hypothesis using an in vivo model is essential to extend the knowledge towards identifying markers of diagnostic and therapeutic value.
Nitrogen Fertilization Elevated Spatial Heterogeneity of Soil Microbial Biomass Carbon and Nitrogen in Switchgrass and Gamagrass Croplands
Authors: Li Jianwei , Guo Chunlan , Jian Siyang , Deng Qi , Yu Chih-Li , Dzantor Kudjo E. , Hui Dafeng 
Published: January 2018

AbstractThe effects of intensive nitrogen (N) fertilizations on spatial distributions of soil microbes in bioenergy croplands remain unknown. To quantify N fertilization effect on spatial heterogeneity of soil microbial biomass carbon (MBC) and N (MBN), we sampled top mineral horizon soils (0-15 cm) using a spatially explicit design within two 15-m2 plots under three fertilization treatments in two bioenergy croplands in a three-year long fertilization experiment in Middle Tennessee, USA. The three fertilization treatments were no N input (NN), low N input (LN: 84 kg N ha−1 in urea) and high N input (HN: 168 kg N ha−1 in urea). The two crops were switchgrass (SG: Panicum virgatum L.) and gamagrass (GG: Tripsacum dactyloides L.). Results showed that N fertilizations little altered central tendencies of microbial variables but relative to LN, HN significantly increased MBC and MBC:MBN (GG only). HN possessed the greatest within-plot variances except for MBN (GG only). Spatial patterns were generally evident under HN and LN plots and much less so under NN plots. Substantially contrasting spatial variations were also identified between croplands (GG > SG) and among variables (MBN, MBC:MBN > MBC). This study demonstrated that spatial heterogeneity is elevated in microbial biomass of fertilized soils likely by uneven fertilizer application in bioenergy crops.
Injection locking at 2f of spin torque oscillators under influence of thermal noise
Authors: Tortarolo M. , Lacoste B. , Hem J. , Dieudonné C. , Cyrille M.-C. , Katine J. A. , Mauri D. , Zeltser A. , Buda-Prejbeanu L. D. , Ebels U. 
Published: January 2018

AbstractIntegration of Spin Torque Nano-Oscillators STNO’s in conventional microwave circuits means that the devices have to meet certain specifications. One of the most important criteria is the phase noise, being the key parameter to evaluate the performance and define possible applications. Phase locking several oscillators together has been suggested as a possible means to decrease phase noise and consequently, the linewidth. In this work we present experiments, numerical simulations and an analytic model to describe the effects of thermal noise in the injection locking of a tunnel junction based STNO. The analytics show the relation of the intrinsic parameters of the STNO with the phase noise level, opening the path to tailor the spectral characteristics by the magnetic configuration. Experiments and simulations demonstrate that in the in-plane magnetized structure, while the frequency is locked, much higher reference currents are needed to reduce the noise by phase locking. Moreover, our analysis shows that it is possible to control the phase noise by the reference microwave current (IRF) and that it can be further reduced by increasing the bias current (IDC) of the oscillator, keeping the reference current in feasible limits for applications.
Isoliquiritigenin blunts osteoarthritis by inhibition of bone resorption and angiogenesis in subchondral bone
Authors: Ji Baochao , Zhang Zhendong , Guo Wentao , Ma Hairong , Xu Boyong , Mu Wenbo , Amat Abdusami , Cao Li 
Published: January 2018

