bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integration and acceleration of virtual microscopy as the key to successful implementation into the routine diagnostic process
Authors: Wienert Stephan , Beil Michael , Saeger Kai , Hufnagl Peter , Schrader Thomas 
Published: January 2009

Abstract

Background
The virtual microscopy is widely accepted in Pathology for educational purposes and teleconsultation but is far from the routine use in surgical pathology due to the technical requirements and some limitations. A technical problem is the limited bandwidth of a usual network and the delayed transmission rate and presentation time on the screen.

Methods
In this study the process of secondary diagnostic was evaluated using the "T.Konsult Pathologie" service of the Professional Association of German Pathologists within the German breast cancer screening program. The characteristics of the access to the WSI (Whole Slide Images) have been analyzed to explore the possibilities of prefetching and caching to reduce the presentation and transfer time with the goal to increase user acceptance. The log files of the web server were analyzed to reconstruct the movements of the pathologist on the WSI and to create the observation path. Using a specialized tool the observation paths were extracted automatically from the log files. The attributes linearity, 3-point-linearity, changes per request, and number of consecutive requests were calculated to design, develop and evaluate different caching and prefetching strategies.

Results
The analysis of the observation paths showed that a complete accordance of two image requests is a very rare event. But more frequently a partial covering of two requested image areas can be found. In total 257 diagnostic paths from 131 WSI have been extracted and analysed. On average a diagnostic path consists of 16 image requests and takes 189 seconds between first and last image request. The mean linearity was 0,41 and the mean 3-point-linearity 0,85. Three different caching algorithms have been compared with respect to hit rate and additional image requests on the WSI server. Tests demonstrated that 95% of the diagnostic paths could be loaded without any deletion of entries in the cache (cache size 12,2 Megapixel). If the image parts are stored after JPEG compression this complies with less than 2 MB.

Discussion
WSI telepathology is a technology which offers the possibility to break the limitations of conventional static telepathology. The complete histological slide may be investigated instead of sets of images of lesions sampled by the presenting pathologist. The benefit is demonstrated by the high diagnostic security of 95% accordance between first and second diagnosis.
Interactions among type I and type II interferon, tumor necrosis factor, and β-estradiol in the regulation of immune response-related gene expressions in systemic lupus erythematosus
Authors: Lee Hooi-Ming , Mima Toru , Sugino Hidehiko , Aoki Chieko , Adachi Yasuo , Yoshio-Hoshino Naoko , Matsubara Kenichi , Nishimoto Norihiro 
Published: January 2009

Abstract
Introduction
Systemic lupus erythematosus (SLE) is a prototypical autoimmune disease characterized by various clinical manifestations. Several cytokines interact and play pathological roles in SLE, although the etiopathology is still obscure. In the present study we investigated the network of immune response-related molecules expressed in the peripheral blood of SLE patients, and the effects of cytokine interactions on the regulation of these molecules.

Methods
Gene expression profiles of peripheral blood from SLE patients and from healthy women were analyzed using DNA microarray analysis. Differentially expressed genes classified into the immune response category were selected and analyzed using bioinformatics tools. Since interactions among TNF, IFNγ, β-estradiol (E2), and IFNα may regulate the expression of interferon-inducible (IFI) genes, stimulating and co-stimulating experiments were carried out on peripheral blood mononuclear cells followed by analysis using quantitative RT-PCR.

Results
Thirty-eight downregulated genes and 68 upregulated genes were identified in the functional category of immune response. Overexpressed IFI genes were confirmed in SLE patient peripheral bloods. Using network-based analysis on these genes, several networks including cytokines – such as TNF and IFNγ – and E2 were constructed. TNF-regulated genes were dominant in these networks, but in vitro TNF stimulation on peripheral blood mononuclear cells showed no differences in the above gene expressions between SLE and healthy individuals. Co-stimulating with IFNα and one of TNF, IFNγ, or E2 revealed that TNF has repressive effects while IFNγ essentially has synergistic effects on IFI gene expressions in vitro. E2 showed variable effects on IFI gene expressions among three individuals.

