bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of Satellite-Based Objective Overshooting Cloud-Top Detection Methods Using CloudSat Cloud Profiling Radar Observations
Authors: Bedka Kristopher M. , Dworak Richard , Brunner Jason , Feltz Wayne 
Published: May 2012

AbstractTwo satellite infrared-based overshooting convective cloud-top (OT) detection methods have recently been described in the literature: 1) the 11-μm infrared window channel texture (IRW texture) method, which uses IRW channel brightness temperature (BT) spatial gradients and thresholds, and 2) the water vapor minus IRW BT difference (WV-IRW BTD). While both methods show good performance in published case study examples, it is important to quantitatively validate these methods relative to overshooting top events across the globe. Unfortunately, no overshooting top database currently exists that could be used in such study. This study examines National Aeronautics and Space Administration CloudSat Cloud Profiling Radar data to develop an OT detection validation database that is used to evaluate the IRW-texture and WV-IRW BTD OT detection methods. CloudSat data were manually examined over a 1.5-yr period to identify cases in which the cloud top penetrates above the tropopause height defined by a numerical weather prediction model and the surrounding cirrus anvil cloud top, producing 111 confirmed overshooting top events. When applied to Moderate Resolution Imaging Spectroradiometer (MODIS)-based Geostationary Operational Environmental Satellite-R Series (GOES-R) Advanced Baseline Imager proxy data, the IRW-texture (WV-IRW BTD) method offered a 76% (96%) probability of OT detection (POD) and 16% (81%) false-alarm ratio. Case study examples show that WV-IRW BTD > 0 K identifies much of the deep convective cloud top, while the IRW-texture method focuses only on regions with a spatial scale near that of commonly observed OTs. The POD decreases by 20% when IRW-texture is applied to current geostationary imager data, highlighting the importance of imager spatial resolution for observing and detecting OT regions.
Evaluation of Cloud Microphysics in JMA-NHM Simulations Using Bin or Bulk Microphysical Schemes through Comparison with Cloud Radar Observations
Authors: Iguchi Takamichi , Nakajima Teruyuki , Khain Alexander P. , Saito Kazuo , Takemura Toshihiko , Okamoto Hajime , Nishizawa Tomoaki , Tao Wei-Kuo 
Published: May 2012

AbstractNumerical weather prediction (NWP) simulations using the Japan Meteorological Agency Nonhydrostatic Model (JMA-NHM) are conducted for three precipitation events observed by shipborne or spaceborne W-band cloud radars. Spectral bin and single-moment bulk cloud microphysics schemes are employed separately for an intercomparative study. A radar product simulator that is compatible with both microphysics schemes is developed to enable a direct comparison between simulation and observation with respect to the equivalent radar reflectivity factor Ze, Doppler velocity (DV), and path-integrated attenuation (PIA). In general, the bin model simulation shows better agreement with the observed data than the bulk model simulation. The correction of the terminal fall velocities of snowflakes using those of hail further improves the result of the bin model simulation. The results indicate that there are substantial uncertainties in the mass–size and size–terminal fall velocity relations of snowflakes or in the calculation of terminal fall velocity of snow aloft. For the bulk microphysics, the overestimation of Ze is observed as a result of a significant predominance of snow over cloud ice due to substantial deposition growth directly to snow. The DV comparison shows that a correction for the fall velocity of hydrometeors considering a change of particle size should be introduced even in single-moment bulk cloud microphysics.
Estimation of Atmospheric Duct Structure Using Radar Sea Clutter
Authors: Zhao Xiaofeng , Huang Sixun 
Published: May 2012

