bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temperature is a key factor in Micromonas–virus interactions
Authors: Demory David , Arsenieff Laure , Simon Nathalie , Six Christophe , Rigaut-Jalabert Fabienne , Marie Dominique , Ge Pei , Bigeard Estelle , Jacquet Stéphan , Sciandra Antoine , Bernard Olivier , Rabouille Sophie , Baudoux Anne-Claire 
Published: January 2017

Abstract
The genus Micromonas comprises phytoplankton that show among the widest latitudinal distributions on Earth, and members of this genus are recurrently infected by prasinoviruses in contrasted thermal ecosystems. In this study, we assessed how temperature influences the interplay between the main genetic clades of this prominent microalga and their viruses. The growth of three Micromonas strains (Mic-A, Mic-B, Mic-C) and the stability of their respective lytic viruses (MicV-A, MicV-B, MicV-C) were measured over a thermal range of 4–32.5 °C. Similar growth temperature optima (Topt) were predicted for all three hosts but Mic-B exhibited a broader thermal tolerance than Mic-A and Mic-C, suggesting distinct thermoacclimation strategies. Similarly, the MicV-C virus displayed a remarkable thermal stability compared with MicV-A and MicV-B. Despite these divergences, infection dynamics showed that temperatures below Topt lengthened lytic cycle kinetics and reduced viral yield and, notably, that infection at temperatures above Topt did not usually result in cell lysis. Two mechanisms operated depending on the temperature and the biological system. Hosts either prevented the production of viral progeny or maintained their ability to produce virions with no apparent cell lysis, pointing to a possible switch in the viral life strategy. Hence, temperature changes critically affect the outcome of Micromonas infection and have implications for ocean biogeochemistry and evolution.
Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome
Authors: Rubino Francesco , Carberry Ciara , Waters Sinéad M , Kenny David , McCabe Matthew S , Creevey Christopher J 
Published: January 2017

Abstract
Many microbes in complex competitive environments share genes for acquiring and utilising nutrients, questioning whether niche specialisation exists and if so, how it is maintained. We investigated the genomic signatures of niche specialisation in the rumen microbiome, a highly competitive, anaerobic environment, with limited nutrient availability determined by the biomass consumed by the host. We generated individual metagenomic libraries from 14 cows fed an ad libitum diet of grass silage and calculated functional isoform diversity for each microbial gene identified. The animal replicates were used to calculate confidence intervals to test for differences in diversity of functional isoforms between microbes that may drive niche specialisation. We identified 153 genes with significant differences in functional isoform diversity between the two most abundant bacterial genera in the rumen (Prevotella and Clostridium). We found Prevotella possesses a more diverse range of isoforms capable of degrading hemicellulose, whereas Clostridium for cellulose. Furthermore, significant differences were observed in key metabolic processes indicating that isoform diversity plays an important role in maintaining their niche specialisation. The methods presented represent a novel approach for untangling complex interactions between microorganisms in natural environments and have resulted in an expanded catalogue of gene targets central to rumen cellulosic biomass degradation.
Self-referenced photonic chip soliton Kerr frequency comb
Authors: Brasch Victor , Lucas Erwan , Jost John D , Geiselmann Michael , Kippenberg Tobias J 
Published: January 2017

AbstractSelf-referencing turns pulsed laser systems into self-referenced frequency combs. Such frequency combs allow counting of optical frequencies and have a wide range of applications. The required optical bandwidth to implement self-referencing is typically obtained via nonlinear broadening in optical fibers. Recent advances in the field of Kerr frequency combs have provided a path toward the development of compact frequency comb sources that provide broadband frequency combs, exhibit microwave repetition rates and are compatible with on-chip photonic integration. These devices have the potential to significantly expand the use of frequency combs. Yet to date, self-referencing of such Kerr frequency combs has only been attained by applying conventional, fiber-based broadening techniques. Here we demonstrate external broadening-free self-referencing of a Kerr frequency comb. An optical spectrum spanning two-thirds of an octave is directly synthesized from a continuous wave laser-driven silicon nitride microresonator using temporal dissipative Kerr soliton formation and soliton Cherenkov radiation. Using this coherent bandwidth and two continuous wave transfer lasers in a 2f–3f self-referencing scheme, we are able to detect the offset frequency of the soliton Kerr frequency comb. By stabilizing the repetition rate to a radio frequency reference, the self-referenced frequency comb is used to count and track the continuous wave pump laser’s frequency. This work demonstrates the principal ability of soliton Kerr frequency combs to provide microwave-to-optical clockworks on a chip.
Signature of type-II Weyl semimetal phase in MoTe2
Authors: Jiang J. , Liu Z.K. , Sun Y. , Yang H.F. , Rajamathi C.R. , Qi Y.P. , Yang L.X. , Chen C. , Peng H. , Hwang C-C. , Sun S.Z. , Mo S-K. , Vobornik I. , Fujii J. , Parkin S.S.P. , Felser C. , Yan B.H. , Chen Y.L. 
Published: January 2017

