bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Transpose-AMIP II Experiment and Its Application to the Understanding of Southern Ocean Cloud Biases in Climate Models
Authors: Williams K. D. , Bodas-Salcedo A. , Déqué M. , Fermepin S. , Medeiros B. , Watanabe M. , Jakob C. , Klein S. A. , Senior C. A. , Williamson D. L. 
Published: November 2012

Abstract
The Transpose-Atmospheric Model Intercomparison Project (AMIP) is an international model intercomparison project in which climate models are run in “weather forecast mode.” The Transpose-AMIP II experiment is run alongside phase 5 of the Coupled Model Intercomparison Project (CMIP5) and allows processes operating in climate models to be evaluated, and the origin of climatological biases to be explored, by examining the evolution of the model from a state in which the large-scale dynamics, temperature, and humidity structures are constrained through use of common analyses.
The Transpose-AMIP II experimental design is presented. The project requests participants to submit a comprehensive set of diagnostics to enable detailed investigation of the models to be performed. An example of the type of analysis that may be undertaken using these diagnostics is illustrated through a study of the development of cloud biases over the Southern Ocean, a region that is problematic for many models. Several models share a climatological bias for too little reflected shortwave radiation from cloud across the region. This is found to mainly occur behind cold fronts and/or on the leading side of transient ridges and to be associated with more stable lower-tropospheric profiles. Investigation of a case study that is typical of the bias and associated meteorological conditions reveals the models to typically simulate cloud that is too optically and physically thin with an inversion that is too low. The evolution of the models within the first few hours suggests that these conditions are particularly sensitive and a positive feedback can develop between the thinning of the cloud layer and boundary layer structure.
An Observation-Based Assessment of Nonlinear Feedback Processes Associated with the Indian Ocean Dipole
Authors: Cai Wenju , Qiu Yun 
Published: November 2012

Abstract
A well-known feature of the Indian Ocean dipole (IOD) is its positive skewness, with cold sea surface temperature (SST) anomalies over the east pole (IODE) exhibiting a larger amplitude than warm SST anomalies. Several mechanisms have been proposed for this asymmetry, but because of a lack of observations the role of various processes remains contentious. Using Argo profiles and other newly available data, the authors provide an observation-based assessment of the IOD skewness. First, the role of a nonlinear dynamical heating process is reaffirmed, which reinforces IODE cold anomalies but damps IODE warm anomalies. This reinforcing effect is greater than the damping effect, further contributing to the skewness. Second, the existence of a thermocline–temperature feedback asymmetry, whereby IODE cold anomalies induced by a shoaling thermocline are greater than warm anomalies associated with a deepening thermocline, is the primary forcing of the IOD skewness. This thermocline–temperature feedback asymmetry is a part of the nonlinear Bjerknes-like positive feedback loop involving winds, SST, and the thermocline, all displaying a consistent asymmetry with a stronger response when IODE SST is anomalously cold. The asymmetry is enhanced by a nonlinear barrier layer response, with a greater thinning associated with IODE cold anomalies than a thickening associated with IODE warm anomalies. Finally, in response to IODE cool anomalies, rainfall and evaporative heat loss diminish and incoming shortwave radiation increases, which results in damping the cool SST anomalies. The damping increases with IODE cold anomalies. Thus, the IOD skewness is generated in spite of a greater damping effect of the SST–cloud–radiation feedback process.
A Comparison of Wind Speed and Forest Damage Associated with Tornadoes in Northern Arizona
Authors: Blanchard David O. 
Published: November 2012

