bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human milk oligosaccharides shorten rotavirus-induced diarrhea and modulate piglet mucosal immunity and colonic microbiota
Authors: Li Min , Monaco Marcia H , Wang Mei , Comstock Sarah S , Kuhlenschmidt Theresa B , Fahey Jr George C , Miller Michael J , Kuhlenschmidt Mark S , Donovan Sharon M 
Published: February 2014

Abstract
The impact of human milk oligosaccharides (HMO) on mucosal immunity, gut microbiota and response to rotavirus (RV) infection was investigated in the piglet model. Newborn piglets were fed with formula alone (FF) or formula supplemented with 4 g l−1 HMO (HMO) or a prebiotic mixture of 9:1 short-chain galactooligosaccharides (3.6 g l−1) and long-chain fructooligosaccharides (0.4 g l−1) (PRE) (n=19–21 per group) for 15 days. Piglets (n=7–8) in each dietary group were orally infected with porcine rotavirus (RV) OSU strain on d10, and stool consistency was assessed daily. Blood, small intestine and colonic contents were collected at day 15. Serum RV-specific antibody concentrations, intestinal histomorphology, RV non-structural protein-4 (NSP4) and cytokine mRNA expression were assessed. Colonic content pH, dry matter (DM) and short-chain fatty acid concentrations were measured. Ascending colonic microbiota was analyzed by 16S rRNA gene v1-3 region pyrosequencing. HMO- and PRE-fed groups had shorter duration of diarrhea than FF piglets. Infection changed intestinal histomorphology, increased serum RV-specific antibody response and intestinal RV NSP4 expression, and modulated ileal cytokine expression. HMO enhanced T helper type 1 (interferon-gamma) and anti-inflammatory (interleukin-10) cytokines in the ileum, while prebiotics promoted RV-specific immunoglobulin M response to the infection. RV infection and HMO supplementation altered intraluminal environment and gut microbiota. HMO increased pH and lowered DM of colonic contents and enhanced the abundance of unclassified Lachnospiraceae, which contains numerous butyrate-producing bacteria. In conclusion, HMO and prebiotics did not prevent the onset of RV infection but reduced the duration of RV-induced diarrhea in piglets, in part, by modulating colonic microbiota and immune response to RV infection.
Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes ‘Gramella forsetii’ KT0803
Authors: Kabisch Antje , Otto Andreas , König Sten , Becher Dörte , Albrecht Dirk , Schüler Margarete , Teeling Hanno , Amann Rudolf I , Schweder Thomas 
Published: February 2014

Abstract
Members of the phylum Bacteroidetes are abundant in many marine ecosystems and are known to have a pivotal role in the mineralization of complex organic substrates such as polysaccharides and proteins. We studied the decomposition of the algal glycans laminarin and alginate by ‘Gramella forsetii’ KT0803, a bacteroidetal isolate from North Sea surface waters. A combined application of isotope labeling, subcellular protein fractionation and quantitative proteomics revealed two large polysaccharide utilization loci (PULs) that were specifically induced, one by alginate and the other by laminarin. These regulons comprised genes of surface-exposed proteins such as oligomer transporters, substrate-binding proteins, carbohydrate-active enzymes and hypothetical proteins. Besides, several glycan-specific TonB-dependent receptors and SusD-like substrate-binding proteins were expressed also in the absence of polysaccharide substrates, suggesting an anticipatory sensing function. Genes for the utilization of the beta-1,3-glucan laminarin were found to be co-regulated with genes for glucose and alpha-1,4-glucan utilization, which was not the case for the non-glucan alginate. Strong syntenies of the PULs of ‘G. forsetii’ with similar loci in other Bacteroidetes indicate that the specific response mechanisms of ‘G. forsetii’ to changes in polysaccharide availability likely apply to other Bacteroidetes. Our results can thus contribute to an improved understanding of the ecological niches of marine Bacteroidetes and their roles in the polysaccharide decomposition part of carbon cycling in marine ecosystems.
Direct exchange of vitamin B12 is demonstrated by modelling the growth dynamics of algal–bacterial cocultures
Authors: Grant Matthew A A , Kazamia Elena , Cicuta Pietro , Smith Alison G 
Published: February 2014

