bluuebunny/crossref_metadata_2025_split huggingface dataset:
Riems influenza a typing array (RITA): An RT-qPCR-based low density array for subtyping avian and mammalian influenza a viruses
Authors: Hoffmann Bernd , Hoffmann Donata , Henritzi Dinah , Beer Martin , Harder Timm C. 
Published: June 2016

AbstractRapid and sensitive diagnostic approaches are of the utmost importance for the detection of humans and animals infected by specific influenza virus subtype(s). Cascade-like diagnostics starting with the use of pan-influenza assays and subsequent subtyping devices are normally used. Here, we demonstrated a novel low density array combining 32 TaqMan® real-time RT-PCR systems in parallel for the specific detection of the haemagglutinin (HA) and neuraminidase (NA) subtypes of avian and porcine hosts. The sensitivity of the newly developed system was compared with that of the pan-influenza assay, and the specificity of all RT-qPCRs was examined using a broad panel of 404 different influenza A virus isolates representing 45 different subtypes. Furthermore, we analysed the performance of the RT-qPCR assays with diagnostic samples obtained from wild birds and swine. Due to the open format of the array, adaptations to detect newly emerging influenza A virus strains can easily be integrated. The RITA array represents a competitive, fast and sensitive subtyping tool that requires neither new machinery nor additional training of staff in a lab where RT-qPCR is already established.
All-Optical Fiber Hanbury Brown & Twiss Interferometer to study 1300 nm single photon emission of a metamorphic InAs Quantum Dot
Authors: Muñoz-Matutano G. , Barrera D. , Fernández-Pousa C.R. , Chulia-Jordan R. , Seravalli L. , Trevisi G. , Frigeri P. , Sales S. , Martínez-Pastor J. 
Published: June 2016

AbstractNew optical fiber based spectroscopic tools open the possibility to develop more robust and efficient characterization experiments. Spectral filtering and light reflection have been used to produce compact and versatile fiber based optical cavities and sensors. Moreover, these technologies would be also suitable to study N-photon correlations, where high collection efficiency and frequency tunability is desirable. We demonstrated single photon emission of a single quantum dot emitting at 1300 nm, using a Fiber Bragg Grating for wavelength filtering and InGaAs Avalanche Photodiodes operated in Geiger mode for single photon detection. As we do not observe any significant fine structure splitting for the neutral exciton transition within our spectral resolution (46 μeV), metamorphic QD single photon emission studied with our all-fiber Hanbury Brown & Twiss interferometer could lead to a more efficient analysis of entangled photon sources at telecom wavelength. This all-optical fiber scheme opens the door to new first and second order interferometers to study photon indistinguishability, entangled photon and photon cross correlation in the more interesting telecom wavelengths.
Timing of population peaks of Norway lemming in relation to atmospheric pressure: A hypothesis to explain the spatial synchrony
Authors: Selås Vidar 
Published: June 2016

AbstractHerbivore cycles are often synchronized over larger areas than what could be explained by dispersal. In Norway, the 3–4 year lemming cycle usually show no more than a one-year time lag between different regions, despite distances of up to 1000 km. If important food plants are forced to reallocate defensive proteins in years with high seed production, spatially synchronized herbivore outbreaks may be due to climate-synchronized peaks in flowering. Because lemming peaks are expected to occur one year after a flowering peak and the formation of flower buds is induced in the year before flowering, a two-year time lag between flower-inducing climate events and lemming peaks is predicted. At Hardangervidda, South Norway, the probability that a year was a population peak year of lemming during 1920–2014 increased with increasing midsummer atmospheric pressure two years earlier, even when the number of years since the previous peak was accounted for.
Dietary fruit, vegetable, fat and red and processed meat intakes and Barrett’s esophagus risk: a systematic review and meta-analysis
Authors: Zhao Zhanwei , Pu Zhongshu , Yin Zifang , Yu Pengfei , Hao Yiming , Wang Qian , Guo Min , Zhao Qingchuan 
Published: June 2016