Conclusions
TNF may repress the abnormal regulation by IFNα in SLE while IFNγ may have a synergistic effect. Interactions between IFNα and one of TNF, IFNγ, or E2 appear to be involved in the pathogenesis of SLE.
No evidence of major effects in several Toll-like receptor gene polymorphisms in rheumatoid arthritis
Authors: Jaen Olivier , Petit-Teixeira Elisabeth , Kirsten Holger , Ahnert Peter , Semerano Luca , Pierlot Céline , Cornelis Francois , Boissier Marie-Christophe , Falgarone Geraldine ,   the European Consortium on Rheumatoid Arthritis Families
Published: January 2009

Abstract
Introduction
The objective was to study the potential genetic contribution of Toll-like receptor (TLR) genes in rheumatoid arthritis (RA). TLRs bind to pathogen-associated molecular patterns, and TLR genes influence both proinflammatory cytokine production and autoimmune responses. Host–pathogen interactions are involved in RA physiopathology.

Methods
We tested SNPs of five TLR genes (TLR9, TLR2, TLR6, TLR1, and TLR4) in a cohort of 100 French families with RA. Genotypes were analyzed using the transmission disequilibrium test. As TLR2, TLR6, and TLR1 are located on chromosome 4, we determined the haplotype relative risk. Analyses were performed in subgroups defined by status for rheumatoid factor, anti-cyclic citrullinated peptide autoantibodies, and erosions.

Results
We found no disequilibrium in allele transmission for any of the SNPs of the five TLR genes. In subgroup analyses, no associations were detected linking TLR9, TLR2, or TLR9/TLR2 to rheumatoid factor, anti-cyclic citrullinated peptide autoantibodies, or erosions. Haplotype analysis of the polymorphisms showed no haplotype associations in any of the subgroups.

Conclusions
We found no evidence of major effects of TLR gene polymorphisms in RA, although we tested different TLR phenotypes. Moreover, no associations were noted with autoantibody production or erosions.
Analysis of the platypus genome suggests a transposon origin for mammalian imprinting
Authors: Pask Andrew J , Papenfuss Anthony T , Ager Eleanor I , McColl Kaighin A , Speed Terence P , Renfree Marilyn B 
Published: January 2009

Abstract
Background
Genomic imprinting is an epigenetic phenomenon that results in monoallelic gene expression. Many hypotheses have been advanced to explain why genomic imprinting evolved in mammals, but few have examined how it arose. The host defence hypothesis suggests that imprinting evolved from existing mechanisms within the cell that act to silence foreign DNA elements that insert into the genome. However, the changes to the mammalian genome that accompanied the evolution of imprinting have been hard to define due to the absence of large scale genomic resources between all extant classes. The recent release of the platypus genome has provided the first opportunity to perform comparisons between prototherian (monotreme; which appear to lack imprinting) and therian (marsupial and eutherian; which have imprinting) mammals.

Results
We compared the distribution of repeat elements known to attract epigenetic silencing across the entire genome from monotremes and therian mammals, particularly focusing on the orthologous imprinted regions. There is a significant accumulation of certain repeat elements within imprinted regions of therian mammals compared to the platypus.

Conclusions
Our analyses show that the platypus has significantly fewer repeats of certain classes in the regions of the genome that have become imprinted in therian mammals. The accumulation of repeats, especially long terminal repeats and DNA elements, in therian imprinted genes and gene clusters is coincident with, and may have been a potential driving force in, the development of mammalian genomic imprinting. These data provide strong support for the host defence hypothesis.
The ethics of dietary supplements and natural health products in pharmacy practice: A systematic documentary analysis
Authors: Boon Heather , Hirschkorn Kristine , Griener Glenn , Cali Michelle 
Published: January 2009

