bluuebunny/crossref_metadata_2025_split huggingface dataset:
Liver X receptors regulate hepatic F4/80
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CD11b+ Kupffer cells/macrophages and innate immune responses in mice
Authors: Endo-Umeda Kaori , Nakashima Hiroyuki , Komine-Aizawa Shihoko , Umeda Naoki , Seki Shuhji , Makishima Makoto 
Published: June 2018

AbstractThe liver X receptors (LXRs), LXRα and LXRβ, are nuclear receptors that regulate lipid homeostasis. LXRs also regulate inflammatory responses in cultured macrophages. However, the role of LXRs in hepatic immune cells remains poorly characterized. We investigated the role of LXRs in regulation of inflammatory responses of hepatic mononuclear cells (MNCs) in mice. Both LXRα and LXRβ were expressed in mouse hepatic MNCs and F4/80+ Kupffer cells/macrophages. LXRα/β-knockout (KO) mice had an increased number of hepatic MNCs and elevated expression of macrophage surface markers and inflammatory cytokines compared to wild-type (WT) mice. Among MNCs, F4/80+CD11b+ cells, not F4/80+CD11b− or F4/80+CD68+ cells, were increased in LXRα/β-KO mice more than WT mice. Isolated hepatic MNCs and F4/80+CD11b+ cells of LXRα/β-KO mice showed enhanced production of inflammatory cytokines after stimulation by lipopolysaccharide or CpG-DNA compared to WT cells, and LXR ligand treatment suppressed lipopolysaccharide-induced cytokine expression in hepatic MNCs. Lipopolysaccharide administration also stimulated inflammatory cytokine production in LXRα/β-KO mice more effectively than WT mice. Thus, LXR deletion enhances recruitment of F4/80+CD11b+ Kupffer cells/macrophages and acute immune responses in the liver. LXRs regulate the Kupffer cell/macrophage population and innate immune and inflammatory responses in mouse liver.
Muscarinic receptor-induced contractions of the detrusor are impaired in TRPC4 deficient mice
Authors: Griffin Caoimhin S. , Thornbury Keith D. , Hollywood Mark A. , Sergeant Gerard P. 
Published: June 2018

AbstractAcetylcholine contracts the bladder by binding to muscarinic M3 receptors on the detrusor, leading to Ca2+ influx via voltage-gated Ca2+ channels. The cellular mechanisms linking these events are poorly understood, but studies have suggested that activation of TRPC4 channels could be involved. The purpose of this study was to investigate if spontaneous and cholinergic-mediated contractions of the detrusor were impaired in TRPC4 deficient (TRPC4−/−) mice. Isometric tension recordings were made from strips of wild-type (WT) and TRPC4−/− detrusor. Spontaneous phasic detrusor contractions were significantly smaller in TRPC4−/− mice compared to wild-type, however no difference in response to exogenous application of 60 mM KCl was observed. Cholinergic responses, induced by electric-field stimulation (EFS), bath application of the cholinergic agonist carbachol, or the acetylcholinesterase inhibitor neostigmine were all significantly smaller in TRPC4−/− detrusor strips than wild-type. Surprisingly, the TRPC4/5 inhibitor ML204 reduced EFS and CCh-evoked contractions in TRPC4−/− detrusor strips. However, TRPC5 expression was up-regulated in these preparations and, in contrast to wild-type, EFS responses were reduced in amplitude by the TRPC5 channel inhibitor clemizole hydrochloride. This study demonstrates that TRPC4 channels are involved in spontaneous and cholinergic-mediated contractions of the murine detrusor. TRPC5 expression is up-regulated in TRPC4−/− detrusor strips, and may partially compensate for loss of TRPC4 channels.
Improving truffle mycelium flavour through strain selection targeting volatiles of the Ehrlich pathway
Authors: Vahdatzadeh Maryam , Splivallo Richard 
Published: June 2018

