bluuebunny/crossref_metadata_2025_split huggingface dataset:
A critical role for FcgammaRIIB in up-regulation of Fas ligand induced by a microbial polysaccharide
Authors: Piccioni M , Monari C , Bevilacqua S , Perito S , Bistoni F , Kozel T R , Vecchiarelli A 
Published: May 2011

SummaryThe microbial capsular polysaccharide glucuronoxylomannan (GXM) from the opportunistic fungus Cryptoccocus neoformans is able to alter the innate and adaptive immune response through multi-faceted mechanisms of immunosuppression. The ability of GXM to dampen the immune response involves the induction of T cell apoptosis, which is dependent on GXM-induced up-regulation of Fas ligand (FasL) on antigen-presenting cells. In this study we elucidate the mechanism exploited by GXM to induce up-regulation of FasL. We demonstrate that (i) the activation of FasL is dependent on GXM interaction with FcgammaRIIB (FcγRIIB); (ii) GXM induces activation of c-Jun NH2-terminal kinase (JNK) and p38 signal transduction pathways via FcγRIIB; (iii) this leads to downstream activation of c-Jun; (iv) JNK and p38 are simultaneously, but independently, activated; (v) FasL up-regulation occurs via JNK and p38 activation; and (vi) apoptosis occurs via FcγRIIB engagement with consequent JNK and p38 activation. Our results highlight a fast track to FasL up-regulation via FcγRIIB, and assign to this receptor a novel anti-inflammatory role that also accounts for induced peripheral tolerance. These results contribute to our understanding of the mechanism of immunosuppression that accompanies cryptococcosis.
Pyrosequencing cut‐off value identifying BRAFV600E mutation in fine needle aspiration samples of thyroid nodules
Authors: Yeo Min‐Kyung , Liang Zhe Long , Oh Taejeong , Moon Youngho , An Sungwhan , Kim Min Kyeong , Kim Koon Soon , Shong Minho , Kim Jin‐Man , Jo Young Suk 
Published: May 2011

SummaryContext  Recently, tremendous efforts have been made towards the development of sensitive techniques to detect the BRAFV600E mutation in fine needle aspiration biopsy (FNAB) samples. However, newly developed quantitative and semi‐quantitative methods, such as dual‐priming oligonucleotide (DPO)‐based multiplex polymerase chain reaction (PCR), have the potential to generate false‐positive (FP) results.Objectives  To eliminate the possibility of FP results, we generated a receiver operating characteristic (ROC) curve to investigate the diagnostic accuracy of pyrosequencing using quantitative data.Design  Cytological diagnoses of 983 thyroid nodules were made according to the Bethesda System 2007. The BRAFV600E mutation was analysed by pyrosequencing, and statistical analyses were performed.Results  Of the 983 nodules, 902 were adopted to evaluate the diagnostic value of pyrosequencing. The number of pathologically confirmed malignancies was 192, of which 182 were papillary thyroid cancer (PTC). By generating an ROC curve, we defined the optimal cut‐off value of the mutant allele peak as 5·95% (area under the curve, 0·849; sensitivity, 0·55; 1‐specificity, 0). When we applied this selective cut‐off value, the number of PTCs positive for BRAFV600E was 99 (54·4% of the total number of PTCs). With cytology alone, the diagnostic sensitivity and specificity of detecting malignancy were 71·2% and 100%, respectively. Pyrosequencing improved the diagnostic sensitivity from 71·2% to 78·5% (McNemar’s test, P < 0·001), without any change in the diagnostic specificity. When ‘suspicious for malignancy’ was considered a positive cytological outcome, pyrosequencing increased the diagnostic sensitivity of cytology from 95·8% to 96·9%; however, this improvement did not show statistical significance (McNemar’s test, P > 0·05).Conclusions  Pyrosequencing is an effective method for detecting the BRAFV600E mutation in FNAB samples. By allowing the optimal cut‐off value to be determined, pyrosequencing improves the diagnostic sensitivity while eliminating the possibility of FP results.
Tyrosine-Phosphorylated Ehrlichia chaffeensis and Ehrlichia canis Tandem Repeat Orthologs Contain a Major Continuous Cross-Reactive Antibody Epitope in Lysine-Rich Repeats
Authors: McBride Jere W. , Zhang Xiaofeng , Wakeel Abdul , Kuriakose Jeeba A. 
Published: May 2011

