bluuebunny/crossref_metadata_2025_split huggingface dataset:
Standards and infrastructure for managing experimental metadata
Authors: Sansone Susanna-Assunta , Rocca-Serra Philippe 
Published: April 2009

Abstract*See also "related poster":http://precedings.nature.com/documents/3144/version/1*Today’s researchers can perform biological and biomedical studies where the same material is run through a wide range of assays, comprising several technologies such as genomics, transcriptomics, proteomics and metabol/nomics (hereafter referred as ‘omics’). To enable others to correctly interpret the complex data sets that result, and the conclusions drawn, it is necessary to provide contextualizing experimental metadata at an appropriate level of granularity.Standards initiatives normally cater to particular domains. However, several synergistic standards activities foster cross-domain harmonization of the three kinds of reporting standard (minimum information checklists, ontologies and file formats). Some 29 groups participate in the "MIBBI":http://www.mibbi.org project, which offers a one-stop shop for those exploring the range of extant ‘minimum information’ checklists, and which fosters integrative development^1^. More than 60 groups participate in the "OBO Foundry":http://www.obofoundry.org ^2^, which coordinates the orthogonal development of ontologies such as "OBI":http://obi-ontology.org for describing experimental (meta)data. And several groups participate in the development of "ISA-Tab":http://isatab.sf.net, a tabular framework for presenting experimental metadata^3^ (analogous to "FuGE":http://fuge.sf.net, a generic data model to underpin various XML file formats^4^).We have developed an infrastructure that leverages the aforementioned synergistic reporting standards to create a common structured representation and storage mechanism for experimental metadata from biological and biomedical investigations ranging from simple single-assay studies to complex, methodologically diverse multi-assay studies.View the "public instance":http://www.ebi.ac.uk/bioinvindex of our ISA-based infrastructure, running at EBI, and/or "download the components":http://isatab.sf.net for your local use.*References*1. Taylor CF, Field D, Sansone SA,… Rocca-Serra P et al. (2008) The MIBBI Project. Nature Biotechnology Aug;26(8):889-896. "http://www.mibbi.org":http://www.mibbi.org2. Smith B, Ashburner M, Rosse C,… Rocca-Serra P, …Sansone SA et al. (2007) The OBO Foundry. Nature Biotechnology Nov;25(11):1251-5. "http://www.obofoundry.org":http://www.obofoundry.org3. Sansone SA, Rocca-Serra P, Brandizi M,… Taylor CF et al. (2008) The First MGED RSBI (ISA-TAB) Workshop. OMICS. Jun;12(2):143-9. "http://isatab.sf.net":http://isatab.sf.net4. Jones AR, Miller M, Aebersold R,… Sansone SA et al. (2007) The Functional Genomics Experiment model (FuGE). Nature Biotechnology Oct;25(10):1127-1133. "http://fuge.sf.net":http://fuge.sf.net
An Ontology To Represent Knowledge On Animal Testing Alternatives
Authors: Wächter Thomas , Sauer Ursula , Doms Andreas , Grune Barbara , Alvers Michael , Spielmann Horst , Schroeder Michael 
Published: April 2009

AbstractEU Directive 86/609/EEC for the protection of laboratory animals obliges scientists to consider whether a planned animal experiment can be replaced, reduced or refined (3Rs principle). To meet this regulatory obligation, scientists must consult the relevant scientific literature prior to any experimental study using laboratory animals. More than 50 million potentially 3Rs relevant documents are spread over the World Wide Web, biomedical literature and patent databases. In April 2008, the beta version of Go3R ("www.Go3R.org":http://www.Go3R.org), the first knowledge-based semantic search engine for alternative methods to animal experiments, was released. Go3R is free of charge and enables scientists and regulatory authorities involved in the planning, authorisation and performance of animal experiments to determine the availability of alternative methods in a fast and comprehensive manner. The technical basis of this search engine is specific 3Rs expert knowledge captured within the Go3R Ontology containing 87,218 labels and synonyms. A total of 16,620 concepts were structured in 28 branches, where 1,227 concepts were newly defined to specifically describe directly 3Rs relevant knowledge. Additionally relevant headings from MeSH where referenced to reflect the topics associated with the definition of Animal Testing Alternatives. Therefore it is distinguished between thematic-defining and directly 3Rs relevant branches. In addition to the assignment of direct parent-child relationships, further relationship types were introduced to allow to model 3Rs relevant domain knowledge. Examples for such knowledge are e.g. (1) the characteristics of cell culture tests methods, which usually utilize “specific cell types” or “cell lines” and are associated with a specific “endpoint” and “endpoint detection method” or (2) named test methods like “PREDISAFE™”, which replaces an animal test namely the “eye irritation test” in rabbits and uses specific cells namely “SIRC Cells” or (3) the “Haemagglutinin-Neuraminidase Protein Assay”, which detects a protein of the “Newcastle disease virus”. Thereby, an article in which e.g. a specific 3Rs method is not explicitly mentioned could still be recognized as relevant for the specific topic searched for in an indirect manner, for example if it mentions specific cells, endpoints or endpoint detection methods, which are relevant for the respective application. The search engine Go3R with its novel ontology is already well recognized by the 3Rs community and will be further maintained and developed.
The cost of linguistic loyalty
Authors: Jenkins Devin L. 
Published: April 2009

