bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variability of Graupel and Snow Observed in Tropical Oceanic Convection by Aircraft during TRMM KWAJEX
Authors: Sukovich Ellen M. , Kingsmill David E. , Yuter Sandra E. 
Published: August 2008

Abstract
Empirical characterization of graupel and snow in precipitating tropical convective clouds is important for refining satellite precipitation retrieval algorithms and cloud-resolving and radiative transfer models. Microphysics data for this analysis were collected by the University of North Dakota (UND) Citation and the National Aeronautics and Space Agency (NASA) DC-8 aircraft during the Tropical Rainfall Measuring Mission (TRMM) Kwajalein Experiment (KWAJEX) in the western tropical Pacific Ocean. An ice particle identification algorithm was applied to two-dimensional optical array probe data for the purpose of identifying ice particle ensembles dominated by graupel or snow particles. These ensembles were accumulated along 1-km flight segments at temperatures below 0°C. A third category, mixed graupel/snow, has characteristics between those of the predominately graupel and snow ensembles and can be used either in combination with the other two categories or separately. Snow particle ensembles compose 80% of UND Citation and 98% of NASA DC-8 ensemble data. For the UND Citation, graupel ensembles compose ∼5% of the total with mixed graupel/snow ensembles composing ∼15%. There were no graupel ensembles in the NASA DC-8 data, which were collected primarily at temperatures &lt;−35°C. Particles too small to classify (&lt;150-μm maximum dimension) compose 56% of UND Citation and 64% of NASA DC-8 particle images. Nearly all these “tiny” particles occur coincident with particles &gt;∼150 μm. Combining data from both aircraft, snow and mixed graupel/snow ensembles were evident over the full range of subfreezing temperatures (from 0° to −65°C) sampled by the aircraft. In contrast, graupel ensembles were present primarily at temperatures &gt;−10°C. Accurate graupel identification was further supported by all graupel ensembles observed either coincident with or within a 10-km horizontal distance of radar-identified convective precipitation structures.
Wavelet Analysis of the Convectively Coupled Equatorial Waves in the Wavenumber–Frequency Domain
Authors: Wong Martin L. M. 
Published: August 2008

Abstract
Wavelet analysis is performed on 31 yr (1975–2007, except 1978 and 1979) of daily outgoing longwave radiation data in the global equatorial region (15°S–15°N). Power spectra in the zonal wavenumber–frequency domain are obtained. With different scales and bandwidths than in previous Fourier-based analysis, peaks of variances that are associated with the various convectively coupled waves are found. Further, possibly because of the ability to resolve shorter waves that have limited zonal extent, significant variances are also found at tropical depression–type scales. However, waves of zonal wavenumber zero cannot be explicitly analyzed.
Tropical SST Response to Global Warming in the Twentieth Century
Authors: Zhu Xiaojie , Liu Zhengyu 
Published: August 2008

Abstract
The trend of sea surface temperature (SST) in the twentieth century is examined in observations and the Intergovernmental Panel on Climate Change (IPCC) twentieth-century simulations. The observed SST neither shows a clear signal of the enhanced equatorial response (EER) warming nor exhibits a clear trend of the El Niño–like warming in the last century. Similarly, the IPCC simulations show neither a clear EER warming nor an El Niño–like warming in the last century. Furthermore, the comparison of heat fluxes in model simulations of the global warming scenario and the twentieth century indicates that the aerosol cooling effect, opposite to the greenhouse gases warming effect, plays an important role in the twentieth century and explains the EER-like signal in the twentieth-century simulations. Therefore, a conclusion that the IPCC model simulations of the twentieth century are consistent with observations within the error bars as well as the future projection of the EER warming pattern in the global warming scenario are validated.
Interannual Variations of East Asian Trough Axis at 500 hPa and its Association with the East Asian Winter Monsoon Pathway
Authors: Wang Lin , Chen Wen , Zhou Wen , Huang Ronghui 
Published: August 2008