ABSTRACT

A small subset of major immunoreactive proteins have been identified in
Ehrlichia chaffeensis
and
Ehrlichia canis
, including three molecularly and immunologically characterized pairs of immunoreactive tandem repeat protein (TRP) orthologs with major continuous species-specific epitopes within acidic tandem repeats (TR) that stimulate strong antibody responses during infection. In this study, we identified a fourth major immunoreactive TR-containing ortholog pair and defined a major cross-reactive epitope in homologous nonidentical 24-amino-acid lysine-rich TRs. Antibodies from patients and dogs with ehrlichiosis reacted strongly with recombinant TR regions, and epitopes were mapped to the N-terminal TR region (18 amino acids) in
E. chaffeensis
and the complete TR (24 amino acids) in
E. canis
. Two less-dominant epitopes were mapped to adjacent glutamate/aspartate-rich and aspartate/tyrosine-rich regions in the acidic C terminus of
E. canis
TRP95 but not in
E. chaffeensis
TRP75. Major immunoreactive proteins in
E. chaffeensis
(75-kDa) and
E. canis
(95-kD) whole-cell lysates and supernatants were identified with TR-specific antibodies. Consistent with other ehrlichial TRPs, the TRPs identified in ehrlichial whole-cell lysates and the recombinant proteins migrated abnormally slow electrophoretically a characteristic that was demonstrated with the positively charged TR and negatively charged C-terminal domains.
E. chaffeensis
TRP75 and
E. canis
TRP95 were immunoprecipitated with anti-pTyr antibody, demonstrating that they are tyrosine phosphorylated during infection of the host cell.
Designing and Implementing the OP and OP2 Web Browsers
Authors: Grier Chris , Tang Shuo , King Samuel T. 
Published: May 2011

Current web browsers are plagued with vulnerabilities, providing hackers with easy access to computer systems via browser-based attacks. Browser security efforts that retrofit existing browsers have had limited success because the design of modern browsers is fundamentally flawed. To enable more secure web browsing, we design and implement a new browser, called the OP web browser, that attempts to improve the state-of-the-art in browser security. We combine operating system design principles with formal methods to design a more secure web browser by drawing on the expertise of both communities. Our design philosophy is to partition the browser into smaller subsystems and make all communication between subsystems simple and explicit. At the core of our design is a small
browser kernel
that manages the browser subsystems and interposes on all communications between them to enforce our new browser security features.

To show the utility of our browser architecture, we design and implement three novel security features. First, we develop flexible security policies that allow us to include browser plugins within our security framework. Second, we use formal methods to prove useful security properties including user interface invariants and browser security policy. Third, we design and implement a browser-level information-flow tracking system to enable post-mortem analysis of browser-based attacks.
In addition to presenting the OP browser architecture, we discuss the design and implementation of a second version of OP, OP2, that includes features from other secure web browser designs to improve on the overall security and performance of OP. To evaluate our design, we implemented OP2 and tested both performance, memory, and filesystem impact while browsing popular pages. We show that the additional security features in OP and OP2 introduce minimal overhead.
Global registration of dynamic range scans for articulated model reconstruction
Authors: Chang Will , Zwicker Matthias 
Published: May 2011

We present the articulated global registration algorithm to reconstruct articulated 3D models from dynamic range scan sequences. This new algorithm aligns multiple range scans simultaneously to reconstruct a full 3D model from the geometry of these scans. Unlike other methods, we express the surface motion in terms of a reduced deformable model and solve for joints and skinning weights. This allows a user to interactively manipulate the reconstructed 3D model to create new animations.
We express the global registration as an optimization of both the alignment of the range scans and the articulated structure of the model. We employ a graph-based representation for the skinning weights that successfully handles difficult topological cases well. Joints between parts are estimated automatically and are used in the optimization to preserve the connectivity between parts. The algorithm also robustly handles difficult cases where parts suddenly disappear or reappear in the range scans. The global registration produces a more accurate registration compared to a sequential registration approach, because it estimates the articulated structure based on the motion observed in all input frames. We show that we can automatically reconstruct a variety of articulated models without the use of markers, user-placed correspondences, segmentation, or template model.
Evaluation of IPCC Models’ Performance in Simulating Late-Twentieth-Century Climatologies and Weather Patterns over North America
Authors: Radić Valentina , Clarke Garry K. C. 
Published: May 2011