AbstractTopological Weyl semimetal (TWS), a new state of quantum matter, has sparked enormous research interest recently. Possessing unique Weyl fermions in the bulk and Fermi arcs on the surface, TWSs offer a rare platform for realizing many exotic physical phenomena. TWSs can be classified into type-I that respect Lorentz symmetry and type-II that do not. Here, we directly visualize the electronic structure of MoTe2, a recently proposed type-II TWS. Using angle-resolved photoemission spectroscopy (ARPES), we unravel the unique surface Fermi arcs, in good agreement with our ab initio calculations that have nontrivial topological nature. Our work not only leads to new understandings of the unusual properties discovered in this family of compounds, but also allows for the further exploration of exotic properties and practical applications of type-II TWSs, as well as the interplay between superconductivity (MoTe2 was discovered to be superconducting recently) and their topological order.
A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea
Authors: Kono Takunari , Mehrotra Sandhya , Endo Chikako , Kizu Natsuko , Matusda Mami , Kimura Hiroyuki , Mizohata Eiichi , Inoue Tsuyoshi , Hasunuma Tomohisa , Yokota Akiho , Matsumura Hiroyoshi , Ashida Hiroki 
Published: January 2017

AbstractTwo enzymes are considered to be unique to the photosynthetic Calvin–Benson cycle: ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), responsible for CO2 fixation, and phosphoribulokinase (PRK). Some archaea possess bona fide RuBisCOs, despite not being photosynthetic organisms, but are thought to lack PRK. Here we demonstrate the existence in methanogenic archaea of a carbon metabolic pathway involving RuBisCO and PRK, which we term ‘reductive hexulose-phosphate’ (RHP) pathway. These archaea possess both RuBisCO and a catalytically active PRK whose crystal structure resembles that of photosynthetic bacterial PRK. Capillary electrophoresis-mass spectrometric analysis of metabolites reveals that the RHP pathway, which differs from the Calvin–Benson cycle only in a few steps, is active in vivo. Our work highlights evolutionary and functional links between RuBisCO-mediated carbon metabolic pathways in methanogenic archaea and photosynthetic organisms. Whether the RHP pathway allows for autotrophy (that is, growth exclusively with CO2 as carbon source) remains unknown.
Mammary stem cells: angels or demons in mammary gland?
Authors: Chen Xueman , Liu Qiang , Song Erwei 
Published: January 2017

AbstractA highly dynamic development process exits within the epithelia of mammary gland, featuring morphogenetic variation during puberty, pregnancy, lactation, and regression. The identification of mammary stem cells (MaSCs) via lineage-tracing studies has substantiated a hierarchical organization of the mammary epithelia. A single MaSC is capable of reconstituting the entirely functional mammary gland upon orthotopic transplantation. Although different mammary cell subpopulations can be candidate cells-of-origin for distinct breast tumor subtypes, it still lacks experimental proofs whether MaSCs, the most primitive cells, are the ‘seeds’ of malignant transformation during most, if not all, tumorigenesis in the breast. Here, we review current knowledge of mammary epithelial hierarchy, highlighting the roles of mammary stem/progenitor cells and breast cancer stem cells (BCSCs) along with their key molecular regulators in organ development and cancer evolution. Clarifying these issues will pave the way for developing novel interventions toward stem/progenitor cells in either prevention or treatment of breast cancer (BrCa).
Etanercept-Synthesising Mesenchymal Stem Cells Efficiently Ameliorate Collagen-Induced Arthritis
Authors: Park Narae , Rim Yeri Alice , Jung Hyerin , Kim Juryun , Yi Hyoju , Kim Youngkyun , Jang Yeonsue , Jung Seung Min , Lee Jennifer , Kwok Seung-Ki , Park Sung-Hwan , Ju Ji Hyeon 
Published: January 2017

