bluuebunny/crossref_metadata_2025_split huggingface dataset:
Statistical Analysis of Forecasting Models across the North Slope of Alaska during the Mixed-Phase Arctic Clouds Experiment
Authors: Yannuzzi Victor T. , Clothiaux Eugene E. , Harrington Jerry Y. , Verlinde Johannes 
Published: June 2009

Abstract
The National Centers for Environmental Prediction’s (NCEP) Eta Model, the models of the European Centre for Medium-Range Weather Forecasts (ECMWF) and the National Aeronautics and Space Administration’s (NASA) Global Modeling and Assimilation Office (GMAO) models, and the Regional Atmospheric Modeling System (RAMS) model are all examined during the Mixed-Phase Arctic Clouds Experiment (MPACE) that took place from 27 September through 22 October 2004. During two intensive observation periods, soundings were launched every 6 h from four sites across the North Slope of Alaska (NSA): Barrow, Atqasuk, Oliktok Point, and Toolik Lake. Measurements of temperature, moisture, and winds, along with surface measurements of radiation and cloud cover, were compared to model outputs from the Eta, ECMWF, GMAO, and RAMS models using the bootstrap statistical technique to ascertain if differences in model performance were statistically significant. Ultimately, three synoptic regimes controlled NSA weather during the MPACE period for varying amounts of time. Each posed a unique challenge to the forecasting models during the study period.
Temperature forecasts for all models were good at the MPACE sites with mean bias errors generally under 2 K, and the models had the fewest significant errors predicting temperature. Forecasting moisture and wind proved to be more difficult for the models, especially aloft in the 500–300-hPa layer. The largest errors occurred in the GMAO model, with significant moist biases of 40% and wind errors of 10 m s−1 or more. The RAMS, Eta, and ECMWF models had smaller moist biases in this layer. Both the Eta and RAMS models overestimated the surface incident shortwave radiation, underestimated longwave radiation, and underestimated cloud cover fraction. Overall, the bootstrapping results coincided with findings from conventional statistical comparisons as model outputs with the largest errors were most likely to be captured and declared statistically significant in the bootstrapping process.
The significant model errors during MPACE were predominantly traced to the inability of the models to simulate disturbances in synoptic regime I, warm or cold biases over higher inland terrain, a warm bias along the NSA coastal waters in the Beaufort Sea, and difficulty in forecasting the intensity of the explosive cyclone in synoptic regime III.
Evaluation of Alberta Hail Growth Model Using Severe Hail Proximity Soundings from the United States
Authors: Jewell Ryan , Brimelow Julian 
Published: June 2009

Abstract
A one-dimensional, coupled hail and cloud model (HAILCAST) is tested to assess its ability to predict hail size. The model employs an ensemble approach when forecasting maximum hail size, uses a sounding as input, and can be run in seconds on an operational workstation. The model was originally developed in South Africa and then improved upon in Canada, using high quality hail verification data for calibration. In this study, the model was run on a spatially and seasonally diverse set of 914 modified severe hail proximity soundings collected within the contiguous United States between 1989 and 2004. Model output was then compared to the maximum observed hail size for each proximity sounding. Basic verification statistics are presented, showing that the HAILCAST model exhibits considerable skill that can be of use to the operational severe weather forecaster.
Chronic myeloid leukemia (CML) with P190BCR-ABL: analysis of characteristics, outcomes, and prognostic significance
Authors: Verma Dushyant , Kantarjian Hagop M. , Jones Dan , Luthra Rajyalakshmi , Borthakur Gautam , Verstovsek Srdan , Rios Mary Beth , Cortes Jorge 
Published: June 2009

