bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Negation Problem
Authors: Schroeder Mark 
Published: September 2008

AbstractThis chapter explores the difficult features of the negation problem for expressivism. The problem is outlined together with the set of tools available to expressivists in order to solve it. A-type and B-type inconsistency in mental states are introduced, and it is argued that only an appeal to A-type inconsistency and to inconsistency-transmitting attitudes could solve this problem by appeal to the kind of assumptions which expressivists will be able to discharge. It is proven, given an assumption implicit in all existing expressivist approaches that a formally adequate expressivist account must appeal to B-type inconsistency. The approaches of Terry Horgan and Mark Timmons, of Allan Gibbard, and Jamie Dreier, are criticized to illustrate why appeals to B-type inconsistency are unsatisfactory.
Predicates and Quantifiers
Authors: Schroeder Mark 
Published: September 2008

AbstractThis chapter shows how to expand the ideas of Chapter 5 for a language involving quantifiers, and offers a more rigorous treatment. Since the contents of states of being for are treated as properties, predicates are treated as semantically contributing functions from objects to properties. Lambda-abstractions are introduced to denote properties, and open lambda-abstractions to denote functions from objects to properties. After improved versions of the main developments in Chapter 5, it is observed that both the treatment of inconsistency and the constructive feature of the semantics turn essentially on the assumption that all sentences in this simple language express the same kind of mental state. From this, it is argued that the only way to incorporate descriptive language is if belief is itself analyzed in terms of being for.
The Limits and Costs of Expressivism
Authors: Schroeder Mark 
Published: September 2008

AbstractThis chapter summarizes the basic insights and arguments needed in order to get this far. It is argued, however, that expressivists will have extraordinary difficulties trying to expand the expressive power of their language beyond that of the predicate calculus. It is shown that most obvious treatments of the past tense and of ‘necessarily’ — constructed on exactly the same model as the accounts of negation, conjunction, and the quantifiers — result in tensed and modal sentences expressing incoherent states of mind, and fail to assign them the right truth conditions on either the approach of Chapter 9 or that of Chapter 10. It is argued, further, that binary quantifiers like ‘most’ cannot be incorporated into biforcated attitude semantics at all. The moral is that the prospects for expressivism are dim. An appendix to the chapter makes suggestions for further research.
The Standard Conception of Composition
Authors: Koslicki Kathrin 
Published: September 2008

AbstractThis chapter is devoted to an exposition of the main concepts and principles of standard mereology, the system originally developed by Stanislaw Leśniewski and introduced into the English-speaking world in the guise of Henry Leonard and Nelson Goodman's ‘Calculus of Individuals’. The main source for this chapter is Peter Simons', Parts: A Study in Ontology, in particular his instructive gradual development of standard mereology, which shows how stronger and stronger principles may be added gradually to a minimal core, until we arrive at the full-strength theory of standard mereology. Despite standard mereology's merits as a formal theory, however, it remains to be seen whether it is of any use to the metaphysician in characterizing ordinary mereological concepts, as they apply to our scientifically informed, common-sense ontology.
Composition as Non‐Identity
Authors: Koslicki Kathrin 
Published: September 2008

AbstractThe positive view adopted later in this book defends a conception of parthood and composition which carries genuine ontological commitment: contrary to the Lewisian Composition-as-Identity model, wholes according to this alternative conception are in no way to be identified with their parts; rather, a commitment to wholes is a commitment to entities that are numerically distinct from their parts. A crucial piece of apparatus which supports this ontologically loaded conception of parthood and composition is a certain style of argument which reasons from Leibniz's Law to the numerical distinctness of wholes and their parts: according to this style of argument, wholes and their parts are numerically distinct by Leibniz's Law, because they do not share all of their properties. This present chapter defends this style of argument for the numerical distinctness of wholes and their parts.
Aristotle's Refinements of Plato's Theory
Authors: Koslicki Kathrin 
Published: September 2008

