bluuebunny/crossref_metadata_2025_split huggingface dataset:
Late measures of microstructural alterations in severe neonatal hypoxic–ischemic encephalopathy by MR diffusion tensor imaging
Authors: Chan Kevin C. , Khong Pek‐lan , Lau Ho‐fai , Cheung Pik‐to , Wu Ed X. 
Published: June 2009

AbstractNeonatal hypoxic–ischemic encephalopathy is a major cause of brain damage in infants, and is associated with periventricular white matter injury and chronic neurological dysfunctions. However, the mechanisms of the chronic white matter injury and reorganization are still unclear. In this study, in vivo diffusion tensor imaging (DTI) was employed to evaluate the late changes of white matter microstructural integrity in the rat brains at 10 weeks after severe neonatal hypoxic–ischemic insults at postnatal day 7. In the fractional anisotropy directionality map, qualitative evaluation showed that a dorsoventrally oriented fiber bundle extended from the corpus callosum into the cyst in the anterior brain, whilst the posterior peri‐infarct areas had similar fiber orientations as the contralateral internal capsule, optic tract and fimbria of hippocampus. Compared to the contralateral hemisphere, significantly higher fractional anisotropy, axial diffusivity and diffusion trace value were observed quantitatively in the distal end of the extended fiber bundle connecting the anterior and posterior white matters rostrocaudally. A significantly lower fractional anisotropy but higher axial and radial diffusivities and trace were also found in the ipsilateral corpus callosum, proximal external capsule and anterior commissure, while slightly lower fractional anisotropy and axial diffusivity were noticed in the ipsilateral internal capsule and optic nerve. It was suggested that increased fractional anisotropy, axial diffusivity and trace characterize white matter reorganization in chronic neonatal hypoxic–ischemic insults, whereas reduction in fractional anisotropy appears to characterize two types of white matter lesions, with significantly higher axial and radial diffusivities and trace being primary and slightly lower axial diffusivity being secondary. Combined with fractional anisotropy directionality map, in vivo DTI provides important indices to differentiate the chronic effects of severe neonatal hypoxic–ischemic injury and recovery globally, quantitatively and non‐invasively.
Health technology assessment in the United States
Authors: Luce Bryan , Cohen Rebecca Singer 
Published: June 2009

Objectives:To describe and explore the reasons for the current health technology assessment (HTA) landscape in the United States.Methods:Relying on multiple historical literature and other documents as well as drawing on personal experiences and observations, we describe, evaluate, and explain the evolving and dynamic HTA-related evidence landscape.Results:The present HTA-related landscape is a product of a dynamic, somewhat turbulent path in the United States. Many early aggressive federal efforts beginning in the 1970s were rejected in the 1980s only to be revived by the mid-1990s and continue to strengthen today, likely due to diffusing private sector political opposition from de-linking HTA from policy decisions (e.g., coverage, clinical guidelines) and omitting economic evaluation. Meanwhile, private sector HTA efforts have remained active during the entire period.Conclusions:The current HTA-related landscape is at least as dynamic as it has been at any point in its turbulent 30-year history and is likely to continue as health reform in the US is debated once again.
Health technology assessment in Italy
Authors: Favaretti Carlo , Cicchetti Americo , Guarrera Giovanni , Marchetti Marco , Ricciardi Walter 
Published: June 2009

Objectives: The aim of this study was to review the history of health technology assessment (HTA) in Italy.Methods: Founded in 1978, the Italian National Health Service (NHS) has been strongly regionalized mainly after a constitutional reform, which started a devolution process. HTA started in the 1980s at the National Institute of Health and in a few University Hospitals, with a focus on big ticket technology: that process was driven by clinical engineers.Results: In recent years, HTA is becoming an important tool for decision-making processes at central, regional, and local levels. In particular, the National Agency for Regional Health Services (AGENAS) and five regions (of twenty-one) are strongly committed to develop HTA initiatives connected with the planning process.Conclusions: At the local level, the hospital-based HTA activity is probably the most important peculiarity of the country and the real driver of the HTA movement.
Gabriel–Ulmer duality and Lawvere theories enriched over a general base
Authors: LACK STEPHEN , POWER JOHN 
Published: June 2009