Abstract
The most common BCR-ABL transcripts in chronic myeloid leukemia (CML) are e13a2(b2a2) and e14a2(b3a2). Other transcripts such as e1a2 are rare and their outcome with tyrosine kinase inhibitors (TKI) therapy is undefined. We analyzed 1292 CML patients and identified 14 with only e1a2 transcripts, 9 in chronic phase (CP), 1 in accelerated phase (AP), and 4 in blast phase (BP). Of the CP, 4 achieved complete hematologic response (CHR); 2, complete cytogenetic response (CCyR); 2, partial cytogenetic response (PCyR), and 1 did not respond to imatinib. Five patients progressed to myeloid BP (3), lymphoid BP (1), or AP (1). The AP patient received various TKIs sequentially and achieved only CHR. BP patients received hyper-CVAD (hyperfractionated cyclophosphamide, vincristine, adriamycin, dexamethasone) plus imatinib/dasatinib or idarubicin plus cytarabine (Ara-C); 2 did not respond, 1 had CCyR, and 1 short-lasting complete molecular response (CMR). Overall, cytogenetic responses lasted 3 to 18 months; only 2 achieved major molecular response (MMR) on TKI. P190BCR-ABL CML is rare and is associated with an inferior outcome to therapy with TKI. These patients need to be identified as high-risk patients.
Protamine sulfate down-regulates thrombin generation by inhibiting factor V activation
Authors: Ni Ainle Fionnuala , Preston Roger J. S. , Jenkins P. Vincent , Nel Hendrik J. , Johnson Jennifer A. , Smith Owen P. , White Barry , Fallon Padraic G. , O'Donnell James S. 
Published: June 2009

AbstractProtamine sulfate is a positively charged polypeptide widely used to reverse heparin-induced anticoagulation. Paradoxically, prospective randomized trials have shown that protamine administration for heparin neutralization is associated with increased bleeding, particularly after cardiothoracic surgery with cardiopulmonary bypass. The molecular mechanism(s) through which protamine mediates this anticoagulant effect has not been defined. In vivo administration of pharmacologic doses of protamine to BALB/c mice significantly reduced plasma thrombin generation and prolonged tail-bleeding time (from 120 to 199 seconds). Similarly, in pooled normal human plasma, protamine caused significant dose-dependent prolongations of both prothrombin time and activated partial thromboplastin time. Protamine also markedly attenuated tissue factor-initiated thrombin generation in human plasma, causing a significant decrease in endogenous thrombin potential (41% ± 7%). As expected, low-dose protamine effectively reversed the anticoagulant activity of unfractionated heparin in plasma. However, elevated protamine concentrations were associated with progressive dose-dependent reduction in thrombin generation. To assess the mechanism by which protamine mediates down-regulation of thrombin generation, the effect of protamine on factor V activation was assessed. Protamine was found to significantly reduce the rate of factor V activation by both thrombin and factor Xa. Protamine mediates its anticoagulant activity in plasma by down-regulation of thrombin generation via a novel mechanism, specifically inhibition of factor V activation.
Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing
Authors: Mane Shrinivasrao P , Evans Clive , Cooper Kristal L , Crasta Oswald R , Folkerts Otto , Hutchison Stephen K , Harkins Timothy T , Thierry-Mieg Danielle , Thierry-Mieg Jean , Jensen Roderick V 
Published: June 2009

Abstract

Background
Transcriptome sequencing using next-generation sequencing platforms will soon be competing with DNA microarray technologies for global gene expression analysis. As a preliminary evaluation of these promising technologies, we performed deep sequencing of cDNA synthesized from the Microarray Quality Control (MAQC) reference RNA samples using Roche's 454 Genome Sequencer FLX.

Results
We generated more that 3.6 million sequence reads of average length 250 bp for the MAQC A and B samples and introduced a data analysis pipeline for translating cDNA read counts into gene expression levels. Using BLAST, 90% of the reads mapped to the human genome and 64% of the reads mapped to the RefSeq database of well annotated genes with e-values ≤ 10-20. We measured gene expression levels in the A and B samples by counting the numbers of reads that mapped to individual RefSeq genes in multiple sequencing runs to evaluate the MAQC quality metrics for reproducibility, sensitivity, specificity, and accuracy and compared the results with DNA microarrays and Quantitative RT-PCR (QRTPCR) from the MAQC studies. In addition, 88% of the reads were successfully aligned directly to the human genome using the AceView alignment programs with an average 90% sequence similarity to identify 137,899 unique exon junctions, including 22,193 new exon junctions not yet contained in the RefSeq database.