Abstract
Damage surveys in the aftermath of tornadoes occurring in the forested regions of the Mogollon Rim in northern Arizona have been assessed using the enhanced Fujita scale (EF scale) damage indicator (DI) and degree of damage (DOD) tables. These surveys often revealed different DODs within close proximity as well as different spatial patterns and areal extent of tree damage exhibiting the same DOD, making the determination of wind speed and EF-scale ratings challenging. A localized tornado outbreak occurred across northern Arizona on 6 October 2010, producing at least 11 tornadoes and substantial areas of forest damage. Remarkably, one of these tornadoes passed over a three-dimensional sonic anemometer. Wind data from this sensor are compared with tree damage in the adjacent forest to assess the performance of the EF-scale metrics for damage to trees.
Axonal loss of white matter in migraine without aura: A tract-based spatial statistics study
Authors: Yu Dahua , Yuan Kai , Qin Wei , Zhao Ling , Dong Minghao , Liu Peng , Yang Xuejuan , Liu Jixin , Sun Jinbo , Zhou Guangyu , von Deneen Karen M , Tian Jie 
Published: November 2012

Aim Multiple diffusion tensor imaging (DTI) derived indices may help to deduce the pathophysiological type of white matter (WM) changes and provide more specific biomarkers of WM neuropathology in the whole brain of migraine patients without aura (MWoA). Methods Twenty MWoA and 20 age-, education- and gender-matched healthy volunteers participated in this study. Tract-based spatial statistics (TBSS) was employed to investigate the WM abnormalities in MWoA by integrating multiple indices, including fractional anisotropy (FA), mean diffusivity (MD), radial diffusivity (RD), and axial diffusivity (AD). Results Compared with healthy controls, MWoA showed significantly lower FA, MD and AD in multiple brain regions, whereas no difference in RD was observed. Specifically, the overlap among the lower FA, MD, and AD was found in the genu, body, and splenium part of the corpus callosum (CC), the right anterior limb of the internal capsule (ALIC) and the posterior limb of the internal capsule (PLIC) in MWoA compared with healthy controls. Additionally, some of the above WM findings were significantly correlated with duration and headache frequency in MWoA. Conclusion Given that decreased AD may suggest axonal loss, our findings may reveal axonal loss in MWoA.
The Effect of Arthroscopic Partial Medial Meniscectomy on Tibiofemoral Stability
Authors: Arno Sally , Hadley Scott , Campbell Kirk A. , Bell Christopher P. , Hall Michael , Beltran Luis S. , Recht Michael P. , Sherman Orrin H. , Walker Peter S. 
Published: November 2012

Background: There is still little known regarding the effects of meniscus resection size on tibiofemoral stability. Purpose: To determine if partial medial meniscectomy of the posterior horn significantly alters tibiofemoral stability as measured by the anterior-posterior (AP) position and laxity of the medial femoral condyle. Study Design: Controlled laboratory study. Methods: Five cadaveric knees were dissected to the capsule, preserving all ligaments and the quadriceps tendon. Each specimen was first tested on a rig where the AP position and laxity of the medial femoral condyle were measured while a range of forces was applied from full extension to 90° of flexion. Magnetic resonance imaging (MRI) at 3 tesla was then performed for baseline measurements of the meniscus before partial meniscectomy. Arthroscopic partial medial meniscectomy aimed at 30% of the posterior horn was then performed, followed by repeat mechanical testing and MRI. The sequence was then repeated for arthroscopic partial meniscectomy aimed at 60% and 100% of the posterior horn of the medial meniscus. Results: The MRI analysis demonstrated that 22% ± 9% of the original width of the posterior horn was removed at the first resection, 46% ± 11% was removed at the second resection, and the third resection was 100% removal of the posterior horn for all specimens. After 22% resection, no significant difference in AP laxity was observed. A statistically significant increase in AP laxity was observed with 46% resection under a 500-N compressive load compared with the intact meniscus. After full resection, significant increases in AP laxity were observed under a 50-N compressive load compared with the intact and 22% and 46% resections. The 22% resection had similar AP positions as the intact knee, whereas the 46% resection and 100% removal of the posterior horn had statistically further posterior AP positions than the intact knee. Conclusion: Partial medial meniscectomy with ≥46% resection of the original width of the posterior horn significantly altered the AP position of the medial femoral condyle and also increased laxity. Clinical Relevance: These mechanical changes may lead to abnormal cartilage loading and early osteoarthritis.
Biomechanical Analysis of Surface-Athlete Impacts on Third-Generation Artificial Turf
Authors: McGhie David , Ettema Gertjan 
Published: November 2012