AbstractThe relationships between dietary fruit, vegetable, fat and red and processed meat intakes and Barrett’s esophagus (BE) risk remain inconclusive. We conducted a systematic review and meta-analysis to summarize the available evidence on these issues. PubMed, EMBASE and the Cochrane Library were searched for studies published from inception through October 2015. A total of eight studies were included in this analysis. Fruit intake was not associated with BE risk (OR = 0.65, 95% CI = 0.37–1.13), but vegetable intake was strongly associated with BE risk (OR = 0.45, 95% CI = 0.29–0.71). Saturated fat, red meat and processed meat intakes were not associated with BE risk with OR = 1.25 (95% CI = 0.82–1.91), OR = 0.85 (95% CI = 0.61–1.17) and OR = 1.03 (95% CI = 0.73–1.46), respectively. Dietary vegetable not fruits intake may be associated with decreased BE risk. Fat and red and processed meat intakes may not contribute to an increased BE risk. Well-designed, large prospective studies with better established dose-response relationships are needed to further validate these issues.
Direct microfabrication of oxide patterns by local electrodeposition of precisely positioned electrolyte: the case of Cu2O
Authors: Wang P. , Roberts R. C. , Ngan A. H. W. 
Published: June 2016

AbstractAn efficient technique for writing 2D oxide patterns on conductive substrates is proposed and demonstrated in this paper. The technique concerns a novel concept for selective electrodeposition, in which a minimum quantity of liquid electrolyte, through an extrusion nozzle, is delivered and manipulated into the desired shape on the substrate, meanwhile being electrodeposited into the product by an applied voltage across the nozzle and substrate. Patterns of primarily Cu2O with 80~90% molar fraction are successfully fabricated on stainless steel substrates using this method. A key factor that allows the solid product to be primarily oxide Cu2O instead of metal Cu – the product predicted by the equilibrium Pourbaix diagram given the unusually large absolute deposition voltage used in this method, is the non-equilibrium condition involved in the process due to the short deposition time. Other factors including the motion of the extrusion nozzle relative to the substrate and the surface profile of the substrate that influence the electrodeposition performance are also discussed.
Molecular characterization of human ABHD2 as TAG lipase and ester hydrolase
Authors: M. Naresh Kumar , V.B.S.C. Thunuguntla , G.K. Veeramachaneni , B. Chandra Sekhar , Guntupalli Swapna , J.S. Bondili 
Published: June 2016

Alterations in lipid metabolism have been progressively documented as a characteristic property of cancer cells. Though, human ABHD2 gene was found to be highly expressed in breast and lung cancers, its biochemical functionality is yet uncharacterized. In the present study we report, human ABHD2 as triacylglycerol (TAG) lipase along with ester hydrolysing capacity. Sequence analysis of ABHD2 revealed the presence of conserved motifs G205XS207XG209 and H120XXXXD125. Phylogenetic analysis showed homology to known lipases, Drosophila melanogaster CG3488. To evaluate the biochemical role, recombinant ABHD2 was expressed in Saccharomyces cerevisiae using pYES2/CT vector and His-tag purified protein showed TAG lipase activity. Ester hydrolase activity was confirmed with pNP acetate, butyrate and palmitate substrates respectively. Further, the ABHD2 homology model was built and the modelled protein was analysed based on the RMSD and root mean square fluctuation (RMSF) of the 100 ns simulation trajectory. Docking the acetate, butyrate and palmitate ligands with the model confirmed covalent binding of ligands with the Ser207 of the GXSXG motif. The model was validated with a mutant ABHD2 developed with alanine in place of Ser207 and the docking studies revealed loss of interaction between selected ligands and the mutant protein active site. Based on the above results, human ABHD2 was identified as a novel TAG lipase and ester hydrolase.
Thyroid hormones inhibit TGF-β signaling and attenuate fibrotic responses
Authors: Alonso-Merino Elvira , Martín Orozco Rosa , Ruíz-Llorente Lidia , Martínez-Iglesias Olaia A. , Velasco-Martín Juan Pedro , Montero-Pedrazuela Ana , Fanjul-Rodríguez Luisa , Contreras-Jurado Constanza , Regadera Javier , Aranda Ana 
Published: June 2016