AbstractTruffles (Tuberspp.) are the fruiting bodies of symbiotic fungi, which are prized food delicacies. The marked aroma variability observed among truffles of the same species has been attributed to a series of factors that are still debated. This is because factors (i.e. genetics, maturation, geographical location and the microbial community colonizing truffles) often co-vary in truffle orchards. Here, we removed the co-variance effect by investigating truffle flavour in axenic cultures of nine strains of the white truffleTuber borchii. This allowed us to investigate the influence of genetics on truffle aroma. Specifically, we quantified aroma variability and explored whether strain selection could be used to improve human-sensed truffle flavour. Our results illustrate that aroma variability among strains is predominantly linked to amino acid catabolism through the Ehrlich pathway, as confirmed by13C labelling experiments. We furthermore exemplified through sensory analysis that the human nose is able to distinguish among strains and that sulfur volatiles derived from the catabolism of methionine have the strongest influence on aroma characteristics. Overall, our results demonstrate that genetics influences truffle aroma much more deeply than previously thought and illustrate the usefulness of strain selection for improving truffle flavour.
Exotic Spartina alterniflora invasion increases CH4 while reduces CO2 emissions from mangrove wetland soils in southeastern China
Authors: Gao Gui Feng , Li Peng Fei , Shen Zhi Jun , Qin Ying Ying , Zhang Xi Min , Ghoto Kabir , Zhu Xue Yi , Zheng Hai Lei 
Published: June 2018

AbstractMangroves are critical in global carbon budget while vulnerable to exotic plant invasion. Spartina alterniflora, one of typical salt marsh plant grows forcefully along the coast of China, has invaded the native mangrove habitats in Zhangjiang Estuary. However, the effects of S. alterniflora invasion on soil carbon gases (CH4 and CO2) emission from mangroves are not fully understood. Accordingly, we conducted a field experiment to investigate the soil CH4 and CO2 emission during growing seasons in 2016 and 2017 at four adjacent wetlands, namely bare mudflat (Mud), Kandelia obovata (KO), Avicennia marina (AM) and S. alterniflora (SA). Potential methane production (PMP), potential methane oxidation (PMO), functional microbial abundance and soil biogeochemical properties were measured simultaneously. Our results indicate that S. alterniflora invasion could dramatically increase soil CH4 emissions mainly due to the enhancement in PMP which facilitated by soil EC, MBC, TOC and mcrA gene abundance. Additionally, S. alterniflora invasion decreases soil CO2 emission. Both heterotrophic microbial respiration (16S rRNA) and methane oxidation (pmoA and ANME-pmoA) are responsible for CO2 emission reduction. Furthermore, S. alterniflora invasion greatly increases GWP by stimulating CH4 emissions. Thus, comparing with mangroves, invasive S. alterniflora significantly (p < 0.001) increases CH4 emission while reduces CO2 emission.
Extremely High Frequency Electromagnetic Fields Facilitate Electrical Signal Propagation by Increasing Transmembrane Potassium Efflux in an Artificial Axon Model
Authors: D’Agostino Simona , Della Monica Chiara , Palizzi Eleonora , Di Pietrantonio Fabio , Benetti Massimiliano , Cannatà Domenico , Cavagnaro Marta , Sardari Dariush , Stano Pasquale , Ramundo-Orlando Alfonsina 
Published: June 2018

AbstractAmong the many biological effects caused by low intensity extremely high frequency electromagnetic fields (EHF-EMF) reported in the literature, those on the nervous system are a promising area for further research. The mechanisms by which these fields alter neural activity are still unclear and thus far there appears to be no frequency dependence regarding neuronal responses. Therefore, properin vitromodels for preliminary screening studies of the interaction between neural cells with EMF are needed. We designed an artificial axon model consisting of a series of parallel RC networks. Each RC network contained an aqueous solution of lipid vesicles with a gradient of potassium (K+) concentration as the functional element. We investigated the effects of EHF-EMF (53.37 GHz–39 mW) on the propagation of the electric impulse. We report that exposure to the EHF-EMF increases the amplitude of electrical signal by inducing a potassium efflux from lipid vesicles. Further, exposure to the EHF-EMF potentiates the action of valinomycin – a K+carrier – increasing the extent of K+transport across the lipid membrane. We conclude that exposure to the EHF-EMF facilitates the electrical signal propagation by increasing transmembrane potassium efflux, and that the model presented is promising for future screening studies of different EMF frequency spectrum bands.
The Emergence of Animal Management in the Southern Levant
Authors: Munro Natalie D. , Bar-Oz Guy , Meier Jacqueline S. , Sapir-Hen Lidar , Stiner Mary C. , Yeshurun Reuven 
Published: June 2018

