bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analytical Solution
for Thermally Fully Developed Combined Electroosmotic and Pressure-Driven Flows in Narrow
Confinements With Thick Electrical Double
Layers
Authors: Dey Ranabir , Chakraborty Debapriya , Chakraborty Suman 
Published: November 2010

Abstract
In the present paper, closed form solutions for the Nusselt number are obtained for hydrodynamically and thermally fully developed combined electroosmotic and pressure-driven flows in narrow confinements for the constant wall heat flux boundary condition. Overcoming the constraints of the standard models that are valid only within thin electrical double layer (EDL) limits, the effects of thick electric double layers are accounted for as a distinctive feature of this model. Along with Joule heating, viscous dissipation effects, which are particularly important for ultrathin channel dimensions (typically conforming to the cases of thick EDLs), are taken into account. The results are presented in terms of appropriate nondimensional parameters depicting the relative EDL thickness with respect to the channel height, as well as relative strengths of Joule heating and viscous dissipation effects.
Characterization of Garvicin ML, a Novel Circular Bacteriocin Produced by
Lactococcus garvieae
DCC43, Isolated from Mallard Ducks (
Anas platyrhynchos
)
Authors: Borrero Juan , Brede Dag A. , Skaugen Morten , Diep Dzung B. , Herranz Carmen , Nes Ingolf F. , Cintas Luis M. , Hernández Pablo E. 
Published: November 2010

ABSTRACT

Lactococcus garvieae
DCC43 produces a bacteriocin, garvicin ML (GarML), with a molecular mass of 6,004.2 Da. Data from
de novo
amino acid sequencing by tandem mass spectrometry and nucleotide sequencing by reverse genetics suggested that the bacteriocin is synthesized as a 63-amino-acid precursor with a 3-amino-acid leader peptide that is removed by cleavage. Subsequently, a covalent linkage between the N and C termini forms the mature version of this novel 60-amino-acid circular bacteriocin.
Spatial Variability in Nitrification Rates and Ammonia-Oxidizing Microbial Communities in the Agriculturally Impacted Elkhorn Slough Estuary, California
Authors: Wankel Scott D. , Mosier Annika C. , Hansel Colleen M. , Paytan Adina , Francis Christopher A. 
Published: November 2010

ABSTRACT

Ammonia oxidation—the microbial oxidation of ammonia to nitrite and the first step in nitrification—plays a central role in nitrogen cycling in coastal and estuarine systems. Nevertheless, questions remain regarding the connection between this biogeochemical process and the diversity and abundance of the mediating microbial community. In this study, we measured nutrient fluxes and rates of sediment nitrification in conjunction with the diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing betaproteobacteria (β-AOB). Sediments were examined from four sites in Elkhorn Slough, a small agriculturally impacted coastal California estuary that opens into Monterey Bay. Using an intact sediment core flowthrough incubation system, we observed significant correlations among NO
3
−
, NO
2
−
, NH
4
+
, and PO
4
3+
fluxes, indicating a tight coupling of sediment biogeochemical processes.
15
N-based measurements of nitrification rates revealed higher rates at the less impacted, lower-nutrient sites than at the more heavily impacted, nutrient-rich sites. Quantitative PCR analyses revealed that β-AOB
amoA
(encoding ammonia monooxygenase subunit A) gene copies outnumbered AOA
amoA
gene copies by factors ranging from 2- to 236-fold across the four sites. Sites with high nitrification rates primarily contained marine/estuarine
Nitrosospira-
like bacterial
amoA
sequences and phylogenetically diverse archaeal
amoA
sequences. Sites with low nitrification rates were dominated by estuarine
Nitrosomonas-
like
amoA
sequences and archaeal
amoA
sequences similar to those previously described in soils. This is the first report measuring AOA and β-AOB
amoA
abundance in conjunction with
15
N-based nitrification rates in estuary sediments.
Microbiome of Fungus-Growing Termites: a New Reservoir for Lignocellulase Genes
Authors: Liu Ning , Yan Xing , Zhang Meiling , Xie Lei , Wang Qian , Huang Yongping , Zhou Xuguo , Wang Shengyue , Zhou Zhihua 
Published: November 2010

