bluuebunny/crossref_metadata_2025_split huggingface dataset:
MOS Uncertainty Estimates in an Ensemble Framework
Authors: Glahn Bob , Peroutka Matthew , Wiedenfeld Jerry , Wagner John , Zylstra Greg , Schuknecht Bryan , Jackson Bryan 
Published: June 2008

Abstract
It is being increasingly recognized that the uncertainty in weather forecasts should be quantified and furnished to users along with the single-value forecasts usually provided. Probabilistic forecasts of “events” have been made in special cases; for instance, probabilistic forecasts of the event defined as 0.01 in. or more of precipitation at a point over a specified time period [i.e., the probability of precipitation (PoP)] have been disseminated to the public by the Weather Bureau/National Weather Service since 1966. Within the past decade, ensembles of operational numerical weather prediction models have been produced and used to some degree to provide probabilistic estimates of events easily dealt with, such as the occurrence of specific amounts of precipitation. In most such applications, the number of ensembles restricts this “enumeration” method, and the ensembles are characteristically underdispersive. However, fewer attempts have been made to provide a probability density function (PDF) or cumulative distribution function (CDF) for a continuous variable. The Meteorological Development Laboratory (MDL) has used the error estimation capabilities of the linear regression framework and kernel density fitting applied to individual and aggregate ensemble members of the Global Ensemble Forecast System of the National Centers for Environmental Prediction to develop PDFs and CDFs. This paper describes the method and results for temperature, dewpoint, daytime maximum temperature, and nighttime minimum temperature. The method produces reliable forecasts with accuracy exceeding the raw ensembles. Points on the CDF for 1650 stations have been mapped to the National Digital Forecast Database 5-km grid and an example is provided.
Emergency Management Decision Making during Severe Weather
Authors: Baumgart Leigh A. , Bass Ellen J. , Philips Brenda , Kloesel Kevin 
Published: June 2008

Abstract
Emergency managers make time-sensitive decisions in order to protect the public from threats including severe weather. Simulation and questionnaires were used to capture the decision-making process of emergency managers during severe weather events. These data were combined with insights from emergency manager instructors, National Weather Service (NWS) forecasters, and experienced emergency managers to develop a descriptive decision-making model of weather information usage, weather assessments, and decisions made during severe weather. This decision-making model can be used to develop better decision support tools, improve training, and to understand how innovative weather information could potentially affect emergency managers’ role of protecting the public.
The Relationship of the Lateral Cord of the Brachial Plexus to the Coracoid Process during Arthroscopic Coracoid Surgery
Authors: Pan Woei-Jack , Teo Yee-Sze , Chang Haw-Chong , Chong Kian-Chun , Karim Sarina Abdul 
Published: June 2008

Background Arthroscopic coracoid decompression is performed for coracoid impingement and has also been advocated for arthroscopic repair of tears of the subscapularis tendon, placing the lateral cord or the musculocutaneous nerve at risk of injury. The dynamic relationship of the lateral cord to the coracoid while the upper limb is in abduction and traction in the shoulder arthroscopy position is not clear. Purpose The purpose of this study was to evaluate the dynamic relationship of the lateral cord of the brachial plexus to the coracoid process during varying degrees of upper limb abduction in traction. Study Design Descriptive laboratory study. Methods and Materials The musculocutaneous nerves of 15 fresh-frozen cadaveric shoulders were carefully dissected and identified without mobilization of the nerve. The musculocutaneous nerve was then injected with radiopaque contrast mixed with methylene blue. The contrast would infiltrate retrogradely into the lateral cord, minimizing mobilization of the lateral cord. The specimens were mounted in the lateral decubitus position with 4.5 kg of traction to the forearm and anteroposterior radiographs were taken at 30° and 60° of abduction. The nearest distance of the lateral cord to the coracoid process was measured off the radiographs and the displacement with increase in shoulder abduction was determined. Results The mean nearest distance between the lateral cord and the coracoid tip at 30° of shoulder abduction was 26.6 ± 5.2 mm and it moved nearer at 60° of abduction to 23.4 ± 5.1 mm; the difference of 3.2 mm was statistically significant ( P < .0005, 95% confidence interval, 2.5–3.9 mm). The shortest distance measured was 14.4 mm in 1 specimen at 60° of abduction. Conclusion The lateral cord moved closer to the coracoid process at 60° than at 30° of abduction under traction during simulated shoulder arthroscopy position using the lateral decubitus position. Clinical Relevance The margin of safety for lateral cord injury during arthroscopic surgery around the coracoid process is improved with lower abduction angles in the lateral decubitus position.
Chronic graft-versus-host disease following umbilical cord blood transplantation: retrospective survey involving 1072 patients in Japan
Authors: Narimatsu Hiroto , Miyakoshi Shigesaburo , Yamaguchi Takuhiro , Kami Masahiro , Matsumura Tomoko , Yuji Koichiro , Murashige Naoko , Kusumi Eiji , Kodama Yuko , Komatsu Tsunehiko , Sakamaki Hisashi , Kouzai Yasushi , Okada Masaya , Osugi Yuko , Kobayashi Ryoji , Inoue Masami , Takahashi Satoshi , Kai Shunro , Kato Koji , Inoue-Nagamura Tokiko , Taniguchi Shuichi , Kato Shunichi 
Published: June 2008