Abstract
Retrieving atmospheric refractivity profiles from the sea surface backscattered radar clutter is known as the refractivity-from-clutter (RFC) technique. Because the relationship between refractivity and radar sea clutter is clearly nonlinear and ill posed, it is difficult to get analytical solutions according to current theories. Previous works treat this problem as a model parameter estimation issue and some optimization algorithms are selected to get approximate solutions. Two main factors that limit the accuracy of the estimation are that 1) the refractive environments are described by using some idealized refractivity parameter models that cannot describe the exact information of the refractivity profile, and 2) accurate modeling of the sea surface radar cross section (RCS) is very difficult. Rather than estimating a few model parameters, this paper puts forward possibilities of using the variational adjoint approach to jointly retrieve the every-height refractivity values and sea surface RCS using radar clutter data. The derivation of the adjoint model is accomplished by an analytical transformation of the parabolic equation (PE) in the continuous domain. Numerical simulations including range-independent and range-dependent RCS cases are presented to demonstrate the ability of this method for RFC estimations. Making use of the refractivity retrievals, propagation loss predictions are also presented.
Reply to “Comments on ‘On the Steadiness of Separating Meandering Currents’”
Authors: Jan van Leeuwen Peter , De Ruijter W. P. M. 
Published: May 2012

Abstract
The authors thank Nof et al. for their comments on the authors’ paper “On the steadiness of separating meandering currents.” The authors’ paper was motivated by a series of papers by Nof et al. Under a certain set of conditions (reduced gravity, steady state, no meridional velocity at outflow, and parallel outflow), Nof et al. showed that a separating and retroflecting frictionless current cannot be steady because of a momentum imbalance. The main conclusion of the authors’ paper was that they agree with the Nof et al. result that a momentum imbalance exists and extended the proof to all possible configurations of retroflecting currents, even including friction. The authors’ results point to a new mechanism for the generation of variability in the ocean that is not related to dynamical instability of the flow.
The main claim in the comments is that the authors incorrectly argued in the appendix that the steady-state solutions presented by Nof et al. in several papers fulfill the extra constraint u2 = g′h. In the original paper, the authors showed that it follows from the geostrophic assumption stated implicitly in all these Nof et al. papers, because the flow is assumed to be parallel. Nof et al. now argue that the flow is only approximately geostrophic in all Nof et al. papers. The authors show in this reply that for steady weakly meandering outflows approximate geostrophy does lead to a momentum imbalance paradox as Nof et al. claim. However, for a steady strongly meandering outflow, approximate geostrophy is not enough and one has to use the method explored by van Leeuwen and De Ruijter to derive a momentum imbalance paradox.
Eddy Subduction and the Vertical Transport Streamfunction
Authors: Lee Mei-Man , Nurser A. J. George 
Published: May 2012

Abstract
Subduction—the transport of fluid across the base of mixed layer—exchanges water masses and tracers between the ocean surface and interior. Eddies can affect subduction in a variety of ways. First, eddies shoal the mixed layer by restratifying water columns through baroclinic instabilities. Second, eddies induce an isopycnic transport that leads to the entrainment of warm waters and subduction of cold waters, which effectively counters the wind-driven overturning circulation. In this study, the authors use an idealized model to examine these two mechanisms by which eddies influence subduction and to discuss how eddy subduction may be better approximated using the concept of vertical transport streamfunction than the conventional meridional transport streamfunction.
An Assessment of Areal Coverage of Severe Weather Parameters for Severe Weather Outbreak Diagnosis
Authors: Shafer Chad M. , Mercer Andrew E. , Richman Michael B. , Leslie Lance M. , Doswell Charles A. 
Published: May 2012