AbstractIsoliquiritigenin (ISL), a natural flavonoid extracted from licorice, has been demonstrated to exert attenuation of osteoclastogenesis and anti-angiogenesis activity in a wide variety of cells. Here, we first evaluated the effects of ISL on pathogenesis of osteoarthritis in a mouse model of OA. The data showed that ISL blunted progression of OA and lowered the Osteoarthritis Research Society International (OARSI)-Modified Making Score and protected the articular cartilage. The thickness of calcified cartilage zone was significantly decreased in ISL-treated ACLT mice compared with vehicle group. ISL increased expression level of lubricin and decreased collagen X (Col X), matrix metalloproteinase-13 (MMP-13). Moreover, ISL reduced aberrant active subchondral bone remodelling, including lowered trabecular pattern factor (Tb.pf) and increased bone volume/tissue volume (BV/TV, %) and thickness of subchondral bone plate (SBP) compared with vehicle-treated group. The results of immunostaining further revealed that ISL directly reduced RANKL-RANK-TRAF6 singling pathway induced osteoclastogenesis, prevented abnormal bone formation through indirect inhibition of TGF-β release. Additionally, ISL exerts anti-angiogenesis effects in subchondral bone through direct suppression of MMP-2. These results indicated that ISL attenuates progression of OA by inhibition of bone resorption and angiogenesis in subchondral bone, indicating that this may be a potential preventive therapy for OA.
Microbial fuel cell assisted band gap narrowed TiO2 for visible light-induced photocatalytic activities and power generation
Authors: Khan Mohammad Ehtisham , Khan Mohammad Mansoob , Min Bong-Ki , Cho Moo Hwan 
Published: January 2018

AbstractThis paper reports a simple, biogenic and green approach to obtain narrow band gap and visible light-active TiO2nanoparticles. Commercial white TiO2(w-TiO2) was treated in the cathode chamber of a Microbial Fuel Cell (MFC), which produced modified light gray TiO2(g-TiO2) nanoparticles. The DRS, PL, XRD, EPR, HR-TEM, and XPS were performed to understand the band gap decline ofg-TiO2. The optical study revealed a significant decrease in the band gap of theg-TiO2(Eg = 2.80 eV) compared to thew-TiO2(Eg = 3.10 eV). The XPS revealed variations in the surface states, composition, Ti4+to Ti3+ratio, and oxygen vacancies in theg-TiO2. The Ti3+and oxygen vacancy-induced enhanced visible light photocatalytic activity ofg-TiO2was confirmed by degrading different model dyes. The enhanced photoelectrochemical response under visible light irradiation further supported the improved performance of theg-TiO2owing to a decrease in the electron transfer resistance and an increase in charge transfer rate. During the TiO2treatment process, electricity generation in MFC was also observed, which was ~0.3979 V corresponding to a power density of 70.39 mW/m2. This study confirms narrow band gap TiO2can be easily obtained and used effectively as photocatalysts and photoelectrode material.
Using DNA origami nanorulers as traceable distance measurement standards and nanoscopic benchmark structures
Authors: Raab Mario , Jusuk Ija , Molle Julia , Buhr Egbert , Bodermann Bernd , Bergmann Detlef , Bosse Harald , Tinnefeld Philip 
Published: January 2018

AbstractIn recent years, DNA origami nanorulers for superresolution (SR) fluorescence microscopy have been developed from fundamental proof-of-principle experiments to commercially available test structures. The self-assembled nanostructures allow placing a defined number of fluorescent dye molecules in defined geometries in the nanometer range. Besides the unprecedented control over matter on the nanoscale, robust DNA origami nanorulers are reproducibly obtained in high yields. The distances between their fluorescent marks can be easily analysed yielding intermark distance histograms from many identical structures. Thus, DNA origami nanorulers have become excellent reference and training structures for superresolution microscopy. In this work, we go one step further and develop a calibration process for the measured distances between the fluorescent marks on DNA origami nanorulers. The superresolution technique DNA-PAINT is used to achieve nanometrological traceability of nanoruler distances following the guide to the expression of uncertainty in measurement (GUM). We further show two examples how these nanorulers are used to evaluate the performance of TIRF microscopes that are capable of single-molecule localization microscopy (SMLM).
Rheumatoid arthritis patient antibodies highly recognize IL-2 in the immune response pathway involving IRF5 and EBV antigens
Authors: Bo Marco , Niegowska Magdalena , Erre Gian Luca , Piras Marco , Longu Maria Giovanna , Manchia Pierangela , Manca Mario , Passiu Giuseppe , Sechi Leonardo A. 
Published: January 2018