ABSTRACT

Fungus-growing termites play an important role in lignocellulose degradation and carbon mineralization in tropical and subtropical regions, but the degradation potentiality of their gut microbiota has long been neglected. The high quality and quantity of intestinal microbial DNA are indispensable for exploring new cellulose genes from termites by function-based screening. Here, using a refined intestinal microbial DNA extraction method followed by multiple-displacement amplification (MDA), a fosmid library was constructed from the total microbial DNA isolated from the gut of a termite growing in fungi. Functional screening for endoglucanase, cellobiohydrolase, β-glucosidase, and xylanase resulted in 12 β-glucosidase-positive clones and one xylanase-positive clone. The sequencing result of the xylanase-positive clone revealed an 1,818-bp open reading frame (ORF) encoding a 64.5-kDa multidomain endo-1,4-β-xylanase, designated Xyl6E7, which consisted of an N-terminal GH11 family catalytic domain, a CBM_4_9 domain, and a
Listeria
-
Bacteroides
repeat domain. Xyl6E7 was a highly active, substrate-specific, and endo-acting alkaline xylanase with considerably wide pH tolerance and stability but extremely low thermostability.
Improved Eco-Friendly Recombinant
Anabaena
sp. Strain PCC7120 with Enhanced Nitrogen Biofertilizer Potential
Authors: Chaurasia Akhilesh Kumar , Apte Shree Kumar 
Published: November 2010

ABSTRACT

Photosynthetic, nitrogen-fixing
Anabaena
strains are native to tropical paddy fields and contribute to the carbon and nitrogen economy of such soils. Genetic engineering was employed to improve the nitrogen biofertilizer potential of
Anabaena
sp. strain PCC7120. Constitutive enhanced expression of an additional integrated copy of the
hetR
gene from a light-inducible promoter elevated HetR protein expression and enhanced functional heterocyst frequency in the recombinant strain. The recombinant strain displayed consistently higher nitrogenase activity than the wild-type strain and appeared to be in homeostasis with compatible modulation of photosynthesis and respiration. The enhanced combined nitrogen availability from the recombinant strain positively catered to the nitrogen demand of rice seedlings in short-term hydroponic experiments and supported better growth. The engineered strain is stable, eco-friendly, and useful for environmental application as nitrogen biofertilizer in paddy fields.
Biochemical Characterization of UDP-Gal:GlcNAc-Pyrophosphate-Lipid β-1,4-Galactosyltransferase WfeD, a New Enzyme fromShigella boydiiType 14 That Catalyzes the Second Step in O-Antigen Repeating-Unit Synthesis
Authors: Xu Changchang , Liu Bin , Hu Bo , Han Yanfang , Feng Lu , Allingham John S. , Szarek Walter A. , Wang Lei , Brockhausen Inka 
Published: November 2010

ABSTRACTThe O antigen is the outer part of the lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria and contains many repeats of an oligosaccharide unit. It contributes to antigenic variability and is essential to the full function and virulence of bacteria.Shigellais a Gram-negative human pathogen that causes diarrhea in humans. The O antigen ofShigella boydiitype 14 consists of repeating oligosaccharide units with the structure [→6-d-Galpα1→4-d-GlcpAβ1→6-d-Galpβ1→4-d-Galpβ1→4-d-GlcpNAcβ1→]n. ThewfeDgene in the O-antigen gene cluster ofShigella boydiitype 14 was proposed to encode a galactosyltransferase (GalT) involved in O-antigen synthesis. We confirmed here that thewfeDgene product is a β4-GalT that synthesizes the Galβ1-4GlcNAcα-R linkage. WfeD was expressed inEscherichia coli, and the activity was characterized by using UDP-[3H]Gal as the donor substrate as well as the synthetic acceptor substrate GlcNAcα-pyrophosphate-(CH2)11-O-phenyl. The enzyme product was analyzed by liquid chromatography-mass spectrometry (LC-MS), high-performance liquid chromatography (HPLC), nuclear magnetic resonance (NMR), and galactosidase digestion. The enzyme was shown to be specific for the UDP-Gal donor substrate and required pyrophosphate in the acceptor substrate. Divalent metal ions such as Mn2+, Ni2+, and, surprisingly, also Pb2+enhanced the enzyme activity. Mutational analysis showed that the Glu101 residue within a DxD motif is essential for activity, possibly by forming the catalytic nucleophile. The Lys211 residue was also shown to be required for activity and may be involved in the binding of the negatively charged acceptor substrate. Our study revealed that the β4-GalT WfeD is a novel enzyme that has virtually no sequence similarity to mammalian β4-GalT, although it catalyzes a similar reaction.
Expressive Exclusion: A Defense
Authors: Bedi Sonu 
Published: November 2010

