bluuebunny/crossref_metadata_2025_split huggingface dataset:
Error Characteristics of Rainfall Measurements by Collocated Joss–Waldvogel Disdrometers
Authors: Tokay Ali , Bashor Paul G. , Wolff Katherine R. 
Published: May 2005

Abstract
Error characteristics of rainfall measurements were studied using six collocated Joss–Waldvogel (JW) disdrometers that are located at NASA’s Wallops Flight Facility. The six disdrometer means of rain rate R, reflectivity Z, and differential reflectivity ZDR, for a given minute were considered as a reference. The maximum deviations of R, Z, and ZDR from the mean in a rain event were 0.6 mm h−1, 1.3 dB, and 0.05 dB, respectively. Rainfall statistics were then examined between disdrometer pairs. The root-mean-square (rms) difference of R, Z, and ZDR between paired disdrometers in a rain event were as high as 3.2 mm h−1, 3.7 dB, and 0.3 dB, respectively. The rms difference of R and ZDR were even higher when the disdrometer observations were stratified based on reflectivity intervals. The differences in disdrometer rainfall measurements have a potential impact when the disdrometers are considered as calibration tools for vertically pointing and scanning radars. The differences between the disdrometer measurements also result in differences in coefficients and exponents of the derived relations between radar parameters and rain rate. Among the four different relations between radar parameters and rain rate, the absolute difference in rain rate |ΔR| from two different JW disdrometers was highest in R(ZH, ZDR) and lowest in R(KDP, ZDR). The other two relations were R(Z) and R(KDP). The |ΔR| increases with increasing horizontally polarized reflectivity ZH, and differential specific phase KDP in both single- and dual-parameter rainfall estimators, while the |ΔR| increases with decreasing ZDR in dual-parameter rainfall estimators. Several sources of JW disdrometer malfunctions were also presented. The hardware problems were the leading cause for the malfunction of the JW disdrometers, as identified by the manufacturer. A single JW disdrometer could have inherent measurement errors that can only be identified in the presence of collocated (preferably two) rain-measuring instruments.
Contribution of Hfe expression in macrophages to the regulation of hepatic hepcidin levels and iron loading
Authors: Makui Hortence , Soares Ricardo J. , Jiang Wenlei , Constante Marco , Santos Manuela M. 
Published: May 2005

Abstract
Hereditary hemochromatosis (HH), an iron overload disease associated with mutations in the HFE gene, is characterized by increased intestinal iron absorption and consequent deposition of excess iron, primarily in the liver. Patients with HH and Hfe-deficient (Hfe-/-) mice manifest inappropriate expression of the iron absorption regulator hepcidin, a peptide hormone produced by the liver in response to iron loading. In this study, we investigated the contribution of Hfe expression in macrophages to the regulation of liver hepcidin levels and iron loading. We used bone marrow transplantation to generate wild-type (wt) and Hfe-/- mice chimeric for macrophage Hfe gene expression. Reconstitution of Hfe-deficient mice with wt bone marrow resulted in augmented capacity of the spleen to store iron and in significantly decreased liver iron loading, accompanied by a significant increase of hepatic hepcidin mRNA levels. Conversely, wt mice reconstituted with Hfe-deficient bone marrow had a diminished capacity to store iron in the spleen but no significant alterations of liver iron stores or hepcidin mRNA levels. Our results suggest that macrophage Hfe participates in the regulation of splenic and liver iron concentrations and liver hepcidin expression. (Blood. 2005;106:2189-2195)
Reduced frequencies and suppressive function of CD4+CD25hi regulatory T cells in patients with chronic lymphocytic leukemia after therapy with fludarabine
Authors: Beyer Marc , Kochanek Matthias , Darabi Kamruz , Popov Alexey , Jensen Markus , Endl Elmar , Knolle Percy A. , Thomas Roman K. , von Bergwelt-Baildon Michael , Debey Svenja , Hallek Michael , Schultze Joachim L. 
Published: May 2005