Abstract
The areal extent of severe weather parameters favorable for significant severe weather is evaluated as a means of identifying major severe weather outbreaks. The first areal coverage method uses kernel density estimation (KDE) to identify severe weather outbreak locations. A selected severe weather parameter value is computed at each grid point within the region identified by KDE. The average, median, or sum value is used to diagnose the event’s severity. The second areal coverage method finds the largest contiguous region where a severe weather parameter exceeds a specified threshold that intersects the KDE region. The severe weather parameter values at grid points within the parameter exceedance region are computed, with the average, median, or sum value used to diagnose the event’s severity. A total of 4057 severe weather outbreaks from 1979 to 2008 are analyzed. An event is considered a major outbreak if it exceeds a selected ranking index score (developed in previous work), and is a minor event otherwise. The areal coverage method is also compared to Storm Prediction Center (SPC) day-1 convective outlooks from 2003 to 2008. Comparisons of the SPC forecasts and areal coverage diagnoses indicate the areal coverage methods have similar skill to SPC convective outlooks in discriminating major and minor severe weather outbreaks. Despite a seemingly large sample size, the rare-events nature of the dataset leads to sample size sensitivities. Nevertheless, the findings of this study suggest that areal coverage should be tested in a forecasting environment as a means of providing guidance in future outbreak scenarios.
Family-Centered Rounds and Communication About Discharge Between Families and Inpatient Medical Teams
Authors: Subramony Anupama , Schwartz Talia , Hametz Patricia 
Published: May 2012

Background. Family-centered rounds (FCRs) are believed to enhance family–medical team communication. Objective. To assess family knowledge of discharge plans on teams conducting FCRs. Methods. Families of inpatients within 24 hours of discharge were surveyed regarding discharge plans; answers were compared with medical documentation. Results. Of 118 families, 70% knew discharge goals, whereas only 41% knew discharge day and 63% knew discharge medications. English speakers were more likely to report knowing discharge goals (adjusted odds ratio [AOR] = 3.9, 95% confidence interval [CI] = 1.2-12.2) and discharge medications (AOR = 3.2, 95% CI = 1.1-9.8) compared with Spanish speakers. Non-Hispanics were more likely to report knowing discharge day compared with Hispanics (AOR = 2.7, 95% CI = 1.1-6.6). Conclusions. Families on teams that conduct FCRs are knowledgeable of discharge goals but less knowledgeable of discharge day and medications. Spanish-speaking and Hispanic families are less likely to report knowing discharge plans compared with English-speaking and non-Hispanic counterparts.
Experiencing Type 2 Diabetes Mellitus
Authors: Salamon Katherine S. , Brouwer Amanda M. , Fox Michelle M. , Olson Kimberly A. , Yelich-Koth Sara L. , Fleischman Katie M. , Hains Anthony A. , Davies W. Hobart , Kichler Jessica C. 
Published: May 2012

Purpose The purpose of this study was to explore the perspectives of adolescents diagnosed with type 2 diabetes mellitus (T2DM) in terms of how youths conceptualized the effect of T2DM on daily life, adjustment to the illness, and motivation related to diabetes self-care management. The aims of the study were to gather essential information in order to develop appropriate intervention techniques and inform future studies intended to understand the psychosocial experiences of youths with T2DM. Methods Eight adolescents diagnosed with T2DM were recruited from an outpatient pediatric diabetes clinic at a Midwestern children’s hospital. A qualitative interview was developed, which was scheduled to last about 30 to 45 minutes. Data were analyzed using the consensual qualitative research methodology, wherein qualitative coders developed core ideas and themes related to the adolescent experience of T2DM. Results Three main themes were identified, including how the youths conceptualized the impact of T2DM, adjustment to self-care, and motivation to perform self-care behaviors. Knowledge related to the cause of T2DM and adjustment to completing self-care behaviors was varied among youths. Few adolescents spoke about motivation sources, although when mentioned, it typically involved witnessing negative health consequences in family members or friends with T2DM. Conclusions The data represent essential initial information related to youths with T2DM, which will help guide in developing future studies designed to understand the psychosocial experiences of youths with T2DM and appropriate intervention techniques. Future research that aims to increase internal and external motivation may be able to subsequently impact adherence to self-care behaviors.
Clinical Indications for Canal Wall‐down Mastoidectomy in a Pediatric Population
Authors: Osborn Alexander J. , Papsin Blake C. , James Adrian L. 
Published: May 2012