AbstractCentral to the freedom of association is the freedom to exclude. In fact, American constitutional law permits associations to discriminate on otherwise prohibited grounds, a principle of expressive discrimination or what I call "expressive exclusion." However, we lack a complete normative defense of it. Too often, expressive exclusion is justifi ed as a simple case of religious accommodation, or a simple case of freedom of association or speech—justifi cations that are defi cient. I argue that expressive exclusion is essential in creating genuine space for democratic dissent. It stands at the intersection of speech, association, and democracy.
Basophils Amplify Type 2 Immune Responses, but Do Not Serve a Protective Role, during Chronic Infection of Mice with the Filarial Nematode Litomosoides sigmodontis
Authors: Torrero Marina N. , Hübner Marc P. , Larson David , Karasuyama Hajime , Mitre Edward 
Published: November 2010

Abstract
Chronic helminth infections induce a type 2 immune response characterized by eosinophilia, high levels of IgE, and increased T cell production of type 2 cytokines. Because basophils have been shown to be substantial contributors of IL-4 in helminth infections, and because basophils are capable of inducing Th2 differentiation of CD4+ T cells and IgE isotype switching in B cells, we hypothesized that basophils function to amplify type 2 immune responses in chronic helminth infection. To test this, we evaluated basophil function using the Litomosoides sigmodontis filaria model of chronic helminth infection in BALB/c mice. Time-course studies showed that eosinophilia, parasite Ag-specific CD4+ T cell production of IL-4 and IL-5 and basophil activation and IL-4 production in response to parasite Ag all peak late (6–8 wk) in the course of L. sigmodontis infection, after parasite-specific IgE has become detectable. Mixed-gender and single-sex worm implantation experiments demonstrated that the relatively late peak of these responses was not dependent on the appearance of circulating microfilariae, but may be due to initial low levels of parasite Ag load and/or habitation of the developing worms in the pleural space. Depletion of basophils throughout the course of L. sigmodontis infection caused significant decreases in total and parasite-specific IgE, eosinophilia, and parasite Ag-driven CD4+ T cell proliferation and IL-4 production, but did not alter total worm numbers. These results demonstrate that basophils amplify type 2 immune responses, but do not serve a protective role, in chronic infection of mice with the filarial nematode L. sigmodontis.
The Role of the Basic Helix-Loop-Helix Transcription FactorDec1in the Regulatory T Cells
Authors: Miyazaki Kazuko , Miyazaki Masaki , Guo Yun , Yamasaki Norimasa , Kanno Masamoto , Honda Zen-ichiro , Oda Hideaki , Kawamoto Hiroshi , Honda Hiroaki 
Published: November 2010

AbstractNaturally occurring regulatory T (Treg) cells play a central role in the maintenance of immune homeostasis and in restraining the development of spontaneous inflammatory responses. However, the underlying mechanisms of Treg homeostasis remain incompletely understood. Of particular note, the IL-2Rα (CD25) is crucial for the homeostasis of Treg cells and the prevention of lymphoproliferative autoimmune disease. In this paper, we report that the basic helix-loop-helix transcription factor Dec1 is involved in the homeostasis of Treg cells and plays a role in their survival or expansion after adoptive transfer to lymphopenic recipients. Hence, it is crucial for the suppression of effector T cell-mediated inflammatory responses. Enforced expression of Dec1 upregulates CD25 expression during thymocyte development and increases the number of Treg cells in the periphery. Dec1 binds the transcription factor Runx1 and colocalizes with Runx1 in Treg cells. Specifically, we demonstrate that in Treg cells the Dec1/Runx1 complex binds to regulatory elements present in the Il-2rα locus. Collectively, these data show how Dec1 mechanistically acts in Treg cells.
A Cell-Impermeable Cyclosporine A Derivative Reduces Pathology in a Mouse Model of Allergic Lung Inflammation
Authors: Balsley Molly A. , Malesevic Miroslav , Stemmy Erik J. , Gigley Jason , Jurjus Rosalyn A. , Herzog Dallen , Bukrinsky Michael I. , Fischer Gunter , Constant Stephanie L. 
Published: November 2010

