bluuebunny/crossref_metadata_2025_split huggingface dataset:
Salmonella enterica serovar Typhi in Japan, 2001–2006: emergence of high-level fluoroquinolone-resistant strains
Authors: MORITA M. , HIROSE K. , TAKAI N. , TERAJIMA J. , WATANABE H. , SAGARA H. , KURAZONO T. , YAMAGUCHI M. , KANAZAWA Y. , OYAIZU T. , IZUMIYA H. 
Published: July 2009

SUMMARYThe phage types and antimicrobial susceptibilities of 226 isolates of Salmonella enterica serovar Typhi from imported cases in Japan between 2001 and 2006 were investigated. Most (93·8%) had travelled to Asian countries, particularly South East Asia. Twenty-one phage types were identified with E1 (30·5%), UVS (15·9%) and B1 (9·3%) being the most common. The frequency of multidrug-resistant strains reached 37·0% in 2006 with phage types E1 and E9 predominating. Almost half (48·2%) of the isolates were resistant to nalidixic acid and two isolates displayed high-level fluoroquinolone resistance. Three mutations, two in gyrA and one in parC, were identified in both isolates.
The anterior temporal lobes and the functional architecture of semantic memory
Authors: SIMMONS W. KYLE , MARTIN ALEX 
Published: July 2009

AbstractRecently, three accounts have emerged on the role of the anterior temporal lobes (ATLs) in semantic memory. One account claims that the ATLs are domain-general semantic hubs, another claims that they underlie knowledge of unique entities specifically, and yet another account claims that they support social conceptual knowledge generally. Here, we review neuropsychological and neuroimaging studies that bear on these three accounts and offer suggestions for future research to elucidate the roles of the ATLs in semantic memory. (JINS, 2009, 15, 645–649.)
Wittgenstein and the problem of consciousness
Authors: Hanfling Oswald 
Published: July 2009

You have a rich inner life of conscious experiences. For example, you have pains and other sensations. And you have sensory experiences, such as that produced by chewing on something bitter. Scientists are currently puzzling over how to explain this inner life in scientific terms. Can we, for example, ‘explain’ consciousness by appealing to certain facts about our brains?Here, Oswald Hanfling explains why he believes the scientific ‘problem’ of ‘explaining’ consciousness is ultimately a pseudo-problem. There is no problem!
My friend was a poem: A philosophical memoir
Authors: Chambers Timothy 
Published: July 2009

The ‘Problem of Evil’ has been the focus of a number of articles in Think. Here, Timothy Chambers offers an unusual perspective on this seemingly intractable difficulty facing theists.‘Did not I weep for him whose day was hard? Was not my soul grieved for the poor? But when I looked for good, evil came; and when I waited for light, darkness came.’
What's in an 'is a' link?
Authors: Hogan William 
Published: July 2009

AbstractIntroductionSeveral researchers have demonstrated that current medical terminologies and ontologies use relations in inconsistent and ambiguous ways,[1] despite Woods’ seminal work that first illustrated the problem.[2] The goal of the present work is to catalog the different ways in which SNOMED CT uses the is a relation. The rationale for creating the catalog is to serve as a basis for systematically improving the semantics of terminologies and ontologies so as to improve their accessibility to machine inference.
Methods
I reviewed the literature to find ontological mistakes that change the interpretation of the is a relation, without respect to any particular terminology. I then reviewed the stated relationships table of SNOMED CT, Jan 2009 version, placing them into categories from the literature, and creating new categories when existing categories did not apply.

Results
I found nine categories of misuse of the is a relation in SNOMED CT (see Table in poster), eight from the literature and one from my analysis. SNOMED CT had an example of every misuse found in the literature.