Abstract
We have little information on chronic graft-versus-host disease (GVHD) after cord blood transplantation (CBT). We investigated its clinical features in 1072 Japanese patients with hematologic malignancies who received a transplant through the Japan Cord Blood Bank Network. The primary end point was to investigate the incidence of any chronic GVHD. Median age of the patients was 33 years (range, 0-79 years). The cumulative incidence of chronic GVHD 2 years after transplantation was 28%. Chronic GVHD was fatal in 29 patients. Multivariate analysis demonstrated that development of chronic GVHD was favorably associated with both overall survival and event-free survival. Multivariate analysis identified risk factors of chronic GVHD: higher patient body weight, higher number of mismatched antigens for GVHD direction, myeloablative preparative regimen, use of mycophenolate mofetil in GVHD prophylaxis, and development of grades II to IV acute GVHD. Although chronic GVHD is a significant problem after CBT, it is associated with improved survival, perhaps due to graft-versus-malignancy effects.
Macrophages contribute to the cellular uptake of von Willebrand factor and factor VIII in vivo
Authors: van Schooten Carina J. , Shahbazi Shirin , Groot Evelyn , Oortwijn Beatrijs D. , van den Berg H. Marijke , Denis Cécile V. , Lenting Peter J. 
Published: June 2008

AbstractVon Willebrand factor (VWF) and factor VIII (FVIII) circulate in a tight noncovalent complex. At present, the cells that contribute to the removal of FVIII and VWF are of unknown identity. Here, we analyzed spleen and liver tissue sections of VWF-deficient mice infused with recombinant VWF or recombinant FVIII. This analysis revealed that both proteins were targeted to cells of macrophage origin. When applied as a complex, both proteins were codirected to the same macrophages. Chemical inactivation of macrophages using gadolinium chloride resulted in doubling of endogenous FVIII levels in VWF-null mice, and of VWF levels in wild-type mice. Moreover, the survival of infused VWF was prolonged almost 2-fold in VWF-deficient mice after gadolinium chloride treatment. VWF and FVIII also bound to primary human macrophages in in vitro tests. In addition, radiolabeled VWF bound to human THP1 macrophages in a dose-dependent, specific, and saturable manner (half-maximal binding at 0.014 mg/mL). Binding to macrophages was followed by a rapid uptake and subsequent degradation of the internalized protein. This process was also visualized using a VWF–green fluorescent protein fusion protein. In conclusion, our data strongly indicate that macrophages play a prominent role in the clearance of the VWF/FVIII complex.
Detection of T lymphocytes with a second-site mutation in skin lesions of atypical X-linked severe combined immunodeficiency mimicking Omenn syndrome
Authors: Wada Taizo , Yasui Masahiro , Toma Tomoko , Nakayama Yuko , Nishida Mika , Shimizu Masaki , Okajima Michiko , Kasahara Yoshihito , Koizumi Shoichi , Inoue Masami , Kawa Keisei , Yachie Akihiro 
Published: June 2008