In a census-related study on language maintenance among the Hispanic/Latino population in the southwest United States, Hudson, Hernández-Chávez and Bills (1995) stated that, given negative correlations between language maintenance and years of education and per capita income, “educational and economic success in the Spanish origin population are purchased at the expense of Spanish language maintenance in the home” (1995: 179). While census figures from 1980 make this statement undeniable for the Southwest, the recent growth of the Spanish-language population in the United States, which has grown by a factor of ~2.5 over the last twenty years, begs a reexamination of these correlations. A recent study on the state of Colorado (McCullough & Jenkins 2005) found a correlational weakening, especially with regard to the relationship between language maintenance and median income. 	The current study follows the model set forth by Hudson et al. (1995) in examining the interrelationship between the measures of count, density, language loyalty and retention based on 2000 census data, as well as the relationship between these metrics and socioeconomic and demographic variables, including income and education. While some relationships existed in 2000 much in the same way that they did in the 1980 data, especially with regard to count and density, the measures of loyalty and retention saw marked reductions in their correlations with social variables.
“A pattern, precedent, and lively warrant”: Emulation, Rhetoric, and Cruel Propriety inTitus Andronicus
Authors: Dickson Vernon Guy 
Published: April 2009

AbstractShakespeare'sTitus Andronicuscritically engages and enacts teachings and patterns of emulation, including those of Quintilian, Roger Ascham, and other contemporary humanists and playwrights, pressing emulation's uses to extremes that suggest that imitative self-fashioning potentially results in monstrous or fragmented characters, decisions, and texts. The professed aim of the grammar-school education, the ability to judge well, is conflicted byTitus's exposure of judgment as itself a contested concept, locked within a circularity of intertextual precedents. Titus's excessive, even parodic, repetition of emulative strategies acts as a rebuttal of seemingly straightforward humanist models of character, judgment, self, and decorum.
“Perplex't Paths”: Youth and Authority in Milton'sMask*
Authors: Greteman Blaine 
Published: April 2009

AbstractThis essay argues that John Milton'sA Mask Presented at Ludlow Castle(1634) is influenced by early modern concepts of childhood in a way that critics have not recognized. Childhood was a problematic concept in contemporary religious, pedagogical, and legal discourses. Children were depicted as models of submission, but prone to impetuous indiscretion, and their path to adult agency was strewn with pitfalls, especially in the liminal period of youth.A Maskengages with and transforms these discourses. It rejects the political quietism routinely associated with childhood and shows that the child's unique sensitivity may offer a route to a particularly powerful kind of voice.
Remote ischaemic pre‐conditioning does not attenuate ischaemic left ventricular dysfunction in humans
Authors: Hoole Stephen P. , Khan Sadia N. , White Paul A. , Heck Patrick M. , Kharbanda Rajesh K. , Densem Cameron G. , Clarke Sarah C. , Shapiro Leonard M. , Schofield Peter M. , O'Sullivan Michael , Dutka David P. 
Published: April 2009