AbstractOur compilation of zooarchaeological data from a series of important archaeological sites spanning the Epipaleolithic through Pre-Pottery Neolithic B periods in the Mediterranean Hills of the southern Levant contributes to major debates about the beginnings of ungulate management in Southwest Asia. The data support an onset of ungulate management practices by the Early PPNB (10,500–10,000 cal. BP), more than 500 years earlier than previously thought for this region. There is a clear developmental connection between reduced hunting intensity and the uptake of ungulate management, confirming that this process began in response to local, density-dependent demographic factors. The early process of goat domestication in the southern Levant appears to have been overwhelmingly local. This may have been true for cattle and pigs as well. Nevertheless, the loose synchrony of animal management trends across Southwest Asia was undoubtedly enabled by large-scale social networks that transmitted knowledge. The results add to growing evidence that animal management processes followed multiple regional evolutionary pathways within the Fertile Crescent.
No yield penalty under favorable conditions paving the way for successful adoption of flood tolerant rice
Authors: Dar Manzoor H. , Zaidi Najam W. , Waza Showkat A. , Verulkar Satish B. , Ahmed T. , Singh P. K. , Roy S. K. Bardhan , Chaudhary Bedanand , Yadav Rambaran , Islam Mirza Mofazzal , Iftekharuddaula Khandakar M. , Roy J. K. , Kathiresan R. M. , Singh B. N. , Singh Uma S. , Ismail Abdelbagi M. 
Published: June 2018

AbstractFlooding is one of the major constraints for rice production in rainfed lowlands, especially in years and areas of high rainfall. Incorporating the Sub1 (Submergence1) gene into high yielding popular varieties has proven to be the most feasible approach to sustain rice production in submergence-prone areas. Introgression of this QTL into popular varieties has resulted in considerable improvement in yield after flooding. However, its impact under non-flooded conditions or years have not been thoroughly evaluated which is important for the farmers to accept and adopt any new version of their popular varieties. The present study was carried out to evaluate the effect of Sub1 on grain yield of rice in different genetic backgrounds, under non-submergence conditions, over years and locations. The study was carried out using head to head trials in farmer’s fields, which enable the farmers to more accurately compare the performance of Sub1 varieties with their recurrent parents under own management. The data generated from different head to head trials revealed that the grain yield of Sub1 varieties was either statistically similar or higher than their non-Sub1 counterparts under non-submergence conditions. Thus, Sub1 rice varieties show no instance of yield penalty of the introgressed gene.
MS analysis of a dilution series of bacteria:phytoplankton to improve detection of low abundance bacterial peptides
Authors: Timmins-Schiffman Emma , Mikan Molly P. , Ting Ying Sonia , Harvey H. Rodger , Nunn Brook L. 
Published: June 2018

AbstractAssigning links between microbial activity and biogeochemical cycles in the ocean is a primary objective for ecologists and oceanographers. Bacteria represent a small ecosystem component by mass, but act as the nexus for both nutrient transformation and organic matter recycling. There are limited methods to explore the full suite of active bacterial proteins largely responsible for degradation. Mass spectrometry (MS)-based proteomics now has the potential to document bacterial physiology within these complex systems. Global proteome profiling using MS, known as data dependent acquisition (DDA), is limited by the stochastic nature of ion selection, decreasing the detection of low abundance peptides. The suitability of MS-based proteomics methods in revealing bacterial signatures outnumbered by phytoplankton proteins was explored using a dilution series of pure bacteria (Ruegeria pomeroyi) and diatoms (Thalassiosira pseudonana). Two common acquisition strategies were utilized: DDA and selected reaction monitoring (SRM). SRM improved detection of bacterial peptides at low bacterial cellular abundance that were undetectable with DDA from a wide range of physiological processes (e.g. amino acid synthesis, lipid metabolism, and transport). We demonstrate the benefits and drawbacks of two different proteomic approaches for investigating species-specific physiological processes across relative abundances of bacteria that vary by orders of magnitude.
Testing for Sufficient-Cause Interactions in Case-Control Studies of Non-Rare Diseases
Authors: Lin Jui-Hsiang , Lee Wen-Chung 
Published: June 2018

AbstractSufficient-cause interaction (also called mechanistic interaction or causal co-action) has received considerable attention recently. Two statistical tests, the ‘relative excess risk due to interaction’ (RERI) test and the ‘peril ratio index of synergy based on multiplicativity’ (PRISM) test, were developed specifically to test such an interaction in cohort studies. In addition, these two tests can be applied in case–control studies for rare diseases but are not valid for non-rare diseases. In this study, we proposed a method to incorporate the information of disease prevalence to estimate the perils of particular diseases. Moreover, we adopted the PRISM test to assess the sufficient-cause interaction in case–control studies for non-rare diseases. The Monte Carlo simulation showed that our proposed method can maintain reasonably accurate type I error rates in all situations. Its powers are comparable to the odds-scale PRISM test and far greater than the risk-scale RERI test and the odds-scale RERI test. In light of its desirable statistical properties, we recommend using the proposed method to test for sufficient-cause interactions between two binary exposures in case–control studies.
Mesenchymal stem cell-mediated Notch2 activation overcomes radiation-induced injury of the hematopoietic system
Authors: Kim Areumnuri , Shim Sehwan , Kim Min-Jung , Myung Jae Kyung , Park Sunhoo 
Published: June 2018