Significance
We show here that binding of the thyroid hormone triiodothyronine to the thyroid hormone receptors (TRs) antagonizes TGF-β/SMAD (mothers against decapentaplegic)-dependent transcription. Transcriptionally inactive TR mutants that do not bind coactivators retained most of the capacity of suppressing transactivation by TGF-β/SMAD, whereas selective mutations in the DNA binding domain abolished this action. TGF-β is a major profibrogenic cytokine, and through this transcriptional mechanism, the hormone-bound TRs act as an endogenous barrier to moderate liver and skin fibrosis. These antagonistic actions on TGF-β/SMAD transcription suggest that TR ligands might be used to block the progression of fibrotic diseases. The natural hormone cannot be used clinically because of severe adverse effects, but novel synthetic ligands with fewer effects might be potentially developed and used.
The relationship between oscillatory EEG activity and the laminar-specific BOLD signal
Authors: Scheeringa René , Koopmans Peter J. , van Mourik Tim , Jensen Ole , Norris David G. 
Published: June 2016

Significance
In this study, we demonstrate that α-, β-, and γ-oscillations can be related to activity in different cortical layers in the human brain. These cortical layers are believed to instantiate feedforward and feedback information streams. Electrophysiological oscillations in α- (8–12 Hz), β- (15–30 Hz), and γ- (40–100 Hz) bands have also been associated with different roles in feedforward and feedback processes and to different cortical layers in nonhuman animals. By simultaneously recording laminar functional MRI (fMRI) and EEG, we could directly link oscillatory signals to activity in cortical layers in humans. This research provides an important neural basis for noninvasive research into the role of cortical layers in information processing using laminar fMRI alone or combined with EEG.
Engineering control of bacterial cellulose production using a genetic toolkit and a new cellulose-producing strain
Authors: Florea Michael , Hagemann Henrik , Santosa Gabriella , Abbott James , Micklem Chris N. , Spencer-Milnes Xenia , de Arroyo Garcia Laura , Paschou Despoina , Lazenbatt Christopher , Kong Deze , Chughtai Haroon , Jensen Kirsten , Freemont Paul S. , Kitney Richard , Reeve Benjamin , Ellis Tom 
Published: June 2016

Significance
Bacterial cellulose is a remarkable material that is malleable, biocompatible, and over 10-times stronger than plant-based cellulose. It is currently used to create materials for tissue engineering, medicine, defense, electronics, acoustics, and fabrics. We describe here a bacterial strain that is readily amenable to genetic engineering and produces high quantities of bacterial cellulose in low-cost media. To reprogram this organism for biotechnology applications, we created a set of genetic tools that enables biosynthesis of patterned cellulose, functionalization of the cellulose surface with proteins, and tunable control over cellulose production. This greatly expands our ability to control and engineer new cellulose-based biomaterials, offering numerous applications for basic research, materials science, and biotechnology.
Dynamic recruitment and activation of ALS-associated TBK1 with its target optineurin are required for efficient mitophagy
Authors: Moore Andrew S. , Holzbaur Erika L. F. 
Published: June 2016

Significance
Mitochondria are key regulators of cellular metabolism and are defective in a number of human disorders. Here, we examine how living cells selectively eliminate damaged mitochondria through the autophagosome-lysosome system. We find that the serine/threonine kinase TANK-binding kinase 1 (TBK1) and its downstream target optineurin (OPTN) are recruited to mitochondria after acute damage, where they coordinate engulfment by autophagosomes. Loss or chemical inhibition of TBK1 stalls mitophagy, resulting in the accumulation of damaged mitochondria. Because mutations in both TBK1 and OPTN are associated with amyotrophic lateral sclerosis and frontotemporal dementia, these results suggest that disordered mitophagy may be associated with selective neurodegeneration.
Sirtuin-dependent reversible lysine acetylation of glutamine synthetases reveals an autofeedback loop in nitrogen metabolism
Authors: You Di , Yin Bin-Cheng , Li Zhi-Hai , Zhou Ying , Yu Wen-Bang , Zuo Peng , Ye Bang-Ce 
Published: June 2016

Significance
Nitrogen availability influences morphogenesis, antibiotic production, and virulence/pathogenicity in actinomycetes. This work provides novel insights into the molecular mechanisms underlying nitrogen metabolism regulation. Glutamine synthetases (GlnA) were acetylated by the acetyltransferase AcuA, which was regulated by the nitrogen regulator GlnR. Acetylation inactivated GlnA4 (GSII). Acetylated GSI-β (GlnA1) exhibited a remarkable ability to directly interact with GlnR and enhance GlnR–DNA binding, thereby modulating target gene transcription in response to nitrogen availability. The results indicated that GSI-β plays a central and essential role in nitrogen metabolism through not only controlling glutamine synthesis but also serving as the nitrogen signal for GlnR activation. These findings substantively extend our understanding of the regulatory mechanisms underlying nitrogen metabolism in actinobacteria, which include antibiotic-producing actinomycetes and pathogenic mycobacteria.
Transposon mutagenesis identifies genes and cellular processes driving epithelial-mesenchymal transition in hepatocellular carcinoma
Authors: Kodama Takahiro , Newberg Justin Y. , Kodama Michiko , Rangel Roberto , Yoshihara Kosuke , Tien Jean C. , Parsons Pamela H. , Wu Hao , Finegold Milton J. , Copeland Neal G. , Jenkins Nancy A. 
Published: June 2016