AbstractMotivated by the search for a body of mathematical theory to support the semantics of computational effects, we first recall the relationship between Lawvere theories and monads onSet. We generalise that relationship fromSetto an arbitrary locally presentable category such asPosetand ωCpoor functor categories such as [Inj,Set] and [Inj, ωCpo]. That involves allowing the arities of Lawvere theories to be extended to being size-restricted objects of the locally presentable category. We develop a body of theory at this level of generality, in particular explaining how the relationship between generalised Lawvere theories and monads extends Gabriel–Ulmer duality.
Implementing a normalizer using sized heterogeneous types
Authors: ABEL ANDREAS 
Published: June 2009

AbstractIn the simply typed λ-calculus, a hereditary substitution replaces a free variable in a normal formrby another normal formsof typea, removing freshly created redexes on the fly. It can be defined by lexicographic induction onaandr, thus giving rise to a structurally recursive normalizer for the simply typed λ-calculus. We implement hereditary substitutions in a functional programming language with sized heterogeneous inductive types$\Fhat$, arriving at an interpreter whose termination can be tracked by the type system of its host programming language.
Big-step normalisation
Authors: ALTENKIRCH THORSTEN , CHAPMAN JAMES 
Published: June 2009

AbstractTraditionally, decidability of conversion for typed λ-calculi is established by showing that small-step reduction is confluent and strongly normalising. Here we investigate an alternative approach employing a recursively defined normalisation function which we show to be terminating and which reflects and preserves conversion. We apply our approach to the simply typed λ-calculus with explicit substitutions and βη-equality, a system which is not strongly normalising. We also show how the construction can be extended to system T with the usual β-rules for the recursion combinator. Our approach is practical, since it does verify an actual implementation of normalisation which, unlike normalisation by evaluation, is first order. An important feature of our approach is that we are using logical relations to establish equational soundness (identity of normal forms reflects the equational theory), instead of the usual syntactic reasoning using the Church–Rosser property of a term rewriting system.
Categorical semantics for arrows
Authors: JACOBS BART , HEUNEN CHRIS , HASUO ICHIRO 
Published: June 2009

AbstractArrows are an extension of the well-established notion of a monad in functional-programming languages. This paper presents several examples and constructions and develops denotational semantics of arrows as monoids in categories of bifunctorsCop×C→C. Observing similarities to monads – which are monoids in categories of endofunctorsC→C– it then considers Eilenberg–Moore and Kleisli constructions for arrows. The latter yields Freyd categories, mathematically formulating the folklore claim ‘Arrows are Freyd categories.’
An induction principle for nested datatypes in intensional type theory
Authors: MATTHES RALPH 
Published: June 2009

AbstractNested datatypes are families of datatypes that are indexed over all types such that the constructors may relate different family members (unlike the homogeneous lists). Moreover, the argument types of the constructors refer to indices given by expressions in which the family name may occur. Especially in this case of true nesting, termination of functions that traverse these data structures is far from being obvious. A joint paper with A. Abel and T. Uustalu (Theor. Comput. Sci., 333 (1–2), 2005, pp. 3–66) proposed iteration schemes that guarantee termination not by structural requirements but just by polymorphic typing. They are generic in the sense that no specific syntactic form of the underlying datatype “functor” is required. However, there was no induction principle for the verification of the programs thus obtained, although they are well known in the usual model of initial algebras on endofunctor categories. The new contribution is a representation of nested datatypes in intensional type theory (more specifically, in the calculus of inductive constructions) that is still generic and covers true nesting, guarantees termination of all expressible programs, and has an induction principle that allows to prove functoriality of monotonicity witnesses (maps for nested datatypes) and naturality properties of iteratively defined polymorphic functions.
U.S. Science Agency Budgets Slated for Increases
Authors: Showstack Randy 
Published: June 2009