AbstractRadiation exposure severely damages the hematopoietic system. Although several radio-protectors have been proposed to prevent radiation-induced damage, most agents have limited efficacy. In the present study, we investigated whether mesenchymal stem cells (MSCs) could contribute to the expansion of hematopoietic cells and mitigate radiation-induced hematopoietic injury in vitro and in vivo. We found that co-culture with MSCs promoted hematopoietic progenitor/stem cell (HPSCs) maintenance by providing a bone marrow-like microenvironment. In addition, we showed that MSCs prevented radiation-induced damage to HPSCs, as evidenced by the lack of DNA damage and apoptosis. Intravenously injected MSCs rapidly migrated to the bone marrow (BM) and prevented loss of BM cellularity, which reduced lethality and ameliorated pancytopenia in the BM of whole body-irradiated mice. We demonstrated that MSC-derived Jagged1 attenuated radiation-induced cytotoxicity of HPSCs, and that this was mediated by Notch signaling and expression of downstream proteins Bcl2 and p63 in HPSCs. In addition, Notch2 depletion significantly reduced the MSC-mediated radio-protective effect in human- and mouse-derived HPSCs. Collectively, our data show that activation of Notch and its associated downstream signaling pathways prevent radiation-induced hematopoietic injury. Therefore, enhancing Jagged1-Notch2 signaling could provide therapeutic benefit by protecting the hematopoietic system against damage after radiation.
Nitric Oxide Controls Constitutive Freezing Tolerance in Arabidopsis by Attenuating the Levels of Osmoprotectants, Stress-Related Hormones and Anthocyanins
Authors: Costa-Broseta Álvaro , Perea-Resa Carlos , Castillo Mari-Cruz , Ruíz M. Fernanda , Salinas Julio , León José 
Published: June 2018

AbstractPlant tolerance to freezing temperatures is governed by endogenous constitutive components and environmental inducing factors. Nitric oxide (NO) is one of the endogenous components that participate in freezing tolerance regulation. A combined metabolomic and transcriptomic characterization of NO-deficientnia1,2noa1–2mutant plants suggests that NO acts attenuating the production and accumulation of osmoprotective and regulatory metabolites, such as sugars and polyamines, stress-related hormones, such as ABA and jasmonates, and antioxidants, such as anthocyanins and flavonoids. Accordingly, NO-deficient plants are constitutively more freezing tolerant than wild type plants.
Ordering of Hollow Ag-Au Nanospheres with Butterfly Wings as a Bio-template
Authors: Guan Yu , Su Huilan , Yang Chengzhi , Wu Lingling , Chen Shikun , Gu Jiajun , Zhang Wang , Zhang Di 
Published: June 2018

AbstractA biological template strategy is implemented for the fabrication of hollow noble metal composite nanospheres within the ordered array nanostructures by introducing butterfly wings to some convenient technique procedure. Butterfly wings are activated by ethylenediamine to increase the reactive sites on the chitin component, on which Ag nanoparticles are in situ formed and serve as “seeds” to direct further incorporation during the following impregnation procedure. Butterfly wings could function as bio-substrate to provide an ordered array and regulate the synthesis process by providing active reaction sites (e.g. -CONH- and -OH). Thus, hollow Ag-Au nanospheres are loaded on the wings’ surface layer and inside the ordered array nanostructures homogeneously, which would have potential applications in surface enhanced Raman scattering (SERS).
Aberration correction considering curved sample surface shape for non-contact two-photon excitation microscopy with spatial light modulator
Authors: Matsumoto Naoya , Konno Alu , Inoue Takashi , Okazaki Shigetoshi 
Published: June 2018