AbstractMesenchymal stem cells (MSCs) have multiple properties including anti-inflammatory and immunomodulatory effects in various disease models and clinical treatments. These beneficial effects, however, are sometimes inconsistent and unpredictable. For wider and proper application, scientists sought to improve MSC functions by engineering. We aimed to invent a novel method to produce synthetic biological drugs from engineered MSCs. We investigated the anti-arthritic effect of engineered MSCs in a collagen-induced arthritis (CIA) model. Biologics such as etanercept are the most successful drugs used in anti-cytokine therapy. Biologics are made of protein components, and thus can be theoretically produced from cells including MSCs. MSCs were transfected with recombinant minicircles encoding etanercept (trade name, Enbrel), which is a tumour necrosis factor α blocker currently used to treat rheumatoid arthritis. We confirmed minicircle expression in MSCs in vitro based on GFP. Etanercept production was verified from the conditioned media. We confirmed that self-reproduced etanercept was biologically active in vitro. Arthritis subsided more efficiently in CIA mice injected with mcTNFR2MSCs than in those injected with conventional MSCs or etanercept only. Although this novel strategy is in a very early conceptual stage, it seems to represent a potential alternative method for the delivery of biologics and engineering MSCs.
Facile synthesis, microstructure and photophysical properties of core-shell nanostructured (SiCN)/BN nanocomposites
Authors: Zhang Qian , Jia Dechang , Yang Zhihua , Cai Delong , Laine Richard M. , Li Qian , Zhou Yu 
Published: January 2017

AbstractIncreasing structural complexity at nanoscale can permit superior control over photophysical properties in the precursor-derived semiconductors. We demonstrate here the synthesis of silicon carbonitride (SiCN)/boron nitride (BN) nanocomposites via a polymer precursor route wherein the cobalt polyamine complexes used as the catalyst, exhibiting novel composite structures and photophysical properties. High Resolution Transmission Electron Microscopy (HRTEM) analysis shows that the diameters of SiCN−BN core−shell nanocomposites and BN shells are 50‒400 nm and 5‒25 nm, respectively. BN nanosheets (BNNSs) are also observed with an average sheet size of 5‒15 nm. The photophysical properties of these nanocomposites are characterized using the UV-Vis and photoluminescence (PL) analyses. The as-produced composites have emission behavior including an emission lifetime of 2.5 ns (±20 ps) longer observed in BN doped SiCN than that seen for SiC nanoparticles. Our results suggest that the SiCN/BN nanocomposites act as semiconductor displaying superior width photoluminescence at wavelengths spanning the visible to near-infrared (NIR) spectral range (400‒700 nm), owing to the heterojunction of the interface between the SiC(N) nanowire core and the BN nanosheet shell.
Lessons from temporal and spatial patterns in global use of N and P fertilizer on cropland
Authors: Bouwman A. F. , Beusen A. H. W. , Lassaletta L. , van Apeldoorn D. F. , van Grinsven H. J. M. , Zhang J. , Ittersum van M. K. 
Published: January 2017

AbstractIn recent decades farmers in high-income countries and China and India have built up a large reserve of residual soil P in cropland. This reserve can now be used by crops, and in high-income countries the use of mineral P fertilizer has recently been decreasing with even negative soil P budgets in Europe. In contrast to P, much of N surpluses are emitted to the environment via air and water and large quantities of N are transported in aquifers with long travel times (decades and longer). N fertilizer use in high-income countries has not been decreasing in recent years; increasing N use efficiency and utilization of accumulated residual soil P allowed continued increases in crop yields. However, there are ecological risks associated with the legacy of excessive nutrient mobilization in the 1970s and 1980s. Landscapes have a memory for N and P; N concentrations in many rivers do not respond to increased agricultural N use efficiency, and European water quality is threatened by rapidly increasing N:P ratios. Developing countries can avoid such problems by integrated management of N, P and other nutrients accounting for residual soil P, while avoiding legacies associated with the type of past or continuing mismanagement of high-income countries, China and India.
Targeting pathogen metabolism without collateral damage to the host
Authors: Haanstra Jurgen R. , Gerding Albert , Dolga Amalia M. , Sorgdrager Freek J. H. , Buist-Homan Manon , du Toit François , Faber Klaas Nico , Holzhütter Hermann-Georg , Szöör Balázs , Matthews Keith R. , Snoep Jacky L. , Westerhoff Hans V. , Bakker Barbara M. 
Published: January 2017