AimsRemote ischaemic pre‐conditioning (RIPC) reduces distant tissue ischaemia reperfusion injury. We tested the hypothesis that RIPC would protect the left ventricle (LV) from ischaemic dysfunction and stunning.Methods and resultsForty‐two patients with single vessel coronary disease and normal LV function were prospectively recruited. Twenty patients had repeated conductance catheter assessment of LV function during serial coronary occlusions with/without RIPC and a further 22 patients underwent serial dobutamine stress echocardiography and tissue Doppler analysis with/without RIPC. Remote ischaemic pre‐conditioning was induced by three 5 min inflations of a blood pressure cuff around the upper arm. RIPC did not diminish the degree of ischaemic LV dysfunction during coronary balloon occlusion (Tau, ms: 59.2 (2.8) vs. 62.8 (2.8), P = 0.15) and there was evidence of cumulative LV dysfunction despite RIPC [ejection fraction (EF), %: 54.3 (5.8) vs. 44.9 (3.7), P = 0.03]. Remote ischaemic pre‐conditioning did not improve contractile recovery during reperfusion (EF, %: 51.7 (3.6) vs. 51.5 (5.7), P = 0.88 and Tau, ms: 55.6 (2.8) vs. 56.0 (2.0), P = 0.85). A neutral effect of RIPC on LV function was confirmed by tissue Doppler analysis of ischaemic segments at peak dobutamine (Vs, cm s−1 control: 8.2 (0.4) vs. RIPC 8.1 (0.4), P = 0.43) and in recovery.ConclusionRIPC does not attenuate ischaemic LV dysfunction in humans.
Pathogenesis of chronic urticaria
Authors: Kaplan A. P. , Greaves M. 
Published: April 2009

SummaryChronic urticaria is defined as the presence of urticaria (hives) for at least 6 weeks with the assumption that it occurs daily or close to it. If we eliminate physical urticarias and urticarial vasculitis from consideration, the remainder can be divided into autoimmune chronic urticaria (45%) and idiopathic chronic urticaria (55%). The autoimmune subgroup is associated with the IgG anti‐IgE receptor α subunit in 35–40% of patients and IgG anti‐IgE in an additional 5–10%. These autoantibodies have been shown to activate blood basophils and cutaneous mast cellsin vitrowith augmentation of basophil activation by complement and release of C5a, in particular. Binding methods (immunoblot and ELISA) yield positives in many autoimmune diseases as well as occasional normal subjects or patients with other forms of urticaria but most such sera are non‐functional. Activation of basophils or mast cells causing histamine release is quite specific for chronic urticaria and defines the autoimmune subgroup. Although pathogenicity is not formally proven, the antibodies cause wealing upon intradermal injection, and removal of the autoantibody leads to remission. A cellular infiltrate is seen to be characterized by mast cell degranulation and infiltration of CD4+T lymphocytes, monocytes, neutrophils, eosinophils, and basophils. The intensity of the infiltrate and clinical severity of the disease (including accompanying angio‐oedema) is more severe in the autoimmune subpopulation. This latter group also has a higher evidence of human leucocyte antigen DR alleles associated with autoimmunity and a 25% incidence of antithyroid antibodies with diagnosed hypothyroidism in some. Hypo‐responsiveness of patients' basophils to anti‐IgE and hyperresponsiveness to serum defines another subpopulation (at least 50%) that overlaps the idiopathic and autoimmune subgroups. Hypo‐responsiveness to anti‐IgE has been shown to be associated with elevated levels of cytoplasmic phosphatases that inhibit degranulation. Reversal of the abnormality is seen with disease remission. Further work will be needed to distinguish whether this is a cause or a consequence of persistent urticaria and to further assess the relationship (or lack thereof) of altered responsiveness (decreased or increased) with the presence or absence of activating autoantibodies.
Programmed death (PD)-1 molecule and its ligand PD-L1 distribution among memory CD4 and CD8 T cell subsets in human immunodeficiency virus-1-infected individuals
Authors: Rosignoli G , Lim C H , Bower M , Gotch F , Imami N 
Published: April 2009