Abstract
X-linked severe combined immunodeficiency (XSCID) is caused by mutations of the common gamma chain (γc) and usually characterized by the absence of T and natural killer (NK) cells. Here, we report an atypical case of XSCID presenting with autologous T and NK cells and Omenn syndrome-like manifestations. The patient carried a splice-site mutation (IVS1+5G>A) that caused most of the mRNA to be incorrectly spliced but produced normally spliced transcript in lesser amount, leading to residual γc expression and development of T and NK cells. The skin biopsy specimen showed massive infiltration of revertant T cells. Those T cells were found to have a second-site mutation and result in complete restoration of correct splicing. These findings suggest that the clinical spectrum of XSCID is quite broad and includes atypical cases mimicking Omenn syndrome, and highlight the importance of revertant mosaicism as a possible cause for variable phenotypic expression.
Analysis of the spatial and temporal characteristics of platelet-delivered factor VIII–based clots
Authors: Neyman Michael , Gewirtz Jamie , Poncz Mortimer 
Published: June 2008

AbstractNormally factor (F) VIII is not expressed in megakaryocytes, but when human FVIII was transgenically expressed in murine megakaryocytes, it was stored in platelet α-granules and released at sites of injury. This platelet FVIII (pFVIII) is effective in correcting hemostasis, even in the presence of circulating inhibitors, so it offers a potential gene therapy strategy for hemophilia A. To understand clot development by pFVIII, we have examined clot response to laser injury in both cremaster arterioles and venules in FVIIInull mice either infused with FVIII or transgenic for pFVIII. In both sets of vessels, pFVIII is at least as effective as infused FVIII. However, there are temporal and spatial differences in fibrin and platelet accumulation within clots depending on how FVIII is delivered. These differences may be related to the temporal and spatial distribution of the α-granular–released FVIII within the developing clot, and may explain the increased frequency and size of embolic events seen with pFVIII. These observations may not only have implications for the use of pFVIII in gene therapy for hemophilia A, but may also have physiologic consequences, explaining why many procoagulant factors are delivered both in the plasma and in platelet α-granules.
The combination approach of SVM and ECOC for powerful identification and classification of transcription factor
Authors: Zheng Guangyong , Qian Ziliang , Yang Qing , Wei Chaochun , Xie Lu , Zhu Yangyong , Li Yixue 
Published: June 2008

AbstractBackgroundTranscription factors (TFs) are core functional proteins which play important roles in gene expression control, and they are key factors for gene regulation network construction. Traditionally, they were identified and classified through experimental approaches. In order to save time and reduce costs, many computational methods have been developed to identify TFs from new proteins and to classify the resulted TFs. Though these methods have facilitated screening of TFs to some extent, low accuracy is still a common problem. With the fast growing number of new proteins, more precise algorithms for identifying TFs from new proteins and classifying the consequent TFs are in a high demand.ResultsThe support vector machine (SVM) algorithm was utilized to construct an automatic detector for TF identification, where protein domains and functional sites were employed as feature vectors. Error-correcting output coding (ECOC) algorithm, which was originated from information and communication engineering fields, was introduced to combine with support vector machine (SVM) methodology for TF classification. The overall success rates of identification and classification achieved 88.22% and 97.83% respectively. Finally, a web site was constructed to let users access our tools (see Availability and requirements section for URL).ConclusionThe SVM method was a valid and stable means for TFs identification with protein domains and functional sites as feature vectors. Error-correcting output coding (ECOC) algorithm is a powerful method for multi-class classification problem. When combined with SVM method, it can remarkably increase the accuracy of TF classification using protein domains and functional sites as feature vectors. In addition, our work implied that ECOC algorithm may succeed in a broad range of applications in biological data mining.
Improving the prediction accuracy in classification using the combined data sets by ranks of gene expressions
Authors: Kim Ki-Yeol , Ki Dong Hyuk , Jeung Hei-Cheul , Chung Hyun Cheol , Rha Sun Young 
Published: June 2008

Abstract

Background
The information from different data sets experimented under different conditions may be inconsistent even though they are performed with the same research objectives. More than that, even when the data sets were generated from the same platform, the data agreement may be affected by the technical variation among the laboratories. In this case, it is necessary to use the combined data set after adjusting the differences between such data sets, for detecting the more reliable information.