AbstractThis chapter examines Aristotle's refinements of Plato's theory of composition. Aristotle is generally sympathetic to the Platonic outlook, but differs over the details. In some cases, Aristotle's more nuanced approach avoids certain of the downfalls of Plato's theory. In other cases, however, the added complexities introduced by Aristotle actually lead to further difficulties of their own. Given that the positive account of composition that is presented in Chapter 7 is broadly Aristotelian in spirit, the overarching goal of this chapter is to find inspiration in Aristotle's insights into matters of mereology, and to separate those features in his treatment of parts and wholes that are timeless and can be taken over by the modern-day mereologist from those that are best left behind.
Structure
Authors: Koslicki Kathrin 
Published: September 2008

AbstractThis chapter isolates and illustrates the general features of the notion of structure by examining the use to which this notion is put in several domains that are especially focused on the study of structure. The particular case-studies examined are taken from the disciplines of mathematics, logic, chemistry, music, and linguistics. Each of these areas conceives of a structure as a sort of entity which (i) makes available positions or places for other object to occupy; and which (ii) places two distinctive sorts of constraints on these positions, type-constraints and configuration-constraints. The two features in (i) and (ii) that have shown themselves to be characteristic of the general notion of structure lead to a distinction between what is taken as variable and what is taken as invariable within a given context.
Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature
Authors: Jadeau Fanny , Bechet Emmanuelle , Cozzone Alain J. , Deléage Gilbert , Grangeasse Christophe , Combet Christophe 
Published: September 2008

Abstract
Motivation: Most of the protein tyrosine kinases found in bacteria have been recently classified in a new family, termed BY-kinase. Indeed, they share no sequence homology with their eukaryotic counterparts and have no known eukaryotic homologues. They are involved in several biological functions (e.g. capsule biosynthesis, antibiotic resistance, virulence mechanism). Thus, they can be considered interesting therapeutic targets to develop new drugs to treat infectious diseases. However, their identification is rendered difficult due to slow progress in their structural characterization and comes most often from biochemical experiments. Moreover BY-kinase sequences are related to many other bacterial proteins involved in several biological functions (e.g. ParA family proteins). Accordingly, their annotations in generalist databases, sequence analysis and classification remain partial and inhomogeneous and there is no bioinformatics resource dedicated to these proteins.
Results: The combination of similarity search with sequence-profile alignment, pattern matching and sliding window computation to detect the tyrosine cluster was used to identify BY-kinase sequences in UniProt Knowledgebase. Cross-validations with keywords searches, pattern matching with several patterns and checking of motifs conservation in multiple sequence alignments were performed. Our pipeline identified 640 sequences as BY-kinases and allowed the definition of a PROSITE pattern that is the signature of the BY-kinases. The sequences identified by our pipeline as BY-kinases share a good sequence similarity with BY-kinases that have already been biochemically characterized, and they all bear the characteristic motifs of the catalytic domain, including the three Walker-like motifs followed by a tyrosine cluster.
Availability: http://bykdb.ibcp.fr
Contact: c.combet@ibcp.fr
FACTA: a text search engine for finding associated biomedical concepts
Authors: Tsuruoka Yoshimasa , Tsujii Jun'ichi , Ananiadou Sophia 
Published: September 2008

Abstract
Summary: FACTA is a text search engine for MEDLINE abstracts, which is designed particularly to help users browse biomedical concepts (e.g. genes/proteins, diseases, enzymes and chemical compounds) appearing in the documents retrieved by the query. The concepts are presented to the user in a tabular format and ranked based on the co-occurrence statistics. Unlike existing systems that provide similar functionality, FACTA pre-indexes not only the words but also the concepts mentioned in the documents, which enables the user to issue a flexible query (e.g. free keywords or Boolean combinations of keywords/concepts) and receive the results immediately even when the number of the documents that match the query is very large. The user can also view snippets from MEDLINE to get textual evidence of associations between the query terms and the concepts. The concept IDs and their names/synonyms for building the indexes were collected from several biomedical databases and thesauri, such as UniProt, BioThesaurus, UMLS, KEGG and DrugBank.
Availability: The system is available at http://www.nactem.ac.uk/software/facta/
Contact: yoshimasa.tsuruoka@manchester.ac.uk
The impact of methadone or buprenorphine treatment and ongoing injection on highly active antiretroviral therapy (HAART) adherence: evidence from the MANIF2000 cohort study
Authors: Roux Perrine , Carrieri M. Patrizia , Villes Virgine , Dellamonica Pierre , Poizot‐Martin Isabelle , Ravaux Isabelle , Spire Bruno 
Published: September 2008