AbstractIn this paper, excitation light wavefront modulation is performed considering the curved sample surface shape to demonstrate high-quality deep observation using two-photon excitation microscopy (TPM) with a dry objective lens. A large spherical aberration typically occurs when the refractive index (RI) interface between air and the sample is a plane perpendicular to the optical axis. Moreover, the curved sample surface shape and the RI mismatch cause various aberrations, including spherical ones. Consequently, the fluorescence intensity and resolution of the obtained image are degraded in the deep regions. To improve them, we designed a pre-distortion wavefront for correcting the aberration caused by the curved sample surface shape by using a novel, simple optical path length difference calculation method. The excitation light wavefront is modulated to the pre-distortion wavefront by a spatial light modulator incorporated in the TPM system before passing through the interface, where the RI mismatch occurs. Thus, the excitation light is condensed without aberrations. Blood vessels were thereby observed up to an optical depth of 2,000 μm in a cleared mouse brain by using a dry objective lens.
Geriatric influenza death (GID) score: a new tool for predicting mortality in older people with influenza in the emergency department
Authors: Chung Jui-Yuan , Hsu Chien-Chin , Chen Jiann-Hwa , Chen Wei-Lung , Lin Hung-Jung , Guo How-Ran , Huang Chien-Cheng 
Published: June 2018

AbstractAlthough influenza may cause death in the geriatric population, the best method for predicting mortality in this population is still unclear. We retrospectively recruited older people (≥65 yr) with influenza visiting the emergency department (ED) of a medical center between January 1, 2010, and December 31, 2015. We performed univariate and multivariate logistic regression to identify independent mortality predictors and then developed a prediction score. Four hundred nine older ED patients with a nearly equal sex ratio were recruited. Five independent mortality predictors were identified: severe coma (Glasgow Coma Scale score ≤8), past histories of cancer and coronary artery disease, elevated C-reactive protein levels (>10 mg/dl), and bandemia (>10% band cells). We divided the patients into three mortality risk and disposition groups: (1) low risk (1.1%; 95% confidence interval [CI], 0.5–3.0%); (2) moderate risk (16.7%; 95% CI, 9.3–28.0%); and (3) high risk (40%; 95% CI, 19.8–64.2%). The area under the receiver operating characteristic curve and the Hosmer-Lemeshow goodness of fit of the GID score were 0.86 and 0.578, respectively. The GID score is an efficient and simple tool for predicting mortality in older ED patients with influenza. Further studies are warranted to validate its use.
Nanosurfaces modulate the mechanism of peri-implant endosseous healing by regulating neovascular morphogenesis
Authors: Khosravi Niloufar , Maeda Azusa , DaCosta Ralph S. , Davies John E. 
Published: June 2018

AbstractNanosurfaces have improved clinical osseointegration by increasing bone/implant contact. Neovascularization is considered an essential prerequisite to osteogenesis, but no previous reports to our knowledge have examined the effect of surface topography on the spatio-temporal pattern of neovascularization during peri-implant healing. We have developed a cranial window model to study peri-implant healing intravitally over clinically relevant time scales as a function of implant topography. Quantitative intravital confocal imaging reveals that changing the topography (but not chemical composition) of an implant profoundly affects the pattern of peri-implant neovascularization. New vessels develop proximal to the implant and the vascular network matures sooner in the presence of an implant nanosurface. Accelerated angiogenesis can lead to earlier osseointegration through the delivery of osteogenic precursors to, and direct formation of bone on, the implant surface. This study highlights a critical aspect of peri-implant healing, but also informs the biological rationale for the surface design of putative endosseous implant materials.
PubMed Phrases, an open set of coherent phrases for searching biomedical literature
Authors: Kim Sun , Yeganova Lana , Comeau Donald C. , Wilbur W. John , Lu Zhiyong 
Published: June 2018

AbstractIn biomedicine, key concepts are often expressed by multiple words (e.g., ‘zinc finger protein’). Previous work has shown treating a sequence of words as a meaningful unit, where applicable, is not only important for human understanding but also beneficial for automatic information seeking. Here we present a collection of PubMed® Phrases that are beneficial for information retrieval and human comprehension. We define these phrases as coherent chunks that are logically connected. To collect the phrase set, we apply the hypergeometric test to detect segments of consecutive terms that are likely to appear together in PubMed. These text segments are then filtered using the BM25 ranking function to ensure that they are beneficial from an information retrieval perspective. Thus, we obtain a set of 705,915 PubMed Phrases. We evaluate the quality of the set by investigating PubMed user click data and manually annotating a sample of 500 randomly selected noun phrases. We also analyze and discuss the usage of these PubMed Phrases in literature search.