bluuebunny/crossref_metadata_2025_split huggingface dataset:
Which staging system to use for gynaecological cancers: a survey with recommendations for practice in the UK
Authors: McCluggage Glenn , Hirschowitz Lynn , Ganesan Raji , Kehoe Sean , Nordin Andrew 
Published: August 2010

AimsThere are two commonly used staging systems for gynaecological cancers, namely Fédération Internationale de Gynécologie et d'Obstétrique (FIGO) and TNM. The authors wished to ascertain which staging system is most commonly used in dealing with gynaecological cancers in the UK.MethodsThe authors undertook a survey among participants in the National Gynaecological Pathology EQA scheme to investigate whether gynaecological pathologists in the UK use FIGO or TNM staging in their routine reporting of gynaecological cancers.ResultsThere were 105 respondents out of 278 participants (38%). Of the analysed results, a majority of respondents (64%) use FIGO staging, while 32% use both FIGO and TNM. 80% of respondents stated that their multidisciplinary team meeting uses FIGO staging, while 18% use both FIGO and TNM. Only an extremely small minority of pathologists and multidisciplinary team meetings use TNM alone. A survey of members of the British Gynaecological Cancer Society revealed similar findings.ConclusionsSince FIGO and TNM are not always equivalent, and there may be confusion when more than one staging system is used, it is recommended that FIGO staging be used for gynaecological cancers. The survey revealed support for the use of TNM, as well as FIGO, only for cervical cancer, since FIGO does not take the lymph node status into account. Given the prevalent practice in the UK, the British Association of Gynaecological Pathologists, British Gynaecological Cancer Society and gynaecological clinical reference group of the National Cancer Intelligence Network recommend that FIGO staging be used for gynaecological cancers with recording of the lymph node status for cervical cancer. This may be done by providing a TNM stage for this cancer type only or by recording the lymph-node status at the multidisciplinary team meeting.
Perspectives on Fred Sanders' Research on Cold Fronts
Authors: Schultz David M. 
Published: August 2010

Abstract
One characteristic of Fred Sanders' research is his ability to take a topic that is believed to be well understood by the research community and show that interesting research problems still exist. Among Sanders' considerable contributions to synoptic meteorology, those concerned with surface cold fronts have been especially influential. After a brief historical review of fronts and frontal analysis, this chapter presents three stages in Sanders' career when he performed research on the structure, dynamics, and analysis of surface cold fronts. First, his 1955 paper, "An investigation of the structure and dynamics of an intense surface frontal zone," was the first study to discuss quantitatively the dynamics of a surface cold front. In the 1960s, Sanders and his students further examined the structure of cold fronts, resulting in the unpublished 1967 report to the National Science Foundation, "Frontal structure and the dynamics of frontogenesis." For a third lime in his career, Sanders published several papers (1995–2005) revisiting the structure and dynamics of cold fronts. His 1967 and 1995–2005 work raises the question of the origin and dynamics of the surface pressure trough and/or wind shift that sometimes precedes the temperature gradient (hereafter called a prefrontal trough or prefrontal wind shift, respectively). Sanders showed that the relationship between this prefrontal feature and the temperature gradient is fundamental to the strength of the front. When the wind shift is coincident with the temperature gradient, frontogenesis (strengthening of the front) results; when the wind shift lies ahead of the temperature gradient, frontolysis (weakening of the front) results. a number of proposed mechanisms for the formation of prefrontal troughs and prefrontal wind shifts exist. Consequently, much research remains to be performed on these topics.
The Application of Fred Sanders' Teaching to Current Research on Extreme Cold-Season Precipitation Events in the Saint Lawrence River Valley Region
Authors: Gyakum John R. 
Published: August 2010

Abstract
Fred Sanders' teaching and research contributions in the area of quasigeostrophic theory are highlighted in this paper. The application of these contributions is made to the topic of extreme cold-season precipitation events in the Saint Lawrence valley in the northeastern United States and southern Quebec.
This research focuses on analyses of Saint Lawrence valley heavy precipitation events. Synoptic- and planetary-scale circulation anomaly precursors are typically identified several days prior to these events. These precursors include transient upper-level troughs, strong moisture transports into the region, and anomalously large precipitable water amounts. The physical insight of Fred Sanders' work is used in the analysis of these composite results. Further details of this insight are provided in analyses of one case of heavy precipitation.
Back to Norway: An Essay
Authors: Emanuel Kerry 
Published: August 2010

