bluuebunny/crossref_metadata_2025_split huggingface dataset:
Basic Diagnosis and Prediction of Persistent Contrail Occurrence Using High-Resolution Numerical Weather Analyses/Forecasts and Logistic Regression. Part I: Effects of Random Error
Authors: Duda David P. , Minnis Patrick 
Published: March 2009

Abstract
Straightforward application of the Schmidt–Appleman contrail formation criteria to diagnose persistent contrail occurrence from numerical weather prediction data is hindered by significant bias errors in the upper-tropospheric humidity. Logistic models of contrail occurrence have been proposed to overcome this problem, but basic questions remain about how random measurement error may affect their accuracy. A set of 5000 synthetic contrail observations is created to study the effects of random error in these probabilistic models. The simulated observations are based on distributions of temperature, humidity, and vertical velocity derived from Advanced Regional Prediction System (ARPS) weather analyses. The logistic models created from the simulated observations were evaluated using two common statistical measures of model accuracy: the percent correct (PC) and the Hanssen–Kuipers discriminant (HKD). To convert the probabilistic results of the logistic models into a dichotomous yes/no choice suitable for the statistical measures, two critical probability thresholds are considered. The HKD scores are higher (i.e., the forecasts are more skillful) when the climatological frequency of contrail occurrence is used as the critical threshold, whereas the PC scores are higher (i.e., the forecasts are more accurate) when the critical probability threshold is 0.5. For both thresholds, typical random errors in temperature, relative humidity, and vertical velocity are found to be small enough to allow for accurate logistic models of contrail occurrence. The accuracy of the models developed from synthetic data is over 85% for the prediction of both contrail occurrence and nonoccurrence, although, in practice, larger errors would be anticipated.
Basic Diagnosis and Prediction of Persistent Contrail Occurrence Using High-Resolution Numerical Weather Analyses/Forecasts and Logistic Regression. Part II: Evaluation of Sample Models
Authors: Duda David P. , Minnis Patrick 
Published: March 2009

Abstract
A probabilistic forecast to accurately predict contrail formation over the conterminous United States (CONUS) is created by using meteorological data based on hourly meteorological analyses from the Advanced Regional Prediction System (ARPS) and the Rapid Update Cycle (RUC) combined with surface and satellite observations of contrails. Two groups of logistic models were created. The first group of models (SURFACE models) is based on surface-based contrail observations supplemented with satellite observations of contrail occurrence. The most common predictors selected for the SURFACE models tend to be related to temperature, relative humidity, and wind direction when the models are generated using RUC or ARPS analyses. The second group of models (OUTBREAK models) is derived from a selected subgroup of satellite-based observations of widespread persistent contrails. The most common predictors for the OUTBREAK models tend to be wind direction, atmospheric lapse rate, temperature, relative humidity, and the product of temperature and humidity.
Toward a Standard Procedure for Validation of Satellite-Derived Cloud Liquid Water Path: A Study with SEVIRI Data
Authors: Greuell W. , Roebeling R. A. 
Published: March 2009

Abstract
Differences between satellite-derived and ground-based values of cloud liquid water path (LWPsat and LWPgr, respectively) in validation studies are partly associated with the validation itself, in particular with scale differences and parallax. This paper aims at establishing standards for validation procedures to minimize these contributions to the differences. To investigate this, LWP values were collected as computed from ground-based microwave radiometer (MWR) summer measurements made at two Cloudnet sites and from the spaceborne Spinning Enhanced Visible and Infrared Imager (SEVIRI) instrument. The large number of all-sky sample pairs (∼2500 after selection) formed an essential condition for the present study. The best validation method was determined by optimum statistical agreement between LWPsat and LWPgr. The method consists of (i) computation of LWPsat by averaging LWP over the pixels surrounding the ground station by means of a Gaussian weight function with a length scale defining the validation area, (ii) computation of LWPgr by averaging the MWR measurements with a Gaussian weight function, by using a time scale that is considerably longer than the time in which the clouds move across the validation area (by a factor of 3–15), and (iii) correcting for parallax. The authors argue that the best length scale for averaging the satellite data is equal to the image resolution. The improvement resulting from the parallax correction was significant at the 99.5% level, but its effect was not significant for a subset of the data for relatively homogeneous cloud fields. Also, there was no significant improvement when, instead of taking a constant, the time scale for averaging the ground data was adjusted to the instantaneous wind field.
Heterogeneous Correlation Modeling Based on the Wavelet Diagonal Assumption and on the Diffusion Operator
Authors: Pannekoucke Olivier 
Published: March 2009