Conclusion
Using the MAQC metrics for evaluating the performance of gene expression platforms, the ExpressSeq results for gene expression levels showed excellent reproducibility, sensitivity, and specificity that improved systematically with increasing shotgun sequencing depth, and quantitative accuracy that was comparable to DNA microarrays and QRTPCR. In addition, a careful mapping of the reads to the genome using the AceView alignment programs shed new light on the complexity of the human transcriptome including the discovery of thousands of new splice variants.
Host cell transcriptional profiling during malaria liver stage infection reveals a coordinated and sequential set of biological events
Authors: Albuquerque Sónia S , Carret Céline , Grosso Ana Rita , Tarun Alice S , Peng Xinxia , Kappe Stefan HI , Prudêncio Miguel , Mota Maria M 
Published: June 2009

Abstract

Background

Plasmodium sporozoites migrate to the liver where they traverse several hepatocytes before invading the one inside which they will develop and multiply into thousands of merozoites. Although this constitutes an essential step of malaria infection, the requirements of Plasmodium parasites in liver cells and how they use the host cell for their own survival and development are poorly understood.

Results
To gain new insights into the molecular host-parasite interactions that take place during malaria liver infection, we have used high-throughput microarray technology to determine the transcriptional profile of P. berghei-infected hepatoma cells. The data analysis shows differential expression patterns for 1064 host genes starting at 6 h and up to 24 h post infection, with the largest proportion correlating specifically with the early stages of the infection process. A considerable proportion of those genes were also found to be modulated in liver cells collected from P. yoelii- infected mice 24 and 40 h after infection, strengthening the data obtained with the in vitro model and highlighting genes and pathways involved in the host response to rodent Plasmodium parasites.

Conclusion
Our data reveal that host cell infection by Plasmodium sporozoites leads to a coordinated and sequential set of biological events, ranging from the initial stage of stress response up to the engagement of host metabolic processes and the maintenance of cell viability throughout infection.
Kalirin12 interacts with dynamin
Authors: Xin Xiaonan , Rabiner Chana A , Mains Richard E , Eipper Betty A 
Published: June 2009

Abstract

Background
Guanine nucleotide exchange factors (GEFs) and their target Rho GTPases regulate cytoskeletal changes and membrane trafficking. Dynamin, a large force-generating GTPase, plays an essential role in membrane tubulation and fission in cells. Kalirin12, a neuronal RhoGEF, is found in growth cones early in development and in dendritic spines later in development.

Results
The IgFn domain of Kalirin12, not present in other Kalirin isoforms, binds dynamin1 and dynamin2. An inactivating mutation in the GTPase domain of dynamin diminishes this interaction and the isolated GTPase domain of dynamin retains the ability to bind Kalirin12. Co-immunoprecipitation demonstrates an interaction of Kalirin12 and dynamin2 in embryonic brain. Purified recombinant Kalirin-IgFn domain inhibits the ability of purified rat brain dynamin to oligomerize in response to the presence of liposomes containing phosphatidylinositol-4,5-bisphosphate. Consistent with this, expression of exogenous Kalirin12 or its IgFn domain in PC12 cells disrupts clathrin-mediated transferrin endocytosis. Similarly, expression of exogenous Kalirin12 disrupts transferrin endocytosis in cortical neurons. Expression of Kalirin7, a shorter isoform which lacks the IgFn domain, was previously shown to inhibit clathrin-mediated endocytosis; the GTPase domain of dynamin does not interact with Kalirin7.

Conclusion
Kalirin12 may play a role in coordinating Rho GTPase-mediated changes in the actin cytoskeleton with dynamin-mediated changes in membrane trafficking.
The impact of a fast track area on quality and effectiveness outcomes: A Middle Eastern emergency department perspective
Authors: Devkaran Subashnie , Parsons Howard , Van Dyke Murray , Drennan Jonathan , Rajah Jaishen 
Published: June 2009

Abstract

Background
Emergency department (ED) overcrowding is a ubiquitous problem with serious public health implications. The fast track area is a novel method which aims to reduce waiting time, patient dissatisfaction and morbidity. |The study objective was to determine the impact of a fast track area (FTA) on both effectiveness measures (i.e. waiting times [WT] and length of stay [LOS]) and quality measures (i.e. LWBS rates and mortality rates) in non-urgent patients. The secondary objective was to assess if a FTA negatively impacted on urgent patients entering the ED.