Abstract
Although the main regulators of leukocyte trafficking are chemokines, another family of chemotactic agents is cyclophilins. Intracellular cyclophilins function as peptidyl-prolyl cis-trans isomerases and are targets of the immunosuppressive drug cyclosporine A (CsA). Cyclophilins can also be secreted in response to stress factors, with elevated levels of extracellular cyclophilins detected in several inflammatory diseases. Extracellular cyclophilins are known to have potent chemotactic properties, suggesting that they might contribute to inflammatory responses by recruiting leukocytes into tissues. The objective of the present study was to determine the impact of blocking cyclophilin activity using a cell-impermeable derivative of CsA to specifically target extracellular pools of cyclophilins. In this study, we show that treatment with this compound in a mouse model of allergic lung inflammation demonstrates up to 80% reduction in inflammation, directly inhibits the recruitment of Ag-specific CD4+ T cells, and works equally well when delivered at 100-fold lower doses directly to the airways. Our findings suggest that cell-impermeable analogs of CsA can effectively reduce inflammatory responses by targeting leukocyte recruitment mediated by extracellular cyclophilins. Specifically blocking the extracellular functions of cyclophilins may provide an approach for inhibiting the recruitment of one of the principal immune regulators of allergic lung inflammation, Ag-specific CD4+ T cells, into inflamed airways and lungs.
Aim2 Deficiency Stimulates the Expression of IFN-Inducible Ifi202, a Lupus Susceptibility Murine Gene within the Nba2 Autoimmune Susceptibility Locus
Authors: Panchanathan Ravichandran , Duan Xin , Shen Hui , Rathinam Vijay A. K. , Erickson Loren D. , Fitzgerald Katherine A. , Choubey Divaker 
Published: November 2010

Abstract
Murine Aim2 and p202 proteins (encoded by the Aim2 and Ifi202 genes) are members of the IFN-inducible p200 protein family. Both proteins can sense dsDNA in the cytoplasm. However, upon sensing dsDNA, only the Aim2 protein through its pyrin domain can form an inflammasome to activate caspase-1 and induce cell death. Given that the p202 protein has been predicted to inhibit the activation of caspase-1 by the Aim2 protein and that increased levels of the p202 protein in female mice of certain strains are associated with lupus susceptibility, we compared the expression of Aim2 and Ifi202 genes between Aim2-deficient and age-matched wild-type mice. We found that the Aim2 deficiency in immune cells stimulated the expression of Ifi202 gene. The increased levels of the p202 protein in cells were associated with increases in the expression of IFN-β, STAT1, and IFN-inducible genes. Moreover, after knockdown of Aim2 expression in the murine macrophage cell line J774.A1, IFN-β treatment of cells robustly increased STAT1 protein levels (compared with those of control cells), increased the activating phosphorylation of STAT1 on Tyr-701, and stimulated the activity of an IFN-responsive reporter. Notably, the expression of Aim2 in non-lupus-prone (C57BL/6 and B6.Nba2-C) and lupus-prone (B6.Nba2-ABC) splenic cells and in a murine macrophage cell line that overexpressed p202 protein was found to be inversely correlated with Ifi202. Collectively, our observations demonstrate an inverse correlation between Aim2 and p202 expressions. We predict that defects in Aim2 expression within immune cells contribute to increased susceptibility to lupus.
Strong and Extremely Strong Ditkin sets for the Banach AlgebrasApr(G) =Ap⋂Lr(G)
Authors: Granirer Edmond E. 
Published: November 2010

AbstractLetAp(G) be the Figa-Talamanca, Herz Banach Algebra onG; thusA2(G) is the Fourier algebra. Strong Ditkin (SD) and Extremely Strong Ditkin (ESD) sets for the Banach algebrasApr(G) are investigated for abelian and nonabelian locally compact groupsG. It is shown that SD and ESD sets forAp(G) remain SD and ESD sets forApr(G), with strict inclusion for ESD sets. The case for the strict inclusion of SD sets is left open.A result on the weak sequential completeness ofA2(F) for ESD setsFis proved and used to show that Varopoulos, Helson, and Sidon sets are not ESD sets forA2r(G), yet they are such forA2(G) for discrete groupsG, for any 1 ≤r≤ 2.A result is given on the equivalence of the sequential and the net definitions of SD or ESD sets forσ-compact groups.The above results are new even ifGis abelian.
Inventory sharing under decentralized preventive transshipments
Authors: Rong Ying , Snyder Lawrence V. , Sun Yang 
Published: November 2010