Discussion
The January 2009 version of SNOMED CT violates its intended interpretation of the is a relation, which is nearly identical to the definition of Smith et al.[1] I cataloged nine categories of misuse of is a, and found an example of each in SNOMED CT. This study demonstrates for the first time that (1) certain common ontological mistakes, not previously identified as causing misuse of is a, lead to ambiguity in the interpretation of is a, (2) the stated relationships of SNOMED CT are the source of mistakes in the use of the is a relation, (3) SNOMED CT has at least one example of every problem with is a elucidated from the broader literature.
References1. Smith B, Ceusters W, Klagges B, et al. Relations in biomedical ontologies. Genome Biol.2005;6(5):R46.2. Woods W. What's in a link: Foundations for semantic networks. In: Bobrow D, Collins A, eds. Representation and understanding. New York: Academic Press; 1975:35-82.
Metarel: An Ontology to Support the Inferencing of Semantic Web Relations within Biomedical Ontologies
Authors: Blondé Ward 
Published: July 2009

AbstractMetarel allows the creation of millions of relational inferences in the RDF Knowledge Base BioGateway, by using five types of SPARUL closure queries. Metarel can be found at "http://www.metarel.org":http://www.metarel.org.
A set of ontologies to drive tools for the control of vector-borne diseases
Authors: Topalis Pantelis , Dialynas Emmanuel , Mitraka Elvira , Deliyanni Elena , Siden-Kiamos Inga , Louis Christos 
Published: July 2009

AbstractWe are developing a set of ontologies that deal with vector-borne diseases and the arthropod vectors that transmit them. For practical reasons (application priorities), we initiated this project with an ontology of insecticide resistance followed by a series of ontologies that describe malaria as well as physiological processes of mosquitoes that are relevant to, and involved in, disease transmission. These will be expanded to encompass other vector-borne diseases as well as non-mosquito vectors. The aim of the whole undertaking, which is worked out in the frame of the international IDO (Infectious Disease Ontology) project, is to provide the community with a set of ontological tools that can be used both in the development of specific databases and, most importantly, in the construction of decision support systems to control these diseases.
SNOMED CT’s Ontological Commitment
Authors: Schulz Stefan , Cornet Ronald 
Published: July 2009

AbstractSNOMED CT is a clinical terminology that describes the meaning of terms by logical axioms. This requires an ontological commitment, i.e. precise agreements about the ontological nature of the entities referred to. We provide evidence that SNOMED implicitly supports at least three different kinds of commitments, viz. (i) independently existing entities, (ii) representational artifacts, and (iii) clinical situations. Our analysis shows how the truth-value of a sentence changes according to one of these perspectives. We argue that a clear understanding of to what kind of entities SNOMED CT concepts extend is crucial for the proper use and maintenance of SNOMED CT.
Providing a Realist Perspective on the eyeGENE Database System
Authors: Ceusters Werner 
Published: July 2009

AbstractOne of the achievements of the eyeGENE Network is a repository of DNA samples of patients with inherited eye diseases and an associated database that tracks key elements of phenotype and genotype information for each patient. Although its database structure serves its direct research needs, eyeGENE has set a goal of enhancing this structure to become increasingly well integrated with medical information standards over time. This goal should be achieved by ensuring semantic interoperability with other information systems but without adopting the incoherencies and inconsistencies found in available biomedical standards. Therefore, eyeGENE’s current pragmatic perspective with focus on data and information, rather than what the information is about, should shift to a realism-based perspective that includes also the portion of reality described, and the competing opinions that clinicians may hold about it. An analysis of eyeGENE’s database structure and user interfaces suggests that such a transition is possible indeed.
Computing the inverse of the neurophysiological spike-response transform
Authors: Brezina Vladimir , Stern Estee , Garcia-Crescioni Keyla , Miller Mark , Peskin Charles 
Published: July 2009