ABSTRACTAims  To date, no data exist assessing the impact of either methadone or buprenorphine on adherence to highly active antiretroviral therapy (HAART) in the long term. This study was conducted in order to evaluate whether receiving take‐home methadone and buprenorphine may ensure better adherence to HAART in individuals infected with human immunodeficiency virus (HIV) through injection drug use (IDU).Design  Longitudinal data on adherence, opioid substitution treatment (OST) and patient behaviours starting from their first HAART prescription were collected for 276 individuals HIV‐infected through drug use (n = 1558 visits).Setting  Out‐patient hospital services delivering HIV care in Marseilles, Avignon, Nice and Ile de France.Measurements  At any given visit, patients were classified both according to the type of OST received and ongoing injection. Patients who reported no injection and no OST over the whole study period were considered as ‘abstinent’ and used as a reference category. A logit model based on generalized estimation equations (GEE) was used to identify predictors of non‐adherence.Findings  After adjustment for alcohol consumption, depression and self‐reported side effects, patients ceasing injection during OST and abstinent patients exhibited comparable adherence. Patients reporting injection, on OST or not, had a twofold and threefold risk, respectively, of non‐adherence compared with abstinent patients (P < 0.01 linear trend). Duration on OST without injecting was associated significantly with virological success.Conclusions  Both access to and effectiveness of OST contribute to sustaining adherence to HAART in HIV‐infected IDUs. These results advocate strongly the need of wider use of OST in countries scaling‐up HAART where HIV is driven by IDUs.
The waterpipe: time for action
Authors: Maziak Wasim 
Published: September 2008

ABSTRACTThe waterpipe, known in many cultures under different shapes and names (e.g. hookah, shisha, narghile), is a centuries‐old tobacco use method that is witnessing a world‐wide surge in popularity. This popularity is most noticeable among youths, and is surpassing cigarette smoking among this group in some societies. Many factors may have contributed to the recent waterpipe spread, including the introduction of sweetened/flavored waterpipe tobacco (known as Maassel), its reduced‐harm perception, the thriving café culture, mass media and the internet. The passage of smoke through water on its way to the smoker underlies much of the common misperception that waterpipe use is less harmful than cigarettes. The health/addictive profile of waterpipe compared to cigarettes is largely unresearched and is likely to be influenced by the properties of smoke, duration and frequency of use, type of tobacco used, volume of smoke inhaled and the contribution of charcoal. However, the accumulation of evidence about the harmful and addictive potential of waterpipe use is outpacing the public health response to this health risk. A timely public health and policy action is needed in order to curb the emerging waterpipe smoking epidemic.
Why should addiction medicine be an attractive field for young physicians?
Authors: Soyka Michael , Gorelick David A. 
Published: September 2008

ABSTRACTAims  The clinical practice and science of addiction are increasingly active fields, which are attracting professionals from diverse disciplines such as psychology and neurobiology. Our scientific knowledge of the pathophysiology of addiction is rapidly growing, along with the variety of effective treatments available to clinicians. Yet, we believe that the medical specialties of addiction medicine/psychiatry are not attracting the interest and enthusiasm of young physicians. What can be done?Methods  We offer the opinions of two experience addiction psychiatrists.Results  In the US, there has been a decline in the number of psychiatrists seeking training or board certification in addiction psychiatry; about one‐third of graduates with such training are not practicing in an addiction psychiatry setting. There is widespread neglect of addiction medicine/psychiatry among the medical profession, academia and national health authorities. This neglect is unfortunate, given the enormous societal costs of addiction (3–5% of the gross domestic product in some developed countries), the substantial unmet need for addiction treatment, and the highly favourable benefit to cost yield (at least 7:1) from treatment.Conclusions  We believe that addiction medicine/psychiatry can be made more attractive for young physicians. Helpful steps include widening acceptance as a medical specialty or subspecialty, reducing the social stigma against people with substance use disorders, expanding insurance coverage and increasing the low rates of reimbursement for physicians. These steps would be easier to take with broader societal (and political) recognition of substance use disorders as a major cause of premature death, morbidity and economic burden.
Development of a full‐genome cDNA clone of Citrus leaf blotch virus and infection of citrus plants
Authors: VIVES MARÍA CARMEN , MARTÍN SUSANA , AMBRÓS SILVIA , RENOVELL ÁGUEDA , NAVARRO LUIS , PINA JOSE ANTONIO , MORENO PEDRO , GUERRI JOSÉ 
Published: September 2008