Background: Excessive repetitive loads are widely believed to be the cause of overload or overuse injuries. On third-generation artificial turf, impacts have been found to vary with surface and shoe properties. Mechanical devices are considered not representative for measuring impact absorption during athletic movements, and pressure insoles have been shown as inaccurate with regard to magnitude of force. Purpose: To compare impact properties between different third-generation artificial turf systems in combination with various cleat configurations in vivo using force plate technology. Study Design: Controlled laboratory study. Methods: Twenty-two male soccer players (mean ± SD: age, 23.1 ± 2.8 y; height, 1.81 ± 0.1 m; body mass, 77.5 ± 6.0 kg) performed 10 short sprints, 5 straight with a sudden stop and 5 with a 90° cut, over a force plate covered with artificial turf for each combination of 3 turf systems and 3 cleat configurations. Results: During stop sprints, peak impact was significantly higher on a recreational-level turf system than professional-level turf systems with and without an underlying shock pad (3.12 body weight [ W] vs 3.01 W and 3.02 W, respectively). During cut sprints, peak impact was significantly higher with traditional round cleats than with turf cleats and bladed cleats (2.99 W vs 2.84 W and 2.87 W, respectively). Conclusion: The results indicate that both an increase in assumed impact-absorbing surface properties and a larger distribution of shorter cleats produced lower impacts during standardized athletic movements. Regardless, none of the shoe-surface combinations yielded peak impacts of an assumed hazardous magnitude. Clinical Relevance: The study provides information on the extent to which various third-generation artificial turf systems and cleat configurations affect impact force, widely believed to be a causative factor for overload and overuse injuries.
Outcome and pathologic classification of children and adolescents with mediastinal large B-cell lymphoma treated with FAB/LMB96 mature B-NHL therapy
Authors: Gerrard Mary , Waxman Ian M. , Sposto Richard , Auperin Anne , Perkins Sherrie L. , Goldman Stanton , Harrison Lauren , Pinkerton Ross , McCarthy Keith , Raphael Martine , Patte Catherine , Cairo Mitchell S. 
Published: November 2012

Abstract
Mediastinal large B-cell lymphoma (MLBL) represents 2% of mature B-cell non-Hodgkin lymphoma in patients ≤ 18 years of age. We analyzed data from childhood and adolescent patients with stage III MLBL (n = 42) and non-MLBL DLBCL (n = 69) treated with Group B therapy in the French-American-British/Lymphome Malins de Burkitt (FAB/LMB) 96 study. MLBL patients had a male/female 26/16; median age, 15.7 years (range, 12.5-19.7); and LDH &lt; 2 versus ≥ 2 × the upper limit of normal, 23:19. Six MLBL patients (14%) had &lt; a 20% response to initial COP (cyclophosphamide, vincristine, and prednisone) therapy. Central pathology revealed approximately 50% with classical features of primary MLBL. Five-year event-free survival for the stage III MLBL and non-MLBL DLBCL groups was 66% (95% confidence interval [CI], 49%-78%) and 85% (95% CI, 71%-92%), respectively (P &lt; .001; 14%). The 5-year overall survival in the 42 MLBL patients was 73% (95% CI, 56%-84%). We conclude that MLBL in adolescent patients is associated with significantly inferior event-free survival compared with stage III non-MLBL DLBCL and can be of multiple histologies. Alternate treatment strategies should be investigated in the future taking into account both adult MLBL approaches and more recent biologic findings in adult MLBL.
How I treat thrombocytopenia in pregnancy
Authors: Gernsheimer Terry , James Andra H. , Stasi Roberto 
Published: November 2012