AbstractObjectivesMany natural health products and dietary supplements are purchased in pharmacies and it has been argued that pharmacists are in the best position to provide patients with evidence-based information about them. This study was designed to identify how the pharmacist's role with respect to natural health products and dietary supplements is portrayed in the literature.MethodA systematic search was conducted in a variety of health databases to identify all literature that pertained to both pharmacy and natural health products and dietary supplements. Of the 786 articles identified, 665 were broad-coded and 259 were subjected to in-depth qualitative content analysis for emergent themes.Key findingsOverwhelmingly, support for the sale of natural health products and dietary supplements in pharmacies is strong. Additionally, a role for pharmacist counselling is underscored. But another recurrent theme is that pharmacists are ill-equipped to counsel patients about these products that are available on their shelves. This situation has led some to question the ethics of pharmacists selling natural health products and dietary supplements and to highlight the existence of an ethical conflict stemming from the profit-motive associated with sales of natural health products and dietary supplements.ConclusionsThis analysis raises concerns about the ethics of natural health products and dietary supplements being sold in pharmacies, and about pharmacists being expected to provide counselling about products of which they have little knowledge.
Effect of component stiffness and deformation on vehicle lateral drift during braking
Authors: Mirza N , Hussain K , Day A J , Klaps J 
Published: January 2009

This article presents a simulation study into effects of compliant (flexible) components (such as the engine subframe and the lower control arm) and their deflections on the characteristics of a vehicle experiencing steering drift during straight-line braking. The vehicle front and rear suspension are modelled using multi-body dynamic analysis software. The front suspension model represents the MacPherson strut design of the vehicle and includes a rack and pinion steering system, brake system, engine subframe, and a powertrain unit. The model has been analysed under two steering control methods: fixed and free control. Suspension characteristics and the effect of deflections arising from the subframe and the lower control arm on these suspension characteristics have been analysed. The simulations confirmed that variation of component stiffness and interactions within components give rise to side-to-side deflections that could affect lateral drift during braking. It is concluded that side-to-side variation of suspension characteristics can have a detrimental effect on lateral drift during braking and that compliant components whose stiffness varies from side to side can cause different side-to-side deflections that can induce and influence variation in suspension characteristics such as toe steer angle that can lead the vehicle during braking.
Interpreting Slug Tests with Large Data Sets
Authors: Chapuis Robert P. 
Published: January 2009

Abstract
Pressure transducers are frequently used to monitor slug tests, and to collect a data set for height Z of water column versus time t. Direct application of the data to draw a velocity graph usually produces a wide scatter, thus limiting the usefulness of the velocity graph method. This paper proposes to interpret the data set in five steps. First, a Z(t) plot is drawn to assess the uncertainty in the Z data. Second, a limited number of data points are selected to reduce the uncertainty to about ±10 % in the velocity graph. Third, the velocity graph is drawn to obtain the hydraulic conductivity k and the piezometric error H0, if any, giving the piezometric level for the test. Fourth, the graph of ln(Z−H0) versus t is drawn to verify its linearity and check the k value of the velocity graph. Fifth, the graph of Z versus log10(t) can be used in a curve fitting process to yield directly both H0 and k, thus providing a second method to interpret the data set, which may be the only one possible when the Z(t) data are inaccurate. Examples are provided to illustrate the five steps and common problems.
Myanmar's Foreign Trade and its Political Consequences
Authors: Alamgir Jalal 
Published: January 2009

Abstract
Analysis of Myanmar's official and unofficial trade suggests that the material bases of independent political power have weakened. Concentration of commercial influence in conjunction with Western trade sanctions has curtailed the potential spread of an independent trading class. Declining trade exposure has also diluted the political power of agriculture, Burma's traditional mainstay, to sustain challenges to the regime.
Historical Meditations in Two Films by John Gianvito
Authors: Rosenbaum Jonathan 
Published: January 2009

Abstract
A comparative essay on two feature-length, hybrid films directed by John Gianvito, The Mad Songs of Fernanda Hussein (2001), which concerns the irreparable effects of the 1991 Gulf War, and Profit Motive and the Whispering Wind (2007), a meditation on the grave sites of American activists.
Beyond the Choir: An Interview with David Simon
Authors: Beck Richard 
Published: January 2009

