bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ensemble Kalman Filter and 4D-Var Intercomparison with the Japanese Operational Global Analysis and Prediction System
Authors: Miyoshi Takemasa , Sato Yoshiaki , Kadowaki Takashi 
Published: February 2010

Abstract
The local ensemble transform Kalman filter (LETKF) is implemented and assessed with the experimental operational system at the Japanese Meteorological Agency (JMA). This paper describes the details of the LETKF system and verification of deterministic forecast skill. JMA has been operating a four-dimensional variational data assimilation (4D-Var) system for global numerical weather prediction since 2005. The main purpose of this study is to make a reasonable comparison between the LETKF and the operational 4D-Var.
Several forecast–analysis cycle experiments are performed to find sensitivity to the parameters of the LETKF. The difference between additive and multiplicative error covariance inflation schemes is investigated. Moreover, an adaptive bias correction method for satellite radiance observations is proposed and implemented, so that the LETKF is equipped with functionality similar to the variational bias correction used in the operational 4D-Var. Finally, the LETKF is compared with the operational 4D-Var. Although forecast verification scores of the two systems relative to each system’s own analyses and to radiosonde observations show some disagreement, the overall conclusion indicates that the LETKF and 4D-Var have essentially comparable performance. The LETKF shows larger temperature bias in the lower troposphere mainly over the ocean, which is related to a well-known JMA model bias that plays an important role in the significant degradation of the forecast scores in the SH. The LETKF suffers less of a performance degradation than 4D-Var in the absence of satellite radiance assimilation. This suggests that better treatment of satellite radiances would be important in future developments toward operational use of the LETKF. Developing both LETKF and 4D-Var at JMA has shown significant benefits by the synergistic effect and is the recommended strategy for the moment.
Assessing the Impacts of Proximity Sounding Criteria on the Climatology of Significant Tornado Environments
Authors: Potvin Corey K. , Elmore Kimberly L. , Weiss Steven J. 
Published: February 2010

Abstract
Proximity sounding studies typically seek to optimize several trade-offs that involve somewhat arbitrary definitions of how to define a “proximity sounding.” More restrictive proximity criteria, which presumably produce results that are more characteristic of the near-storm environment, typically result in smaller sample sizes that can reduce the statistical significance of the results. Conversely, the use of broad proximity criteria will typically increase the sample size and the apparent robustness of the statistical analysis, but the sounding data may not necessarily be representative of near-storm environments, given the presence of mesoscale variability in the atmosphere. Previous investigations have used a wide range of spatial and temporal proximity criteria to analyze severe storm environments. However, the sensitivity of storm environment climatologies to the proximity definition has not yet been rigorously examined.
In this study, a very large set (∼1200) of proximity soundings associated with significant tornado reports is used to generate distributions of several parameters typically used to characterize severe weather environments. Statistical tests are used to assess the sensitivity of the parameter distributions to the proximity criteria. The results indicate that while soundings collected too far in space and time from significant tornadoes tend to be more representative of the larger-scale environment than of the storm environment, soundings collected too close to the tornado also tend to be less representative due to the convective feedback process. The storm environment itself is thus optimally sampled at an intermediate spatiotemporal range referred to here as the Goldilocks zone. Implications of these results for future proximity sounding studies are discussed.
Sialic acid mediated transcriptional modulation of a highly conserved sialometabolism gene cluster in Haemophilus influenzae and its effect on virulence
Authors: Jenkins Gaynor A , Figueira Marisol , Kumar Gaurav A , Sweetman Wendy A , Makepeace Katherine , Pelton Stephen I , Moxon Richard , Hood Derek W 
Published: February 2010

Abstract

Background
Sialic acid has been shown to be a major virulence determinant in the pathogenesis of otitis media caused by the bacterium Haemophilus influenzae. This study aimed to characterise the expression of genes required for the metabolism of sialic acid and to investigate the role of these genes in virulence.

Results
Using qRT-PCR, we observed decreased transcriptional activity of genes within a cluster that are required for uptake and catabolism of 5-acetyl neuraminic acid (Neu5Ac), when bacteria were cultured in the presence of the sugar. We show that these uptake and catabolic genes, including a sialic acid regulatory gene (siaR), are highly conserved in the H. influenzae natural population. Mutant strains were constructed for seven of the nine genes and their influence upon LPS sialylation and resistance of the bacteria to the killing effect of normal human serum were assessed. Mutations in the Neu5Ac uptake (TRAP transporter) genes decreased virulence in the chinchilla model of otitis media, but the attenuation was strain dependent. In contrast, mutations in catabolism genes and genes regulating sialic acid metabolism (siaR and crp) did not attenuate virulence.