SummaryHuman immunodeficiency virus (HIV)-1 causes T cell anergy and affects T cell maturation. Various mechanisms are responsible for impaired anti-HIV-1-specific responses: programmed death (PD)-1 molecule and its ligand PD-L1 are negative regulators of T cell activity and their expression is increased during HIV-1 infection. This study examines correlations between T cell maturation, expression of PD-1 and PD-L1, and the effects of their blockade. Peripheral blood mononuclear cells (PBMC) from 24 HIV-1+ and 17 uninfected individuals were phenotyped for PD-1 and PD-L1 expression on CD4+ and CD8+ T cell subsets. The effect of PD-1 and PD-L1 blockade on proliferation and interferon (IFN)-γ production was tested on eight HIV-1+ patients. Naive (CCR7+CD45RA+) CD8+ T cells were reduced in HIV-1 aviraemic (P = 0·0065) and viraemic patients (P = 0·0130); CD8 T effector memory subsets [CCR7-CD45RA–(TEM)] were increased in HIV-1+ aviraemic (P = 0·0122) and viraemic (P = 0·0023) individuals versus controls. PD-1 expression was increased in CD4 naive (P = 0·0496), central memory [CCR7+CD45RA– (TCM); P = 0·0116], TEM (P = 0·0037) and CD8 naive T cells (P = 0·0133) of aviraemic HIV-1+versus controls. PD-L1 was increased in CD4 TEMRA (CCR7-CD45RA+, P = 0·0119), CD8 TEM (P = 0·0494) and CD8 TEMRA (P = 0·0282) of aviraemic HIV-1+versus controls. PD-1 blockade increased HIV-1-specific proliferative responses in one of eight patients, whereas PD-L1 blockade restored responses in four of eight patients, but did not increase IFN-γ-production. Alteration of T cell subsets, accompanied by increased PD-1 and PD-L1 expression in HIV-1 infection contributes to anergy and impaired anti-HIV-1-specific responses which are not rescued when PD-1 is blocked, in contrast to when PD-L1 is blocked, due possibly to an ability to bind to receptors other than PD-1.
Attenuation of massive cytokine response to the staphylococcal enterotoxin B superantigen by the innate immunomodulatory protein lactoferrin
Authors: Hayworth J L , Kasper K J , Leon-Ponte M , Herfst C A , Yue D , Brintnell W C , Mazzuca D M , Heinrichs D E , Cairns E , Madrenas J , Hoskin D W , McCormick J K , Haeryfar S M M 
Published: April 2009

SummaryStaphylococcal enterotoxin B (SEB) is a pyrogenic exotoxin and a potent superantigen which causes massive T cell activation and cytokine secretion, leading to profound immunosuppression and morbidity. The inhibition of SEB-induced responses is thus considered a goal in the management of certain types of staphylococcal infections. Lactoferrin (LF) is a multi-functional glycoprotein with both bacteriostatic and bactericidal activities. In addition, LF is known to have potent immunomodulatory properties. Given the anti-microbial and anti-inflammatory properties of this protein, we hypothesized that LF can modulate T cell responses to SEB. Here, we report that bovine LF (bLF) was indeed able to attenuate SEB-induced proliferation, interleukin-2 production and CD25 expression by human leucocyte antigen (HLA)-DR4 transgenic mouse T cells. This inhibition was not due to bLF’s iron-binding capacity, and could be mimicked by the bLF-derived peptide lactoferricin. Cytokine secretion by an engineered SEB-responsive human Jurkat T cell line and by peripheral blood mononuclear cells from healthy donors was also inhibited by bLF. These findings reveal a previously unrecognized property of LF in modulation of SEB-triggered immune activation and suggest a therapeutic potential for this naturally occurring protein during toxic shock syndrome.
Modeling larval Calanus finmarchicus on Georges Bank: time‐varying mortality rates and a cannibalism hypothesis
Authors: NEUHEIMER A. B. , GENTLEMAN W. C. , GALLOWAY C. L. , JOHNSON C. L. 
Published: April 2009