Significance
Epithelial-mesenchymal transition (EMT) contributes to metastasis and chemoresistance in patients with hepatocellular carcinoma (HCC), but the genes driving EMT are poorly understood. Here, we describe a transposon mutagenesis screen that made it possible to identify 233 candidate cancer genes (CCGs) that are enriched for genes driving EMT in HCC. Twenty-three CCGs are predicted to function early in tumorigenesis, and alterations in these genes are associated with poor HCC patient survival. Validation studies showed that deregulation of the most highly mutated CCGs activates an EMT program that enhances HCC cell migration and also confers sorafenib resistance. Thus, transposon mutagenesis appears to provide an excellent resource for identifying genes regulating EMT in human HCC and for potentially identifying new drug targets for HCC.
Berkeley and the Perception of Ideas
Authors: Odegard Douglas 
Published: June 2016

It is important to try to understand Berkeley's exact position on what it is for someone to perceive an idea. He is frequently presented as holding that to perceive an idea is to be confronted by an object which is in some sense mind-dependent and private, and, if taken in a certain way, such a remark is not inaccurate. But the interpretation which renders it accurate needs to be specified and this is a task which awaits completion. Until it is completed, questions like ‘Can Berkeley account for everything we, as plain men, legitimately want to say?’, ‘Are his arguments against the possibility of mind-independent material substances sound?’, and ‘Is he right to hold that the ideas involved in different sense modalities are always different?’, cannot be finally resolved.George Pitcher, in “Minds and Ideas in Berkeley”, makes a good start on the problem, but he does not consider a sufficient number of alternative analyses of ‘So and so perceives such and such an idea’. As a result he fails to pinpoint the exact analysis which Berkeley himself would favour.
The Firm But Untidy Correlativity of Rights and Obligations
Authors: Braybrooke David 
Published: June 2016

The correlativity of rights and obligations is one of the few stock topics in the basic repertory of English-speaking philosophy th-t is considered suitable for assignment to philosophers specializing in political philosophy (even so it is a topic that must be shared with ethics). It is a topic perennially discussed, chiefly (I think) for reasons that have little to do with its importance: namely, just because it is a recognized topic and because it appears to be a safely tidy one that lends itself readily to being tidied up further by formal or quasi-formal considerations. For my part, I wish more effort went into discussing less tractable subjects like the individuation of rights and their delimitation vis-à-vis one another.What I have to contribute to the subject of correlativity, returning to the scene of my comments on David Lyons’ paper, “The Correlativity of Rights and Duties,” is mainly a stint of annual or biennial repair-work, designed to restore the obvious — the truth that rights do imply obligations and cannot be understood without accepting this implication.
Primary and Secondary Qualities
Authors: Campbell Keith 
Published: June 2016

The philosophy of primary and secondary qualities is in a state of some confusion. There is no agreement as to the basis upon which the two classes of quality may be distinguished—a host of features, as diverse as perceptible by more than one sense and belonging to the definition of matter, are offered as the mark of the primary. There is not even agreement on which qualities belong to which group. Shape, size and solidity are generally held to be primary, while colours, smells, and the like (I) are favoured secondary candidates. But for large numbers of qualities, for example being acidic, malleable, rust-proof—or, among perceptible qualities, glistening and vibrating—we are offered no effective guidance.Inevitably, in such a situation, we are without clear answers to the questions; Why should any distinction be made between primaries and secondaries? Must all qualities be the one or the other? To the solution of which problems does the distinction serve as a preliminary step? What special relationship is there between primary qualities and scientific theory, or between secondary qualities and peculiarities in perception?
Sensation and Synecdoche
Authors: Matthews Gareth B. 
Published: June 2016