AbstractRheumatoid arthritis (RA) is a chronic autoimmune disease characterized by a progressive joint damage due to largely unknown environmental factors acting in concert with risk alleles conferring genetic susceptibility. A major role has been attributed to viral infections that include past contacts with Epstein-Barr virus (EBV) and, more recently, to non-protein coding sequences of human endogenous retrovirus K (HERV-K) integrated in the human genome. Molecular mimicry between viral and self proteins is supposed to cause the loss of immune tolerance in predisposed hosts. There are evidences that anti-IL-2 antibodies (Abs) are present in subjects affected by autoimmune diseases and may be responsible for alterations in regulatory T cell responses. In this study, we evaluated the levels of Abs against IL-2, viral epitopes and interferon regulatory factor 5 (IRF5) in 140 RA patients and 137 healthy controls (HCs). Ab reactivity reached the highest levels for IRF5, EBV and IL-2 (56%, 44% and 39%, respectively) in RA with significantly lower values among HCs (7–9%, p < 0.0001), which suggests a possible cross-reaction between IRF5/EBV homologous antigens and shifts in T cell balance disrupted by anti-IL-2 Abs.
Ordered states in the Kitaev-Heisenberg model: From 1D chains to 2D honeycomb
Authors: Agrapidis Cliò Efthimia , van den Brink Jeroen , Nishimoto Satoshi 
Published: January 2018

AbstractWe study the ground state of the 1D Kitaev-Heisenberg (KH) model using the density-matrix renormalization group and Lanczos exact diagonalization methods. We obtain a rich ground-state phase diagram as a function of the ratio between Heisenberg (J = cosϕ) and Kitaev (K = sinϕ) interactions. Depending on the ratio, the system exhibits four long-range ordered states: ferromagnetic-z, ferromagnetic-xy, staggered-xy, Néel-z, and two liquid states: Tomonaga-Luttinger liquid and spiral-xy. The two Kitaev points $${\boldsymbol{\phi }}{\boldsymbol{=}}\frac{{\boldsymbol{\pi }}}{{\bf{2}}}$$
ϕ
=

π
2

and $${\boldsymbol{\varphi }}{\boldsymbol{=}}\frac{{\bf{3}}{\boldsymbol{\pi }}}{{\bf{2}}}$$
φ
=

3
π

2

are singular. The ϕ-dependent phase diagram is similar to that for the 2D honeycomb-lattice KH model. Remarkably, all the ordered states of the honeycomb-lattice KH model can be interpreted in terms of the coupled KH chains. We also discuss the magnetic structure of the K-intercalated RuCl3, a potential Kitaev material, in the framework of the 1D KH model. Furthermore, we demonstrate that the low-lying excitations of the 1D KH Hamiltonian can be explained within the combination of the known six-vertex model and spin-wave theory.
Investigating the origins of eastern Polynesians using genome-wide data from the Leeward Society Isles
Authors: Hudjashov Georgi , Endicott Phillip , Post Helen , Nagle Nano , Ho Simon Y. W. , Lawson Daniel J. , Reidla Maere , Karmin Monika , Rootsi Siiri , Metspalu Ene , Saag Lauri , Villems Richard , Cox Murray P. , Mitchell R. John , Garcia-Bertrand Ralph L. , Metspalu Mait , Herrera Rene J. 
Published: January 2018

AbstractThe debate concerning the origin of the Polynesian speaking peoples has been recently reinvigorated by genetic evidence for secondary migrations to western Polynesia from the New Guinea region during the 2nd millennium BP. Using genome-wide autosomal data from the Leeward Society Islands, the ancient cultural hub of eastern Polynesia, we find that the inhabitants’ genomes also demonstrate evidence of this episode of admixture, dating to 1,700–1,200 BP. This supports a late settlement chronology for eastern Polynesia, commencing ~1,000 BP, after the internal differentiation of Polynesian society. More than 70% of the autosomal ancestry of Leeward Society Islanders derives from Island Southeast Asia with the lowland populations of the Philippines as the single largest potential source. These long-distance migrants into Polynesia experienced additional admixture with northern Melanesians prior to the secondary migrations of the 2nd millennium BP. Moreover, the genetic diversity of mtDNA and Y chromosome lineages in the Leeward Society Islands is consistent with linguistic evidence for settlement of eastern Polynesia proceeding from the central northern Polynesian outliers in the Solomon Islands. These results stress the complex demographic history of the Leeward Society Islands and challenge phylogenetic models of cultural evolution predicated on eastern Polynesia being settled from Samoa.
Role of Particle Entanglement in the Violation of Bell Inequalities
Authors: Wasak Tomasz , Smerzi Augusto , Chwedeńczuk Jan 
Published: January 2018