The Obama administration released more details on 7 May about its proposed US$3.6 trillion federal budget for fiscal year (FY) 2010 and the planned significant increases for science agencies and for research and development (see Eos, 90(10), 83, 2009). The budget, which needs to be approved by Congress, includes $147.6 billion for research and development, an increase of $555 million, or 0.4%, above the enacted 2009 budget. In addition, the 2009 budget includes $18.3 billion in stimulus spending for research and development through the American Recovery and Reinvestment Act (ARRA).John Holdren, director of the White House Office of Science and Technology Policy and Assistant to the President for Science and Technology, said the FY 2009 and proposed 2010 budgets are among the two largest research and development investments in the nation's history, in real terms. “We in the science and technology community have done better than just about any other constituency in the budget,” Holdren explained in a 7 May budget overview briefing, noting that virtually every science agency is doing better now than it was doing 2 years ago. “We have, in the White House, a president who gets it, believes and gets that investments in science and technology are just that: investments that will pay off.”
Trace Fossil Analysis
Authors: Hasiotis Stephen T. 
Published: June 2009

Today, the study of trace fossils—ichnology— is an important subdiscipline of geology at the interface of paleontology and sedimentology, mostly because of the efforts of Adolf Seilacher. His ability to synthesize various aspects of ichnology and produce a hierarchy of marine ichna and sedimentary facies has made ichnology useful worldwide in interpreting paleodiversity, rates of sedimentation, oxygenation of bottom water and sediment pore water, and depositional energy.Seilacher's book Trace Fossil Analysis provides a glimpse into the mind, methodology, and insights of the father of modern ichnology, generated from his course notes as a professor and a guest lecturer. The title sounds misleading—readers looking for up‐to‐date principles and approaches to trace fossil analysis in marine and continental strata will be disappointed. In his preface, however, Seilacher clearly gives direction for the use of his text: “This is a course book— meaning that it is intended to confer not knowledge, but skill.” Thus, it is not meant as a total compilation of all trace fossils, ichnotaxonomy, ichnological interpretations, applications, or the most relevant and up‐to‐date references. Rather, it takes the reader on a personal journey, explaining how trace fossils are understood in the context of their three‐dimensional (3‐D) morphology and sedimentary facies.
New Study For Climate Modeling, Analyses, and Scenarios
Authors: Lowe Jason A. , Hewitt Chris D. , van Vuuren Detlef P. , Johns Tim C. , Stehfest Elke , Royer Jean‐François , van der Linden Paul J. 
Published: June 2009

The European Commission is funding the ENSEMBLES project, which aims to provide policy makers with information from the latest climate modeling, analyses, and scenarios. Currently, the most comprehensive estimates of climate change are made using general circulation models (GCMs) and Earth system models, but these have been used mostly to simulate futures that do not factor in climate mitigation policy. The results of these simulations typically show global average warming greatly exceeding the European Union (EU) climate policy target of 2°C above preindustrial levels, with associated large impacts on human and natural systems.To date, simple climate models typically have been used to assess the emissions trajectories that are required for meeting this target. The ENSEMBLES project is the first international multiclimate model intercomparison using a politically relevant aggressive mitigation scenario, referred to as E1 (Figures 1a and 1b). This scenario leads to a peak in the carbon dioxide (CO2) equivalent concentration in the atmosphere at around 535 parts per million (ppm) in 2045 before eventually stabilizing at around 450 ppm during the 22nd century. The climate models used are generally improved or extended versions of models contributing to the Intergovernmental Panel on Climate Change's (IPCC) Fourth Assessment Report.
Linking Extreme Weather to Climate Variability and Change: International Group on Attribution of Climate‐Related Events (ACE); Boulder, Colorado, 26 January 2009
Authors: Stott Peter , Trenberth Kevin 
Published: June 2009