AbstractGlobally suppressed T-cell function has been described in many patients with cancer to be a major hurdle for the development of clinically efficient cancer immunotherapy. Inhibition of antitumor immune responses has been mainly linked to inhibitory factors present in cancer patients. More recently, increased frequencies of CD4+CD25hi regulatory T cells (Treg cells) have been described as an additional mechanism reducing immunity. We assessed 73 patients with B-cell chronic lymphocytic leukemia (CLL) and 42 healthy controls and demonstrated significantly increased frequencies of cytotoxic T lymphocyte-associated protein 4 (CTLA4+)–, Forkhead box P3 (FOXP3+)–, glucocorticoid-induced tumor necrosis factor receptor-related protein (GITR+)–, CD62L+–, transforming growth factor β1 (TGF-β1+)–, interleukin 10 (IL-10+)–Treg cells in patients with CLL, with highest frequencies in untreated or progressing patients presenting with extended disease. Most surprisingly, in the majority of patients with CLL treated with fludarabine-containing therapy regimens the inhibitory function of Treg cells was decreased or even abrogated. In addition, frequencies of Treg cells were significantly decreased after therapy with fludarabine. In light of similar findings for cyclophosphamide the combination of fludarabine and cyclophosphamide might be further exploited in strategies reducing immunosuppression prior to cancer immunotherapy.
Interplay between P2Y1, P2Y12, and P2X1 receptors in the activation of megakaryocyte cation influx currents by ADP: evidence that the primary megakaryocyte represents a fully functional model of platelet P2 receptor signaling
Authors: Tolhurst Gwen , Vial Catherine , Léon Catherine , Gachet Christian , Evans Richard J. , Mahaut-Smith Martyn P. 
Published: May 2005

AbstractThe difficulty of conducting electrophysiologic recordings from the platelet has restricted investigations into the role of ion channels in thrombosis and hemostasis. We now demonstrate that the well-established synergy between P2Y1 and P2Y12 receptors during adenosine diphosphate (ADP)–dependent activation of the platelet αIIbβ3 integrin also exists in murine marrow megakaryocytes, further supporting the progenitor cell as a bona fide model of platelet P2 receptor signaling. In patch clamp recordings, ADP (30 μM) stimulated a transient inward current at –70 mV, which was carried by Na+ and Ca2+ and was amplified by phenylarsine oxide, a potentiator of certain transient receptor potential (TRP) ion channels by phosphatidylinositol 4,5-bisphosphate depletion. This initial current decayed to a sustained phase, upon which repetitive transient inward cation currents with pre-dominantly P2X1-like kinetics were super-imposed. Abolishing P2X1-receptor activity prevented most of the repetitive currents, consistent with their activation by secreted adenosine triphosphate (ATP). Recordings in P2Y1-receptor–deficient megakaryocytes demonstrated an essential requirement of this receptor for activation of all ADP-evoked inward currents. However, P2Y12 receptors, through the activation of PI3-kinase, played a synergistic role in both P2Y1 and P2X1-receptor–dependent currents. Thus, direct stimulation of P2Y1 and P2Y12 receptors, together with autocrine P2X1 activation, is responsible for the activation of nonselective cation currents by the platelet agonistADP.
Forced aggregation of defined numbers of human embryonic stem cells into embryoid bodies fosters robust, reproducible hematopoietic differentiation
Authors: Ng Elizabeth S. , Davis Richard P. , Azzola Lisa , Stanley Edouard G. , Elefanty Andrew G. 
Published: May 2005

AbstractTo realize the therapeutic potential of human embryonic stem cells (hESCs), it is necessary to regulate their differentiation in a uniform and reproducible manner. We have developed a method in which known numbers of hESCs in serum-free medium were aggregated by centrifugation to foster the formation of embryoid bodies (EBs) of uniform size (spin EBs). These spin EBs differentiated efficiently and synchronously, as evidenced by the sequential expression of molecular markers representing stem cells, primitive streak, and mesoderm. In the presence of hematopoietic growth factors, reproducible differentiation was achieved with blood cells formed in more than 90% of EBs. Using chimeric EBs generated from mixtures of green fluorescence protein–positive (GFP+) and GFP– hESCs in a clonogenic assay, hematopoietic precursor frequency was estimated to be approximately 1:500 input cells. This method of EB formation provides a generally applicable means for modulating and objectively monitoring the directed differentiation of hESCs.
Interleukin-17A mRNA and protein expression within cells from the human bronchoalveolar space after exposure to organic dust
Authors: Ivanov Stefan , Palmberg Lena , Venge Per , Larsson Kjell , Lindén Anders 
Published: May 2005

Abstract
Background
In mice, the cytokine interleukin (IL)-17A causes a local accumulation of neutrophils within the bronchoalveolar space. IL-17A may thereby also contribute to an increased local proteolytic burden. In the current study, we determined whether mRNA for IL-17A is elevated and protein expression of IL-17A occurs locally in inflammatory cells within the human bronchoalveolar space during severe inflammation caused by organic dust. We also assessed the expression of the elastinolytic protease MMP-9 in this airway compartment.