Conclusion
The commensal and pathogenic behaviour of H. influenzae involves LPS sialylation that can be influenced by a complex regulatory interplay of sialometabolism genes.
Chlamydia trachomatis antigens in enteroendocrine cells and macrophages of the small bowel in patients with severe irritable bowel syndrome
Authors: Dlugosz Aldona , Törnblom Hans , Mohammadian Ghazaleh , Morgan Gareth , Veress Béla , Edvinsson Benjamin , Sandström Gunnar , Lindberg Greger 
Published: February 2010

Abstract

Background
Inflammation and immune activation have repeatedly been suggested as pathogentic factors in irritable bowel syndrome (IBS). The driving force for immune activation in IBS remains unknown. The aim of our study was to find out if the obligate intracellular pathogen Chlamydia could be involved in the pathogenesis of IBS.

Methods
We studied 65 patients (61 females) with IBS and 42 (29 females) healthy controls in which IBS had been excluded. Full thickness biopsies from the jejunum and mucosa biopsies from the duodenum and the jejunum were stained with a monoclonal antibody to Chlamydia lipopolysaccharide (LPS) and species-specific monoclonal antibodies to C. trachomatis and C. pneumoniae. We used polyclonal antibodies to chromogranin A, CD68, CD11c, and CD117 to identify enteroendocrine cells, macrophages, dendritic, and mast cells, respectively.

Results

Chlamydia LPS was present in 89% of patients with IBS, but in only 14% of healthy controls (p < 0.001) and 79% of LPS-positive biopsies were also positive for C. trachomatis major outer membrane protein (MOMP). Staining for C. pneumoniae was negative in both patients and controls. Chlamydia LPS was detected in enteroendocrine cells of the mucosa in 90% of positive biopsies and in subepithelial macrophages in 69% of biopsies. Biopsies taken at different time points in 19 patients revealed persistence of Chlamydia LPS up to 11 years. The odds ratio for the association of Chlamydia LPS with presence of IBS (43.1; 95% CI: 13.2-140.7) is much higher than any previously described pathogenetic marker in IBS.

Conclusions
We found C. trachomatis antigens in enteroendocrine cells and macrophages in the small bowel mucosa of patients with IBS. Further studies are required to clarify if the presence of such antigens has a role in the pathogenesis of IBS.
Survey of HBsAg-positive pregnant women and their infants regarding measures to prevent maternal-infantile transmission
Authors: Guo Yan , Liu Jianqiong , Meng Liping , Meina Hu , Du Yukai 
Published: February 2010

AbstractBackgroundIntrauterine infection is the main contributor to maternal-infantile transmission of HBV. This is a retrospective study of 158 HBsAg-positive pregnant women who delivered children from Jan 1st, 2004 to Dec.31th, 2006 in Wuhan City, China. We investigated the measures taken to prevent maternal-infantile transmission of hepatitis B virus and the infection status of children.MethodsHBsAg-positive pregnant women were selected by a random sampling method when they accepted prenatal care in district-level Maternal and Child Health Hospitals. On a voluntary basis, these women completed questionnaires by face-to-face or phone interviews. The collected data were used to evaluate the immunization programs that pregnant women had received for preventing hepatitis B maternal-infantile transmission.ResultsAmong the 158 women, 143(90.5%) received Hepatitis B immune globulin during pregnancy, and 86.0% of their children were given Hepatitis B immune globulin and Hepatitis B vaccine. The rate of cesarean section was 82.3%, and 28.5% of these were aimed at preventing HBV infection. The rate of bottle feeding was 51.9%, and 89.0% of bottle feeding cases were for the purpose of preventing HBV infection. There were 71 cases of participants who were HBeAg-positive. Compared with the HBsAg+ HBeAg- group (only HBsAg-positive), the HBsAg + HBeAg+ group (HBsAg-positive and HBeAg-positive) had significantly higher rates of the caesarean section and bottle feeding resulting from hepatitis B (P< 0.05). Five cases were HBsAg-positive by Umbilical Cord Blood detection. The intrauterine infection rate of newborns was 6.7%. The chronic HBV rate of children was 4.0%.ConclusionMost HBsAg positive pregnant women have a growing awareness of maternal-infantile transmission of Hepatitis B virus and are receiving some form of preventative treatment, like combined immunization. Caesarean and bottle feeding are very common, often primarily to prevent transmission. Relatively few intrauterine infections were identified in this sample, but many infants did not appear to seroconvert after vaccination.
Prevalence of HPV infection among Greek women attending a gynecological outpatient clinic
Authors: Stamataki Petroula , Papazafiropoulou Athanasia , Elefsiniotis Ioannis , Giannakopoulou Margarita , Brokalaki Hero , Apostolopoulou Eleni , Sarafis Pavlos , Saroglou George 
Published: February 2010