Abstract
The advent of the polar front theory of cyclones in Norway early in the last century held that the development of fronts and air masses is central to understanding midlatitude weather phenomena. While work on fronts continues to this day, the concept of air masses has been largely forgotten, superseded by the idea of a continuum. The Norwegians placed equal emphasis on the thermodynamics of airmass formation and on the dynamical processes that moved air masses around; today, almost all the emphasis is on dynamics, with little published literature on diabatic processes acting on a large scale. In this essay, the author argues that a lack of understanding of large-scale diabatic processes leads to an incomplete picture of the atmosphere and contributes to systematic errors in medium- and long-range weather forecasts. At the same time, modern concepts centered around potential vorticity conservation and inversion lead one to a redefinition of the term "air mass" that may have some utility in conceptualizing atmospheric physics and in weather forecasting.
Functional characterization of a 13-bp deletion (c.-1522_-1510del13) in the promoter of the von Willebrand factor gene in type 1 von Willebrand disease
Authors: Othman Maha , Chirinian Yvette , Brown Christine , Notley Colleen , Hickson Nicholas , Hampshire Daniel , Buckley Suzanne , Waddington Simon , Parker Alan L. , Baker Andrew , James Paula , Lillicrap David 
Published: August 2010

Abstract
We have studied the effect of a 13-bp deletion in the promoter of the von Willebrand factor (VWF) gene in a patient with type 1 von Willebrand disease. The index case has a VWF:Ag of 0.49 IU/mL and is heterozygous for the deletion. The deletion is located 48 bp 5′ of the transcription start site, and in silico analysis, electrophoretic mobility shift assays, and chromatin immunoprecipitation studies all predict aberrant binding of Ets transcription factors to the site of the deletion. Transduction of reporter gene constructs into blood outgrowth endothelial cells showed a 50.5% reduction in expression with the mutant promoter (n = 16, P < .001). A similar 40% loss of transactivation was documented in transduced HepG2 cells. A similar marked reduction of transgene expression was shown in the livers of mice injected with the mutant promoter construct (n = 8, P = .003). Finally, in studies of BOEC mRNA, the index case showed a 4.6-fold reduction of expression of the VWF transcript associated with the deletion mutation. These studies show that the 13-bp deletion mutation alters the binding of Ets (and possibly GATA) proteins to the VWF promoter and significantly reduces VWF expression, thus playing a central pathogenic role in the type 1 von Willebrand disease phenotype in the index case.
When Toll-like receptor and T-cell receptor signals collide: a mechanism for enhanced CD8 T-cell effector function
Authors: Geng Degui , Zheng Liqin , Srivastava Ratika , Asprodites Nicole , Velasco-Gonzalez Cruz , Davila Eduardo 
Published: August 2010

AbstractEmerging reports reveal that activating Toll-like receptor-2 (TLR2)–MyD88 signals in CD8 T lymphocytes enhances cytokine production and cytotoxicity; however, the signaling pathway remains undefined. In the present study, we examined the physiologic significance and molecular mechanisms involved in this process. We found that TLR2 engagement on T-cell receptor transgenic CD8 OT-1 T cells increased T-bet transcription factor levels consequently, augmenting effector transcript and protein levels both in vivo and in vitro. In contrast, TLR2 agonist did not costimulate TLR2−/−OT-1 or MyD88−/−OT-1 T cells. Elevated T-bet levels in TLR2-MyD88–activated T cells was a consequence of increased biosynthesis resulting from the enhanced acti- vation of the mammalian target of the rapamycin (mTOR) pathway. Inhibiting mTOR, Akt, or protein kinase C in T cells abolished the costimulatory effects of the TLR2 agonist. In vivo, activating TLR2–MyD88 signals in T cells increased effector-molecule levels and enhanced the clearance of Listeria monocytogenes-Ova. These results help define a signaling pathway linking the TLR-MyD88 and mTOR pathway in an Akt- and protein kinase C–dependent manner. These results highlight a critical role for MyD88 signaling in T-cell activation and cytotoxicity. Furthermore, these findings offer the opportunity for improving the efficacy of vaccines and T cell–based immunotherapies by targeting TLR-MyD88 signaling within T cells.
Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images
Authors: Helmuth Jo A , Paul Grégory , Sbalzarini Ivo F 
Published: August 2010