AbstractThe development of drugs that can inactivate disease-causing cells (e.g. cancer cells or parasites) without causing collateral damage to healthy or to host cells is complicated by the fact that many proteins are very similar between organisms. Nevertheless, due to subtle, quantitative differences between the biochemical reaction networks of target cell and host, a drug can limit the flux of the same essential process in one organism more than in another. We identified precise criteria for this ‘network-based’ drug selectivity, which can serve as an alternative or additive to structural differences. We combined computational and experimental approaches to compare energy metabolism in the causative agent of sleeping sickness, Trypanosoma brucei, with that of human erythrocytes, and identified glucose transport and glyceraldehyde-3-phosphate dehydrogenase as the most selective antiparasitic targets. Computational predictions were validated experimentally in a novel parasite-erythrocytes co-culture system. Glucose-transport inhibitors killed trypanosomes without killing erythrocytes, neurons or liver cells.
SMIM1 variants rs1175550 and rs143702418 independently modulate Vel blood group antigen expression
Authors: Christophersen Mikael K. , Jöud Magnus , Ajore Ram , Vege Sunitha , Ljungdahl Klara W. , Westhoff Connie M. , Olsson Martin L. , Storry Jill R. , Nilsson Björn 
Published: January 2017

AbstractThe Vel blood group antigen is expressed on the red blood cells of most individuals. Recently, we described that homozygosity for inactivating mutations in SMIM1 defines the rare Vel-negative phenotype. Still, Vel-positive individuals show great variability in Vel antigen expression, creating a risk for Vel blood typing errors and transfusion reactions. We fine-mapped the regulatory region located in SMIM1 intron 2 in Swedish blood donors, and observed a strong correlation between expression and rs1175550 as well as with a previously unreported tri-nucleotide insertion (rs143702418; C > CGCA). While the two variants are tightly linked in Caucasians, we separated their effects in African Americans, and found that rs1175550G and to a lesser extent rs143702418C independently increase SMIM1 and Vel antigen expression. Gel shift and luciferase assays indicate that both variants are transcriptionally active, and we identified binding of the transcription factor TAL1 as a potential mediator of the increased expression associated with rs1175550G. Our results provide insight into the regulatory logic of Vel antigen expression, and extend the set of markers for genetic Vel blood group typing.
Fluorescence assay of dihydroorotate dehydrogenase that may become a cancer biomarker
Authors: Yin Sheng , Kabashima Tsutomu , Zhu Qinchang , Shibata Takayuki , Kai Masaaki 
Published: January 2017

AbstractWe developed an assay method for measuring dihydroorotate dehydrogenase (DHODH) activity in cultured HeLa cells and fibroblasts, and in stage III stomach cancer and adjacent normal tissues from the same patient. The assay comprised enzymatic reaction of DHODH with a large amount of dihydroorotic acid substrate, followed by fluorescence (FL) detection specific for orotic acid using the 4-trifluoromethyl-benzamidoxime fluorogenic reagent. The DHODH activities in the biologically complex samples were readily measured by the assay method. Our data indicate significantly higher DHODH activity in HeLa cells (340 ± 25.9 pmol/105 cells/h) than in normal fibroblasts (54.1 ± 7.40 pmol/105 cells/h), and in malignant tumour tissue (1.10 ± 0.19 nmol/mg total proteins/h) than in adjacent normal tissue (0.24 ± 0.11 nmol/mg total proteins/h). This is the first report that DHODH activity may be a diagnostic biomarker for cancer.
Molecular phylogeny of a novel human adenovirus type 8 strain causing a prolonged, multi-state keratoconjunctivitis epidemic in Germany
Authors: Hage Elias , Espelage Werner , Eckmanns Tim , Lamson Daryl M. , Pantó Laura , Ganzenmueller Tina , Heim Albert 
Published: January 2017