AbstractA mild thrombocytopenia is relatively frequent during pregnancy and has generally no consequences for either the mother or the fetus. Although representing no threat in the majority of patients, thrombocytopenia may result from a range of pathologic conditions requiring closer monitoring and possible therapy. Two clinical scenarios are particularly relevant for their prevalence and the issues relating to their management. The first is the presence of isolated thrombocytopenia and the differential diagnosis between primary immune thrombocytopenia and gestational thrombocytopenia. The second is thrombocytopenia associated with preeclampsia and its look-alikes and their distinction from thrombotic thrombocytopenic purpura and the hemolytic uremic syndrome. In this review, we describe a systematic approach to the diagnosis and treatment of these disease entities using a case presentation format. Our discussion includes the antenatal and perinatal management of both the mother and fetus.
Biased agonism of protease-activated receptor 1 by activated protein C caused by noncanonical cleavage at Arg46
Authors: Mosnier Laurent O. , Sinha Ranjeet K. , Burnier Laurent , Bouwens Eveline A. , Griffin John H. 
Published: November 2012

AbstractActivated protein C (APC) exerts endothelial cytoprotective actions that require protease-activated receptor 1 (PAR1), whereas thrombin acting via PAR1 causes endothelial disruptive, proinflammatory actions. APC's activities, but not thrombin's, require PAR1 located in caveolae. PAR1 is a biased 7-transmembrane receptor because G proteins mediate thrombin's signaling, whereas β-arrestin 2 mediates APC's signaling. Here we elucidate novel mechanisms for APC's initiation of signaling. Biochemical studies of APC's protease specificity showed that APC cleaved PAR1 sequences at both Arg41 and Arg46. That PAR1 cleavage at Arg46 can occur on cells was supported by APC's cleavage of N-terminal-SEAP-tagged R41Q-PAR1 but not R41Q/R46Q-PAR1 mutants transfected into cells and by anti-PAR1 epitope mapping of APC-treated endothelial cells. A synthetic peptide composing PAR1 residues 47-66, TR47, stimulated protective signaling in endothelial cells as reflected in Akt and glycogen synthase kinase 3β phosphorylation, Ras-related C3 botulinum toxin substrate 1 activation, and barrier stabilization effects. In mice, the TR47 peptide reduced VEGF-induced vascular leakage. These in vitro and in vivo data imply that the novel PAR1 N-terminus beginning at residue Asn47, which is generated by APC cleavage at Arg46, mediates APC's cytoprotective signaling and that this unique APC-generated N-terminal peptide tail is a novel biased agonist for PAR1.
Clustering of time-course gene expression profiles using normal mixture models with autoregressive random effects
Authors: Wang Kui , Ng Shu Kay , McLachlan Geoffrey J 
Published: November 2012

Abstract

Background
Time-course gene expression data such as yeast cell cycle data may be periodically expressed. To cluster such data, currently used Fourier series approximations of periodic gene expressions have been found not to be sufficiently adequate to model the complexity of the time-course data, partly due to their ignoring the dependence between the expression measurements over time and the correlation among gene expression profiles. We further investigate the advantages and limitations of available models in the literature and propose a new mixture model with autoregressive random effects of the first order for the clustering of time-course gene-expression profiles. Some simulations and real examples are given to demonstrate the usefulness of the proposed models.

Results
We illustrate the applicability of our new model using synthetic and real time-course datasets. We show that our model outperforms existing models to provide more reliable and robust clustering of time-course data. Our model provides superior results when genetic profiles are correlated. It also gives comparable results when the correlation between the gene profiles is weak. In the applications to real time-course data, relevant clusters of coregulated genes are obtained, which are supported by gene-function annotation databases.