Abstract

Background
Sub-cellular structures interact in numerous direct and indirect ways in order to fulfill cellular functions. While direct molecular interactions crucially depend on spatial proximity, other interactions typically result in spatial correlations between the interacting structures. Such correlations are the target of microscopy-based co-localization analysis, which can provide hints of potential interactions. Two complementary approaches to co-localization analysis can be distinguished: intensity correlation methods capitalize on pattern discovery, whereas object-based methods emphasize detection power.

Results
We first reinvestigate the classical co-localization measure in the context of spatial point pattern analysis. This allows us to unravel the set of implicit assumptions inherent to this measure and to identify potential confounding factors commonly ignored. We generalize object-based co-localization analysis to a statistical framework involving spatial point processes. In this framework, interactions are understood as position co-dependencies in the observed localization patterns. The framework is based on a model of effective pairwise interaction potentials and the specification of a null hypothesis for the expected pattern in the absence of interaction. Inferred interaction potentials thus reflect all significant effects that are not explained by the null hypothesis. Our model enables the use of a wealth of well-known statistical methods for analyzing experimental data, as demonstrated on synthetic data and in a case study considering virus entry into live cells. We show that the classical co-localization measure typically under-exploits the information contained in our data.

Conclusions
We establish a connection between co-localization and spatial interaction of sub-cellular structures by formulating the object-based interaction analysis problem in a spatial statistics framework based on nearest-neighbor distance distributions. We provide generic procedures for inferring interaction strengths and quantifying their relative statistical significance from sets of discrete objects as provided by image analysis methods. Within our framework, an interaction potential can either refer to a phenomenological or a mechanistic model of a physico-chemical interaction process. This increased flexibility in designing and testing different hypothetical interaction models can be used to quantify the parameters of a specific interaction model or may catalyze the discovery of functional relations.
Microarray meta-analysis database (M2DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database
Authors: Cheng Wei-Chung , Tsai Min-Lung , Chang Cheng-Wei , Huang Ching-Lung , Chen Chaang-Ray , Shu Wun-Yi , Lee Yun-Shien , Wang Tzu-Hao , Hong Ji-Hong , Li Chia-Yang , Hsu Ian C 
Published: August 2010

Abstract

Background
Over the past decade, gene expression microarray studies have greatly expanded our knowledge of genetic mechanisms of human diseases. Meta-analysis of substantial amounts of accumulated data, by integrating valuable information from multiple studies, is becoming more important in microarray research. However, collecting data of special interest from public microarray repositories often present major practical problems. Moreover, including low-quality data may significantly reduce meta-analysis efficiency.

Results
M2DB is a human curated microarray database designed for easy querying, based on clinical information and for interactive retrieval of either raw or uniformly pre-processed data, along with a set of quality-control metrics. The database contains more than 10,000 previously published Affymetrix GeneChip arrays, performed using human clinical specimens. M2DB allows online querying according to a flexible combination of five clinical annotations describing disease state and sampling location. These annotations were manually curated by controlled vocabularies, based on information obtained from GEO, ArrayExpress, and published papers. For array-based assessment control, the online query provides sets of QC metrics, generated using three available QC algorithms. Arrays with poor data quality can easily be excluded from the query interface. The query provides values from two algorithms for gene-based filtering, and raw data and three kinds of pre-processed data for downloading.

Conclusion
M2DB utilizes a user-friendly interface for QC parameters, sample clinical annotations, and data formats to help users obtain clinical metadata. This database provides a lower entry threshold and an integrated process of meta-analysis. We hope that this research will promote further evolution of microarray meta-analysis.
RNA Interference inhibits Hepatitis B Virus of different genotypes in Vitro and in Vivo
Authors: Zhang Ya-Li , Cheng Tong , Cai Yi-Jun , Yuan Quan , Liu Che , Zhang Tao , Xia De-Zhen , Li Rui-Yin , Yang Lian-Wei , Wang Ying-Bin , Yeo Anthony ET , Shih James Wai-Kuo , Zhang Jun , Xia Ning-shao 
Published: August 2010

Abstract

Background
Hepatitis B virus (HBV) infection increases the risk of liver disease and hepatocellular carcinoma. Small interfering RNA (siRNA) can be a potential new tool for HBV therapy. Given the high heterogeneity of HBV strains and the sensitivity towards sequences changes of siRNA, finding a potent siRNA inhibitor against the conservative site on the HBV genome is essential to ensure a therapeutic application.