Abstract
The authors analyze the performance of 22 Intergovernmental Panel on Climate Change (IPCC) global climate models (GCMs) over all of North America and its western subregion using several different evaluation metrics. They assess the model skill in simulating climatologies of several climate variables and the skill in simulating the daily synoptic patterns. The evaluation is performed by comparing the model output with the North American Regional Reanalysis (NARR) over the period 1980–99. One set of metrics, based on root-mean-square errors and variance ratios, compares modeled versus the NARR mean annual cycle and interannual variability. Based on these measures the three top performing models are the ECHAM5–Max Planck Institute Ocean Model (MPI-OM), the third climate configuration of the Met Office Unified Model (HadCM3), and the Canadian Centre for Climate Modelling and Analysis (CCCma) Coupled General Circulation Model, version 3.1 [CGCM3.1(T47)]. Models that perform well over all North America also perform well over its western subregion. However, the model ranking is sensitive to the choice of climate variable. For another evaluation measure the method of self-organizing maps was applied to classify the characteristic daily patterns of sea level pressure over the region. The evaluation consists of correlating the frequencies of these patterns, as generated in GCMs, with the frequencies in the NARR over the baseline period. Most of the models are successful in simulating the frequencies of daily anomaly patterns from the 20-yr-average daily pattern. However, very few GCMs are able to reproduce the occurrences of characteristic daily weather patterns in the NARR on seasonal basis over the baseline period. In terms of relative performance, the three top performing models are the Meteorological Research Institute (MRI) CGCM2.3.2, ECHAM5–MPI-OM, and the Model for Interdisciplinary Research on Climate 3.2, high-resolution version [MIROC3.2(hires)]. The model skill in simulating daily synoptic patterns is not strongly linked to the skill in simulating the climatologies of selected variables. Despite the large scatter of model performance across all the metrics, some models consistently rank high [e.g., ECHAM5–MPI-OM and MIROC3.2(medres)]. Likewise, some models consistently rank low [e.g., the Community Climate System Model, version 3 (CCSM3) and the Goddard Institute for Space Studies Model E-R (GISS-ER)] independently of the evaluation measures, domain size, and climate variable of interest.
The Response of Quasigeostrophic Oceanic Vortices to Tropical Cyclone Forcing
Authors: Jaimes Benjamin , Shay Lynn K. , Halliwell George R. 
Published: May 2011

Abstract
The response of quasigeostrophic (QG) oceanic vortices to tropical cyclone (TC) forcing is investigated using an isopycnic ocean model. Idealized oceanic currents and wind fields derived from observational data acquired during Hurricane Katrina are used to initialize this model. It is found that the upwelling response is a function of the curl of wind-driven acceleration of oceanic mixed layer (OML) currents rather than a function of the wind stress curl. Upwelling (downwelling) regimes prevail under the TC’s eye as it translates over cyclonic (anticyclonic) QG vortices. OML cooling of ~1°C occurs over anticyclones because of the combined effects of downwelling, instantaneous turbulent entrainment over the deep warm water column (weak stratification), and vertical dispersion of near-inertial energy. By contrast, OML cooling of ~4°C occurs over cyclones due to the combined effects of upwelling, instantaneous turbulent entrainment over regions of tight vertical thermal gradients (strong stratification), and trapping of near-inertial energy that enhances vertical shear and mixing at the OML base. The rotational rate of the QG vortex affects the dispersion of near-inertial waves. As rotation is increased in both cyclones and anticyclones, the near-inertial response is shifted toward more energetic frequencies that enhance vertical shear and mixing. TC-induced temperature anomalies in QG vortices propagate westward with time, deforming the cold wake. Therefore, to accurately simulate the impact of TC-induced OML cooling and feedback mechanisms on storm intensity, coupled ocean–atmosphere TC models must resolve geostrophic ocean eddy location as well as thermal, density, and velocity structures.
Bereaved relatives’ views about participating in cancer research
Authors: Koffman Jonathan , Higginson Irene J , Hall Sue , Riley Julia , McCrone Paul , Gomes Barbara 
Published: May 2011