Methods
The study took place in a 500 bed, urban, tertiary care hospital in Abu Dhabi, United Arab Emirates. This was a quasi-experimental, which examined the impact of a FTA on a pre-intervention control group (January 2005) (n = 4,779) versus a post-intervention study group (January 2006) (n = 5,706).

Results
Mean WTs of Canadian Triage Acuity Scale (CTAS) 4 patients decreased by 22 min (95% CI 21 min to 24 min, P < 0.001). Similarly, mean WTs of CTAS 5 patients decreased by 28 min (95% CI 19 min to 37 min, P < 0.001) post FTA. The mean WTs of urgent patients (CTAS 2/3) were also significantly reduced after the FTA was opened (P < 0.001). The LWBS rate was reduced from 4.7% to 0.7% (95% CI 3.37 to 4.64; P < 0.001). Opening a FTA had no significant impact on mortality rates (P = 0.88).

Conclusion
The FTA improved ED effectiveness (WTs and LOS) and quality measures (LWBS rates) whereas mortality rate remained unchanged.
Deaths among tuberculosis cases in Shanghai, China: who is at risk?
Authors: Shen Xin , DeRiemer Kathryn , Yuan Zheng'an , Shen Mei , Xia Zhen , Gui Xiaohong , Wang Lili , Mei Jian 
Published: June 2009

Abstract

Background
Information about the risk factors associated with death caused by tuberculosis (TB) or death with TB would allow improvements in the clinical care of TB patients and save lives. The present study sought to identify characteristics associated with increased risk of death during anti-TB treatment in Shanghai, a city in China with one of the country's highest TB mortality rates.

Methods
We evaluated deaths among culture positive pulmonary TB cases that were diagnosed in Shanghai during 2000–2004 and initiated anti-TB therapy. Demographic, clinical, mycobacteriological information and treatment outcomes were routinely collected through a mandatory reporting system.

Results
There were 7,999 culture positive pulmonary cases reported during the study period. The overall case fatality rate was 5.5% (440 cases), and approximately half (50.5%) of the deaths were attributed to causes other than TB. Eighty-six percent of the deaths were among TB cases age ≥ 60 years. The significant independent risk factors for mortality during anti-TB treatment were advancing age, male sex, sputum smear positivity, and the presence of a comorbidity.

Conclusion
More vigorous clinical management and prevention strategies by both the TB control program and other public health programs are essential to improve TB treatment outcomes. Earlier suspicion, diagnosis and treatment of TB, especially among persons older than 60 years of age and those with a comorbid condition, could reduce deaths among TB patients.
Risk of latent tuberculosis infection in children living in households with tuberculosis patients: a cross sectional survey in remote northern Lao People's Democratic Republic
Authors: Nguyen Tuan H , Odermatt Peter , Slesak Gunther , Barennes Hubert 
Published: June 2009

Abstract

Background
Tuberculosis is highly prevalent in Laos (289 per 100,000). We evaluated the risk of latent tuberculosis infection (LTBI) among children (0–15 years) living with tuberculosis patients in rural northern Laos.

Methods
In a cross sectional survey of 30 randomly selected villages, 72 tuberculosis patients were traced and their 317 contacts (148 were children) investigated using a questionnaire, a tuberculin skin tests (positive: > = 10 mm), a 3-day sputum examination for acid-fast bacilli (AFB), and chest radiography.

Results
None of the 148 contact-children received prophylaxis, one had cervical tuberculosis; the risk for LTBI was 31.0%. Awareness of the infectiousness of tuberculosis was low among patients (31%) and their contacts (31%), and risky behavior was common. After multivariate logistic analysis, increased LTBI was found in children with contact with sputum positive adults (OR: 3.3, 95% CI: 1.4–7.7), patients highly positive sputum prior to treatment (AFB >2+; OR: 4.7, 95% CI: 1.7–12.3), and living in ethnic minorities (OR: 5.4, 95% CI: 2.2–13.6).