Abstract
This article discusses several models for background error correlation matrices using the wavelet diagonal assumption and the diffusion operator. The most general properties of filtering local correlation functions, with wavelet formulations, are recalled. Two spherical wavelet transforms based on Legendre spectrum and a gridpoint spherical wavelet transform are compared. The latter belongs to the class of second-generation wavelets. In addition, a nonseparable formulation that merges the wavelets and the diffusion operator model is formally proposed. This hybrid formulation is illustrated in a simple two-dimensional framework. These three formulations are tested in a toy experiment on the sphere: a large ensemble of perturbed forecasts is used to simulate a true background error ensemble, which gives a reference. This ensemble is then applied to compute the required parameters for each model. A randomization method is utilized in order to diagnose these different models. In particular, their ability to represent the geographical variations of the local correlation functions is studied by diagnosis of the local length scale. The results from these experiments show that the spectrally based wavelet formulation filters the geographical variations of the local correlation length scale but it is less able to represent the anisotropy. The gridpoint-based wavelet formulation is also able to represent some parts of the geographical variations but it appears that the correlation functions are dependent on the grid. Finally, the formulation based on the diffusion represents quite well the local length scale.
Reply
Authors: Knippertz Peter , Fink Andreas H. , Pohle Susan 
Published: March 2009

AbstractHydrostatic tendency equations of pressure and geopotential have been used in various forms since the beginning of the twentieth century. In contrast to classical mass flux divergence formulations, all forms that involve vertical integrals of temperature tendencies contain an additional term related to geopotential tendency at the upper limit of the integral. In many previous studies, including a recent work by two of the authors on a case of unusual wintertime precipitation in tropical West Africa, it has been assumed that there exists a pressure level in the stratosphere (usually 100 or 50 hPa) where these tendencies become negligible. This assumption implies a direct relation between net column heating and surface pressure fall. Prompted by a critique of Spengler and Egger, the validity of the concept of a stratospheric level of insignificant dynamics is tested here for the previously studied case on the basis of operational analyses from the ECMWF. At least for low latitudes, significant tendencies with some spatial and temporal variations are found up to 10 hPa, which renders a general neglect of this term on a fixed pressure level problematic. These results call for a more detailed investigation of the dynamical causes of the analyzed tendencies, a reevaluation of some previous work, and a more careful design of future studies on this subject.
Is forced use of the paretic upper limb beneficial? A randomized pilot study during subacute post-stroke recovery
Authors: Hammer Ann , Lindmark Birgitta 
Published: March 2009