ObjectiveTo establish clinically derived indications for performing canal wall‐up or canal wall‐down surgery when treating children with cholesteatoma.Study DesignCase series with chart review.SettingTertiary care academic pediatric otolaryngology practice.Subjects and MethodsRetrospective review of 420 children who underwent 700 procedures for cholesteatoma between 1996 and 2010.ResultsThe canal wall was preserved in 89.5% of cases. Common reasons for removing the canal wall were to provide access to the disease, extensive erosion of key structures, and the desire to avoid further surgery. The mean pure‐tone average (PTA) for the canal wall‐up group was 30 dB, whereas the canal wall‐down group had a mean PTA of 45 dB. A matched‐pairs analysis demonstrated that the better performance of the canal wall‐up group was independent of preoperative hearing levels. Furthermore, although the presence of the stapes did influence hearing results, the canal wall‐up procedure yielded better results even when the condition of the stapes was taken into account. The number needed to treat with canal wall‐up to prevent 1 case of hearing loss (ie, mean threshold >30 dB) would be around 6. The need for revision surgery was higher in the canal wall‐up group (51%) compared with the canal wall‐down group (21%).ConclusionIn the setting of adequate follow‐up and open access to surgical resources, most children with cholesteatoma can be managed with an intact canal wall technique. The authors believe that the better audiometric outcomes and easier postoperative care outweigh the need for revision surgery in this group.
Outcomes 5 years after response to rituximab therapy in children and adults with immune thrombocytopenia
Authors: Patel Vivek L. , Mahévas Matthieu , Lee Soo Y. , Stasi Roberto , Cunningham-Rundles Susanna , Godeau Bertrand , Kanter Julie , Neufeld Ellis , Taube Tillmann , Ramenghi Ugo , Shenoy Shalini , Ward Mary J. , Mihatov Nino , Patel Vinay L. , Bierling Philippe , Lesser Martin , Cooper Nichola , Bussel James B. 
Published: May 2012

AbstractTreatments for immune thrombocytopenic purpura (ITP) providing durable platelet responses without continued dosing are limited. Whereas complete responses (CRs) to B-cell depletion in ITP usually last for 1 year in adults, partial responses (PRs) are less durable. Comparable data do not exist for children and 5-year outcomes are unavailable. Patients with ITP treated with rituximab who achieved CRs and PRs (platelets > 150 × 109/L or 50-150 × 109/L, respectively) were selected to be assessed for duration of their response; 72 adults whose response lasted at least 1 year and 66 children with response of any duration were included. Patients had baseline platelet counts < 30 × 109/L; 95% had ITP of > 6 months in duration. Adults and children each had initial overall response rates of 57% and similar 5-year estimates of persisting response (21% and 26%, respectively). Children did not relapse after 2 years from initial treatment whereas adults did. Initial CR and prolonged B-cell depletion predicted sustained responses whereas prior splenectomy, age, sex, and duration of ITP did not. No novel or substantial long-term clinical toxicity was observed. In summary, 21% to 26% of adults and children with chronic ITP treated with standard-dose rituximab maintained a treatment-free response for at least 5 years without major toxicity. These results can inform clinical decision-making.
Inhibition of the mTORC2 and chaperone pathways to treat leukemia
Authors: Zhang Fan , Lazorchak Adam S. , Liu Dou , Chen Fangping , Su Bing 
Published: May 2012