Results
Forty short hairpin RNA (shRNA) expression plasmids were constructed to target conserved regions among nine HBV genotypes. HBV 1.3-fold genome plasmids carrying various genotypes were co-transfected with shRNA plasmids into either Huh7 cells or mice. The levels of various viral markers were examined to assess the anti-HBV efficacy of siRNA. Four (B245, B376, B1581 and B1789) were found with the ability to potently inhibit HBV RNA, DNA, surface antigen (HBsAg), e antigen (HBeAg) and core antigen (HBcAg) expression in HBV genotypes A, B, C, D and I (a newly identified genotype) in Huh7 cells and in mice. No unusual cytotoxicity or off-target effects were noted.

Conclusions
Such siRNA suggests an alternate way of inhibiting various HBV genotypes in vitro and in vivo, promising advances in the treatment of HBV.
The clinical Pseudomonas fluorescens MFN1032 strain exerts a cytotoxic effect on epithelial intestinal cells and induces Interleukin-8 via the AP-1 signaling pathway
Authors: Madi Amar , Lakhdari Omar , Blottière Hervé M , Guyard-Nicodème Muriel , Le Roux Karine , Groboillot Anne , Svinareff Pascal , Doré Joel , Orange Nicole , Feuilloley Marc GJ , Connil Nathalie 
Published: August 2010

AbstractBackgroundPseudomonas fluorescensis present in low number in the intestinal lumen and has been proposed to play a role in Crohn's disease (CD). Indeed, a highly specific antigen, I2, has been detected in CD patients and correlated to the severity of the disease. We aimed to determine whetherP. fluorescenswas able to adhere to human intestinal epithelial cells (IECs), induce cytotoxicity and activate a proinflammatory response.ResultsBehaviour of the clinical strainP. fluorescensMFN1032 was compared to that of the psychrotrophic strainP. fluorescensMF37 and the opportunistic pathogenP. aeruginosaPAO1. Both strains ofP. fluorescenswere found to adhere on Caco-2/TC7 and HT-29 cells. Their cytotoxicity towards these two cell lines determined by LDH release assays was dose-dependent and higher for the clinical strain MFN1032 than for MF37 but lower thanP. aeruginosaPAO1. The two strains ofP. fluorescensalso induced IL-8 secretion by Caco-2/TC7 and HT-29 cellsviathe AP-1 signaling pathway whereasP. aeruginosaPAO1 potentially used the NF-κB pathway.ConclusionsThe present work shows, for the first time, thatP. fluorescensMFN1032 is able to adhere to IECs, exert cytotoxic effects and induce a proinflammatory reaction. Our results are consistent with a possible contribution ofP. fluorescensin CD and could explain the presence of specific antibodies against this bacterium in the blood of patients.
When decisions of others matter to me: an electrophysiological analysis
Authors: Marco-Pallarés Josep , Krämer Ulrike M , Strehl Saskia , Schröder Andrea , Münte Thomas F 
Published: August 2010

Abstract

Background
Actions of others may have immediate consequences for oneself. We probed the neural responses associated with the observation of another person's action using event-related potentials in a modified gambling task. In this task a "performer" bet either a higher or lower number and could win or lose this amount. Three different groups of "observers" were also studied. The first (neutral) group simply observed the performer's action, which had no consequences for the observers. In the second (parallel) group, wins/losses of the performer were paralleled by similar wins and losses by the observer. In the third (reverse) group, wins of the performer led to a loss of the observer and vice versa.

Results
ERPs of the performers showed a mediofrontal feedback related negativity (FRN) to losses. The neutral and parallel observer groups did similarly show an FRN response to the performer's losses with a topography indistinguishable from that seen in the performers. In the reverse group, however, the FRN occurred for wins of the performer which translated to losses for the observer.