SUMMARY Citrus leaf blotch virus (CLBV), a member of the family Flexiviridae, has a ~9‐kb single‐stranded, positive‐sense genomic RNA encapsidated by a 41‐kDa coat protein. CLBV isolates are associated with symptom production in citrus including leaf blotching of Dweet tangor and stem pitting in Etrog citron (Dweet mottle disease), and some isolates are associated with bud union crease on trifoliate rootstocks, but Koch's postulates for this virus were not fulfilled. A full‐genome cDNA of CLBV isolate SRA‐153, which induces bud union crease, was placed under the T7 promoter (clone T7‐CLBV), or between the 35S promoter and the Nos‐t terminator, with or without a ribozyme sequence downstream of the CLBV sequence (clones 35SRbz‐CLBV and 35S‐CLBV). RNA transcripts from T7‐CLBV failed to infect Etrog citron and Nicotiana occidentalis and N. benthamiana plants, whereas agro‐inoculation with binary vectors carrying 35SRbz‐CLBV or 35S‐CLBV, and the p19 silencing suppressor, caused systemic infection and production of normal CLBV virions. Virus accumulation was similar in citron plants directly agro‐infiltrated, or mechanically inoculated with wild‐type or 35SRbz‐CLBV‐derived virions from Nicotiana, and the three sources incited the symptoms characteristic of Dweet mottle disease, but not bud union crease. Our results show that (1) virions derived from an infectious clone show the same replication, movement and pathogenicity characteristics as the wild‐type CLBV; (2) CLBV is the causal agent of Dweet mottle disease but not of the bud union crease syndrome; and (3) for the first time an RNA virus could be successfully agro‐inoculated on citrus plants. This infectious clone may become a useful viral vector for citrus genomic studies.
Maize food allergy: a double‐blind placebo‐controlled study
Authors: Scibilia J. , Pastorello E. A. , Zisa G. , Ottolenghi A. , Ballmer‐Weber B. , Pravettoni V. , Scovena E. , Robino A. , Ortolani C. 
Published: September 2008

SummaryBackground
Maize allergy is not very common especially in Europe. The number of studies that address IgE mediated maize allergy is all too few.Objective
Evaluate subjects with a history of maize allergy by double‐blind, placebo‐controlled food challenge; identify the spectrum of symptoms manifested during challenge; determine the lowest provocation dose (PD) during challenge; determine the performance characteristics of maize skin prick test and specific IgE.Methods
Twenty‐seven patients with a history of maize allergy were enrolled to be evaluated by skin test, specific IgE and double‐blind placebo‐controlled maize challenge.Results
Forty‐eight percent of the patients were challenge positive. PD range was 0.1–25 g. Fifty‐four percent of the maize allergic subjects had a PD that was 2.5 g; two subjects reacted to 100 mg of maize. Comparison of maize specific IgE levels and skin test results to the challenge results revealed the following (specific IgE level/skin testing): sensitivity 1.00/0.846, specificity 0.077/0.384, positive predictive value 0.520/0.579, and negative predictive value 1.00/0.714.Conclusion
Maize is a cause of IgE‐mediated allergic reactions to foods in adults and children. Nearly half of the subjects recruited were confirmed by challenge to be allergic to maize. Twenty‐three percent of the positive challenge patients manifested symptoms that involved two organ systems, thus fulfilling the criteria for maize induced anaphylaxis. Maize is allergenic and can pose a risk for symptomatic food allergy at a dose of 100 mg.
Maternal tolerance achieved during pregnancy is transferred to the offspring via breast milk and persistently protects the offspring from allergic asthma
Authors: Polte T. , Hansen G. 
Published: September 2008

