bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictability Associated with the Downstream Impacts of the Extratropical Transition of Tropical Cyclones: Methodology and a Case Study of Typhoon Nabi (2005)
Authors: Harr Patrick A. , Anwender Doris , Jones Sarah C. 
Published: January 2008

Abstract
Measures of the variability among ensemble members from the National Centers for Environmental Prediction ensemble prediction system are examined with respect to forecasts of the extratropical transition (ET) of Typhoon Nabi over the western North Pacific during September 2005. In this study, variability among ensemble members is used as a proxy for predictability. The time–longitude distribution of standard deviations among 500-hPa height fields from the ensemble members is found to increase across the North Pacific following the completion of the extratropical transition. Furthermore, the increase in ensemble standard deviation is organized such that an increase is associated with the extratropical transition and another increase extends downstream from the ET event. The organization and amplitude of the standard deviations increase from 144 h until approximately 72–48 h prior to the completion of the extratropical transition, and then decrease as the forecast interval decreases.
An empirical orthogonal function analysis of potential temperature on the dynamic tropopause is applied to ensemble members to identify the spatial and temporal organization of centers of variability related to the extratropical transition. The principal components are then used in a fuzzy cluster analysis to examine the grouping of forecast sequences in the collection of ensemble members. The number of forecast groups decreases as the forecast interval to the completion of the ET decreases. However, there is a systematic progression of centers of variability downstream of the ET event. Once the variability associated with the ET begins to decrease, the variability downstream of the ET event also begins to decrease.
Synoptic Control of Mesoscale Precipitating Systems in the Pacific Northwest
Authors: Roebber Paul J. , Swanson Kyle L. , Ghorai Jugal K. 
Published: January 2008

AbstractThis research examines whether an adequate representation of flow features on the synoptic scale allows for the skillful inference of mesoscale precipitating systems. The focus is on the specific problem of landfalling systems on the west coast of the United States for a variety of synoptic types that lead to significant rainfall. The methodology emphasizes rigorous hypothesis testing within a controlled hindcast setting to quantify the significance of the results. The role of lateral boundary conditions is explicitly accounted for by the study.The hypotheses that (a) uncertainty in the large-scale analysis and (b) upstream buffer size have no impact on the skill of precipitation simulations are each rejected at a high level of confidence, with the results showing that mean precipitation skill is higher where low analysis uncertainty exists and for small nested grids. This indicates that an important connection exists between the quality of the synoptic information and predictability at the mesoscale in this environment, despite the absence of such information in the initialization or boundary conditions. Further, the flow-through of synoptic information strongly constrains the evolution of the mesoscale such that a small upstream buffer produces superior results consistent with the higher quality of the information crossing the boundary. Some preliminary evidence that synoptic type has an influence on precipitation skill is also found. The implications of these results for data assimilation, forecasting, and climate modeling are discussed.
Systematic Error Correction of Dynamical Seasonal Prediction of Sea Surface Temperature Using a Stepwise Pattern Project Method
Authors: Kug Jong-Seong , Lee June-Yi , Kang In-Sik 
Published: January 2008

Abstract
Every dynamical climate prediction model has significant errors in its mean state and anomaly field, thus degrading its performance in climate prediction. In addition to correcting the model’s systematic errors in the mean state, it is also possible to correct systematic errors in the predicted anomalies by means of dynamical or statistical postprocessing. In this study, a new statistical model has been developed based on the pattern projection method in order to empirically correct the dynamical seasonal climate prediction. The strength of the present model lies in the objective and automatic selection of optimal predictor grid points. The statistical model was applied to systematic error correction of SST anomalies predicted by Seoul National University’s (SNU) coupled GCM and evaluated in terms of temporal correlation skill and standardized root-mean-square error. It turns out that the statistical error correction improves the SST prediction over most regions of the global ocean with most forecast lead times up to 6 months. In particular, the SST predictions over the western Pacific and Indian Ocean are improved significantly, where the SNU coupled GCM shows a large error.
An Ensemble-Based Four-Dimensional Variational Data Assimilation Scheme. Part I: Technical Formulation and Preliminary Test
Authors: Liu Chengsi , Xiao Qingnong , Wang Bin 
Published: January 2008