Objective: To evaluate the effect of two weeks of forced use of the paretic upper limb, as a supplement to the rehabilitation programme in the subacute phase after stroke, on self-rated use of that limb. Design: A randomized, non-blind, parallel group, clinical, before-and-after trial. A forced use group and a conventional group were followed up one and three months after intervention. Setting: In- and outpatient units of rehabilitation at a University Hospital. Subjects: Thirty patients were allocated to two groups, 15 in each, 1—6 months (mean 2.4) after stroke onset. Twenty-six patients completed the study. Interventions: The patients of both groups participated in two weeks of daily training on weekdays. In addition, the forced use group wore a restraining sling on the non-paretic arm for up to 6 hours per weekday. Main measure: The Motor Activity Log; patients scored 0—5 for 30 daily tasks concerning both amount of use and quality of movement. Results: The forced use group tended to achieve larger improvements immediately post-intervention, but this was not clearly demonstrated. The small differences also levelled out up to the three-month follow-up, with both groups earning an approximately 1.0 score point on both scales of the Motor Activity Log. Conclusions: This pilot study did not reveal any additional benefit of forced use on self-rated performance in daily use of the paretic upper limb. Both groups performed fairly extensive, active training with a similar duration, amount and content.
What does a structured review of the effectiveness of exercise interventions for persons with multiple sclerosis tell us about the challenges of designing trials?
Authors: Asano M , Dawes DJ , Arafah A , Moriello C , Mayo NE 
Published: March 2009

Objective The goal of this review is to ascertain the extent to which the current body of research on the role of exercise in multiple sclerosis (MS) provides sufficiently strong evidence to guide regular exercise prescription. Methods We searched CINAHL, COCHRANE, EMBASE, and MEDLINE between 1950 and December 2007 with combinations of MeSH terms and keywords. We assessed the methodological quality of selected randomized controlled trials (RCTs) of exercise interventions using the Physiotherapy Evidence Database scale and evaluated the effects of the exercise interventions by calculating effect sizes (ES) for the target outcomes. Results Eleven RCTs met the criteria, all with acceptable methodological quality. The ES ranged from −0.36 to 3.50 on the target outcomes. Only one study had 95% confidence intervals clearly excluding a value of 0. Measures of body functions and structures and activities were the most common target outcomes of interventions. Conclusion Although there was some evidence to support positive effects of exercise on physical and psychosocial functioning and on quality of life, our review revealed insufficient research in this area, making it difficult to guide regular exercise prescription. Furthermore, it also emphasizes the methodological challenges in these RCTs leading us to believe that there is a great need for high quality RCTs in this area, contributing evidence for regular exercise and physical activity prescription for persons with MS.
Anti-α-glucose–based glycan IgM antibodies predict relapse activity in multiple sclerosis after the first neurological event
Authors: Freedman MS , Laks J , Dotan N , Altstock RT , Dukler A , Sindic CJM 
Published: March 2009

Background There is no specific serum-based biomarker for the diagnosis or prognosis of relapsing-remitting multiple sclerosis (RRMS). Objective We investigated whether levels of IgM antibodies to Glc(α1,4)Glc(α) (GAGA4) or to a panel of four glucose-based glycans could differentiate MS from other neurological diseases (OND) or predict risk of early relapse following first presentation (FP) of RRMS. Methods Retrospective analysis of 440 sera samples of three cohorts: A) FP-RRMS ( n = 44), OND ( n = 44); B) FP-RRMS ( n = 167), OND ( n = 85); and C) FP ( n = 100). Anti-GAGA4 IgM levels were measured by enzyme immunoassay in cohort-A and cohort-B. Cohort-C IgM antibodies to glucose-based glycan panel were measured by immunofluorescence. Results FP-RRMS had higher levels of anti-GAGA4 IgM than OND patients (cohort-A, P = 0.01; cohort-B, P = 0.0001). Sensitivity and specificity were 27% and 97% for cohort-A; and 26% and 90% for cohort-B, respectively. In cohort-C, 58 patients experienced early relapse (<24 months), 31 had late relapse (≥24 months), and 11 did not experience second attack during follow-up. Kaplan–Meier curves demonstrated decrease in time to next relapse for patients positive for the antibody panel ( P = 0.02, log rank). Conclusions Serum anti-GAGA4 IgM discerns FP-RRMS patients from OND patients. Higher levels of serum anti-α-glucose IgM in FP patients predict imminent early relapse.
A proliferation-inducing ligand mediates follicular lymphoma B-cell proliferation and cyclin D1 expression through phosphatidylinositol 3-kinase–regulated mammalian target of rapamycin activation
Authors: Gupta Mamta , Dillon Stacey R. , Ziesmer Steven C. , Feldman Andrew L. , Witzig Thomas E. , Ansell Stephen M. , Cerhan James R. , Novak Anne J. 
Published: March 2009