Abstract
The growth dynamics of populations of interacting species in the aquatic environment is of great importance, both for understanding natural ecosystems and in efforts to cultivate these organisms for industrial purposes. Here we consider a simple two-species system wherein the bacterium Mesorhizobium loti supplies vitamin B12 (cobalamin) to the freshwater green alga Lobomonas rostrata, which requires this organic micronutrient for growth. In return, the bacterium receives photosynthate from the alga. Mathematical models are developed that describe minimally the interdependence between the two organisms, and that fit the experimental observations of the consortium. These models enable us to distinguish between different mechanisms of nutrient exchange between the organisms, and provide strong evidence that, rather than undergoing simple lysis and release of nutrients into the medium, M. loti regulates the levels of cobalamin it produces, resulting in a true mutualism with L. rostrata. Over half of all microalgae are dependent on an exogenous source of cobalamin for growth, and this vitamin is synthesised only by bacteria; it is very likely that similar symbiotic interactions underpin algal productivity more generally.
Quantum phases in circuit QED with a superconducting qubit array
Authors: Zhang Yuanwei , Yu Lixian , Liang J. -Q , Chen Gang , Jia Suotang , Nori Franco 
Published: February 2014

AbstractCircuit QED on a chip has become a powerful platform for simulating complex many-body physics. In this report, we realize a Dicke-Ising model with an antiferromagnetic nearest-neighbor spin-spin interaction in circuit QED with a superconducting qubit array. We show that this system exhibits a competition between the collective spin-photon interaction and the antiferromagnetic nearest-neighbor spin-spin interaction and then predict four quantum phases, including: a paramagnetic normal phase, an antiferromagnetic normal phase, a paramagnetic superradiant phase and an antiferromagnetic superradiant phase. The antiferromagnetic normal phase and the antiferromagnetic superradiant phase are new phases in many-body quantum optics. In the antiferromagnetic superradiant phase, both the antiferromagnetic and superradiant orders can coexist and thus the system possesses "Equation missing" symmetry. Moreover, we find an unconventional photon signature in this phase. In future experiments, these predicted quantum phases could be distinguished by detecting both the mean-photon number and the magnetization.
Oxidation modifies the structure and function of the extracellular matrix generated by human coronary artery endothelial cells
Authors: Chuang Christine Y. , Degendorfer Georg , Hammer Astrid , Whitelock John M. , Malle Ernst , Davies Michael J. 
Published: February 2014

ECM (extracellular matrix) materials, such as laminin, perlecan, type IV collagen and fibronectin, play a key role in determining the structure of the arterial wall and the properties of cells that interact with the ECM. The aim of the present study was to investigate the effect of peroxynitrous acid, an oxidant generated by activated macrophages, on the structure and function of the ECM laid down by HCAECs (human coronary artery endothelial cells) in vitro and in vivo. We show that exposure of HCAEC-derived native matrix components to peroxynitrous acid (but not decomposed oxidant) at concentrations &gt;1 μM results in a loss of antibody recognition of perlecan, collagen IV, and cell-binding sites on laminin and fibronectin. Loss of recognition was accompanied by decreased HCAEC adhesion. Real-time PCR showed up-regulation of inflammation-associated genes, including MMP7 (matrix metalloproteinase 7) and MMP13, as well as down-regulation of the laminin α2 chain, in HCAECs cultured on peroxynitrous acid-treated matrix compared with native matrix. Immunohistochemical studies provided evidence of co-localization of laminin with 3-nitrotyrosine, a biomarker of peroxynitrous acid damage, in type II–III/IV human atherosclerotic lesions, consistent with matrix damage occurring during disease development in vivo. The results of the present study suggest a mechanism through which peroxynitrous acid modifies endothelial cell-derived native ECM proteins of the arterial basement membrane in atherosclerotic lesions. These changes to ECM and particularly perlecan and laminin may be important in inducing cellular dysfunction and contribute to atherogenesis.
Crystallographic structure of the turbine C-ring from spinach chloroplast F-ATP synthase
Authors: Balakrishna Asha Manikkoth , Seelert Holger , Marx Sven-Hendric , Dencher Norbert A. , Grüber Gerhard 
Published: February 2014

In eukaryotic and prokaryotic cells, F-ATP synthases provide energy through the synthesis of ATP. The chloroplast F-ATP synthase (CF1FO-ATP synthase) of plants is integrated into the thylakoid membrane via its FO-domain subunits a, b, b’ and c. Subunit c with a stoichiometry of 14 and subunit a form the gate for H+-pumping, enabling the coupling of electrochemical energy with ATP synthesis in the F1 sector.
Here we report the crystallization and structure determination of the c14-ring of subunit c of the CF1FO-ATP synthase from spinach chloroplasts. The crystals belonged to space group C2, with unit-cell parameters a=144.420, b=99.295, c=123.51 Å, and β=104.34° and diffracted to 4.5 Å resolution. Each c-ring contains 14 monomers in the asymmetric unit. The length of the c-ring is 60.32 Å, with an outer ring diameter 52.30 Å and an inner ring width of 40 Å.
Time–frequency method to reduce contamination by ionospheric fast frequency modulation for HF skywave radars
Authors: Chengyu Hou , Tian Xia , Qian Bao 
Published: February 2014