AbstractThroughout the North Atlantic, the copepod Calanus finmarchicus dominates the zooplankton biomass, linking primary production and higher trophic levels. On Georges Bank, the peak abundance of larval (naupliar) stages occurs in March–April and represents a potential source of prey for cod and haddock larvae. Following this maximum, naupliar abundance declines dramatically, reaching a minimum in May and increasing again in June. Explaining the naupliar seasonal cycle is critical for predicting climate effects on C. finmarchicus dynamics, including whether environmental variability may lead to a mismatch with larval fish. Here, an age‐within‐stage population dynamics model is used to investigate the factors controlling the temporal variation of C. finmarchicus nauplii in three Georges Bank sub‐regions. The model incorporates temperature‐ and food‐dependent development and egg production, as well as female abundance derived from the US Global Ocean Ecosystem Dynamics (GLOBEC) program. Use of field‐estimated constant mortality rates overestimates May abundances by as much as an order of magnitude. These data/model discrepancies can not be explained by temperature or food‐limitation effects on physiological rates. Instead, accurate simulation requires use of time‐varying early stage mortalities, which differ from published estimates in both magnitude and trend. These mortality rates are correlated with C. finmarchicus female abundance, implying cannibalism as a possible regulatory factor. Thus, the biological control of predation (including cannibalism) must be considered to predict the effects of climate on C. finmarchicus and associated larval fish populations.
Nurse and parent partnership during children’s vaccinations: a conversation analysis
Authors: Plumridge Elizabeth , Goodyear‐Smith Felicity , Ross Jim 
Published: April 2009

AbstractTitle.  Nurse and parent partnership during children’s vaccinations: a conversation analysis. Aim.  This paper is a report of a study conducted to examine the elements of partnership and communication between nurses and parents during actual events of immunization.Background.  Childhood immunizations require collaboration with parents, who may be anxious about immunization safety or subjecting their children to painful procedures.Methods.  Ten interactions during immunization events from six purposively selected general practices were videoed in 2005, giving 168 minutes of talk. Conversation analysis was conducted on talk during the short phase of injection administration.Findings.  During the immunization event nurse and mother talked to the baby/toddler rather than each other. Concurrent talk acted as a chorus, marked by sing‐sing prosody, shared laughter and talk or reassuring noises. In coordinated talk nurse and parent took turns. Although overlap might occur, the actions accomplished by each speaker were different. Nurses most commonly cued bravery or stoicism to the child and stressed the progress made in administering the injections. In the less common pattern when pain was recognized as inevitable and there was no stress on stoicism and progress towards completion, the child displayed more distress and began crying before the injection.Conclusion.  Communication skills and rapport are core to nursing work. What happens at the micro‐level of turn‐taking, where prosody and the actions achieved in talk, is of key importance. Our study suggests ‘small talk’ is of major importance – a practical professional skill in which nurses not only align with parents but simultaneously cue both mother and child about how the immunization should be conducted.
Extending immunofluorescence detection limits in whole paraffin‐embedded formalin fixed tissues using hyperspectral confocal fluorescence imaging
Authors: CONSTANTINOU P. , DACOSTA R.S. , WILSON B.C. 
Published: April 2009

SummaryA major problem in microscopic imaging of ex vivo tissue sections stained with fluorescent agents (e.g. antibodies, peptides) is the confounding presence of background tissue autofluorescence. Autofluorescence limits (1) the accuracy of differentiating background signals from single and multiple fluorescence labels and (2) reliable quantification of fluorescent signals. Advanced techniques such as hyperspectral imaging and spectral unmixing can be applied to essentially remove this autofluorescent signal contribution, and this work attempts to quantify the effectiveness of autofluorescence spectral unmixing in a tumour xenograft model. Whole‐specimen single‐channel fluorescence images were acquired using excitation wavelengths of 488 nm (producing high autofluorescence) and 568 nm (producing negligible autofluorescence). These single‐channel data sets are quantified against hyperspectral images acquired at 488 nm using a prototype whole‐slide hyperspectral fluorescence scanner developed in our facility. The development and further refinement of this instrument will improve the quantification of weak fluorescent signals in fluorescence microscopy studies of ex vivo tissues in both preclinical and clinical applications.
An improved dynamic model of tuning fork probe for scanning probe microscopy
Authors: NG B.P. , ZHANG Y. , KOK S.W. , SOH Y.C. 
Published: April 2009

SummaryThis paper presents a two coupled oscillators model to describe the dynamics of a tuning fork with a probe attached. The two coupled oscillators are unbalanced only in their effective masses and the damping ratios. By applying a frequency domain system identification approach in experimental investigation of various probe attachment cases, a good accuracy of the model is demonstrated. The effectiveness of the model is further demonstrated in quantitative analysis of the noise performance and the sensitivity of force sensing with a tuning fork probe. Compared with existing models, the proposed model can more accurately characterize the dynamics of a tuning fork probe.