AbstractBackgroundHuman papillomavirus (HPV) infection is a causative factor for cervical cancer. Early detection of high risk HPV types might help to identify women at high risk of cervical cancer. The aim of the present study was to examine the HPV prevalence and distribution in cervical smears in a sample of Greek women attending a gynecological outpatient clinic and to explore the determinants of the infection.MethodsA total of 225 women were studied. All women underwent a regular gynecological control. 35 HPV types were studied; 6, 11, 16, 18, 26, 31, 33, 35, 39, 40, 42, 43, 44, 45, 51, 52, 53, 54, 56, 58, 59, 61, 62, 66, 68, 70, 71, 72, 73, 81, 82, 83, 84, 85 and 89. Also, basic demographic information, sociodemographic characteristics and sexual behavior were recorded.ResultsHPV was detected in 22.7% of the study population. The percentage of the newly diagnosed women with HPV infection was 17.3%. HPV-16 was the most common type detected (5.3%) followed by HPV-53 (4.9%). 66.2% of the study participants had a Pap test during the last year without any abnormalities. HPV infection was related positively with alcohol consumption (OR: 2.19, 95% CI: 1.04-4.63, P = 0.04) and number of sexual partners (OR: 2.16, 95% CI: 1.44-3.25, P < 0.001), and negatively with age (OR: 0.93, 95% CI: 0.87-0.99, P = 0.03), and monthly income (OR: 0.63, 95% CI: 0.44-0.89, P = 0.01).ConclusionThe prevalence of HPV in women attending an outpatient clinic is high. Number of sexual partners and alcohol consumption were the most significant risk factors for HPV infection, followed by young age and lower income.
In situ detection of Gag-specific CD8+cells in the GI tract of SIV infected Rhesus macaques
Authors: Tjernlund Annelie , Zhu Jia , Laing Kerry , Diem Kurt , McDonald David , Vazquez Julio , Cao Jianhong , Ohlen Claes , McElrath M Juliana , Picker Louis J , Corey Lawrence 
Published: February 2010

AbstractBackgroundSIV and HIV predominantly replicate in lymphoid tissue, but the study of virus specific CD8+T cells in intact lymphoid tissue is difficult, as traditionalin situtetramer staining requires fresh tissue.ResultsIn this report, we demonstrate a novel technique using Qdot 655-conjugated peptide-MHC multimers to directly visualize SIV specific cells in cryopreserved tissue biopsies from chronically SIVmac239 infected Rhesus macaques. Qdot 655 multimers showed similar sensitivity and specificity to APC-conjugated tetramers by flow cytometry analysis, but yielded ten-fold higher signal intensity when imaged by fluorescence microscopy. Using this technique, we detected CD8+T cells which recognize an immunodominant epitope (Gag CM9) in the spleen, lymph nodes, ileum and colon. In all these tissues, the Gag CM9 positive cells were mainly located in the extra follicular T cell zone. In the ileum and colon, we found Gag CM9 positive cells concentrated in Peyer's patches and solitary lymphoid follicles, a pattern of localization not previously described.ConclusionsThe use of Qdot multimers provide an anatomic and quantitative evaluation of SIV specific CD8+T cell responses in SIV pathogenesis, and may prove useful to studies of SIV specific CD8+T cell responses elicited by vaccines and other immunotherapies in the non-human primate model.
Absolute Measurements of Photoluminescence Quantum Yields of 1-Halonaphthalenes in 77 K Rigid Solution Using an Integrating Sphere Instrument
Authors: Kobayashi Atsushi , Suzuki Kengo , Yoshihara Toshitada , Tobita Seiji 
Published: February 2010