The unstable and time‐varying property of the ionosphere causes a frequency modulation on the high frequency sky‐wave radar echo signals. When the modulation period is of 10 s or smaller, it is called the fast phase‐path modulation. This sort of modulation will result in the broadening, the splitting and even the overlapping of the spectra, which makes target detection and sea‐state remote sensing hard. Hence, it is necessary to decontaminate the echo signals before the coherent integration process. In this study, the pseudo Wigner‐Ville distribution is proposed as a means of estimating the ionospheric frequency modulation. A frequency weighting method is used to obtain the instantaneous frequency (IF) from the time–frequency distribution and an adaptive low‐pass filter is introduced to purify the IF. Then, the amplitude difference between the two first‐order Bragg peaks is adopted in the weighting process to obtain the phase compensation function. To improve the compensation effect, an optimising process is proposed. The simulation results show that the method can improve the quality of the spectra for the target detection and remote sensing efficiently even in the cases of a high sea‐state.
Anomalous water diffusion in salt solutions
Authors: Ding Yun , Hassanali Ali A. , Parrinello Michele 
Published: February 2014

Significance
Liquid water remains one of the most important environments in which physical, chemical, and biological processes occur. One such process involves the solvation of ions. Understanding the perturbation that ions make on the hydrogen bond network of water remains an open question. Here, using state-of-the-art simulation methods, we show that treating the electronic degrees of freedom explicitly is required to reproduce the experimentally observed water diffusion trends in CsI and NaCl solutions, where ab initio water is characterized by dynamic heterogeneity. We find that the ions do not disrupt the network in any significant manner and provide some nuances to classical ideas in physical chemistry regarding the “structure-making” and “structure-breaking” properties of ions.
Using kinematic properties of pre-planetary nebulae to constrain engine paradigms
Authors: Blackman Eric G. , Lucchini Scott 
Published: February 2014

Abstract
Some combination of binary interactions and accretion plausibly conspire to produce the ubiquitous collimated outflows from planetary nebulae (PN) and their presumed pre-PN (PPN) precursors. But which accretion engines are viable? The difficulty in observationally resolving the engines warrants the pursuit of indirect constraints. We show how kinematic outflow data for 19 PPN can be used to determine the minimum required accretion rates. We consider main-sequence (MS) and white dwarf (WD) accretors and five example accretion rates inferred from published models to compare with the minima derived from outflow momentum conservation. While our primary goal is to show the method in anticipation of more data and better theoretical constraints, taking the present results at face value already rules out modes of accretion: Bondi–Hoyle–Lyttleton (BHL) wind accretion and wind Roche lobe overflow (M-WRLOF, based on Mira parameters) are too feeble for all 19/19 objects for an MS accretor. For a WD accretor, BHL is ruled out for 18/19 objects and M-WRLOF for 15/19 objects. RLOF from the primary at the Red Rectangle level can accommodate 7/19 objects, though RLOF modes with higher accretion rates are not yet ruled out. Accretion modes operating from within common envelope evolution can accommodate all 19 objects, if jet collimation can be maintained. Overall, sub-Eddington rates for an MS accretor are acceptable but 8/19 would require super-Eddington rates for a WD.
A new cold sub-Saturnian candidate planet orbiting GJ 221
Authors: Tuomi Mikko 
Published: February 2014

Abstract
We re-analyse the recently published High-Accuracy Radial velocity Planet Searcher (HARPS) and Planet Finder Spectrograph (PFS) velocities of the nearby K dwarf GJ 221 that have been reported to contain the signatures of two planets orbiting the star. Our goal is to see whether the earlier studies discussing the system fell victims of false negative detections. We perform the analyses by using an independent statistical method based on posterior samplings and model comparisons in the Bayesian framework that is known to be more sensitive to weak signals of low-mass planets. According to our analyses, we find strong evidence in favour of a third candidate planet in the system corresponding to a cold sub-Saturnian planet with an orbital period of 500 d and a minimum mass of 29 M⊕. Application of sub-optimal signal detection methods can leave low-amplitude signals undetected in radial velocity time series. Our results suggest that the estimated statistical properties of low-mass planets can thus be biased because several signals corresponding to low-mass candidate planets may have gone unnoticed. This also suggests that the occurrence rates of such planets based on radial velocity surveys might be underestimated.
First Report of Leek yellow stripe virus in Allium sativum in Western India
Authors: Gawande S. J. , Gurav V. S. , Ingle A. A. , Gopal J. 
Published: February 2014