Climate change is likely to be manifested on societies around the world mainly through changes in extremes. As a result, the scientific community faces an increasing demand for regularly updated appraisals of evolving climate conditions and extreme weather. Such information would be immensely beneficial for adaptation planning.A group of climate scientists representing the United Kingdom, the United States, Australia, Canada, and South Africa assembled on 26 January 2009 at the National Center for Atmospheric Research (NCAR), in Colorado, to discuss how to meet this challenge. This first meeting of the International Group on Attribution of Climate‐Related Events (ACE) was sponsored by the Science and Innovation Network of the U.K. Foreign and Commonwealth Office (FCO) and NCAR and was organized in collaboration with the U.S. National Oceanic and Atmospheric Administration (NOAA), the Met Office Hadley Centre, and the University of Oxford.
An Alaska Soil Carbon Database: Database Collaborator's Meeting; Fairbanks, Alaska, 4 March 2009
Authors: Johnson Kristofer , Harden Jennifer 
Published: June 2009

Soil carbon pools in northern high‐latitude regions and their response to climate changes are highly uncertain, and collaboration is required from field scientists and modelers to establish baseline data for carbon cycle studies. The Global Change Program at the U.S. Geological Survey has funded a 2‐year effort to establish a soil carbon network and database for Alaska based on collaborations from numerous institutions.To initiate a community effort, a workshop for the development of an Alaska soil carbon database was held at the University of Alaska Fairbanks. The database will be a resource for spatial and biogeochemical models of Alaska ecosystems and will serve as a prototype for a nationwide community project: the National Soil Carbon Network (http://www.soilcarb.net). Studies will benefit from the combination of multiple academic and government data sets. This collaborative effort is expected to identify data gaps and uncertainties more comprehensively. Future applications of information contained in the database will identify specific vulnerabilities of soil carbon in Alaska to climate change, disturbance, and vegetation change.
Principles of Metamorphic Petrology
Authors: Williams Michael L. 
Published: June 2009

The field of metamorphic petrology has seen spectacular advances in the past decade, including new X‐ray mapping techniques for characterizing metamorphic rocks and minerals, new internally consistent thermobarometers, new software for constructing and viewing phase diagrams, new methods to date metamorphic processes, and perhaps most significant, revised petrologic databases and the ability to calculate accurate phase diagrams and pseudosections. These tools and techniques provide new power and resolution for constraining pressure‐temperature (P‐T) histories and tectonic events.Two books have been fundamental for empowering petrologists and structural geologists during the past decade. Frank Spear's Metamorphic Phase Equilibria and Pressure‐Temperature‐Time Paths, published in 1993, builds on his seminal papers to provide a quantitative framework for P‐T path analysis. Spear's book lays the foundation for modern quantitative metamorphic analysis. Cees Passchier and Rudolph Trouw's Microtectonics, published in 2005, with its superb photos and figures, provides the tools and the theory for interpreting deformation textures and inferring deformation processes.
Crystal structure of an inverting GH 43 1,5-α-L-arabinanase from Geobacillus stearothermophilus complexed with its substrate
Authors: Alhassid Anat , Ben-David Alon , Tabachnikov Orly , Libster Dima , Naveh Einat , Zolotnitsky Gennady , Shoham Yuval , Shoham Gil 
Published: June 2009