Abstract
In this interview, David Simon, executive producer and writer (together with Ed Burns), talks about Generation Kill, the seven-part HBO adaptation of Evan Wright's book about the 2003 U.S. invasion of Iraq and the early days of occupation. Simon emphasizes the desire to stay as faithful as possible to the book as well as discussing particular characters and scenes.
Small tumor size as favorable prognostic factor after adrenalectomy in Conn's adenoma
Authors: Giacchetti Gilberta , Ronconi Vanessa , Rilli Silvia , Guerrieri Mario , Turchi Federica , Boscaro Marco 
Published: January 2009

ObjectivePrimary aldosteronism (PA) due to aldosterone-producing adenoma (APA) is the most common curable form of secondary hypertension.DesignIn order to evaluate blood pressure outcome after adrenalectomy for APA and to identify new favorable prognostic factors, data from 42 consecutive APA patients who underwent adrenalectomy were collected from 2005 to 2007.MethodsRenin-angiotensin-aldosterone system (upright and postsaline infusion test), serum and urinary electrolytes, office and ambulatory blood pressure monitoring were evaluated at baseline and after a follow-up of 2.7±2.2 years. Drug history and adenoma size at morphological evaluation were also collected.ResultsMultiple regression analysis showed that, before surgery, patients with a small adenoma (diameter <20 mm) displayed higher postsaline aldosterone values (P=0.0001), and lower serum potassium levels (P=0.020), than patients with adenoma >20 mm. Before surgery, mineralocorticoid receptor (MR) antagonists were used in patients with small APA in greater percentage than patients with bigger adenomas (64 vs 30% respectively,P=0.037). At follow-up, blood pressure normalized in 63% of the subjects. Recovered patients had a shorter duration of hypertension (P=0.038), and a smaller adenoma size (P=0.035). Receiver operating characteristic curves showed that a duration of hypertension ≤6 years and an APA size <20 mm were the best predictors of blood pressure normalization. Patients with APA <20 mm showed the complete restoration of blood pressure circadian rhythm.ConclusionsThe presence of APA <20 mm, duration of hypertension equal or less than 6 years, and preoperative MR antagonists use are favorable prognostic factors for hypertension recovery after adrenalectomy.
Critical period of sensitivity for effects of cadmium on frog growth and development
Authors: Gross Jackson A. , Johnson Pieter T. J. , Prahl Lili K. , Karasov William H. 
Published: January 2009

Abstract
Cadmium is a ubiquitous pollutant in aquatic environments that can alter organismal physiology and ecology. Previous experiments found that ecological Cd exposures increased the growth and development of two North American anurans. However, the generality of these effects among species, the time period over which they occur, and the mechanisms responsible remain conjectural. The goal of the present study was to determine the critical period of sensitivity of Rana pipiens exposed to ecologically relevant levels of Cd. We exposed tadpoles to Cd (0 [control], 1.0, and 10.0 μg/L) from Gosner stage (GS) 25 to metamorphic climax. We assessed effects of Cd on amphibian length, survival, and development during premetamorphosis (GS 25–30) and prometamorphosis (GS 31–42). After 14 d of exposure, we staged tadpoles and recorded snout-vent length. Tadpoles were then pooled according to treatment and stage (GS ≤ 29 or GS ≥ 30) and allowed to undergo metamorphic development. Tadpoles exposed to 10 μg/L were significantly larger and more advanced in development by 14 d. Survival to forelimb emergence exceeded 90% in all treatments, and time to metamorphic climax was not different from that in controls. Body burdens of Cd were positively correlated with increasing treatment. Early amphibian development (premetamorphosis) was shown to be the critical period of sensitivity for growth and development. Whereas the freshwater criterion for Cd appears to be protective for survival, a lack of knowledge remains about the sublethal effects of chronic exposures of metal pollutants, especially as they relate to tissue concentrations at various stages of amphibian life history.
New Downhole-Fluid-Analysis Tool for Improved Reservoir Characterization
Authors: Dong C. , O'Keefe M. D. , Elshahawi H. , Hashem M. , Williams S. , Stensland D. , Hegeman P. , Vasques R. , Terabayashi T. , Mullins O. , Donzier E. 
Published: January 2009