Garlic (Allium sativum L.) is an important bulbous spice crop in India as well as other parts of world. Garlic is well known for its medicinal properties. Degeneration due to viral infections is one of the important constraints in exploiting its yield potential. Leek yellow stripe virus (LYSV), genus Potyvirus, family Potyviridae, is a prominent virus known to infect garlic worldwide (4). During July 2013, potyvirus-like symptoms such as mosaic, streaking, stunting, mottling of leaves were observed on garlic cv. G-41 and landrace Ranibennur local, collected from Karnataka, India, and maintained at the Directorate of Onion and Garlic Research, Rajgurunagar, Pune, India. The incidence of symptomatic plants was estimated at 70% for Ranibennur local and 68% for cv. G-41. The symptomatic leaves were sampled diagonally from the field. Twenty symptomatic plants per cultivar with each sample was composited from young, middle, and lower (basal) leaves of the plant. These samples were tested by double-antibody sandwich (DAS)-ELISA for LYSV using commercially available kit (Agdia Inc., Elkhart, IN). ELISA-positive plants were further subjected to molecular studies. Total RNA from the infected leaf samples were extracted by RNeasy Plant Mini kit (Qiagen GmbH, Hilden, Germany) and assayed by reverse transcription (RT)-PCR using primer pair LYSV-F 2 (5′-GCACCATACAGTGAATTGAG-3′) (1), LYSV-R (5′-GCCTCGCGCGCTCTAA-3′) (3) to amplify 874 bases of partial Nib and partial coat protein gene. The amplified product of 874 bp derived from A. sativum isolate was purified (QIAquick PCR Purification Kit, Qiagen) and cloned using vector pDrive (Qiagen). The recombinant clones were sequenced and submitted in NCBI database (GenBank Accession No. KF850539). The sequence analysis performed on CLC Main Workbench Version 6.8.4 gave confirmation of LYSV. Further, phylogenetic analysis of the 874-nt sequence revealed the highest nucleotide identity (80 to 82%) with LYSV isolates (DQ925453, JN127339, AB005611, and JX429965). To the best of our knowledge, this is the first report of natural infection of garlic by LYSV in western India. LYSV is known to cause direct losses in garlic and other related Allium spp. Up to 54% reduction in bulb weight was observed due to single infection of this virus (2). Hence, our first report about this virus has significant impact on garlic production scenario, if this virus found to be widespread in the country. For this, additional surveys and genotype screenings are needed to obtain a better understanding of the potential impact of LYSV on garlic production in India. References: (1) H. Fidan and S. Baloglu. Plant Dis. 93:672, 2009. (2) H. Lot et al. Plant Dis. 82:1381, 1998. (3) P. Lunello et al. J. Virol. Methods. 118:15, 2004. (4) H. R. Pappu et al. Plant Dis. 89:205, 2005.
First Report of Sugarcane yellow leaf virus Infecting Barley in Tunisia
Authors: Bouallegue M. , Mezghani-Khemakhem M. , Makni H. , Makni M. 
Published: February 2014