Methods
Six healthy, non-smoking human volunteers were exposed to organic dust in a swine confinement, a potent stimulus of neutrophil accumulation within the human bronchoalveolar space. Bronchoalveolar lavage (BAL) fluid was harvested 2 weeks before and 24 hours after the exposure and total and differential counts were conducted for inflammatory BAL cells. Messenger RNA for IL-17A was measured using reverse transcript polymerase chain reaction-enzyme linked immunoassay (RT-PCR-ELISA). Intracellular immunoreactivity (IR) for IL-17A and MMP-9, respectively, was determined in BAL cells.

Results
The exposure to organic dust caused more than a forty-fold increase of mRNA for IL-17A in BAL cells. IL-17A immunoreactivity was detected mainly in BAL lymphocytes, and the number of these IL-17A expressing lymphocytes displayed an eight-fold increase, even though not statistically significant. The increase in IL-17A mRNA was associated with a substantial increase of the number of BAL neutrophils expressing MMP-9 immunoreactivity.

Conclusion
Exposure to organic dust increases local IL-17A mRNA and because there is intracellular expression in BAL lymphocytes, this suggests that IL-17A protein can originate from lymphocytes within the human bronchoalveolar space. The fact that the increased IL-17A mRNA is associated with an increased number of MMP-9-expressing neutrophils is compatible with IL-17A increasing the local proteolytic burden through its neutrophil-accumulating effect.
GENETAG: a tagged corpus for gene/protein named entity recognition
Authors: Tanabe Lorraine , Xie Natalie , Thom Lynne H , Matten Wayne , Wilbur W John 
Published: May 2005

Abstract

Background
Named entity recognition (NER) is an important first step for text mining the biomedical literature. Evaluating the performance of biomedical NER systems is impossible without a standardized test corpus. The annotation of such a corpus for gene/protein name NER is a difficult process due to the complexity of gene/protein names. We describe the construction and annotation of GENETAG, a corpus of 20K MEDLINE® sentences for gene/protein NER. 15K GENETAG sentences were used for the BioCreAtIvE Task 1A Competition.

Results
To ensure heterogeneity of the corpus, MEDLINE sentences were first scored for term similarity to documents with known gene names, and 10K high- and 10K low-scoring sentences were chosen at random. The original 20K sentences were run through a gene/protein name tagger, and the results were modified manually to reflect a wide definition of gene/protein names subject to a specificity constraint, a rule that required the tagged entities to refer to specific entities. Each sentence in GENETAG was annotated with acceptable alternatives to the gene/protein names it contained, allowing for partial matching with semantic constraints. Semantic constraints are rules requiring the tagged entity to contain its true meaning in the sentence context. Application of these constraints results in a more meaningful measure of the performance of an NER system than unrestricted partial matching.

Conclusion
The annotation of GENETAG required intricate manual judgments by annotators which hindered tagging consistency. The data were pre-segmented into words, to provide indices supporting comparison of system responses to the "gold standard". However, character-based indices would have been more robust than word-based indices. GENETAG Train, Test and Round1 data and ancillary programs are freely available at ftp://ftp.ncbi.nlm.nih.gov/pub/tanabe/GENETAG.tar.gz. A newer version of GENETAG-05, will be released later this year.
Identifying gene and protein mentions in text using conditional random fields
Authors: McDonald Ryan , Pereira Fernando 
Published: May 2005

Abstract

Background
We present a model for tagging gene and protein mentions from text using the probabilistic sequence tagging framework of conditional random fields (CRFs). Conditional random fields model the probability P(t|o) of a tag sequence given an observation sequence directly, and have previously been employed successfully for other tagging tasks. The mechanics of CRFs and their relationship to maximum entropy are discussed in detail.

