bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relative Humidity Effect on the High-Frequency Attenuation of Water Vapor Flux Measured by a Closed-Path Eddy Covariance System
Authors: Mammarella Ivan , Launiainen Samuli , Gronholm Tiia , Keronen Petri , Pumpanen Jukka , Rannik Üllar , Vesala Timo 
Published: March 2009

AbstractIn this study the high-frequency loss of carbon dioxide (CO2) and water vapor (H2O) fluxes, measured by a closed-path eddy covariance system, were studied, and the related correction factors through the cospectral transfer function method were calculated. As already reported by other studies, it was found that the age of the sampling tube is a relevant factor to consider when estimating the spectral correction of water vapor fluxes. Moreover, a time-dependent relationship between the characteristic time constant (or response time) for water vapor and the ambient relative humidity was disclosed. Such dependence is negligible when the sampling tube is new, but it becomes important already when the tube is only 1 yr old and increases with the age of the tube. With a new sampling tube, the correction of water vapor flux measurements over a Scots pine forest in Hyytiälä, Finland, amounted on average to 7%. After 4 yr the correction increased strongly, ranging from 10%–15% during the summer to 30%–40% in wintertime, when the relative humidity is typically high. For this site the effective correction improved the long-term energy and water balance.Results suggest that the relative humidity effect on high-frequency loss of water vapor flux should be taken into account and that the effective transfer function should be estimated experimentally at least once per year. On the other hand, this high correction can be avoided by a correct choice and periodic maintenance of the eddy covariance system tube, for example, by cleaning or changing it at least once per year.
Investigation of Microphysical Parameterizations of Snow and Ice in Arctic Clouds during M-PACE through Model–Observation Comparisons
Authors: Solomon Amy , Morrison Hugh , Persson Ola , Shupe Matthew D. , Bao Jian-Wen 
Published: March 2009

Abstract
In this study the Weather Research Forecast model is used with 1-km horizontal grid spacing to investigate the microphysical properties of Arctic mixed-phase stratocumulus. Intensive measurements taken during the Department of Energy Atmospheric Radiation Measurement Program Mixed-Phase Arctic Cloud Experiment (M-PACE) on the North Slope of Alaska, during 9–12 October 2004, are used to verify the microphysical characteristics of the model’s simulation of mixed-phase clouds (MPCs). A series of one- and two-moment bulk microphysical cloud schemes are tested to identify how the treatment of snow and ice affects the maintenance of cloud liquid water at low temperatures. The baseline two-moment simulation results in realistic liquid water paths and in size distributions of snow reasonably similar to observations. With a one-moment simulation for which the size distribution intercept parameter for snow is fixed at values taken from the two-moment simulation, reasonable snow size distributions are again obtained but the cloud liquid water is reduced because the one-moment scheme couples the number concentration to the mixing ratio. The one-moment scheme with the constant snow intercept parameter set to a value typical of midlatitude frontal clouds results in a substantial underprediction of the liquid water path. In the simulations, the number concentration of small ice crystals is found to be underestimated by an order of magnitude. A sensitivity test with the concentration of ice particles larger than 53 μm increased to the observed value results in underprediction of the liquid water path. If ice (not snow) is the primary driver for the depletion of cloud liquid water, then the results of this study suggest that the feedbacks among ice–snow–cloud liquid water may be misrepresented in the model.
Evaluation of Planetary Boundary Layer Parameterizations in Tropical Cyclones by Comparison of In Situ Observations and High-Resolution Simulations of Hurricane Isabel (2003). Part II: Inner-Core Boundary Layer and Eyewall Structure
Authors: Nolan David S. , Stern Daniel P. , Zhang Jun A. 
Published: March 2009