Abstract
A proliferation-inducing ligand (APRIL), as well as its receptors transmembrane activator and calcium-modulating cyclophilin ligand (CAML) interactor (TACI) and B-cell maturation antigen (BCMA), has been shown to be important in B-cell biology, and overexpression of APRIL in mice results in development of lymphoma. Limited data are available on APRIL-specific signaling responses, but knockout models suggest that signaling through TACI is critical to B-cell homeostasis. To better understand the mechanism by which APRIL exerts its effects and how it may contribute to lymphomagenesis, we sought to characterize the outcome of APRIL-TACI interactions. In support of murine studies, we find that APRIL induces proliferation of human patient follicular lymphoma (FL) B cells in a TACI-dependent manner. This study also shows that APRIL is expressed within the tumor microenvironment and that, upon engagement with TACI, APRIL mediates activation of the phosphatidylinositol 3-kinase (PI3K) pathway. Activation of PI3K via APRIL results in phosphorylation of Akt and mammalian target of rapamycin (mTOR) and the mTOR-specific substrates p70S6 kinase and 4E-binding protein 1 in a TACI-dependent manner. APRIL-mediated signaling also results in phosphorylation of Rb and up-regulation of cyclin D1. These studies are the first to characterize APRIL-TACI–specific signaling and suggest a role for this ligand-receptor pair in FL B-cell growth.
The mouse Runx1 +23 hematopoietic stem cell enhancer confers hematopoietic specificity to both Runx1 promoters
Authors: Bee Thomas , Ashley Emma L.K. , Bickley Sorrel R.B. , Jarratt Andrew , Li Pik-Shan , Sloane-Stanley Jackie , Göttgens Berthold , de Bruijn Marella F.T.R. 
Published: March 2009

AbstractThe transcription factor Runx1 plays a pivotal role in hematopoietic stem cell (HSC) emergence, and studies into its transcriptional regulation should give insight into the critical steps of HSC specification. Recently, we identified the Runx1 +23 enhancer that targets reporter gene expression to the first emerging HSCs of the mouse embryo when linked to the heterologous hsp68 promoter. Endogenous Runx1 is transcribed from 2 alternative promoters, P1 and P2. Here, we examined the in vivo cis-regulatory potential of these alternative promoters and asked whether they act with and contribute to the spatiotemporal specific expression of the Runx1 +23 enhancer. Our results firmly establish that, in contrast to zebrafish runx1, mouse Runx1 promoter sequences do not confer any hematopoietic specificity in transgenic embryos. Yet, both mouse promoters act with the +23 enhancer to drive reporter gene expression to sites of HSC emergence and colonization, in a +23-specific pattern.
JNets: Exploring networks by integrating annotation
Authors: MacPherson Jamie I , Pinney John W , Robertson David L 
Published: March 2009

AbstractBackgroundA common method for presenting and studying biological interaction networks is visualization. Software tools can enhance our ability to explore network visualizations and improve our understanding of biological systems, particularly when these tools offer analysis capabilities. However, most published network visualizations are static representations that do not support user interaction.ResultsJNets was designed as a network visualization tool that incorporates annotation to explore the underlying features of interaction networks. The software is available as an application and a configurable applet that can provide a flexible and dynamic online interface to many types of network data. As a case study, we use JNets to investigate approved drug targets present within the HIV-1 Human protein interaction network. Our software highlights the intricate influence that HIV-1 has on the host immune response.ConclusionJNets is a software tool that allows interaction networks to be visualized and studied remotely, from within a standard web page. Therefore, using this free software, network data can be presented in an enhanced, interactive format. More information about JNets is available athttp://www.manchester.ac.uk/bioinformatics/jnets.
Photo-activation of the hydrophobic probe iodonaphthylazide in cells alters membrane protein function leading to cell death
Authors: Viard Mathias , Garg Himanshu , Blumenthal Robert , Raviv Yossef 
Published: March 2009