AbstractConsider the transform from a discrete neuronal spike train to a continuous neurophysiological response such as postsynaptic membrane voltage or muscle contraction. Often, we can record only the response. Here we therefore ask about the inverse of this transform: given the response, how can we estimate from it the spike train that produced it? In previous work, we have developed a kernel-based "decoding" method for system identification of the forward transform. Using several variant approaches based on this method, here we demonstrate how to identify the spike train, in the minimal case from just the response, with synthetic as well as real synaptic and neuromuscular data.
Clonal Complexes in Biomedical Ontologies
Authors: Goldfain Albert , Cowell Lindsay , Smith Barry 
Published: July 2009

AbstractAn accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Se-quence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.
Social or Academic Language Intervention? You Don’t Have To Choose
Authors: Robinson Lee , Westby Carol 
Published: July 2009

AbstractStudents with a variety of types of language impairments exhibit deficits that affect both social interactions and academic performance. Two types of theory of mind underlie social and academic language skills: interpersonal and intrapersonal. In this article, the authors describe strategies for developing interpersonal and intrapersonal theory of mind abilities with the goal of promoting the inferencing skills essential for comprehension of social and academic language.
Teaching Conversation Skills to Children With High Functioning Autism/Asperger Syndrome
Authors: Breit-Smith Allison , Murray Donna S. 
Published: July 2009

Abstract
This article discusses the conversational abilities of children diagnosed with High functioning autism/Asperger’s syndrome in the context of the broader social deficits associated with the disorder and describes how social skills training groups might address conversation skill difficulties in this population. We present a template for how speech-language pathologists might structure a social skills training group to increase conversational responding in children with high functioning autism/Asperger’s syndrome.
Assessment and Treatment of Pragmatic Disorders: Integrating Linguistic and Neurocognitive Perspectives
Authors: Abdelal Ahmed M. 
Published: July 2009

AbstractThe increasing demand for pragmatic intervention, paucity of standardized diagnostic tools targeting this domain, and the impressive advances in neuroscientific research over the past decade have made it necessary for us to re-examine the way we conduct assessment and treatment of pragmatic disorders. This article uses a case study format to summarize an intervention framework that views pragmatics as an integrative, neurocognitive-linguistic domain.
The Communication Neuroscience Laboratories at the University of Kansas: An Overview
Authors: Barlow Steven M. 
Published: July 2009

AbstractThe Communication Neuroscience Laboratories (CNL) celebrates its 25th anniversary in 2009 with a brief overview of past and current research projects concerned with the sensorimotor development and control of orofacial and laryngeal systems subserving speech, vocalization, suck, oromotor, and aeroingestive behaviors in health and disease across the human life span. A key ingredient in the multidimensional study lines described in this review is the assembly and nurturing of a strong multidisciplinary research team involving students and research faculty from communication sciences, biology, neuroscience, bioengineering, computer science, neurology, radiology and medical physics, neonatology, nursing, pediatrics, and physical therapy. The transfer of technology from bench to bedside (or even cribside) is another important function. An example of an innovation from the CNL is highlighted by a new therapeutic sensorimotor entrainment intervention (NTrainer) that helps premature infants with feeding disorders develop ororhythmic (suck) skills. When possible, project lines are directed toward patient-oriented research and innovative interventions aimed at driving mechanisms of brain plasticity to improve communication/ oromotor function, neurodevelopmental outcomes, or both.
Orofacial Biomechanics and Speech Motor Control
Authors: Chu Shin Ying , Barlow Steven M. 
Published: July 2009

Abstract
The mechanical properties (e.g., mass, stiffness, viscoelasticity) of bone, cartilage, muscle, tendon, ligament, fat, and skin among articulatory subsystems involved in speech and gesture collectively influence all aspects of movement and must be accounted for in the selection and sequencing of motor program elements. Damage or disease processes affecting peripheral or central nervous system function, or both, can affect muscle coordination and alter muscle stiffness. Therefore, the biomechanics of orofacial and vocal tract structures should be taken into account when considering the movement patterns and network signaling in the neuromotor control system in health and disease. The purpose of this report is to summarize our evolving approach to and application of orofacial biomechanics in the context of movement disorders associated with dysarthria and craniofacial anomalies. We describe a new application for mapping stiffness in the lips for clinical application in pediatric and adult populations.
Obstetric outcome in women with hepatitis C virus infection and thyroid dysfunction
Authors: KUMAR ASHOK , AGARWAL KRISHNA , GUPTA RAM KUMAR , KAR PREMASHISH 
Published: July 2009