Abstract
Applying a flow-dependent background error covariance (𝗕 matrix) in variational data assimilation has been a topic of interest among researchers in recent years. In this paper, an ensemble-based four-dimensional variational (En4DVAR) algorithm, designed by the authors, is presented that uses a flow-dependent background error covariance matrix constructed by ensemble forecasts and performs 4DVAR optimization to produce a balanced analysis. A great advantage of this En4DVAR design over standard 4DVAR methods is that the tangent linear and adjoint models can be avoided in its formulation and implementation. In addition, it can be easily incorporated into variational data assimilation systems that are already in use at operational centers and among the research community.
A one-dimensional shallow water model was used for preliminary tests of the En4DVAR scheme. Compared with standard 4DVAR, the En4DVAR converges well and can produce results that are as good as those with 4DVAR but with far less computation cost in its minimization. In addition, a comparison of the results from En4DVAR with those from other data assimilation schemes [e.g., 3DVAR and ensemble Kalman filter (EnKF)] is made. The results show that the En4DVAR yields an analysis that is comparable to the widely used variational or ensemble data assimilation schemes and can be a promising approach for real-time applications.
In addition, experiments were carried out to test the sensitivities of EnKF and En4DVAR, whose background error covariance is estimated from the same ensemble forecasts. The experiments indicated that En4DVAR obtained reasonably sound analysis even with larger observation error, higher observation frequency, and more unbalanced background field.
Visualization of microtubule growth in living platelets reveals a dynamic marginal band with multiple microtubules
Authors: Patel-Hett Sunita , Richardson Jennifer L. , Schulze Harald , Drabek Ksenija , Isaac Natasha A. , Hoffmeister Karin , Shivdasani Ramesh A. , Bulinski J. Chloë , Galjart Niels , Hartwig John H. , Italiano Joseph E. 
Published: January 2008

AbstractThe marginal band of microtubules maintains the discoid shape of resting blood platelets. Although studies of platelet microtubule coil structure conclude that it is composed of a single microtubule, no investigations of its dynamics exist. In contrast to previous studies, permeabilized platelets incubated with GTP-rhodamine-tubulin revealed tubulin incorporation at 7.9 (± 1.9) points throughout the coil, and anti-EB1 antibodies stained 8.7 (± 2.0) sites, indicative of multiple free microtubules. To pursue this result, we expressed the microtubule plus-end marker EB3-GFP in megakaryocytes and examined its behavior in living platelets released from these cells. Time-lapse microscopy of EB3-GFP in resting platelets revealed multiple assembly sites within the coil and a bidirectional pattern of assembly. Consistent with these findings, tyrosinated tubulin, a marker of newly assembled microtubules, localized to resting platelet microtubule coils. These results suggest that the resting platelet marginal band contains multiple highly dynamic microtubules of mixed polarity. Analysis of microtubule coil diameters in newly formed resting platelets indicates that microtubule coil shrinkage occurs with aging. In addition, activated EB3-GFP–expressing platelets exhibited a dramatic increase in polymerizing microtubules, which travel outward and into filopodia. Thus, the dynamic microtubules associated with the marginal band likely function during both resting and activated platelet states.
GraphCrunch: A tool for large network analyses
Authors: Milenković Tijana , Lai Jason , Pržulj Nataša 
Published: January 2008