AbstractThe German infectious disease surveillance system revealed an increase of epidemic keratoconjunctivitis (EKC) from an average of 320 cases/year (2001 to 2010) up to 2146 and 1986 cases in 2012 and 2013, respectively. From November 2011 until December 2013 (epidemic period) 85% of typed isolates were human adenovirus type 8 (HAdV-D8), whereas only low level circulation (19%) of HAdV-D8 was observed outside the epidemic period. In order to investigate whether a novel monophyletic HAdV-D8 strain prevailed during the epidemic period, complete genomic sequences of 23 HAdV-D8 isolates were generated by deep sequencing and analyzed phylogenetically. For comparison, eight HAdV-D8 isolates from outside the epidemic period were sequenced. HAdV-D8 isolates of the epidemic period had a very high sequence identity of at least 99.9% and formed a monophyletic cluster with two subclusters. A single outlier was closely related to HAdV-D8 strains isolated prior to the epidemic period. Circulation of the epidemic strain was detected as early as 2010 but not after the epidemic period in 2014. In conclusion, molecular phylogeny of complete genomic sequences proved a monophyletic HAdV-D8 epidemic. However, co-circulation of other HAdV types as well as better reporting may have contributed to the huge increase of reported cases.
HMGB1-induced autophagy: a new pathway to maintain Treg function during chronic hepatitis B virus infection
Authors: Cheng Li-sha , Li Jing , Liu Yun , Wang Fu-ping , Wang Si-qi , She Wei-min , Wu Sheng-di , Qi Xiao-long , Zhou Yong-ping , Jiang Wei 
Published: January 2017

High-mobility group box-1 (HMGB1) protein, as one of the well-known damage-associated molecular pattern molecules (DAMPs), is enriched in chronic hepatitis B virus (HBV) infection and has a context-dependent role in autophagy, a highly conserved self-digestive process in response to environmental stress. Recent mouse studies indicate that autophagy is highly active in regulatory T (Treg)-cells. In the present study, we evaluated spontaneous and induced autophagy of peripheral Treg cells from 98 patients with chronic hepatitis B (CHB), by measuring levels of lipidated form of microtubule-associated light chain 3 (LC3-II, marker for closed autophagosomes) and observing autophagic vacuoles (AV) with transmission electron microscope. No significant difference was found in spontaneous autophagy of either Treg or CD4+ naive cells when comparing CHB patients with healthy subjects, apart from CHB-Treg showed significantly higher autophagic activity after activation by anti-CD3–CD28 beads. Besides, incubation of CHB-Treg cells with CHB-serum greatly maintained their autophagic behaviour, which could be significantly diminished by blocking HMGB1 with the neutralizing antibody. Further, we characterized time- and dose-dependent effects by recombinant HMGB1 protein on autophagy of CHB-Treg cells. We also documented a significant up-regulation of HMGB1 and its receptors [toll-like receptor (TLR4), receptor for advanced glycation end-product (RAGE)] in both peripheral and intra-hepatic microenvironments of CHB patients. Moreover, the RAGE–extracellular regulated protein kinases (ERK) axis and rapamycin-sensitive components of mammalian target of rapamycin (mTOR) pathways were demonstrated in vitro to be involved in HMGB1-induced autophagy of Treg cells. Additionally, HMGB1-induced autophagy could maintain cell survival and functional stability of CHB-Treg cells. Our findings could open new perspectives in developing therapeutic strategies to activate specific anti-HBV immunity by diminishing Treg autophagy.
The Effects of Directional Processing on Objective and Subjective Listening Effort
Authors: Picou Erin M. , Moore Travis M. , Ricketts Todd A. 
Published: January 2017

PurposeThe purposes of this investigation were (a) to evaluate the effects of hearing aid directional processing on subjective and objective listening effort and (b) to investigate the potential relationships between subjective and objective measures of effort.MethodSixteen adults with mild to severe hearing loss were tested with study hearing aids programmed with 3 settings: omnidirectional, fixed directional, and bilateral beamformer. A dual-task paradigm and subjective ratings were used to assess objective and subjective listening effort, respectively, in 2 signal-to-noise ratios. Testing occurred in rooms with either low or moderate reverberation.ResultsDirectional processing improved subjective and objective listening effort, although benefit for objective effort was found only in moderate reverberation. Subjective reports of work and tiredness were more highly correlated with word recognition performance than objective listening effort. However, subjective ratings about control were significantly correlated with objective listening effort.ConclusionsDirectional microphone technology in hearing aids has the potential to improve listening effort in moderately reverberant environments. In addition, subjective questions that probe a listener's desire to exercise control may be a viable method for eliciting ratings that are significantly related to objective listening effort.