Conclusion
The study supports the importance of contact tracing in remote settings with high TB prevalence. Suggestions to improve the children's detection rate, the use of existing guidelines, chemoprophylaxis of contact-children and the available interventions in Laos are discussed. Improving education and awareness of the infectiousness of TB in patients is urgently needed to reduce TB transmission.
The INSIG2 rs7566605 genetic variant does not play a major role in obesity in a sample of 24,722 individuals from four cohorts
Authors: Bressler Jan , Fornage Myriam , Hanis Craig L , Kao Wen Hong Linda , Lewis Cora E , McPherson Ruth , Dent Robert , Mosley Thomas H , Pennacchio Len A , Boerwinkle Eric 
Published: June 2009

Abstract

Background
In a genome-wide association study performed in the Framingham Offspring Cohort, individuals homozygous for the rs7566605 C allele located upstream of insulin-induced gene 2 (INSIG2) were reported to incur an increased risk of obesity. This finding was later replicated in four out of five populations examined. The goal of the study reported here was to assess the role of the INSIG2 single nucleotide polymorphism (SNP) in susceptibility to obesity in the prospective longitudinal Atherosclerosis Risk in Communities (ARIC) study (n = 14,566) and in three other cohorts: the Coronary Artery Risk Development in Young Adults (CARDIA) study (n = 3,888), the Genetic Epidemiology Network of Arteriopathy (GENOA) study (n = 4,766), and extremely obese and lean individuals ascertained at the University of Ottawa (n = 1,502). The combined study sample is comprised of 24,722 white, African-American, and Mexican-American participants.

Methods
Differences in mean body mass index (BMI) and other anthropometric measures including weight, waist circumference, and waist-to-hip ratio were assessed by a general linear model in individuals categorized by INSIG2 rs7566605 genotype. Multivariable logistic regression was used to predict the risk of obesity (BMI ≥ 30 kg/m2).

Results
There was no discernable variation in the frequencies of the three INSIG2 SNP genotypes observed between white, Hispanic, and African-American obese individuals and non-obese study subjects. When the relationship between rs7566605 and BMI considered either as a categorical variable or a continuous variable was examined, no significant association with obesity was found for participants in any of the four study populations or in a combined analysis (p = 0.38) under a recessive genetic model. There was also no association between the INSIG2 polymorphism and the obesity-related quantitative traits except for a reduced waist-to-hip ratio in white ARIC study participants homozygous for the C allele, and an increased waist-to-hip ratio in African-Americans in the ARIC cohort with the same genotype (p = 0.04 and p = 0.01, respectively). An association with waist-to-hip ratio was not seen when the combined study sample was analyzed (p = 0.74).

Conclusion
These results suggest that the INSIG2 rs7566605 variant does not play a major role in determining obesity risk in a racially and ethnically diverse sample of 24,722 individuals from four cohorts.
Mammographic density and epithelial histopathologic markers
Authors: Verheus Martijn , Maskarinec Gertraud , Erber Eva , Steude Jana S , Killeen Jeffrey , Hernandez Brenda Y , Cline J Mark 
Published: June 2009

Abstract

Background
We explored the association of mammographic density, a breast cancer risk factor, with hormonal and proliferation markers in benign tissue from tumor blocks of pre-and postmenopausal breast cancer cases.

Methods
Breast cancer cases were recruited from a case-control study on breast density. Mammographic density was assessed on digitized prediagnostic mammograms using a computer-assisted method. For 279 participants of the original study, we obtained tumor blocks and prepared tissue microarrays (TMA), but benign tissue cores were only available for 159 women. The TMAs were immunostained for estrogen receptor alpha (ERα) and beta (ERβ), progesterone receptor (PR), HER2/neu, Ki-67, and Proliferating Cell Nuclear Antigen (PCNA). We applied general linear models to compute breast density according to marker expression.

Results
A substantial proportion of the samples were in the low or no staining categories. None of the results was statistically significant, but women with PR and ERβ staining had 3.4% and 2.4% higher percent density. The respective values for Caucasians were 5.7% and 11.6% but less in Japanese women (3.5% and -1.1%). Percent density was 3.4% higher in women with any Ki-67 staining and 2.2% in those with positive PCNA staining.

Conclusion
This study detected little evidence for an association between mammographic density and expression of steroid receptors and proliferation markers in breast tissue, but it illustrated the problems of locating tumor blocks and benign breast tissue samples for epidemiologic research. Given the suggestive findings, future studies examining estrogen effects in tissue, cell proliferation, and density in the breast may be informative.