Abstract
This is the second of a two-part study of the representation of the planetary boundary layer (PBL) in high-resolution Weather Research and Forecast Model (WRF) simulations of Hurricane Isabel (2003). The Yonsei University (YSU) PBL parameterization and the Mellor–Yamada–Janjić (MYJ) PBL parameterization are evaluated by direct comparison to in situ data obtained by research aircraft. The numerical model, simulation design, details of the PBL schemes, and the representation of the boundary layer in the outer-core were presented in Part I. This part presents a detailed study of the inner-core PBL, including its axisymmetric and asymmetric structures, and comparisons to analyses of dropsonde data from previous studies.
Although neither PBL scheme was designed specifically for hurricane conditions, their simulated boundary layers are reasonably good representations of the observed boundary layer. Both schemes reproduce certain unique features of the hurricane boundary layer, such as the separate depths of the well-mixed layer and the inflow layer, and the pronounced wind speed maxima near the top of the inflow layer. Modification of the original YSU and MYJ schemes to have ocean roughness lengths more in agreement with recent studies considerably improves the results of both schemes. Even with these improvements, the MYJ consistently produces larger frictional tendencies in the boundary layer than the YSU scheme, leading to a stronger low-level inflow and a stronger azimuthal wind maximum at the top of the boundary layer. For both schemes, differences in the low-level asymmetries between the simulated and observed wind fields appear to be related to eyewall asymmetries forced by environmental wind shear.
The effects of varying horizontal and vertical resolutions are also considered. Increasing the vertical resolution in the PBL results in minor improvements in the inner-core structures. Increasing the horizontal resolution around the eyewall also leads to improved boundary layers, as well as an improvement of the vertical structure of the inner-core wind field.
A summary and discussion of the results of both Parts I and II is provided.
Infectious complications from full extension endobronchial ultrasound transbronchial needle aspiration
Authors: Haas A. R. 
Published: March 2009

The development of a convex probe endobronchial ultrasound (CP-EBUS) videobronchoscope to allow real-time transbronchial needle aspiration (TBNA) has been a significant advance in minimally invasive lung cancer staging and diagnosis. Several recent studies have demonstrated CP-EBUS-TBNA to have recovery rivalling that of the current gold standard, cervical mediastinoscopy. These same studies have indicated that the safety of this procedure has no reported complications.The present case study presents two infectious complications from full extension endobronchial ultrasound transbronchial needle aspiration and discusses possible aetiologies of these infections, as well as implications for future application of this technology.
An improved ontological representation of dendritic cells as a paradigm for all cell types
Authors: Masci Anna Maria , Arighi Cecilia N , Diehl Alexander D , Lieberman Anne E , Mungall Chris , Scheuermann Richard H , Smith Barry , Cowell Lindsay G 
Published: March 2009

Abstract

Background
Recent increases in the volume and diversity of life science data and information and an increasing emphasis on data sharing and interoperability have resulted in the creation of a large number of biological ontologies, including the Cell Ontology (CL), designed to provide a standardized representation of cell types for data annotation. Ontologies have been shown to have significant benefits for computational analyses of large data sets and for automated reasoning applications, leading to organized attempts to improve the structure and formal rigor of ontologies to better support computation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL's utility for computation and for cross-species data integration.

Results
To enhance the CL's utility for computational analyses, we developed a method for the ontological representation of cells and applied this method to develop a dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. We avoid multiple uses of is_a by linking DC-CL terms to terms in other ontologies via additional, formally defined relations such as has_function.

Conclusion
This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. Accordingly, we propose our method as a general strategy for the ontological representation of cells. DC-CL is available from http://www.obofoundry.org.
Human parainfluenza virus type 2 (HPIV2) induced host ADAM8 expression in human salivary adenocarcinoma cell line (HSY) during cell fusion
Authors: Ma Guo-Feng , Miettinen Simo , Porola Pauliina , Hedman Klaus , Salo Jari , Konttinen Yrjö T 
Published: March 2009

Abstract

Background
The aim of the study was to investigate expression of ADAMs (A Disintegrin and A Metalloproteinase) of host cell origin during cell-cell fusion induced by human parainfluenza virus type 2 (HPIV2).

Results
Induction of host cell ADAM9 was observed in GMK cells, but the applicability of this model was restricted by lack of cross-reactivity of the anti-human ADAM8 antibodies with the corresponding green monkey antigens. HSG cells were not susceptible to HPIV2 virus infection. In contrast, in human parotid gland HSY cells, a natural host cell for paramyxoviruses, HPIV2 induced ADAM8 expression. ADAM8 staining increased dramatically over time from 7.9 ± 3% at zero hours to 99.2 ± 0.8% at 72 hours (p = 0.0001). Without HPIV2 the corresponding percentages were only 7.7% and 8.8%. Moreover, ADAM8 positive cells formed bi- (16.2%) and multinuclear cells (3.5%) on day one and the corresponding percentages on day three were 15.6% for binuclear and 57.2% for multinuclear cells.