SummaryBackground
Maternal, more than paternal, asthma is a risk factor for the development of asthma in children. Recently, epidemiologic studies have shown that environmental exposures during pregnancy might influence the development of childhood asthma and allergies.Objective
The aim of the present study was to investigate whether the induction of tolerance against a specific antigen during pregnancy prevents in the offspring the development of allergic asthma in response to this antigen.Methods
Balb/c mice were orally tolerized with ovalbumin (OVA) during pregnancy. The offspring of tolerized and naïve mothers were immunized with OVA at 6 weeks and 4 months of age and analysed in our murine asthma model.Results
While the offspring of naïve mice developed increased AHR, eosinophilic airway inflammation, T‐helper type 2 cytokine production and high serum IgE levels in response to OVA sensitization, the offspring of tolerized mice were almost completely protected from asthma, even when immunized as late as 4 months after birth. Breastfeeding was crucial for protection because tolerance was only observed when the offspring were nursed by their own mothers and not when nursed by naïve wet‐nurses. Allergen‐specific IgG1 antibodies were exclusively increased in the breast milk of tolerant mothers and serum of protected pups, indirectly supporting its important role in tolerance transfer from the mother to the offspring. Sensitization of the F1 generation from OVA‐tolerized mothers with a heterologous allergen enhanced the immune response to this antigen.Conclusion
Our results demonstrate that mucosal allergen contact during pregnancy modifies the asthma and allergy risk of the offspring mediated via breast milk. This observation may suggest that the time window for primary prevention strategies starts even before early childhood during pregnancy.
Important roles of tachykinins in the development of allergic nasal hyperresponsiveness in guinea‐pigs
Authors: Nabe T. , Tsuzuike N. , Ohtani Y. , Mizutani N. , Watanabe S. , Fujii M. , Yoshimura M. , Nagasawa M. , Kohno S. 
Published: September 2008

SummaryBackground
Although it has been suggested that the use of tachykinin receptor antagonists might prove to be an effective treatment for allergic rhinitis (AR), they are not used clinically. Therefore, we decided to examine the effects of tachykinin receptor antagonists on AR symptoms in an appropriate experimental model.Objective
To evaluate newly developed tachykinin receptor antagonists in a Japanese cedar pollen‐induced AR model and to determine their effect on allergen‐induced sneezing, nasal blockage, and nasal hyperresponsiveness (NHR).Methods
Sensitized guinea‐pigs were challenged by forced inhalation of pollen once every week. Sneezing and nasal blockage were observed after pollen challenges. NHR (nasal blockage) to an intranasal application of leukotriene D4 was assessed 2 days after an antigen challenge. We also evaluated whether intranasal dosing with a tachykinin causes NHR. NK1 and NK2 receptor antagonists were administered before an intranasal treatment with antigen or tachykinin. Amounts of tachykinins present in nasal cavity lavage fluid were measured by an enzyme immunoassay.Results
Although an NK1 and NK2 receptor dual antagonist showed no effect on pollen‐induced sneezing and biphasic nasal blockage, it did completely suppress the development of NHR. Experiments using specific NK1 or NK2 receptor antagonists revealed that NK2 receptor activation was preferentially involved in the development of hyperresponsiveness. Increases in the levels of substance P (SP) and neurokinin A (NKA) in the nasal tissue were noted 20 min–1 h after the challenge. Intranasal instillation of either SP or NKA‐induced NHR, which was almost completely inhibited by NK2 receptor antagonists and partially inhibited by NK1 receptor antagonists.Conclusions
SP and NKA, which are released early after the challenge, mediate the development of NHR by preferentially activating NK2 receptors. Therefore, NK2 receptor antagonists might prove to be effective treatment of AR.