Summary
Downhole fluid analysis (DFA) has emerged as a key technique for characterizing the distribution of reservoir-fluid properties and determining zonal connectivity across the reservoir. Information from profiling the reservoir fluids enables sealing barriers to be proved and compositional grading to be quantified; this information cannot be obtained from conventional wireline logs. The DFA technique has been based largely on optical spectroscopy, which can provide estimates of filtrate contamination, gas/oil ratio (GOR), pH of formation water, and a hydrocarbon composition in four groups: methane (C1), ethane to pentane (C2–5), hexane and heavier hydrocarbons (C6+), and carbon dioxide (CO2). For single-phase assurance, it is possible to detect gas liberation (bubblepoint) or liquid dropout (dewpoint) while pumping reservoir fluid to the wellbore, before filling a sample bottle.
In this paper, a new DFA tool is introduced that substantially increases the accuracy of these measurements. The tool uses a grating spectrometer in combination with a filter-array spectrometer. The range of compositional information is extended from four groups to five groups: C1, ethane (C2), propane to pentane (C3–5), C6+, and CO2. These spectrometers, together with improved compositional algorithms, now make possible a quantitative analysis of reservoir fluid with greater accuracy and repeatability. This accuracy enables comparison of fluid properties between wells for the first time, thus extending the application of fluid profiling from a single-well to a multiwall basis. Field-based fluid characterization is now possible.
In addition, a new measurement is introduced—in-situ density of reservoir fluid. Measuring this property downhole at reservoir conditions of pressure and temperature provides important advantages over surface measurements. The density sensor is combined in a package that includes the optical spectrometers and measurements of fluid resistivity, pressure, temperature, and fluorescence that all play a vital role in determining the exact nature of the reservoir fluid.
Extensive tests at a pressure/volume/temperature (PVT) laboratory are presented to illustrate sensor response in a large number of live-fluid samples. These tests of known fluid compositions were conducted under pressurized and heated conditions to simulate reservoir conditions. In addition, several field examples are presented to illustrate applicability in different environments.
A Brief Introduction to Algebraic Set Theory
Authors: Awodey Steve 
Published: January 2009

AbstractThis brief article is intended to introduce the reader to the field of algebraic set theory, in which models of set theory of a new and fascinating kind are determined algebraically. The method is quite robust, applying to various classical, intuitionistic, and constructive set theories. Under this scheme some familiar set theoretic properties are related to algebraic ones, while others result from logical constraints. Conventional elementary set theories are complete with respect to algebraic models, which arise in a variety of ways, such as topologically, type-theoretically, and through variation. Many previous results from topos theory involving realizability, permutation, and sheaf models of set theory are subsumed, and the prospects for further such unification seem bright.
A Natural Axiomatization of Computability and Proof of Church's Thesis
Authors: Dershowitz Nachum , Gurevich Yuri 
Published: January 2009

AbstractChurch's Thesis asserts that the only numeric functions that can be calculated by effective means are the recursive ones, which are the same, extensionally, as the Turing-computable numeric functions. The Abstract State Machine Theorem states that every classical algorithm is behaviorally equivalent to an abstract state machine. This theorem presupposes three natural postulates about algorithmic computation. Here, we show that augmenting those postulates with an additional requirement regarding basic operations gives a natural axiomatization of computability and a proof of Church's Thesis, as Gödel and others suggested may be possible. In a similar way, but with a different set of basic operations, one can prove Turing's Thesis, characterizing the effective string functions, and—in particular—the effectively-computable functions on string representations of numbers.
Reconsidering Ordered Pairs
Authors: Scott Dana , McCarty Dominic 
Published: January 2009

AbstractThe well known Wiener-Kuratowski explicit definition of the ordered pair, which sets (x,y) = {{x}, {x,y}}, works well in many set theories but fails for those with classes which cannot be members of singletons. With the aid of the Axiom of Foundation, we propose arecursivedefinition of ordered pair which addresses this shortcoming and also naturally generalizes to ordered tuples of greater length. There are many advantages to the new definition, for it allows for uniform definitions working equally well in a wide range of models for set theories. In ZFC and closely related theories, the rank of an ordered pair of twoinfinite setsunder the new definition turns out to be equal to the maximum of the ranks of the sets.