AbstractEntanglement between two separate systems is a necessary resource to violate a Bell inequality in a test of local realism. We demonstrate that to overcome the Bell bound, this correlation must be accompanied by the entanglement between the constituent particles. This happens whenever a super-selection rule prohibits coherences between states with different total number of particles and thus imposes a constraint on feasible local operations in each sub-system. We show that the necessary entanglement between the particles might solely result from their indistinguishability. We also give an example of both mode and particle-entangled pure state, which does not violate any Bell inequality. Our result reveals a fundamental relation between the non-locality and the particle entanglement.
Aging extension and modifications of lipid metabolism in the monogonont rotifer Brachionus koreanus under chronic caloric restriction
Authors: Lee Min-Chul , Park Jun Chul , Yoon Deok-Seo , Han Jeonghoon , Kang Sujin , Kamizono Shohei , Om Ae-Son , Shin Kyung-Hoon , Hagiwara Atsushi , Lee Jae-Seong 
Published: January 2018

AbstractTo examine the interrelationship of aging extension and modification of lipid metabolism under chronic caloric restriction (CCR; reduced concentration of the green algae Tetraselmis suecica) in the monogonont rotifer Brachionus koreanus, we assessed life cycle parameters, fatty acid composition, and expression of sirtuin and genes related to lipid metabolism. B. koreanus in the 5% T. suecica group showed an increased life span but decreased reproduction. Based on this finding, we chose 5% T. suecica for further experiments and compared the data with those for 100% T. suecica. Upregulation of sirtuin gene expression was observed under CCR. In addition, despite the reduction in the amount of total fatty acid (FA) and the area of triacylglycerol, increases in the ratios of saturated fatty acid and monounsaturated fatty acid (MUFA) to total FA in 5%-exposed B. koreanus were observed. Furthermore, mRNA expression analysis confirmed that CCR promoted the synthesis of MUFA through Δ9 desaturase. Moreover, expression of the docosahexaenoic acid (DHA) synthesizing gene Δ4 desaturase was also upregulated, together with DHA content. These data suggest that CCR modified protein acetylation and lipid metabolism, leading to a decrease in reproduction and consequently resulting in life span extension.
MRI/Fluorescence bimodal amplification system for cellular GSH detection and tumor cell imaging based on manganese dioxide nanosheet
Authors: Yuan Dandan , Ding Lairong , Sun Zhaomei , Li Xuemei 
Published: January 2018

AbstractHere, we report a novel magnetic resonance imaging (MRI)/fluorescence bimodal amplification platform for the detection of glutathione (GSH) on the basis of redoxable manganese dioxide (MnO2) nanosheets, which can be readily applied as a DNA nanocarrier, fluorescence quencher, and intracellular GSH-activated MRI contrast agent. The binding of aptamers that absorbed on the MnO2 nanosheets to their target can facilitating the endocytosis of target-nanoprobes. Once endocytosed, the MnO2 nanosheets can react with cellular GSH, resulting in the disintegration of nanosheets to generate plenty of Mn2+ ions for MRI and releases the primers which were adsorbed on the MnO2 nanosheets. Then the rolling circle amplification (RCA) reaction was initiated to amplify the fluorescence signal. In addition, after treatment with GSH, the MnO2 nanosheets were reduced and then most of the fluorescence was recovered. Therefore, this MnO2 nanoprobe exhibits excellent selectivity, suggesting a potential detection platform for analyzing the glutathione level in cells.
Spatiotemporal patterning of EpCAM is important for murine embryonic endo- and mesodermal differentiation
Authors: Sarrach Sannia , Huang Yuanchi , Niedermeyer Sebastian , Hachmeister Matthias , Fischer Laura , Gille Sebastian , Pan Min , Mack Brigitte , Kranz Gisela , Libl Darko , Merl-Pham Juliane , Hauck Stefanie M. , Paoluzzi Tomada Elisa , Kieslinger Matthias , Jeremias Irmela , Scialdone Antonio , Gires Olivier 
Published: January 2018