Sometimes in THE CONCEPT OF MIND Gilbert Ryle describes what he is up to in a way which is quite unhelpful. The following passage will serve as an example of what I mean:To talk of a person’s mind is not to talk of a repository which is permitted to house objects that something called ‘the physical world’ is forbidden to house; it is to talk of the person’s abilities, liabilities and inclinations to do and undergo certain sorts of things, and of the doing and undergoing of these things in the ordinary world, (p. 199)I call this passage unhelpful because it commits the fallacy of false alternatives. It would have us think that talk of a person's mind is either (1) talk of a special non-physical repository or else (2) talk of a person's abilities, liabilities, inclinations, etc.—but not both. Yet surely talk of the mind as a non-physical repository might be one way of talking about a person's abilities, liabilities, inclinations, etc.Perhaps what Ryle should have said is that to speak of the mind as a non-physical repository that houses special, mental objects is a figurative way of putting what could be reported literally in talk of a person’s abilities, liabilities, inclinations, etc. Certainly that is a point Ryle tries to make in his book. Indeed it is a major burden of THE CONCEPT OF MIND to identify and analyze those figures of speech, or tropes, in which mental activities and capacities are commonly reported and described. The idea seems to be that we are misled philosophically by our failure to recognize the tropological character of what we commonly say about the mind and by our naivete as to how the tropes work.
Remembering the Past of Another
Authors: Puccetti Roland 
Published: June 2016

There has been a tendency in recent literature on personal identity to treat puzzle cases as unfair intrusions upon the discussion, like proposing to play chess without the Queen. Thus Terence Penelhum speaks of ‘imaginary worlds’ where our normal criteria do not hold and Sydney Shoemaker refers approvingly to G. C. Nerlich's dictum that it is a universal truth of our world, and not of ‘all possible worlds', that only by being identical with a witness to past events can one have the knowledge of them we have in memory.I would agree that where puzzle cases involve changing basic features of our physical universe, e.g. in having people's bodies go out of existence in one place and reappear in another, as recently envisaged by J. M. Shorter, there is some point in talking of ‘imaginary’ or ‘possible’ worlds. But where puzzle cases propose no such basic changes but ground the discussion in physiological possibilities, however unfeasible technologically, this seems an arbitrarily harsh description. It would be like Nineteenth Century philosophers saying talk of flying machines and heart transplants belongs, not to another age merely, but to other worlds.
God and Rationality
Authors: Solomon Robert C. 
Published: June 2016

Is belief in God rational? Over a century ago, Hegel (following Kant) and Søren Kierkegaard established one set of parameters for discussing that question, but in a language that appears opaque to many philosophers today. Very recently, Alvin Plantinga, James Ross, and George Mavrodes have been debating similar issues in a modern analytic idiom. In this essay, I want to use this modern philosophical language in an attempt to clarify certain issues surrounding the relevant notion of “rationality” and related notions essential to the natural theologian, and in so doing attempt to make presentable the dispute between Hegel and Kierkegaard.For our purposes here, I take “rationality” to be predicated of an epistemological concept of belief, even if, as I believe, any such notion would have to be a special case and a logical derivative of a more general notion of “rationality” as primarily practical.
La méthode cartésienne et l'interprétation de P.A. Schouls
Authors: Duchesneau François 
Published: June 2016

Monsieur Schouls a établi un certain nombre de points, avec lesquels je me declarerai d'accord. Je crois qu'il a raison d'affirmrr que pour Locke, le fondement de toute connaissance au niveau initial de l'expérience est un divers de la sensation ou de la réflexion formé par des combinations d'idées unies ensemble. D'autre part, la description de la maniere dont l'esprit acquiert la connaissance générale (general knowledge) par un processus d'abstraction et done d'analyse me semble conforme à l'épistémologie de Locke.Mais je crois que par ce processus, l'esprit atteint seulement le niveau de la connaissance générale; la connaissance générale elle-même consiste dans la démonstration (reasoning) et, meme si la démonstration se raméné à une chaîne d'intuitions, conformément au modèle cartésien des Regulae, c'est seulement dans l'illatio que l'on peut situer ce que M. Schouls qualifie de synthèse: c'est cette illatio qui constitue proprement la science.D'où le problème de cette éthique démontrable dont il faudrait établir, conformément à cette thèse, le mode de formation “synthétique” à partir d'axiomes et de principes.