Sugarcane yellow leaf virus (ScYLV) causes severe leaf symptoms in sugarcane (Saccharum spp.). It is a single-stranded RNA virus assigned to the genus Polerovirus, family Luteoviridae (1). ScYLV is transmitted by two aphid species, Melanaphis sacchari and Rhopalosiphum maidis. Although barley (Hordeum vulgare), oats (Avena sativa), and wheat (Triticum spp.) are susceptible to ScYLV when experimentally inoculated (3), this virus, related serologically to Barley yellow dwarf virus (BYDV)-RPV (4), has never been detected naturally in these cereals. In this study, 240 barley leaves were randomly collected from six fields in Tunisia following a north-south trend during the high infestation periods (March/April) in the 2013 growing season. Samples were tested by DAS-ELISA, using three antibodies (Bioreba AG, Switzerland), two of them, BYDV-B and BYDV-F, specific to luteoviruses corresponding to BYDV-PAV and BYDV-MAV, respectively, and the third one, BYDV-RPV, specific to the polerovirus synonymous to Cereal yellow dwarf virus (CYDV)-RPV. Based on DAS-ELISA, 30 samples were found positive for B/CYDV infection; 17 out of the 30 infected samples contained a single serotype, BYDV-PAV, and 13 out of the 30 infected samples contained two serotypes, PAV and RPV. Total RNA was extracted from all positive samples, and RT-PCR of the viral CP gene was performed with Lu1/Lu4 primers (2). A product of 531 bp was cloned and sequenced. The identities among the sequences determined varied between 80 to 100%, and from the 17 samples containing BYDV-PAV, six distinct BYDV-PAV sequences were revealed and named PAV-TN1 to PAV-TN6 (GenBank Accession No. JX402453 to JX402457 and KF271792). Fortuitously, all 13 positive samples corresponding to the serotypes PAV-RPV exhibited 98.7 to 99.3% identity with ScYLV isolates. These 13 samples contained three distinct sequences that were named ScYLV-Tun1 to ScYLV-Tun3 (GenBank Accession No. KF836888 to KF836890). Of the 17 PAV-positive samples collected, six were infected with PAV-TN1, four with PAV-TN2, four with PAV-TN3, one with PAV-TN4, one with PAV-TN5, and the last one with PAV-TN6. Of the 13 ScYLV-positive samples, seven were infected with ScYLV-Tun1, four with ScYLV-Tun2, and two with ScYLV-Tun3. Phylogenetic analysis showed that PAV-TN sequences formed a very tight cluster (>98%) corresponding to BYDV subspecies PAV-II, whereas all three Tunisian ScYLV sequences were clustered together. This study provides the first report of ScYLV isolates infecting barley crops in Tunisia, and confirms serological cross-reactivity between ScYLV and BYDV-RPV when commercial antibodies against BYDV-RPV are used. References: (1) C. J. D'Arcy and L. L. Domier. Page 891 in: Virus Taxonomy, 8th Report of the ICTV. C. M. Fauquet et al., eds. Springer-Verlag, New York, 2005. (2) N. L. Robertson and R. French. J. Gen. Virol. 72:1473, 1991. (3) S. Schenck and A. T. Lehrer. Plant Dis. 84:1085, 2000. (4) J. Vega et al. Plant Dis. 81:21, 1997.
Effects of node position on regeneration of stolon fragments in congeneric invasive and native Alternanthera species in China
Authors: Song Yao‐Bin , Zhou Meng‐Yao , Dai Wen‐Hong , Jiang Dan , Li Wen‐Bing , Dong Ming 
Published: February 2014

AbstractVegetative regeneration plays an important role in the adaptation of clonal plants in frequently disturbed habitats, but few studies have compared vegetative regeneration capacity of invasive clonal plants with that of their native congeners. Vegetative regeneration capacity from shoot nodes can also be affected by the position of the nodes, but this appears little studied. We conducted a greenhouse experiment with Alternanthera philoxeroides, a highly invasive species in China, and its native congener A. sessilis to test the difference in vegetative regeneration capacity of stolon nodes at five different positions (i.e. 3rd, 4th, 5th, 6th and 7th node starting from the apex of the stolon). At the end of the experiment, we counted and harvested all regenerated plants and determined their biomass and allocation. Both species could successfully regenerate from stolon fragments and node position significantly affected regeneration rate and subsequent growth. However, the vegetative regeneration capacity of A. philoxeroides was not higher than that of A. sessilis. These results suggest that vegetative regeneration from stolon fragments may not be a trait that can explain the invasiveness of A. philoxeroides.
Correlation between infection by ophiostomatoid fungi and the presence of subterranean termites in loblolly pine (Pinus taedaL.) roots
Authors: Riggins John J. , Little Nathan S. , Eckhardt Lori G. 
Published: February 2014

AbstractObservations of subterranean termites feeding in pine sapwood containing ophiostomatoid fungi prompted the present study aiming to investigate the effect of infection byLeptographiumfungi on the probability of encountering subterranean termites in loblolly pine (Pinus taedaL.) roots.Root samples were collected from 2350 loblolly pine trees inAlabama,Texas,Louisiana andMississippi using hand tools. The presence or absence of subterranean termites in the roots was recorded. Samples were plated onmalt extract agarandcycloheximide‐streptomycin malt agarand incubated to determine which, if any, fungal species were present.The presence ofLeptographium procerum,Leptographium terebrantisor both was significantly associated with an increased presence of subterranean termites in loblolly pine roots.The results obtained in the present study indicate that complex ecological interactions may exist between ophiostomatoid fungi, as carried by root‐feeding bark beetles, and subterranean termites.