Abstract
Constitutive activation of the kinases Akt or protein kinase C (PKC) in blood cancers promotes tumor-cell proliferation and survival and is associated with poor patient survival. The mammalian target of rapamycin (mTOR) complex 2 (mTORC2) regulates the stability of Akt and conventional PKC (cPKC; PKCα and PKCβ) proteins by phosphorylating the highly conserved turn motif of these proteins. In cells that lack mTORC2 function, the turn motif phosphorylation of Akt and cPKC is abolished and therefore Akt and cPKC protein stability is impaired. However, the chaperone protein HSP90 can stabilize Akt and cPKC, partially rescuing the expression of these proteins. In the present study, we investigated the antitumor effects of inhibiting mTORC2 plus HSP90 in mouse and human leukemia cell models and show that the HSP90 inhibitor 17-allylaminogeldanamycin (17-AAG) preferentially inhibits Akt and cPKC expression and promotes cell death in mTORC2 deficient pre-B leukemia cells. Furthermore, we show that 17-AAG selectively inhibits mTORC2 deficient leukemia cell growth in vivo. Finally, we show that the mTOR inhibitors rapamycin and pp242 work together with 17-AAG to inhibit leukemia cell growth to a greater extent than either drug alone. These studies provide a mechanistic and clinical rationale to combine mTOR inhibitors with chaperone protein inhibitors to treat human blood cancers.
PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods
Authors: Francisco Alexandre P , Vaz Cátia , Monteiro Pedro T , Melo-Cristino José , Ramirez Mário , Carriço João A 
Published: May 2012

Abstract

Background
With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it.

Results
PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available.

Conclusions
PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net.
Genovar: a detection and visualization tool for genomic variants
Authors: Jung Kwang Su , Moon Sanghoon , Kim Young Jin , Kim Bong-Jo , Park Kiejung 
Published: May 2012

Abstract

Background
Along with single nucleotide polymorphisms (SNPs), copy number variation (CNV) is considered an important source of genetic variation associated with disease susceptibility. Despite the importance of CNV, the tools currently available for its analysis often produce false positive results due to limitations such as low resolution of array platforms, platform specificity, and the type of CNV. To resolve this problem, spurious signals must be separated from true signals by visual inspection. None of the previously reported CNV analysis tools support this function and the simultaneous visualization of comparative genomic hybridization arrays (aCGH) and sequence alignment. The purpose of the present study was to develop a useful program for the efficient detection and visualization of CNV regions that enables the manual exclusion of erroneous signals.

Results
A JAVA-based stand-alone program called Genovar was developed. To ascertain whether a detected CNV region is a novel variant, Genovar compares the detected CNV regions with previously reported CNV regions using the Database of Genomic Variants (DGV, http://projects.tcag.ca/variation) and the Single Nucleotide Polymorphism Database (dbSNP). The current version of Genovar is capable of visualizing genomic data from sources such as the aCGH data file and sequence alignment format files.

Conclusions
Genovar is freely accessible and provides a user-friendly graphic user interface (GUI) to facilitate the detection of CNV regions. The program also provides comprehensive information to help in the elimination of spurious signals by visual inspection, making Genovar a valuable tool for reducing false positive CNV results. Availability: http://genovar.sourceforge.net/.
Assessing and predicting protein interactions by combining manifold embedding with multiple information integration
Authors: Lei Ying-Ke , You Zhu-Hong , Ji Zhen , Zhu Lin , Huang De-Shuang 
Published: May 2012

Abstract

Background
Protein-protein interactions (PPIs) play crucial roles in virtually every aspect of cellular function within an organism. Over the last decade, the development of novel high-throughput techniques has resulted in enormous amounts of data and provided valuable resources for studying protein interactions. However, these high-throughput protein interaction data are often associated with high false positive and false negative rates. It is therefore highly desirable to develop scalable methods to identify these errors from the computational perspective.

Results
We have developed a robust computational technique for assessing the reliability of interactions and predicting new interactions by combining manifold embedding with multiple information integration. Validation of the proposed method was performed with extensive experiments on densely-connected and sparse PPI networks of yeast respectively. Results demonstrate that the interactions ranked top by our method have high functional homogeneity and localization coherence.

Conclusions
Our proposed method achieves better performances than the existing methods no matter assessing or predicting protein interactions. Furthermore, our method is general enough to work over a variety of PPI networks irrespectively of densely-connected or sparse PPI network. Therefore, the proposed algorithm is a much more promising method to detect both false positive and false negative interactions in PPI networks.