Conclusion
ADAM8, well recognized for participation in cell-to-cell fusion especially in osteoclast formation, is up-regulated upon formation of multinuclear giant cells after HPIV2 induction in HSY cells. The virus-HSY cell system provides a novel experimental model for study of the molecular mechanism of cell fusion events.
Reconstructing the ubiquitin network - cross-talk with other systems and identification of novel functions
Authors: Venancio Thiago M , Balaji S , Iyer Lakshminarayan M , Aravind L 
Published: March 2009

Abstract
Background
The ubiquitin system (Ub-system) can be defined as the ensemble of components including Ub/ubiquitin-like proteins, their conjugation and deconjugation apparatus, binding partners and the proteasomal system. While several studies have concentrated on structure-function relationships and evolution of individual components of the Ub-system, a study of the system as a whole is largely lacking.

Results
Using numerous genome-scale datasets, we assemble for the first time a comprehensive reconstruction of the budding yeast Ub-system, revealing static and dynamic properties. We devised two novel representations, the rank plot to understand the functional diversification of different components and the clique-specific point-wise mutual-information network to identify significant interactions in the Ub-system.

Conclusions
Using these representations, evidence is provided for the functional diversification of components such as SUMO-dependent Ub-ligases. We also identify novel components of SCF (Skp1-cullin-F-box)-dependent complexes, receptors in the ERAD (endoplasmic reticulum associated degradation) system and a key role for Sus1 in coordinating multiple Ub-related processes in chromatin dynamics. We present evidence for a major impact of the Ub-system on large parts of the proteome via its interaction with the transcription regulatory network. Furthermore, the dynamics of the Ub-network suggests that Ub and SUMO modifications might function cooperatively with transcription control in regulating cell-cycle-stage-specific complexes and in reinforcing periodicities in gene expression. Combined with evolutionary information, the structure of this network helps in understanding the lineage-specific expansion of SCF complexes with a potential role in pathogen response and the origin of the ERAD and ESCRT systems.
Gender differences in the association between childhood abuse and psychosis
Authors: Fisher Helen , Morgan Craig , Dazzan Paola , Craig Thomas K. , Morgan Kevin , Hutchinson Gerard , Jones Peter B. , Doody Gillian A. , Pariante Carmine , McGuffin Peter , Murray Robin M. , Leff Julian , Fearon Paul 
Published: March 2009

BackgroundStudies demonstrating an association between childhood trauma and psychosis in adulthood have not systematically explored gender differences.AimsTo investigate gender differences in the prevalence of childhood sexual and physical abuse among people with psychosis in comparison with healthy controls.MethodThe Childhood Experiences of Care and Abuse Questionnaire was completed to elicit experiences of sexual and physical abuse during childhood in first-episode psychosis cases and population-based controls.ResultsAmong women, those in the cases group were twice as likely to report either physical or sexual abuse compared with controls following adjustment for all confounders. In particular, the effect of physical abuse in women was stronger and more robust than that for sexual abuse. A similar trend was found for psychotic-like experiences in the female control group. No association was found in men.ConclusionsReports of severe childhood physical or sexual abuse were associated with psychosis in women but not in men.
Mental health implications of detaining asylum seekers: systematic review
Authors: Robjant Katy , Hassan Rita , Katona Cornelius 
Published: March 2009