Results
The proposed method combines data sets posterior to the discretization of data sets based on the ranks of the gene expression ratios, and the statistical method is applied to the combined data set for predictive gene selection. The efficiency of the proposed method was evaluated using five colon cancer related data sets, which were experimented using cDNA microarrays with different RNA sources, and one experiment utilized oligonucleotide arrays. NCI-60 cell lines data sets were used, which were performed with two different platforms of cDNA microarrays and Affymetrix HU6800 oligonucleotide arrays. The combined data set by the proposed method predicted the test data sets more accurately than the separated data sets did. The biological significant genes were detected from the combined data set, which were missed on the separated data sets.

Conclusion
By transforming gene expressions using ranks, the proposed method is not influenced by systematic bias among chips and normalization method. The method may be especially more useful to find predictive genes from data sets which have different scale in gene expressions.
Venezuelan equine encephalitis virus infection causes modulation of inflammatory and immune response genes in mouse brain
Authors: Sharma Anuj , Bhattacharya Bhaskar , Puri Raj K , Maheshwari Radha K 
Published: June 2008

Abstract

Background
Neurovirulent Venezuelan equine encephalitis virus (VEEV) causes lethal encephalitis in equines and is transmitted to humans by mosquitoes. VEEV is highly infectious when transmitted by aerosol and has been developed as a bio-warfare agent, making it an important pathogen to study from a military and civilian standpoint. Molecular mechanisms of VEE pathogenesis are poorly understood. To study these, the gene expression profile of VEEV infected mouse brains was investigated. Changes in gene expression were correlated with histological changes in the brain. In addition, a molecular framework of changes in gene expression associated with progression of the disease was studied.

Results
Our results demonstrate that genes related to important immune pathways such as antigen presentation, inflammation, apoptosis and response to virus (Cxcl10, CxCl11, Ccl5, Ifr7, Ifi27 Oas1b, Fcerg1,Mif, Clusterin and MHC class II) were upregulated as a result of virus infection. The number of over-expressed genes (>1.5-fold level) increased as the disease progressed (from 197, 296, 400, to 1086 at 24, 48, 72 and 96 hours post infection, respectively).

Conclusion
Identification of differentially expressed genes in brain will help in the understanding of VEEV-induced pathogenesis and selection of biomarkers for diagnosis and targeted therapy of VEEV-induced neurodegeneration.
Chloroplast DNA sequence of the green alga Oedogonium cardiacum (Chlorophyceae): Unique genome architecture, derived characters shared with the Chaetophorales and novel genes acquired through horizontal transfer
Authors: Brouard Jean-Simon , Otis Christian , Lemieux Claude , Turmel Monique 
Published: June 2008

Abstract

Background
To gain insight into the branching order of the five main lineages currently recognized in the green algal class Chlorophyceae and to expand our understanding of chloroplast genome evolution, we have undertaken the sequencing of chloroplast DNA (cpDNA) from representative taxa. The complete cpDNA sequences previously reported for Chlamydomonas (Chlamydomonadales), Scenedesmus (Sphaeropleales), and Stigeoclonium (Chaetophorales) revealed tremendous variability in their architecture, the retention of only few ancestral gene clusters, and derived clusters shared by Chlamydomonas and Scenedesmus. Unexpectedly, our recent phylogenies inferred from these cpDNAs and the partial sequences of three other chlorophycean cpDNAs disclosed two major clades, one uniting the Chlamydomonadales and Sphaeropleales (CS clade) and the other uniting the Oedogoniales, Chaetophorales and Chaetopeltidales (OCC clade). Although molecular signatures provided strong support for this dichotomy and for the branching of the Oedogoniales as the earliest-diverging lineage of the OCC clade, more data are required to validate these phylogenies. We describe here the complete cpDNA sequence of Oedogonium cardiacum (Oedogoniales).

Results
Like its three chlorophycean homologues, the 196,547-bp Oedogonium chloroplast genome displays a distinctive architecture. This genome is one of the most compact among photosynthetic chlorophytes. It has an atypical quadripartite structure, is intron-rich (17 group I and 4 group II introns), and displays 99 different conserved genes and four long open reading frames (ORFs), three of which are clustered in the spacious inverted repeat of 35,493 bp. Intriguingly, two of these ORFs (int and dpoB) revealed high similarities to genes not usually found in cpDNA. At the gene content and gene order levels, the Oedogonium genome most closely resembles its Stigeoclonium counterpart. Characters shared by these chlorophyceans but missing in members of the CS clade include the retention of psaM, rpl32 and trnL(caa), the loss of petA, the disruption of three ancestral clusters and the presence of five derived gene clusters.