Results
We employ a diverse feature set containing standard orthographic features combined with expert features in the form of gene and biological term lexicons to achieve a precision of 86.4% and recall of 78.7%. An analysis of the contribution of the various features of the model is provided.
Systematic feature evaluation for gene name recognition
Authors: Hakenberg Jörg , Bickel Steffen , Plake Conrad , Brefeld Ulf , Zahn Hagen , Faulstich Lukas , Leser Ulf , Scheffer Tobias 
Published: May 2005

Abstract
In task 1A of the BioCreAtIvE evaluation, systems had to be devised that recognize words and phrases forming gene or protein names in natural language sentences. We approach this problem by building a word classification system based on a sliding window approach with a Support Vector Machine, combined with a pattern-based post-processing for the recognition of phrases. The performance of such a system crucially depends on the type of features chosen for consideration by the classification method, such as pre- or postfixes, character n-grams, patterns of capitalization, or classification of preceding or following words. We present a systematic approach to evaluate the performance of different feature sets based on recursive feature elimination, RFE. Based on a systematic reduction of the number of features used by the system, we can quantify the impact of different feature sets on the results of the word classification problem. This helps us to identify descriptive features, to learn about the structure of the problem, and to design systems that are faster and easier to understand. We observe that the SVM is robust to redundant features. RFE improves the performance by 0.7%, compared to using the complete set of attributes. Moreover, a performance that is only 2.3% below this maximum can be obtained using fewer than 5% of the features.
An inter-platform repeatability study investigating real-time amplification of plasmid DNA
Authors: Donald Carol E , Qureshi Fizza , Burns Malcolm J , Holden Marcia J , Blasic Joseph R , Woolford Alison J 
Published: May 2005

Abstract
Background
The wide variety of real-time amplification platforms currently available has determined that standardisation of DNA measurements is a fundamental aspect involved in the comparability of results.
Statistical analysis of the data arising from three different real-time platforms was conducted in order to assess inter-platform repeatability. On three consecutive days two PCR reaction mixes were used on each of the three amplification platforms – the LightCycler®, ABI PRISM® 7700 and Rotor Gene 3000™. Real-time PCR amplification using a fluorogenic 5' exonuclease assay was performed in triplicate on negative controls and DNA plasmid dilutions of 108–102 copies to give a total of 24 reactions per PCR experiment.

Results
The results of the statistical analyses indicated that the platform with the most precise repeatability was the ABI PRISM® 7700 when coupled with the FastStart PCR reaction mix. It was also found that there was no obvious relationship between plasmid copy number and repeatability. An ANOVA approach identified the factors that significantly affected the results, in descending order of magnitude, as: plasmid copy number, platform, PCR reaction mix and day (on which the experiment was performed).

Conclusion
In order to deliver useful, informative genetic tests, standardisation of real-time PCR detection platforms to provide repeatable, reliable results is warranted. In addition, a better understanding of inter-assay and intra-assay repeatability is required.
The subcutaneous movements of filarial infective larvae are impaired in vaccinated hosts in comparison to primary infected hosts
Authors: Babayan Simon A , Attout Tarik , Vuong Phat N , Le Goff Laetitia , Gantier Jean-Charles , Bain Odile 
Published: May 2005

AbstractOur aim in this study was to observe the movements of filarial infective larvae following inoculation into the mammalian host and to assess the effect of vaccination on larval migration, in situ. Here we present recordings of larvae progressing through the subcutaneous tissues and inguinal lymph node of primary infected or vaccinated mice. We used the filaria Litomosoides sigmodontis in BALB/c mice that were necropsied 6 hours after the challenge inoculation of 200 larvae. Subcutaneous tissue sections were taken from the inoculation site and larvae were filmed in order to quantify their movements. Our analyses showed that the subcutaneous larvae were less motile in the vaccinated mice than in primary-infected mice and had more leucocytes attached to the cuticle. We propose that this reduced motility may result in the failure of a majority of larvae to evade the inflammatory reaction, thereby being a possible mechanism involved in the early vaccine-induced protection.
Economic and biological costs of cardiac imaging
Authors: Picano Eugenio 
Published: May 2005