Background: Bereaved relatives are considered to be a vulnerable group and there is debate as to whether it is ethical to engage them in research at a time that can be difficult for them. Aim: We conducted a cross-sectional study using cognitive interviewing with the aim of exploring the acceptability of a mortality follow-back survey among bereaved relatives of recently deceased cancer patients to inform the development of a large-scale survey about end-of-life care. Results: Thirty-three next-of-kin of recently deceased cancer patients were invited to participate in a face-to-face interview, or to complete a postal questionnaire. At the end, they were asked about their views of engaging in the study. Nine bereaved relatives participated in a face-to-face interview and 11 completed the postal questionnaire. Eleven relatives reported it was helpful to take part in the study; of these, six did not consider it distressing, and five stated whilst it had been distressing it had been helpful. Thoughts about bringing back memories, altruism and therapeutic value emerged. Conclusions: We have new evidence that although engaging in follow-back surveys can evoke distress, many participants report it to be a positive experience. We therefore believe that this approach is acceptable when conducted sensitively.
An observational study to determine the prevalence of alcohol use disorders in advanced cancer patients
Authors: Webber Katherine , Davies Andrew N 
Published: May 2011

Context: observational studies in North America suggest alcohol dependence is a common problem in advanced cancer patients and is associated with a high burden of physical and psychological symptoms. The prevalence of all types of alcohol use disorders, and the relationship between alcohol use disorders and symptoms, has not been studied. Objectives: this observational, cross-sectional study was designed to determine the prevalence of alcohol use disorders in patients with advanced cancer and establish if such patients have a higher symptom burden. Methods: sequential patients referred to the palliative medicine team at a United Kingdom cancer centre completed the Alcohol Use Disorders Identification Test, Hospital Anxiety and Depression Scale (HADS) and Memorial Symptom Assessment Scale-Short Form (MSAS-SF). Results: 120 patients participated in the study. Twenty-two (18%) patients screened positively for the presence of an alcohol use disorder. This study found no significant association between alcohol use disorders and the presence of anxiety ( P = 0.38) or depression ( P = 0.81) on the HADS or the global distress index subscale ( P = 0.142), physical symptom distress index subscale ( P = 0.734), or the psychological distress index subscale ( P = 0.154) on the MSAS-SF. Current smoking status was the only independent predictor for the presence of an alcohol use disorder ( P < 0.001). Seven (6%) patients screened positively for high-risk alcohol use disorders. Current smoking status ( P < 0.001) and male gender ( p < 0.001) were independent predictors of this problem. Conclusions: alcohol use disorders in this cohort of patients were not associated with a higher symptom burden, and the prevalence was lower than the general United Kingdom population.
Vibration analysis of oil-injected twin-screw compressors using simple simulated waveforms
Authors: Fujiwara A , Matsuo K , Yamashita H 
Published: May 2011

There are few published references on the practical diagnosis of oil-injected twin-screw compressors. In most cases of diagnosis on this type of compressors, usual methods that deal with machine elements, gears, rotational parts, rolling element bearings, couplings, and so on, are employed. These methods are certainly effective but not specified for diagnosis of oil-injected twin-screw compressors. The purpose of this study is to develop an effective tool for diagnosis of vibrations in oil-injected twin-screw compressors. Vibrations in this type of compressors vary with the quality of machining and operating conditions. Therefore, it is difficult to establish a systematic method of analysing vibration data in all practical conditions. This paper reports on a method developed to diagnose lobe meshing vibrations on this type of compressors using synthesized waveform models. Typical vibration waveforms are synthesized from basic waves with measured data and simple assumptions. These synthesized waveforms are then used to diagnose lobe mesh and resonance vibration problems in the compressors, after being modulated into modified waveform models. Waveforms synthesized by this method were fairly in good agreement with measured waveforms, indicating that this method is an effective tool in diagnosing lobe mesh vibration problems. There is no verified method or information on the diagnosis of lobe mesh vibrations in oil-injected screw compressors; this method, therefore, offers a effective analysis.
Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing
Authors: Durban Jordi , Juárez Paula , Angulo Yamileth , Lomonte Bruno , Flores-Diaz Marietta , Alape-Girón Alberto , Sasa Mahmood , Sanz Libia , Gutiérrez José M , Dopazo Joaquín , Conesa Ana , Calvete Juan J 
Published: May 2011