Arabinanases are glycosidases that hydrolyse α-(1→5)- arabinofuranosidic linkages found in the backbone of the pectic polysaccharide arabinan. Here we describe the biochemical characterization and the enzyme–substrate crystal structure of an inverting family 43 arabinanase from Geobacillus stearothermophilus T-6 (AbnB). Based on viscosity and reducing power measurements, and based on product analysis for the hydrolysis of linear arabinan by AbnB, the enzyme works in an endo mode of action. Isothermal titration calorimetry studies of a catalytic mutant with various arabino-oligosaccharides suggested that the enzyme active site can accommodate at least five arabinose units. The crystal structure of AbnB was determined at 1.06 Å (1 Å=0.1 nm) resolution, revealing a single five-bladed-β-propeller fold domain. Co-crystallization of catalytic mutants of the enzyme with different substrates allowed us to obtain complex structures of AbnBE201A with arabinotriose and AbnBD147A with arabinobiose. Based on the crystal structures of AbnB together with its substrates, the position of the three catalytic carboxylates: Asp27, the general base; Glu201, the general acid; and Asp147, the pKa modulator, is in agreement with their putative catalytic roles. In the complex structure of AbnBE201A with arabinotriose, a single water molecule is located 2.8 Å from Asp27 and 3.7 Å from the anomeric carbon. The position of this water molecule is kept via hydrogen bonding with a conserved tyrosine (Tyr229) that is 2.6 Å distant from it. The location of this molecule suggests that it can function as the catalytic water molecule in the hydrolysis reaction, resulting in the inversion of the anomeric configuration of the product.
Applications of Exercise Science in Dysphagia Rehabilitation
Authors: Burkhead Lori M. 
Published: June 2009

Abstract
Dysphagia clinicians are charged with improving strength, skill, and endurance in order to rehabilitate oropharyngeal swallowing. The obvious method is exercise training. Dysphagia clinicians often use trial-and-error and experience to develop effective regimens. This article is intended to invoke broader and more accurate perspectives from our colleagues in exercise science.
Effects of Chemoradiotherapy on Tongue Function in Patients With Head and Neck Cancer
Authors: Lazarus Cathy L. 
Published: June 2009

AbstractIn this review article, the effects of radiotherapy ± chemotherapy on tissues and on oropharyngeal swallowing are reviewed. In addition, normal tongue function for swallowing is reviewed, as are the effects of tongue exercise programs designed to improve tongue strength and swallow functioning. Current literature on swallow exercise programs for head and neck cancer patients is provided. Also discussed are potential new avenues for research in this population.
Food For Thought: Self-Criticism and Raising the Bar of Dysphagia Practice
Authors: Murray Joe 
Published: June 2009

AbstractThe assessment and treatment of swallowing disorders have become central to the practice of the medical speech-language pathologist. The outcomes associated with swallowing and swallowing disorders are severe with aspiration pneumonia, malnutrition and dehydration, and reduced quality of life among the most concerning. Clinicians practicing in this area possess unequal skills, training, and experience, and there is considerable variation in practice in the field. This article focuses on variation and error in swallowing assessment with attention to reliability and accuracy of the videofluoroscopic swallowing assessment. In this self-critical overview of the practice, recommendations are made for developing a standardized assessment protocol, shared lexicon, and specialty recognition in the area of swallowing and swallowing disorders.
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
Authors: Zang Chongzhi , Schones Dustin E. , Zeng Chen , Cui Kairong , Zhao Keji , Peng Weiqun 
Published: June 2009

AbstractMotivation: Chromatin states are the key to gene regulation and cell identity. Chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-Seq) is increasingly being used to map epigenetic states across genomes of diverse species. Chromatin modification profiles are frequently noisy and diffuse, spanning regions ranging from several nucleosomes to large domains of multiple genes. Much of the early work on the identification of ChIP-enriched regions for ChIP-Seq data has focused on identifying localized regions, such as transcription factor binding sites. Bioinformatic tools to identify diffuse domains of ChIP-enriched regions have been lacking.Results: Based on the biological observation that histone modifications tend to cluster to form domains, we present a method that identifies spatial clusters of signals unlikely to appear by chance. This method pools together enrichment information from neighboring nucleosomes to increase sensitivity and specificity. By using genomic-scale analysis, as well as the examination of loci with validated epigenetic states, we demonstrate that this method outperforms existing methods in the identification of ChIP-enriched signals for histone modification profiles. We demonstrate the application of this unbiased method in important issues in ChIP-Seq data analysis, such as data normalization for quantitative comparison of levels of epigenetic modifications across cell types and growth conditions.Availability: http://home.gwu.edu/∼wpeng/Software.htmContact: wpeng@gwu.eduSupplementary information: Supplementary data are available at Bioinformatics online.