AbstractObjectives. To determine the incidence of thyroid abnormality in pregnant women with hepatitis C virus (HCV) infection and evaluate pregnancy outcomes with respect to thyroid function status. Design. Prospective cohort study. Setting. Tertiary care hospital. Population. Pregnant women with HCV infection. Methods. Seventy‐eight HCV positive women had radioimmunoassay thyroid function tests. All were followed until delivery. Pregnancy outcomes were compared in women with and without subclinical hypothyroidism. Main outcome measures. Maternal and perinatal outcomes. Results. Of 78 anti‐HCV antibody positive pregnant women, 13 (16.7%) had abnormal thyroid‐stimulating hormone (TSH) (>5 mIU/L; hypothyroid group) and the remaining 65 (83.3%) had normal TSH values (euthyroid group). None had abnormal free T4 levels. None showed evidence of fetal distress in labor or fetal asphyxia. In the hypothyroid group, 23% compared to 6.2% in euthyroid group underwent cesarean section (p = 0.07). The incidence of preterm delivery (7.7% vs. 24.6%; p = 0.28), mean gestation at delivery (38.2±1.8 vs. 37.5±1.8 weeks, p = 0.19), and birthweight (2,687±430 g vs. 2,846±379 g, p = 0.18) was comparable. Neonatal nursery admissions were comparable. Conclusion. The presence of subclinical hypothyroidism in pregnant women with HCV infection does not adversely affect short‐term pregnancy outcomes.
Geochemical constraints on the Palaeocene–Miocene evolution of eastern Azerbaijan, with implications for the South Caspian basin and eastern Paratethys
Authors: Johnson C. L. , Hudson S. M. , Rowe H. D. , Efendiyeva M. A. 
Published: July 2009

ABSTRACTFine‐grained Palaeogene–early Neogene strata of the South Caspian basin, specifically the Oligocene–Lower Miocene Maikop Series, are responsible for the bulk of hydrocarbon generation in the region. Despite the magnitude of oil and gas currently attributed to the source interval offshore, geochemical evaluation of 376 outcrop samples from the northern edge of the Kura basin (onshore eastern Azerbaijan) indicates that depositional conditions in these proximal strata along the basin margins were dominantly oxic to mildly suboxic/anoxic throughout three major depositional stages: the Palaeocene–Eocene, Oligocene–early Middle Miocene and late Middle–Late Miocene. Palaeocene–Eocene samples have low average total organic carbon (TOC) values (0.3%), with higher total inorganic carbon (TIC) values (average=2.6%), extremely low sulphur content (0.2%) and relatively high detrital input as indicated by Fe/Al and Ti/Al ratios. C–S–Fe associations, along with relatively lower concentrations of redox‐sensitive trace elements (e.g. V, Ni, Mo, U) indicate dominantly oxic environments of deposition during much of the Palaeocene–Eocene. A pronounced geochemical shift occurred near the Eocene–Oligocene boundary, and continued through the Early Miocene. Specifically, this interval is characterized by a distinct increase in TOC (ranging from 0.1 to 6.3% with an average of 1.5%), C–S–Fe associations that reveal an abrupt relative increase of carbon and sulphur with respect to iron‐dominated Palaeocene–Eocene samples, and higher concentrations of redox‐sensitive trace metals. These changes suggest that a shift away from unrestricted marine conditions and towards more variable salinity conditions occurred coincident with the initial collision of the Arabian plate and partial closure of the Paratethys ocean. Despite periodic basin restriction, the majority of Upper Eocene–Lower Miocene strata in the northern Kura basin record oxic to slightly dysoxic conditions.
Testing the predictive adaptive response in a host‐parasite system
Authors: Devevey Godefroy , Bize Pierre , Fournier Sara , Person Emilie , Christe Philippe 
Published: July 2009