AbstractBackgroundThe recent explosion in biological and other real-world network data has created the need for improved tools for large network analyses. In addition to well establishedglobalnetwork properties, several new mathematical techniques for analyzinglocalstructural properties of large networks have been developed. Small over-represented subgraphs, called networkmotifs, have been introduced to identify simple building blocks of complex networks. Small induced subgraphs, calledgraphlets, have been used to develop "network signatures" that summarize network topologies. Based on these network signatures, two new highly sensitive measures of network local structural similarities were designed: therelative graphlet frequency distance(RGF-distance) and thegraphlet degree distribution agreement(GDD-agreement).Finding adequate null-models for biological networks is important in many research domains. Network properties are used to assess the fit of network models to the data. Various network models have been proposed. To date, there does not exist a software tool that measures the above mentioned local network properties. Moreover, none of the existing tools compare real-world networks against a series of network models with respect to these local as well as a multitude of global network properties.ResultsThus, we introduce GraphCrunch, a software tool that finds well-fitting network models by comparing large real-world networks against random graph models according to various network structural similarity measures. It has unique capabilities of finding computationally expensive RGF-distance and GDD-agreement measures. In addition, it computes several standard global network measures and thus supports the largest variety of network measures thus far. Also, it is the first software tool that compares real-world networks against a series of network models and that has built-in parallel computing capabilities allowing for a user specified list of machines on which to perform compute intensive searches for local network properties. Furthermore, GraphCrunch is easily extendible to include additional network measures and models.ConclusionGraphCrunch is a software tool that implements the latest research on biological network models and properties: it compares real-world networks against a series of random graph models with respect to a multitude of local and global network properties. We present GraphCrunch as a comprehensive, parallelizable, and easily extendible software tool for analyzing and modeling large biological networks. The software is open-source and freely available athttp://www.ics.uci.edu/~bio-nets/graphcrunch/. It runs under Linux, MacOS, and Windows Cygwin. In addition, it has an easy to use on-line web user interface that is available from the above web page.
Cyclooxygenase-2 overexpression is common in serrated and non-serrated colorectal adenoma, but uncommon in hyperplastic polyp and sessile serrated polyp/adenoma
Authors: Kawasaki Takako , Nosho Katsuhiko , Ohnishi Mutsuko , Suemoto Yuko , Glickman Jonathan N , Chan Andrew T , Kirkner Gregory J , Mino-Kenudson Mari , Fuchs Charles S , Ogino Shuji 
Published: January 2008

Abstract

Background
Cyclooxygenase-2 (COX-2, PTGS2) plays an important role in colorectal carcinogenesis. COX-2 overexpression in colorectal cancer is inversely associated with microsatellite instability (MSI) and the CpG island methylator phenotype (CIMP). Evidence suggests that MSI/CIMP+ colorectal cancer may arise through the serrated tumorigenic pathway through various forms of serrated neoplasias. Therefore, we hypothesized that COX-2 may play a less important role in the serrated pathway.

Methods
By immunohistochemistry, we assessed COX-2 expression in 24 hyperplastic polyps, 7 sessile serrated polyp/adenomas (SSA), 5 mixed polyps with SSA and adenoma, 27 traditional serrated adenomas, 515 non-serrated adenomas (tubular adenoma, tubulovillous adenoma and villous adenoma), 33 adenomas with intramucosal carcinomas, 96 adenocarcinomas with serration (corkscrew gland) and 111 adenocarcinomas without serration.

Results
Strong (2+) COX-2 overexpression was more common in non-serrated adenomas (28% = 143/515) than in hyperplastic polyps (4.2% = 1/24, p = 0.008) and serrated polyps (7 SSAs and 5 mixed polyps) (0% = 0/12, p = 0.04). Furthermore, any (1+/2+) COX-2 overexpression was more frequent in non-serrated adenomas (60% = 307/515) than in hyperplastic polyps (13% = 3/24, p < 0.0001) and serrated polyps (SSAs and mixed polyps) (25% = 3/12, p = 0.03). Traditional serrated adenomas and non-serrated adenomas showed similar frequencies of COX-2 overexpression. Regardless of serration, COX-2 overexpression was frequent (~85%) in colorectal adenocarcinomas. Tumor location was not significantly correlated with COX-2 overexpression, although there was a trend towards higher frequencies of COX-2 overexpression in distal tumors (than proximal tumors) among hyperplastic polyps, SSAs, mixed polyps, traditional serrated adenomas and adenocarcinomas.