AbstractWe consider preventive transshipments between two stores in a decentralized system with two demand subperiods. Replenishment orders are made before the first subperiod, and the stores may make transshipments to one another between the subperiods. We prove that the transshipment decision has a dominant strategy, called a control‐band conserving transfer policy, under which each store chooses a quantity to transship in or out that will keep its second‐subperiod starting inventory level within a range called a control band. We prove that the optimal replenishment policy is a threshold policy in which the threshold depends on the capacity level at the other store. Finally, we prove that there does not exist a transfer price that coordinates the decentralized supply chain. Our research also explains many of the differences between preventive and emergency transshipments, including differences in the optimal transfer policies and the existence or nonexistence of transfer prices that coordinate the system. © 2010 Wiley Periodicals, Inc. Naval Research Logistics, 2010
Adaptive random search for continuous simulation optimization
Authors: Andradóttir Sigrún , Prudius Andrei A. 
Published: November 2010

AbstractWe present, analyze, and compare three random search methods for solving stochastic optimization problems with uncountable feasible regions. Our adaptive search with resampling (ASR) approach is a framework for designing provably convergent algorithms that are adaptive and may consequently involve local search. The deterministic and stochastic shrinking ball (DSB and SSB) approaches are also convergent, but they are based on pure random search with the only difference being the estimator of the optimal solution [the DSB method was originally proposed and analyzed by Baumert and Smith]. The three methods use different techniques to reduce the effects of noise in the estimated objective function values. Our ASR method achieves this goal through resampling of already sampled points, whereas the DSB and SSB approaches address it by averaging observations in balls that shrink with time. We present conditions under which the three methods are convergent, both in probability and almost surely, and provide a limited computational study aimed at comparing the methods. Although further investigation is needed, our numerical results suggest that the ASR approach is promising, especially for difficult problems where the probability of identifying good solutions using pure random search is small. © 2010 Wiley Periodicals, Inc. Naval Research Logistics, 2010
THE POOR INQUIRY AND IRISH SOCIETY – A CONSENSUS THEORY OF TRUTH
Authors: Ciosáin Niall Ó 
Published: November 2010

ABSTRACTThe most detailed contemporary ethnographic representation of early nineteenth-century Ireland can be found in the reports produced by the Poor Inquiry of 1833–6. Despite their richness, however, these reports remained marginal to contemporary policy discussions and public debate. This is normally, and correctly, attributed to the unpopularity and impracticability of the specific recommendations of the Inquiry. This paper argues that the marginalisation of the reports was also due to their discursive originality. It focuses on the voluminous oral evidence which was collected and published by the Inquiry. This evidence was taken in public from large groups representing all social classes, and much of it was printed verbatim. This method was unique among state reports of the nineteenth century in the United Kingdom, and unusual in social discourse more generally. It emerged from an equally unusual conception of truth as social consensus, a theory which the Inquiry adopted in order to overcome what it saw as the socially fragmented nature of representation in Ireland.
IRISH SOCIAL THOUGHT AND THE RELIEF OF POVERTY, 1847–1880
Authors: Gray Peter 
Published: November 2010

ABSTRACTThis paper investigates the way in which the ‘problem of poverty’ in Ireland was encountered, constructed and debated by members of the Irish intellectual and political elite in the decades between the Great Famine and the outbreak of the land war in the late 1870s. This period witnessed acute social upheavals in Ireland, from the catastrophic nadir of the Famine, through the much-vaunted economic recovery of the 1850s–1860s, to the near-famine panic of the late 1870s (itself prefigured by a lesser agricultural crisis in 1859–63). The paper focuses on how a particular elite group – the ‘Dublin School’ of political economists and their circle, and most prominently William Neilson Hancock and John Kells Ingram – sought to define and investigate the changing ‘problem’, shape public attitudes towards the legitimacy of welfare interventions and lobby state officials in the making of poor law policy in this period. It suggests that the crisis of 1859–63 played a disproportionate role in the reevaluation of Irish poor relief and in promoting a campaign for an ‘anglicisation’ of poor law measures and practice in Ireland.