Abstract
Medical imaging market consists of several billion tests per year worldwide. Out of these, at least one third are cardiovascular procedures. Keeping in mind that each test represents a cost, often a risk, and a diagnostic hypothesis, we can agree that every unnecessary and unjustifiable test is one test too many. Small individual costs, risks, and wastes multiplied by billions of examinations per year represent an important population, society and environmental burden. Unfortunately, the appropriateness of cardiac imaging is extra-ordinarily low and there is little awareness in patients and physicians of differential costs, radiological doses, and long term risks of different imaging modalities. For a resting cardiac imaging test, being the average cost (not charges) of an echocardiogram equal to 1 (as a cost comparator), the cost of a CT is 3.1x, of a SPECT 3.27x, of a Cardiovascular Magnetic Resonance imaging 5.51x, of a PET 14.03x, and of a right and left heart catheterization 19.96x. For stress cardiac imaging, compared with the treadmill exercise test equal to 1 (as a cost comparator), the cost of stress echocardiography is 2.1x and of a stress SPECT scintigraphy is 5.7x. Biohazards and downstream long-term costs linked to radiation-induced oncogenesis should also be considered. The radiation exposure is absent in echo and magnetic resonance, and corresponds to 500 chest x rays for a sestamibi cardiac stress scan and to 1150 chest x rays for a thallium scan. The corresponding extra-risk in a lifetime of fatal cancer is 1 in 2000 exposed patients for a sestamibi stress and 1 in 1000 for a thallium scan. Increased awareness of economic, biologic, and environmental costs of cardiac imaging will hopefully lead to greater appropriateness, wisdom and prudence from both the prescriber and the practitioner. In this way, the sustainability of cardiac imaging will eventually improve.
Evaluation of autoantibodies to common and neuronal cell antigens in Chronic Fatigue Syndrome
Authors: Vernon Suzanne D , Reeves William C 
Published: May 2005

Abstract
People with chronic fatigue syndrome (CFS) suffer from multiple symptoms including fatigue, impaired memory and concentration, unrefreshing sleep and musculoskeletal pain. The exact causes of CFS are not known, but the symptom complex resembles that of several diseases that affect the immune system and autoantibodies may provide clues to the various etiologies of CFS. We used ELISA, immunoblot and commercially available assays to test serum from subjects enrolled in a physician-based surveillance study conducted in Atlanta, Georgia and a population-based study in Wichita, Kansas for a number of common autoantibodies and antibodies to neuron specific antigens. Subsets of those with CFS had higher rates of antibodies to microtubule-associated protein 2 (MAP2) (p = 0.03) and ssDNA (p = 0.04). There was no evidence of higher rates for several common nuclear and cellular antigens in people with CFS. Autoantibodies to specific host cell antigens may be a useful approach for identifying subsets of people with CFS, identify biomarkers, and provide clues to CFS etiologies.
RNA interference: more than a research tool in the vertebrates' adaptive immunity
Authors: Mak Johnson 
Published: May 2005

Abstract
In recent years, RNA silencing, usage of small double stranded RNAs of ~21 – 25 base pairs to regulate gene expression, has emerged as a powerful research tool to dissect the role of unknown host cell factors in this 'post-genomic' era. While the molecular mechanism of RNA silencing has not been precisely defined, the revelation that small RNA molecules are equipped with this regulatory function has transformed our thinking on the role of RNA in many facets of biology, illustrating the complexity and the dynamic interplay of cellular regulation. As plants and invertebrates lack the protein-based adaptive immunity that are found in jawed vertebrates, the ability of RNA silencing to shut down gene expression in a sequence-specific manner offers an explanation of how these organisms counteract pathogen invasions into host cells. It has been proposed that this type of RNA-mediated defence mechanism is an ancient form of immunity to offset the transgene-, transposon- and virus-mediated attack. However, whether 1) RNA silencing is a natural immune response in vertebrates to suppress pathogen invasion; or 2) vertebrate cells have evolved to counteract invasion in a 'RNA silencing' independent manner remains to be determined. A number of recent reports have provided tantalizing clues to support the view that RNA silencing functions as a physiological response to regulate viral infection in vertebrate cells. Amongst these, two manuscripts that are published in recent issues of Science and Immunity, respectively, have provided some of the first direct evidences that RNA silencing is an important component of antiviral defence in vertebrate cells. In addition to demonstrating RNA silencing to be critical to vertebrate innate immunity, these studies also highlight the potential of utilising virus-infection systems as models to refine our understanding on the molecular determinants of RNA silencing in vertebrate cells.