Conclusion
COX-2 overexpression is infrequent in hyperplastic polyp, SSA and mixed polyp with SSA and adenoma, compared to non-serrated and serrated adenoma. COX-2 overexpression becomes more frequent as tumors progress to higher grade neoplasias. Our observations suggest that COX-2 may play a less significant role in the serrated pathway of tumorigenesis; however, COX-2 may still play a role in later stage of the serrated pathway.
Self-excision of the BAC sequences from the recombinant Marek's disease virus genome increases replication and pathogenicity
Authors: Zhao Yuguang , Petherbridge Lawrence , Smith Lorraine P , Baigent Sue , Nair Venugopal 
Published: January 2008

Abstract
Cloning of full length genomes of herpesviruses as bacterial artificial chromosomes (BAC) has greatly facilitated the manipulation of the genomes of several herpesviruses to identify the pathogenic determinants. We have previously reported the construction of the BAC clone (pRB-1B5) of the highly oncogenic Marek's disease virus (MDV) strain RB-1B, which has proven to be a valuable resource for elucidating several oncogenic determinants. Despite the retention of the BAC replicon within the genome, the reconstituted virus was able to induce tumours in susceptible chickens. Nevertheless, it was unclear whether the presence of the BAC influenced the full oncogenic potential of the reconstituted virus. To maximize the closeness of BAC-derived virus to the parental RB-1B strain, we modified the existing pRB-1B5 clone by restoring the Us2 and by introducing SV40-cre cassette within the lox P sites of the mini-F plasmid, to allow self-excision of the plasmid sequences in chicken cells. The reconstituted virus from the modified clone showed significant improvement in replication in vitro and in vivo. Excision of the BAC sequences also enhanced the pathogenicity to levels similar to that of the parental virus, as the cumulative incidence of Marek's disease in groups infected with the recombinant and the parental viruses showed no significant differences. Thus, we have been able to make significant improvements to the existing BAC clone of this highly oncogenic virus which would certainly increase its usefulness as a valuable tool for studies on identifying the oncogenic determinants of this major avian pathogen.
Identification of gene interactions associated with disease from gene expression data using synergy networks
Authors: Watkinson John , Wang Xiaodong , Zheng Tian , Anastassiou Dimitris 
Published: January 2008

AbstractBackgroundAnalysis of microarray data has been used for the inference of gene-gene interactions. If, however, the aim is the discovery of disease-related biological mechanisms, then the criterion for defining such interactions must be specifically linked to disease.ResultsHere we present a computational methodology that jointly analyzes two sets of microarray data, one in the presence and one in the absence of a disease, identifying gene pairs whose correlation with disease is due to cooperative, rather than independent, contributions of genes, using the recently developed information theoretic measure of synergy. High levels of synergy in gene pairs indicates possible membership of the two genes in a shared pathway and leads to a graphical representation of inferred gene-gene interactions associated with disease, in the form of a "synergy network." We apply this technique on a set of publicly available prostate cancer expression data and successfully validate our results, confirming that they cannot be due to pure chance and providing a biological explanation for gene pairs with exceptionally high synergy.ConclusionThus, synergy networks provide a computational methodology helpful for deriving "disease interactomes" from biological data. When coupled with additional biological knowledge, they can also be helpful for deciphering biological mechanisms responsible for disease.
Serum keratan sulfate transiently increases in the early stage of osteoarthritis during strenuous running of rats: protective effect of intraarticular hyaluronan injection
Authors: Tang Tao , Muneta Takeshi , Ju Young-Jin , Nimura Akimoto , Miyazaki Kyosuke , Masuda Hiroyuki , Mochizuki Tomoyuki , Sekiya Ichiro 
Published: January 2008

Abstract
Introduction
Osteoarthritis is influenced by genetic and environment factors, including mechanical stress; however, the relationship between running and the development of osteoarthritis remains a matter of controversy. We investigated whether osteoarthritic change could be obtained in a rat strenuous running model, whether serum keratan sulfate in rats could be detected by HPLC and was associated with onset or progression of osteoarthritis, and whether hyaluronan injection suppressed development of osteoarthritis and elevation of serum keratan sulfate.

Methods
Wistar rats were forced to run 30 km in 6 weeks on a treadmill machine. Articular cartilage of the knees was evaluated macroscopically and immunohistologically. Serum keratan sulfate was examined every week by HPLC. The effect of weekly knee injection of hyaluronan was also investigated.

Results
Cartilage surfaces stained with India ink became irregular, metachromasia by safranin-O staining appeared to be almost lost, and Mankin's score significantly worsened after 30 km of running. Serum keratan sulfate in rats was detected by HPLC and transiently increased (peaked at 3 to 4 weeks) along with depletion of keratan sulfate in cartilage tissue. Hyaluronan treatment suppressed morphological progression of osteoarthritis and elevation of serum keratan sulfate.