Conclusion
The Oedogonium chloroplast genome disclosed additional characters that bolster the evidence for a close alliance between the Oedogoniales and Chaetophorales. Our unprecedented finding of int and dpoB in this cpDNA provides a clear example that novel genes were acquired by the chloroplast genome through horizontal transfers, possibly from a mitochondrial genome donor.
Genome-wide transcriptional changes induced by phagocytosis or growth on bacteria in Dictyostelium
Authors: Sillo Alessio , Bloomfield Gareth , Balest Alessandra , Balbo Alessandra , Pergolizzi Barbara , Peracino Barbara , Skelton Jason , Ivens Alasdair , Bozzaro Salvatore 
Published: June 2008

AbstractBackgroundPhagocytosis plays a major role in the defense of higher organisms against microbial infection and provides also the basis for antigen processing in the immune response. Cells of the model organismDictyosteliumare professional phagocytes that exploit phagocytosis of bacteria as the preferred way to ingest food, besides killing pathogens. We have investigatedDictyosteliumdifferential gene expression during phagocytosis of non-pathogenic bacteria, using DNA microarrays, in order to identify molecular functions and novel genes involved in phagocytosis.ResultsThe gene expression profiles of cells incubated for a brief time with bacteria were compared with cells either incubated in axenic medium or growing on bacteria. Transcriptional changes during exponential growth in axenic medium or on bacteria were also compared. We recognized 443 and 59 genes that are differentially regulated by phagocytosis or by the different growth conditions (growth on bacteria vs. axenic medium), respectively, and 102 genes regulated by both processes. Roughly one third of the genes are up-regulated compared to macropinocytosis and axenic growth. Functional annotation of differentially regulated genes with different tools revealed that phagocytosis induces profound changes in carbohydrate, aminoacid and lipid metabolism, and in cytoskeletal components. Genes regulating translation and mitochondrial biogenesis are mostly up-regulated. Genes involved in sterol biosynthesis are selectively up-regulated, suggesting a shift in membrane lipid composition linked to phagocytosis. Very few changes were detected in genes required for vesicle fission/fusion, indicating that the intracellular traffic machinery is mostly in common between phagocytosis and macropinocytosis. A few putative receptors, including GPCR family 3 proteins, scaffolding and adhesion proteins, components of signal transduction and transcription factors have been identified, which could be part of a signalling complex regulating phagocytosis and adaptational downstream responses.ConclusionThe results highlight differences between phagocytosis and macropinocytosis, and provide the basis for targeted functional analysis of new candidate genes and for comparison studies with transcriptomes during infection with pathogenic bacteria.
Mast cell activation is characterized by upregulation of a functional anaphylatoxin C5a receptor
Authors: Soruri Afsaneh , Grigat Jasmin , Kiafard Ziba , Zwirner Jörg 
Published: June 2008

AbstractBackgroundMast cells (MC) are key effector cells of allergic diseases and resistance to helminthic parasites and induce or amplify diverse innate and adaptive immune responses. The signals controlling MC mobilization during inflammation are not fully understood.ResultsSince anaphylatoxins are attractive candidates as MC chemoattractants, we investigated expression and function of anaphylatoxin receptors in murine MC. Precursor cell-derived MC cultured with IL-3 in the presence or absence of SCF did not express significant amounts of surface C5a receptor (C5aR) or C3a receptor (C3aR). MC required approximately 4 h of stimulation with Ag (DNP-albumin, following preincubation with IgE anti-DNP), ionomycin, or PMA to enable a strong chemotactic response towards C5a, paralleled by a distinct C5aR upregulation. Likewise, C5a induced intracellular calcium fluxes solely in activated MC. In contrast, C3a proved to be a weak MC chemotaxin and unable to increase intracellular calcium. Primary peritoneal MC did not express detectable amounts of anaphylatoxin receptors, however, similar to precursor cell-derived MC, stimulation with Ag or ionomycin for 4 h induced a prominent surface expression of C5aR whereas C3aR remained undetectable.ConclusionCollectively, our results suggest that Ag-dependent as well as -independent activation induces an inflammatory MC phenotype which is distinguished by neoexpression of a functional C5aR as a novel effector mechanism in MC-mediated pathogenesis.