Conclusions
Our new model under our extension of the EMMIX-WIRE procedure is more reliable and robust for clustering time-course data because it adopts a random effects model that allows for the correlation among observations at different time points. It postulates gene-specific random effects with an autocorrelation variance structure that models coregulation within the clusters. The developed R package is flexible in its specification of the random effects through user-input parameters that enables improved modelling and consequent clustering of time-course data.
Pre-capture multiplexing improves efficiency and cost-effectiveness of targeted genomic enrichment
Authors: Shearer A Eliot , Hildebrand Michael S , Ravi Harini , Joshi Swati , Guiffre Angelica C , Novak Barbara , Happe Scott , LeProust Emily M , Smith Richard JH 
Published: November 2012

Abstract

Background
Targeted genomic enrichment (TGE) is a widely used method for isolating and enriching specific genomic regions prior to massively parallel sequencing. To make effective use of sequencer output, barcoding and sample pooling (multiplexing) after TGE and prior to sequencing (post-capture multiplexing) has become routine. While previous reports have indicated that multiplexing prior to capture (pre-capture multiplexing) is feasible, no thorough examination of the effect of this method has been completed on a large number of samples. Here we compare standard post-capture TGE to two levels of pre-capture multiplexing: 12 or 16 samples per pool. We evaluated these methods using standard TGE metrics and determined the ability to identify several classes of genetic mutations in three sets of 96 samples, including 48 controls. Our overall goal was to maximize cost reduction and minimize experimental time while maintaining a high percentage of reads on target and a high depth of coverage at thresholds required for variant detection.

Results
We adapted the standard post-capture TGE method for pre-capture TGE with several protocol modifications, including redesign of blocking oligonucleotides and optimization of enzymatic and amplification steps. Pre-capture multiplexing reduced costs for TGE by at least 38% and significantly reduced hands-on time during the TGE protocol. We found that pre-capture multiplexing reduced capture efficiency by 23 or 31% for pre-capture pools of 12 and 16, respectively. However efficiency losses at this step can be compensated by reducing the number of simultaneously sequenced samples. Pre-capture multiplexing and post-capture TGE performed similarly with respect to variant detection of positive control mutations. In addition, we detected no instances of sample switching due to aberrant barcode identification.

Conclusions
Pre-capture multiplexing improves efficiency of TGE experiments with respect to hands-on time and reagent use compared to standard post-capture TGE. A decrease in capture efficiency is observed when using pre-capture multiplexing; however, it does not negatively impact variant detection and can be accommodated by the experimental design.
Unusual domain architecture of aminoacyl tRNA synthetases and their paralogs from Leishmania major
Authors: Gowri V S , Ghosh Indira , Sharma Amit , Madhubala Rentala 
Published: November 2012

AbstractBackgroundLeishmania major, a protozoan parasite, is the causative agent of cutaneous leishmaniasis. Due to the development of resistance against the currently available anti-leishmanial drugs, there is a growing need for specific inhibitors and novel drug targets. In this regards, aminoacyl tRNA synthetases, the linchpins of protein synthesis, have received recent attention among the kinetoplastid research community. This is the first comprehensive survey of the aminoacyl tRNA synthetases, their paralogs and other associated proteins fromL. major.ResultsA total of 26 aminoacyl tRNA synthetases were identified using various computational and bioinformatics tools. Phylogenetic analysis and domain architectures of theL. majoraminoacyl tRNA synthetases suggest a probable archaeal/eukaryotic origin. Presence of additional domains or N- or C-terminal extensions in 11 aminoacyl tRNA synthetases fromL. majorsuggests possibilities such as additional tRNA binding or oligomerization or editing activity. Five freestanding editing domains were identified inL. major. Domain assignment revealed a novel asparagine tRNA synthetase paralog, asparagine synthetase A which has been so far reported from prokaryotes and archaea.ConclusionsA comprehensive bioinformatic analysis revealed 26 aminoacyl tRNA synthetases and five freestanding editing domains inL. major. Identification of two EMAP (endothelial monocyte-activating polypeptide) II-like proteins similar to human EMAP II-like proteins suggests their participation in multisynthetase complex formation. While the phylogeny of tRNA synthetases suggests a probable archaeal/eukaryotic origin, phylogeny of asparagine synthetase A strongly suggests a bacterial origin. The unique features identified in this work provide rationale for designing inhibitors against parasite aminoacyl tRNA synthetases and their paralogs.