Abstract

Background
A long term research goal of venomics, of applied importance for improving current antivenom therapy, but also for drug discovery, is to understand the pharmacological potential of venoms. Individually or combined, proteomic and transcriptomic studies have demonstrated their feasibility to explore in depth the molecular diversity of venoms. In the absence of genome sequence, transcriptomes represent also valuable searchable databases for proteomic projects.

Results
The venom gland transcriptomes of 8 Costa Rican taxa from 5 genera (Crotalus, Bothrops, Atropoides, Cerrophidion, and Bothriechis) of pitvipers were investigated using high-throughput 454 pyrosequencing. 100,394 out of 330,010 masked reads produced significant hits in the available databases. 5.165,220 nucleotides (8.27%) were masked by RepeatMasker, the vast majority of which corresponding to class I (retroelements) and class II (DNA transposons) mobile elements. BLAST hits included 79,991 matches to entries of the taxonomic suborder Serpentes, of which 62,433 displayed similarity to documented venom proteins. Strong discrepancies between the transcriptome-computed and the proteome-gathered toxin compositions were obvious at first sight. Although the reasons underlaying this discrepancy are elusive, since no clear trend within or between species is apparent, the data indicate that individual mRNA species may be translationally controlled in a species-dependent manner. The minimum number of genes from each toxin family transcribed into the venom gland transcriptome of each species was calculated from multiple alignments of reads matched to a full-length reference sequence of each toxin family. Reads encoding ORF regions of Kazal-type inhibitor-like proteins were uniquely found in Bothriechis schlegelii and B. lateralis transcriptomes, suggesting a genus-specific recruitment event during the early-Middle Miocene. A transcriptome-based cladogram supports the large divergence between A. mexicanus and A. picadoi, and a closer kinship between A. mexicanus and C. godmani.

Conclusions
Our comparative next-generation sequencing (NGS) analysis reveals taxon-specific trends governing the formulation of the venom arsenal. Knowledge of the venom proteome provides hints on the translation efficiency of toxin-coding transcripts, contributing thereby to a more accurate interpretation of the transcriptome. The application of NGS to the analysis of snake venom transcriptomes, may represent the tool for opening the door to systems venomics.
Novel transposable elements from Anopheles gambiae
Authors: Fernández-Medina Rita D , Struchiner Cláudio J , Ribeiro José MC 
Published: May 2011

Abstract
Background
Transposable elements (TEs) are DNA sequences, present in the genome of most eukaryotic organisms that hold the key characteristic of being able to mobilize and increase their copy number within chromosomes. These elements are important for eukaryotic genome structure and evolution and lately have been considered as potential drivers for introducing transgenes into pathogen-transmitting insects as a means to control vector-borne diseases. The aim of this work was to catalog the diversity and abundance of TEs within the Anopheles gambiae genome using the PILER tool and to consolidate a database in the form of a hyperlinked spreadsheet containing detailed and readily available information about the TEs present in the genome of An. gambiae.

Results
Here we present the spreadsheet named AnoTExcel that constitutes a database with detailed information on most of the repetitive elements present in the genome of the mosquito. Despite previous work on this topic, our approach permitted the identification and characterization both of previously described and novel TEs that are further described in detailed.

Conclusions
Identification and characterization of TEs in a given genome is important as a way to understand the diversity and evolution of the whole set of TEs present in a given species. This work contributes to a better understanding of the landscape of TEs present in the mosquito genome. It also presents a novel platform for the identification, analysis, and characterization of TEs on sequenced genomes.