Abstract
A new apparatus to determine the absolute luminescence quantum yield of organic molecules in 77 K rigid solution is developed by using an integrating sphere (IS). Using this apparatus the fluorescence and phosphorescence quantum yields of 1-halogenated naphthalenes in 77 K rigid solutions are measured to determine the rate constants for the spin-forbidden radiative and nonradiative transitions.
Variation at 8q24 and 9p24 and Risk of Epithelial Ovarian Cancer
Authors: White Kristin L. , Sellers Thomas A. , Fridley Brooke L. , Vierkant Robert A. , Phelan Catherine M. , Tsai Ya-Yu , Kalli Kimberly R. , Berchuck Andrew , Iversen Edwin S. , Hartmann Lynn C. , Liebow Mark , Armasu Sebastian , Fredericksen Zachary , Larson Melissa C. , Duggan David , Couch Fergus J. , Schildkraut Joellen M. , Cunningham Julie M. , Goode Ellen L. 
Published: February 2010

AbstractThe chromosome 8q24 region (specifically, 8q24.21.a) is known to harbor variants associated with risk of breast, colorectal, prostate, and bladder cancers. In 2008, variants rs10505477 and rs6983267 in this region were associated with increased risk of invasive ovarian cancer (p < 0.01); however, three subsequent ovarian cancer reports of 8q24 variants were null. Here, we used a multi-site case-control study of 940 ovarian cancer cases and 1,041 controls to evaluate associations between these and other single-nucleotide polymorphisms (SNPs) in this 8q24 region, as well as in the 9p24 colorectal cancer associated-region (specifically, 9p24.1.b). A total of 35 SNPs from previous reports and additional tagging SNPs were assessed using an Illumina GoldenGate array and analyzed using logistic regression models, adjusting for population structure and other potential confounders. We observed no association between genotypes and risk of ovarian cancer considering all cases, invasive cases, or invasive serous cases. For example, at 8q24 SNPs rs10505477 and rs6983267, analyses yielded per-allele invasive cancer odds ratios of 0.95 (95% confidence interval (CI) 0.82–1.09, p trend 0.46) and 0.97 (95% CI 0.84–1.12, p trend 0.69), respectively. Analyses using an approach identical to that of the first positive 8q24 report also yielded no association with risk of ovarian cancer. In the 9p24 region, no SNPs were associated with risk of ovarian cancer overall or with invasive or invasive serous disease (all p values > 0.10). These results indicate that the SNPs studied here are not related to risk of this gynecologic malignancy and that the site-specific nature of 8q24.21.a associations may not include ovarian cancer.
Worldwide Timing of Growth Faltering: Revisiting Implications for Interventions
Authors: Victora Cesar Gomes , de Onis Mercedes , Hallal Pedro Curi , Blössner Monika , Shrimpton Roger 
Published: February 2010

OBJECTIVE:
Our goal was to describe worldwide growth-faltering patterns by using the new World Health Organization (WHO) standards.

METHODS:
We analyzed information available from the WHO Global Database on Child Growth and Malnutrition, comprising data from national anthropometric surveys from 54 countries. Anthropometric data comprise weight-for-age, length/height-for-age, and weight-for-length/height z scores. The WHO regions were used to aggregate countries: Europe and Central Asia; Latin America and the Caribbean; North Africa and Middle East; South Asia; and sub-Saharan Africa.

RESULTS:
Sample sizes ranged from 1000 to 47 000 children. Weight for length/height starts slightly above the standard in children aged 1 to 2 months and falters slightly until 9 months of age, picking up after that age and remaining close to the standard thereafter. Weight for age starts close to the standard and falters moderately until reaching approximately −1 z at 24 months and remaining reasonably stable after that. Length/height for age also starts close to the standard and falters dramatically until 24 months, showing noticeable bumps just after 24, 36, and 48 months but otherwise increasing slightly after 24 months.

CONCLUSIONS:
Comparison of child growth patterns in 54 countries with WHO standards shows that growth faltering in early childhood is even more pronounced than suggested by previous analyses based on the National Center for Health Statistics reference. These findings confirm the need to scale up interventions during the window of opportunity defined by pregnancy and the first 2 years of life, including prevention of low birth weight and appropriate infant feeding practices.
Ismételt májresectio, a modern daganatsebészet egyik kihívásar
Authors: Jakab Ferenc , Mersich Tamás 
Published: February 2010