BackgroundThe number of asylum seekers, refugees and internally displaced people worldwide is rising. Western countries are using increasingly restrictive policies, including the detention of asylum seekers, and there is concern that this is harmful.AimsTo investigate mental health outcomes among adult, child and adolescent immigration detainees.MethodA systematic review was conducted of studies investigating the impact of immigration detention on the mental health of children, adolescents and adults, identified by a systematic search of databases and a supplementary manual search of references.ResultsTen studies were identified. All reported high levels of mental health problems in detainees. Anxiety, depression and posttraumatic stress disorder were commonly reported, as were self-harm and suicidal ideation. Time in detention was positively associated with severity of distress. There is evidence for an initial improvement in mental health occurring subsequent to release, although longitudinal results have shown that the negative impact of detention persists.ConclusionsThis area of research is in its infancy and studies are limited by methodological constraints. Findings consistently report high levels of mental health problems among detainees. There is some evidence to suggest an independent adverse effect of detention on mental health.
Intrauterine testosterone exposure and risk for disordered eating
Authors: Baker Jessica H. , Lichtenstein Paul , Kendler Kenneth S. 
Published: March 2009

SummaryPrevious research has suggested that prenatal testosterone exposure masculinises disordered eating by comparing opposite- and same-gender twins. The objective of the current study is to replicate this finding using a sample of 439 identical and 213 fraternal females, 461 identical and 344 fraternal males, and 361 males and 371 females from opposite-gender twin pairs. Disordered eating was compared across twin types using the Eating Disorder Inventory–2. Inconsistent with previous findings, a main effect of co-twin gender was not found. Our results raise questions about the validity of prior evidence of the impact of prenatal testosterone exposure on patterns of disordered eating.
Molecular Response to Cetuximab and Efficacy of Preoperative Cetuximab-Based Chemoradiation in Rectal Cancer
Authors: Debucquoy Annelies , Haustermans Karin , Daemen Anneleen , Aydin Selda , Libbrecht Louis , Gevaert Olivier , De Moor Bart , Tejpar Sabine , McBride William H. , Penninckx Freddy , Scalliet Pierre , Stroh Christopher , Vlassak Soetkin , Sempoux Christine , Machiels Jean-Pascal 
Published: March 2009

Purpose To characterize the molecular pathways activated or inhibited by cetuximab when combined with chemoradiotherapy (CRT) in rectal cancer and to identify molecular profiles and biomarkers that might improve patient selection for such treatments. Patients and Methods Forty-one patients with rectal cancer (T3-4 and/or N+) received preoperative radiotherapy (1.8 Gy, 5 days/wk, 45 Gy) in combination with capecitabine and cetuximab (400 mg/m2 as initial dose 1 week before CRT followed by 250 mg/m2 /wk for 5 weeks). Biopsies and plasma samples were taken before treatment, after cetuximab but before CRT, and at the time of surgery. Proteomics and microarrays were used to monitor the molecular response to cetuximab and to identify profiles and biomarkers to predict treatment efficacy. Results Cetuximab on its own downregulated genes involved in proliferation and invasion and upregulated inflammatory gene expression, with 16 genes being significantly influenced in microarray analysis. The decrease in proliferation was confirmed by immunohistochemistry for Ki67 (P = .01) and was accompanied by an increase in transforming growth factor-α in plasma samples (P < .001). Disease-free survival (DFS) was better in patients if epidermal growth factor receptor expression was upregulated in the tumor after the initial cetuximab dose (P = .02) and when fibro-inflammatory changes were present in the surgical specimen (P = .03). Microarray and proteomic profiles were predictive of DFS. Conclusion Our study showed that a single dose of cetuximab has a significant impact on the expression of genes involved in tumor proliferation and inflammation. We identified potential biomarkers that might predict response to cetuximab-based CRT.
Prospective Risk-Adjusted [18F]Fluorodeoxyglucose Positron Emission Tomography and Computed Tomography Assessment of Radiation Response in Head and Neck Cancer
Authors: Moeller Benjamin J. , Rana Vishal , Cannon Blake A. , Williams Michelle D. , Sturgis Erich M. , Ginsberg Lawrence E. , Macapinlac Homer A. , Lee J. Jack , Ang K. Kian , Chao K.S. Clifford , Chronowski Gregory M. , Frank Steven J. , Morrison William H. , Rosenthal David I. , Weber Randal S. , Garden Adam S. , Lippman Scott M. , Schwartz David L. 
Published: March 2009