Conclusion
Rat strenuous running induced osteoarthritis. Serum keratan sulfate was associated with progression of osteoarthritis. Weekly intraarticular injection of hyaluronan controlled the development of osteoarthritis, and the effect was reflected by serum keratan sulfate.
Electrical protein detection in cell lysates using high-density peptide-aptamer microarrays
Authors: Evans David , Johnson Steven , Laurenson Sophie , Davies A Giles , Ko Ferrigno Paul , Wälti Christoph 
Published: January 2008

Abstract
Background
The dissection of biological pathways and of the molecular basis of disease requires devices to analyze simultaneously a staggering number of protein isoforms in a given cell under given conditions. Such devices face significant challenges, including the identification of probe molecules specific for each protein isoform, protein immobilization techniques with micrometer or submicrometer resolution, and the development of a sensing mechanism capable of very high-density, highly multiplexed detection.

Results
We present a novel strategy that offers practical solutions to these challenges, featuring peptide aptamers as artificial protein detectors arrayed on gold electrodes with feature sizes one order of magnitude smaller than existing formats. We describe a method to immobilize specific peptide aptamers on individual electrodes at the micrometer scale, together with a robust and label-free electronic sensing system. As a proving proof of principle experiment, we demonstrate the specific recognition of cyclin-dependent protein kinases in whole-cell lysates using arrays of ten electrodes functionalized with individual peptide aptamers, with no measurable cross-talk between electrodes. The sensitivity is within the clinically relevant range and can detect proteins against the high, whole-cell lysate background.

Conclusion
The use of peptide aptamers selected in vivo to recognize specific protein isoforms, the ability to functionalize each microelectrode individually, the electronic nature and scalability of the label-free detection and the scalability of the array fabrication combine to yield the potential for highly multiplexed devices with increasingly small detection areas and higher sensitivities that may ultimately allow the simultaneous monitoring of tens or hundreds of thousands of protein isoforms.
Phase I/II Trial of Weekly Intravenous 130-nm Albumin-Bound Paclitaxel As Initial Chemotherapy in Patients With Stage IV Non–Small-Cell Lung Cancer
Authors: Rizvi Naiyer A. , Riely Gregory J. , Azzoli Christopher G. , Miller Vincent A. , Ng Kenneth K. , Fiore John , Chia Gloria , Brower Martin , Heelan Robert , Hawkins Michael J. , Kris Mark G. 
Published: January 2008

Purpose Nanoparticle albumin-bound paclitaxel (NAB-paclitaxel) is an albumin-bound formulation of paclitaxel that has demonstrated improved efficacy compared with paclitaxel in the treatment of metastatic breast cancer. We undertook this trial to determine the maximum-tolerated dose (MTD) and single-agent activity of NAB-paclitaxel administered on a weekly basis to patients with stage IV non–small-cell lung cancer (NSCLC). Patients and Methods This was an open-label, single-arm, phase I/II study. Patients were treated with NAB-paclitaxel intravenously during 30 minutes without corticosteroid or antihistamine premedications on days 1, 8, and 15 of a 28-day cycle. Radiologic tumor assessment was performed every 8 weeks. Results Dose levels of 100 and 125 mg/m2 were tolerated without dose-limiting toxicities (DLTs). At 150 mg/m2 the MTD was exceeded; two of three patients experienced a DLT (grade 3 sensory neuropathy and febrile neutropenia). The 125 mg/m2 dose level was expanded and determined to be the MTD. A total of 40 patients were treated at 125 mg/m2. The objective response rate was 30% (12 of 40 patients; 95% CI, 16% to 44%), median time to progression was 5 months (95% CI, 3 to 8 months), and median overall survival was 11 months (95% CI, 7 months to not reached). The 1-year survival was 41%. Conclusion NAB-paclitaxel 125 mg/m2 administered on days 1, 8, and 15 of a 28-day cycle was well tolerated and demonstrated encouraging single-agent activity. No corticosteroid premedication was administered and no hypersensitivity reactions were seen. Additional studies of single-agent NAB-paclitaxel as well as platinum-based combinations are warranted.