Summary1. Harsh environmental conditions experienced during development can reduce the performance of the same individuals in adulthood. However, the ‘predictive adaptive response’ hypothesis postulates that if individuals adapt their phenotype during development to the environments where they are likely to live in the future, individuals exposed to harsh conditions in early life perform better when encountering the same harsh conditions in adulthood compared to those never exposed to these conditions before.2. Using the common vole (Microtus arvalis) as study organism, we tested how exposure to flea parasitism during the juvenile stage affects the physiology (haematocrit, resistance to oxidative stress, resting metabolism, spleen mass, and testosterone), morphology (body mass, testis mass) and motor performance (open field activity and swimming speed) of the same individuals when infested with fleas in adulthood. According to the ‘predictive adaptive response’ hypothesis, we predicted that voles parasitized at the adult stage would perform better if they had already been parasitized with fleas at the juvenile stage.3. We found that voles exposed to fleas in adulthood had a higher metabolic rate if already exposed to fleas when juvenile, compared to voles free of fleas when juvenile and voles free of fleas in adulthood. Independently of juvenile parasitism, adult parasitism impaired adult haematocrit and motor performances. Independently of adult parasitism, juvenile parasitism slowed down crawling speed in adult female voles.4. Our results suggest that juvenile parasitism has long‐term effects that do not protect from the detrimental effects of adult parasitism. On the contrary, experiencing parasitism in early‐life incurs additional costs upon adult parasitism measured in terms of higher energy expenditure, rather than inducing an adaptive shift in the developmental trajectory.5. Hence, our study provides experimental evidence for long term costs of parasitism. We found no support for a predictive adaptive response in this host‐parasite system.
Are competitive effect and response two sides of the same coin, or fundamentally different?
Authors: Wang Ping , Stieglitz Tara , Zhou Dao Wei , Cahill Jr James F 
Published: July 2009

Summary 1. The ability to suppress neighbour growth and the ability to withstand growth suppression are widely viewed as two forms of competition, competitive effect and competitive response. 2. We conducted a greenhouse experiment to determine whether these two forms of competition were functionally linked, and to determine which plant traits are associated with effect and response competitive abilities among seedlings of 22 perennial North American prairie species. We further explored the trait‐function relationship by growing plants under different soil fertilities and with different neighbour species. 3. To determine competitive abilities, we used a phytometer approach with two phytometer species: Poa pratensis and Achillea millefolium grown in competition with each of the 22 focal species under low and high fertility. Root and shoot morphological traits were measured and principal component analyses were used to reduce the dimensionality of the data. Three axes were extracted, which roughly corresponded to size, root and shoot architecture. 4. The hierarchy of competitive effect ability of the target species did not vary with either soil fertility or neighbour identity, while the hierarchies of competitive response abilities were highly variable among the treatments. Competitive effect ability was closely associated with size‐related traits under high nutrient conditions, and with root‐related traits under low nutrient conditions. In contrast, few plant traits axes were related to competitive response. 5. These findings indicate significant differences between competitive effect and response ability. We suggest competitive effect ability is a consistent trait of a species, linked to specific plant traits. In contrast, we found little evidence to support the idea that competitive response ability is itself a species trait, and instead it appears this may be simply a collection of different ways of avoiding or tolerating competition and/or low nutrient conditions. Supporting this argument was a lack of any consistency in which traits were associated with competitive response ability. 6. We recognize the limitations of a single study of seedlings under greenhouse conditions. However, we suggest these findings indicate a need to critically examine current assumptions about plant competition, how it is defined, and the traits which control a species’ competitive ability.