Purpose [18F]Fluorodeoxyglucose positron emission tomography (FDG-PET)/computed tomography (CT) imaging may improve assessment of radiation response in patients with head and neck cancer, but it is not yet known for which patients this is most useful. We conducted a prospective trial to identify patient populations likely to benefit from the addition of functional imaging to the assessment of radiotherapy response. Patients and Methods Ninety-eight patients with locally advanced cancer of the oropharynx, larynx, or hypopharynx were prospectively enrolled and treated with primary radiotherapy, with or without chemotherapy. Patients underwent FDG-PET/CT and contrast-enhanced CT imaging 8 weeks after completion of treatment. Functional and anatomic imaging response was correlated with clinical and pathologic response. Imaging accuracy was then compared between imaging modalities. Results Although postradiation maximum standard uptake values were significantly higher in nonresponders compared with responders, the positive and negative predictive values of FDG-PET/CT scanning were similar to those for CT alone in the unselected study population. Subset analyses revealed that FDG-PET/CT outperformed CT alone in response assessment for patients at high risk for treatment failure (those with human papillomavirus [HPV] –negative disease, nonoropharyngeal primaries, or history of tobacco use). No benefit to FDG-PET/CT was seen for low-risk patients lacking these features. Conclusion These data do not support the broad application of FDG-PET/CT for radiation response assessment in unselected head and neck cancer patients. However, FDG-PET/CT may be the imaging modality of choice for patients with highest risk disease, particularly those with HPV-negative tumors. Optimal timing of FDG-PET/CT imaging after radiotherapy merits further investigation.
Newer Antidepressants and Gabapentin for Hot Flashes: An Individual Patient Pooled Analysis
Authors: Loprinzi Charles L. , Sloan Jeff , Stearns Vered , Slack Rebecca , Iyengar Malini , Diekmann Brent , Kimmick Gretchen , Lovato James , Gordon Paul , Pandya Kishan , Guttuso Thomas , Barton Debra , Novotny Paul 
Published: March 2009

Purpose Nonhormonal treatment options have been investigated as treatments for hot flashes, a major clinical problem in many women. Starting in 2000, a series of 10 individual double-blind placebo-controlled studies has evaluated newer antidepressants and gabapentin for treating hot flashes. This current project was developed to conduct an individual patient pooled analysis of the data from these published clinical trials. Patients and Methods Individual patient data were collected from the various study investigators who published their study results between 2000 and 2007. Between-study heterogeneity for study characteristics and patient populations was tested via χ2 tests before a pooled analysis. The primary end point, the change in hot flash activity from baseline to week 4, for each agent was calculated via both weighted and unweighted approaches, using the size of the study as the weight. Basic summary statistics were produced for hot flash score and frequency using the following three statistics: raw change, percent reduction, and whether or not a 50% reduction was achieved. Results This study included seven trials of newer antidepressants and three trials of gabapentin. The optimal doses (defined by individual study results) of the newer antidepressants paroxetine, venlafaxine, fluoxetine, and sertraline decreased hot flash scores by 41%, 33%, 13%, and 3% to 18% compared with the corresponding placebo arms, respectively. The three gabapentin trials decreased hot flashes by 35% to 38% compared with the corresponding placebo arms. Conclusion Some newer antidepressants and gabapentin, within 4 weeks of therapy initiation, decrease hot flashes more than placebo.
The prevalence of hallux valgus and its association with foot pain and function in a rural Korean community
Authors: Cho N. H. , Kim S. , Kwon D.-J. , Kim H. A. 
Published: March 2009

There are few data available regarding the association between hallux valgus and pain or functional limitation. We determined the prevalence of hallux valgus in a rural Korean population aged between 40 and 69 years, and its association with pain and function. A total of 563 subjects was examined using the foot health status questionnaire, the Short Form-36 questionnaire and weight-bearing anteroposterior radiographs. Hallux valgus was present in 364 subjects (64.7%). It did not significantly correlate with age and was more common in women. Of the 364 subjects, 48 (13.2%) had moderate or greater deformity, defined as a hallux valgus angle > 25°. This was significantly associated with pain, worse function and worse foot health. The putative risk factors associated with painful hallux valgus were female gender, low educational attainment and the presence of pain in the knee.