Conclusions
Taking into account previous experiments, we suggest that the FRN response in observers is driven by two evaluative processes (a) related to the benefit/loss for oneself and (b) related to the benefit/loss of another person.
Multi-agent modeling of the South Korean avian influenza epidemic
Authors: Kim Taehyong , Hwang Woochang , Zhang Aidong , Sen Surajit , Ramanathan Murali 
Published: August 2010

Abstract

Background
Several highly pathogenic avian influenza (AI) outbreaks have been reported over the past decade. South Korea recently faced AI outbreaks whose economic impact was estimated to be 6.3 billion dollars, equivalent to nearly 50% of the profit generated by the poultry-related industries in 2008. In addition, AI is threatening to cause a human pandemic of potentially devastating proportions. Several studies show that a stochastic simulation model can be used to plan an efficient containment strategy on an emerging influenza. Efficient control of AI outbreaks based on such simulation studies could be an important strategy in minimizing its adverse economic and public health impacts.

Methods
We constructed a spatio-temporal multi-agent model of chickens and ducks in poultry farms in South Korea. The spatial domain, comprised of 76 (37.5 km × 37.5 km) unit squares, approximated the size and scale of South Korea. In this spatial domain, we introduced 3,039 poultry flocks (corresponding to 2,231 flocks of chickens and 808 flocks of ducks) whose spatial distribution was proportional to the number of birds in each province. The model parameterizes the properties and dynamic behaviors of birds in poultry farms and quarantine plans and included infection probability, incubation period, interactions among birds, and quarantine region.

Results
We conducted sensitivity analysis for the different parameters in the model. Our study shows that the quarantine plan with well-chosen values of parameters is critical for minimize loss of poultry flocks in an AI outbreak. Specifically, the aggressive culling plan of infected poultry farms over 18.75 km radius range is unlikely to be effective, resulting in higher fractions of unnecessarily culled poultry flocks and the weak culling plan is also unlikely to be effective, resulting in higher fractions of infected poultry flocks.

Conclusions
Our results show that a prepared response with targeted quarantine protocols would have a high probability of containing the disease. The containment plan with an aggressive culling plan is not necessarily efficient, causing a higher fraction of unnecessarily culled poultry farms. Instead, it is necessary to balance culling with other important factors involved in AI spreading. Better estimations for the containment of AI spreading with this model offer the potential to reduce the loss of poultry and minimize economic impact on the poultry industry.
TLR9 expression in glioma tissues correlated to glioma progression and the prognosis of GBM patients
Authors: Wang Chao , Cao Shouqiang , Yan Ying , Ying Qiao , Jiang Tao , Xu Ke , Wu Anhua 
Published: August 2010

AbstractBackgroundOur study aims to evaluate the expression of TLR9 in glioma tissues, examine the association between TLR9 expression, clinicopathological variables, and glioma patient outcome, we further characterized the direct effects of TLR9 agonist CpG ODN upon the proliferation and invasion of glioma cellsin vitro.MethodsRT-PCR and immunofluorescence were used to determine the expression of TLR9 in glioma cell lines and clinical glioma samples. Tissue microarry and immunohistochemistry were applied to evaluated TLR9 expression in 292 newly diagnosed glioma and 13 non-neoplastic brain tissues. We further investigated the effect of CpG ODN on the proliferation and invasion of glioma cellsin vitrowith MTT assays and matrigel transwell assay respectively.ResultsRT-PCR showed that TLR9 expressed in all the glioma samples and glioma cell lines we examined. The tissue array analysis indicated that TLR9 expression is correlated with malignancy of glioma (p < 0.01). Multivariate Cox regression analysis revealed that TLR9 expression is an independent prognostic factor for PFS of GBM patients(P = 0.026). TLR9 agonist CpG ODN has no significant effect on glioma proliferation, but matrigel transwell analysis showed that TLR9 agonist CpG ODN can significantly enhance glioma invasionin vitro.ConclusionsOur data indicated that TLR9 expression increases according to the histopathological grade of glioma, and the TLR9 expression level is related to the PFS of GBM patients. In addition, our findings warrant caution in the directly injection of TLR9 agonist CpG ODN into glioma tissues for the glioma immunotherapy.