AbsztraktA colorectalis daganatok májáttéteinek sebészi és onkológiai kezelésében az elmúlt húsz év jelentős fejlődést hozott. Noha a kemoterápiás arzenál soha nem látott módon fejlődik, hosszú távú túlélést csak sikeresen (R0), műtétileg resecált beteg remélhet. Ugyanakkor komoly problémát jelent a közel 60%-ban jelentkező daganatkiújulás. A szerzők áttekintik az Uzsoki utcai Kórház Sebészeti-Érsebészeti Osztályán 1995 és 2009 között colorectalis carcinoma (CRC) májáttétje (CLM) miatt operált, és daganatkiújulás miatt ismételten operált betegeiket. Saját tapasztalataik és a legújabb irodalom tükrében összefoglalják azokat a tényezőket, speciális daganatsebészeti és onkológiai szempontokat, melyek az ismételt májresectiót valódi kihívássá teszik. A legújabb eredmények – melyeket a saját adataink is alátámasztanak – alapján kimondható, hogy amennyiben az ismételt májresectio R0 intencióval elvégezhető, a beteg 5 éves túlélése nem különbözik az egyszer resecált betegcsoportétól. Így a daganatos beteg kezelését irányító onkoteamek feladata a kiújult CLM esetében is az, hogy a multidiszciplinaritást kihasználva a beteget resecálható “helyzetbe hozza”.
Visual Assessment of the Spine Bruckel Instrument, a Novel Status Tool to Reflect Appearance of the Spine in Patients with Ankylosing Spondylitis
Authors: PODBIELSKI DOMINIK W. , BRUCKEL JANE , POMEROY EMMA , INMAN ROBERT D. , WARREN ROBERT W. , SAVAGE LAURIE M. , RICHARDSON JENNY , PAPACHRISTOS ANGELO , MOGG REBECCA J. , STONE MILLICENT A. 
Published: February 2010

Objective.The Visual Assessment of the Spine Bruckel Instrument (VASBI) is a new status tool developed by the Spondylitis Association of America and the University of Toronto to reflect spinal appearance in patients with ankylosing spondylitis (AS). Our objective was to validate the VASBI according to the Outcome Measures in Rheumatoid Arthritis Clinical Trials filter (truth, discrimination, and feasibility).Methods.Three hundred patients with AS were asked to rate their degree of perceived spinal deformity using the VASBI. To evaluate construct validity, VASBI scores were compared with functional outcome, spinal mobility, and radiographic spinal damage. Test-retest reliability was evaluated using kappa statistic (κ).Results.Patient VASBI demonstrated strong correlation with spinal mobility (r = 0.543) and moderate correlation with functional impairment (r = 0.490) and structural damage (r = 0.309). Reliability for VASBI was very good (κ = 0.973, p < 0.001).Conclusion.The VASBI is a novel tool with practical applications in a busy clinical setting as it simplifies assessment of AS spinal deformity. Our study demonstrates that the VASBI has good feasibility, construct validity, and reliability.
A method for reverse interactome analysis: High‐resolution mapping of interdomain interaction network in Dam1 complex and its specific disorganization based on the interaction domain expression
Authors: Ikeuchi Akinori , Nakano Hideo , Kamiya Takuma , Yamane Tsuneo , Kawarasaki Yasuaki 
Published: February 2010

AbstractAn experimental methodology that facilitates functional analysis of numerous protein–protein interactions, which have been found in genome‐wide interactome researches, has long been awaited. We propose herein an antagonistic inhibition‐based approach. The antagonizing polypeptide is generated in the course of interaction domain mapping based on yeast 2‐hybrid (Y2H) screening coupled with in vitro convergence of the Y2H‐selected fragments, which is performed in a formatted procedure. Using the coupled methodology, we first performed a high‐resolution mapping of an interdomain interaction network within budding yeast's Dam1 complex. Dam1 complex is a kinetochore protein complex composed of 10 essential subunits including Spc34p and Spc19p. The high‐resolution mapping revealed the overall network structure within the complex for the first time: Dam1 components form into two separated subnetworks on N‐terminal scaffolding domains of Spc34p and Spc19p, and the coiled‐coil interaction in their C‐terminal domains connects the subnetworks. Secondly, we show that the domain fragments converged in the high‐resolution mapping acted as potent inhibitors for the endogenous interactions when episomally overexpressed. The in vivo Dam1 interaction targeting with the fragments conferred a similar phenotype on the host cells; a critical and irreversible damage, which was accompanied with disturbed budding and chromosome mis‐segregation as a result of disorganized spindle. These phenotypes were strongly related to the cellular function of the Dam1 complex. The results and approach we demonstrated herein not only shed light on the Dam1 molecular architecture but also pave the road to reverse‐interactome analysis and discoveries of novel drugs that target disease‐related protein–protein interactions. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010