Abstract

Background
Photo-activation of the hydrophobic membrane probe 1, 5 iodonaphthylazide (INA) by irradiation with UV light (310–380 nm) results in the covalent modification of transmembrane anchors of membrane proteins. This unique selectivity of INA towards the transmembrane anchor has been exploited to specifically label proteins inserted in membranes. Previously, we have demonstrated that photo-activation of INA in enveloped viruses resulted in the inhibition of viral membrane protein-induced membrane fusion and viral entry into cells. In this study we show that photo-activation of INA in various cell lines, including those over-expressing the multi-drug resistance transporters MRP1 or Pgp, leads to cell death. We analyzed mechanisms of cell killing by INA-UV treatment. The effects of INA-UV treatment on signaling via various cell surface receptors, on the activity of the multi-drug resistance transporter MRP1 and on membrane protein lateral mobility were also investigated.

Results
INA treatment of various cell lines followed by irradiation with UV light (310–380 nm) resulted in loss of cell viability in a dose dependent manner. The mechanism of cell death appeared to be apoptosis as indicated by phosphatidylserine exposure, mitochondrial depolarization and DNA fragmentation. Inhibition by pan-caspase inhibitors and cleavage of caspase specific substrates indicated that at low concentrations of INA apoptosis was caspase dependent. The INA-UV treatment showed similar cell killing efficacy in cells over-expressing MRP1 function as control cells. Efflux of an MRP1 substrate was blocked by INA-UV treatment of the MRP1-overexpressing cells. Although INA-UV treatment resulted in inhibition of calcium mobilization triggered by chemokine receptor signaling, Akt phosphorylation triggered by IGF1 receptor signaling was enhanced. Furthermore, fluorescence recovery after photobleaching experiments indicated that INA-UV treatment resulted in reduced lateral mobility of a seven transmembrane G protein-coupled receptor.

Conclusion
INA is a photo-activable agent that induces apoptosis in various cancer cell lines. It reacts with membrane proteins to alter the normal physiological function resulting in apoptosis. This activity of INA maybe exploited for use as an anti-cancer agent.
Preventing falls in older multifocal glasses wearers by providing single-lens distance glasses: the protocol for the VISIBLE randomised controlled trial
Authors: Haran Mark J , Lord Stephen R , Cameron Ian D , Ivers Rebecca Q , Simpson Judy M , Lee Bonsan B , Porwal Mamta , Kwan Marcella MS , Severino Connie 
Published: March 2009

Abstract

Background
Recent research has shown that wearing multifocal glasses increases the risk of trips and falls in older people. The aim of this study is to determine whether the provision of single-lens distance glasses to older multifocal glasses wearers, with recommendations for wearing them for walking and outdoor activities, can prevent falls. We will also measure the effect of the intervention on health status, lifestyle activities and fear of falling, as well as the extent of adherence to the program.

Methods/Design
Approximately 580 older people who are regular wearers of multifocal glasses people will be recruited. Participants will be randomly allocated to either an intervention group (provision of single lens glasses, with counselling and advice about appropriate use) or a control group (usual care). The primary outcome measure will be falls (measured with 13 monthly calendars). Secondary measures will be quality of life, falls efficacy, physical activity levels and adverse events.

Discussions
The study will determine the impact of providing single-lens glasses, with advice about appropriate use, on preventing falls in older regular wearers of multifocal glasses. This pragmatic intervention, if found to be effective, will guide practitioners with regard to recommending appropriate glasses for minimising the risk of falls in older people.

Trial Registration
The protocol for this study was registered with the Clinical Trials.gov Protocol Registration System on June 7th 2006 (#350855).