AbstractEpithelial cell adhesion molecule EpCAM is expressed in pluripotent embryonic stem cells (ESC)in vitro, but is repressed in differentiated cells, except epithelia and carcinomas. Molecular functions of EpCAM, possibly imposing such repression, were primarily studied in malignant cells and might not apply to non-pathologic differentiation. Here, we comprehensively describe timing and rationale for EpCAM regulation in early murine gastrulation and ESC differentiation using single cell RNA-sequencing datasets,in vivoandin vitromodels including CRISPR-Cas9-engineered ESC-mutants. We demonstrate expression of EpCAM in inner cell mass, epiblast, primitive/visceral endoderm, and strict repression in the most primitive, nascent Flk1+mesoderm progenitors at E7.0. Selective expression of EpCAM was confirmed at mid-gestation and perinatal stages. The rationale for strict patterning was studied in ESC differentiation. Gain/loss-of-function demonstrated supportive functions of EpCAM in achieving full pluripotency and guided endodermal differentiation, but repressive functions in mesodermal differentiation as exemplified with cardiomyocyte formation. We further identified embryonic Ras (ERas) as novel EpCAM interactor of EpCAM and an EpCAM/ERas/AKT axis that is instrumental in differentiation regulation. Hence, spatiotemporal patterning of EpCAM at the onset of gastrulation, resulting in early segregation of interdependent EpCAM+endodermal and EpCAM−/vimentin+mesodermal clusters represents a novel regulatory feature during ESC differentiation.
Design, Bioactivity and structure-activity of 3-Arylpropionate Derivatives as Potential High-Efficient Acaricides against Psoroptes Cuniculi
Authors: Chen Dongdong , Tian Ye , Xu Mingxuan , Wang Xinyuan , Li Ding , Miao Fang , Yang Xinjuan , Zhou Le 
Published: January 2018

AbstractA series of 3-aryl propionic esters and their analogues were designed and evaluated for acaricidal activity in vitro against Psoroptes cuniculi, a mange mite. The structure–activity relationship (SAR) was also discussed. The results showed that 6 compounds possessed the excellent activity (LC50 = 0.17–0.24 mM, LT50 = 1.5–2.9 h), superior to ivermectin (LC50 = 0.28 mM, LT50 = 8.9 h) (P < 0.05), a standard drug. Furthermore, 7 compounds showed the good activity (LC50 = 0.25–0.37 mM, LT50 < 3.9 h), slightly lower or close to that of ivermectin. One compound displayed super-fast acaricidal property, far superior to ivermectin. SAR analysis found that the ester group is vital for the activity and the small steric hindrance adjacent to the ester group is advantageous for the high activity. The <C4 linear alcohol esters can give the higher activity. The substituents on the 3-phenyl ring or replacement of the 3-phenyl with heterocyclic aryl generally decreases the activity. The position of the ester group in the ester chain also influences the activity, where the 3-phenyl propionate and the benzoate had the highest and lowest activity, respectively. Thus, 3-arylpropionates emerged as new and promising high-efficient acaricide candidates.
DNA structure at the plasmid origin-of-transfer indicates its potential transfer range
Authors: Zrimec Jan , Lapanje Aleš 
Published: January 2018

AbstractHorizontal gene transfer via plasmid conjugation enables antimicrobial resistance (AMR) to spread among bacteria and is a major health concern. The range of potential transfer hosts of a particular conjugative plasmid is characterised by its mobility (MOB) group, which is currently determined based on the amino acid sequence of the plasmid-encoded relaxase. To facilitate prediction of plasmid MOB groups, we have developed a bioinformatic procedure based on analysis of the origin-of-transfer (oriT), a merely 230 bp long non-coding plasmid DNA region that is the enzymatic substrate for the relaxase. By computationally interpreting conformational and physicochemical properties of the oriT region, which facilitate relaxase-oriT recognition and initiation of nicking, MOB groups can be resolved with over 99% accuracy. We have shown that oriT structural properties are highly conserved and can be used to discriminate among MOB groups more efficiently than the oriT nucleotide sequence. The procedure for prediction of MOB groups and potential transfer range of plasmids was implemented using published data and is available at http://dnatools.eu/MOB/plasmid.html.