AbstractInterannual variations of the East Asian trough (EAT) axis at 500 hPa are studied with the European Centre for Medium-Range Weather Forecasts 40-yr reanalysis data. The associated circulation pattern and pathway of the East Asian winter monsoon (EAWM) with the EAT axis tilt are specially investigated with a trough axis index, which is closely related to the midlatitude baroclinic process and mainly represents the intensity of the eddy-driven jet over the East Asia–North Pacific sector. When the tilt of EAT is smaller than normal, the EAWM prefers to take the southern pathway and less cold air moves to the central North Pacific. However, the EAWM prefers the eastern pathway and brings more cold air to the North Pacific when the tilt of EAT is larger than normal. These differences induce pronounced changes in both the precipitation and the surface air temperature over East and Southeast Asia. Furthermore, the tilt status of the EAT has a significant modulation effect on the regional climate anomalies related to the intensity of the EAWM. The findings suggest an increase in the temperature anomaly associated with the EAWM intensity and a clear northward–southward shift in its pattern in anomalous tilt phase of the EAT. In addition, the modulation tends to be confined mainly to East Asia and expanded to a larger area during the weak and the strong EAWM winters, respectively. The possible reasons for interannual variations of the EAT tilt are discussed, and it is speculated that the midlatitude air–sea interaction in the North Pacific plays a dominant role. This study on the EAT tilt may enrich knowledge of the East Asian winter monsoon beyond the conventional intensity index and may be helpful to improve regional climate prediction in East Asia.
Quality Control of Large Argo Datasets
Authors: Gaillard Fabienne , Autret Emmanuelle , Thierry Virginie , Galaup Philippe , Coatanoan Christine , Loubrieu Thomas 
Published: August 2008

Abstract
Argo floats have significantly improved the observation of the global ocean interior, but as the size of the database increases, so does the need for efficient tools to perform reliable quality control. It is shown here how the classical method of optimal analysis can be used to validate very large datasets before operational or scientific use. The analysis system employed is the one implemented at the Coriolis data center to produce the weekly fields of temperature and salinity, and the key data are the analysis residuals. The impacts of the various sensor errors are evaluated and twin experiments are performed to measure the system capacity in identifying these errors. It appears that for a typical data distribution, the analysis residuals extract 2/3 of the sensor error after a single analysis. The method has been applied on the full Argo Atlantic real-time dataset for the 2000–04 period (482 floats) and 15% of the floats were detected as having salinity drifts or offset. A second test was performed on the delayed mode dataset (120 floats) to check the overall consistency, and except for a few isolated anomalous profiles, the corrected datasets were found to be globally good. The last experiment performed on the Coriolis real-time products takes into account the recently discovered problem in the pressure labeling. For this experiment, a sample of 36 floats, mixing well-behaved and anomalous instruments of the 2003–06 period, was considered and the simple test designed to detect the most common systematic anomalies successfully identified the deficient floats.
Addressing circadian rhythm disturbances in depressed patients
Authors: Lam RW 
Published: August 2008

Abstract Desynchronisation of normal circadian rhythms, including the sleep–wake rhythm, is common in major depressive disorder (MDD). The association between sleep disturbances and depression has long been recognised. Disturbed sleep is a diagnostic criterion for MDD, and insomnia commonly precedes the onset of symptomatic mood disorders. Disruptions of the sleep–wake cycle (sleep architecture and timing) are residual symptoms that may prevent the attainment of high-quality remission and delay recovery from MDD. Therefore, early recognition and treatment of sleep disturbances may be important for the treatment and prevention of recurrent depression. Evidence suggests that melatonergic (MT1 and MT2) and the 5-HT2C serotonergic receptor subtypes are important modulators of circadian rhythmicity. Agomelatine is the first melatonergic antidepressant; an agonist of melatonin MT1 and MT2 receptors, with additional antagonist properties at the 5-HT2C receptors. Agomelatine combines antidepressant efficacy including quality and efficiency of sleep, with a more favourable side-effect profile than current antidepressant treatments, including neutral effects on sexual function, bodyweight and the absence of discontinuation symptoms. These positive features provide a novel approach to the treatment of depression and the attainment of high-quality remission in MDD.
Arthroscopic Treatment of Chronic Osteochondral Lesions of the Talus
Authors: Ferkel Richard D. , Zanotti Robert M. , Komenda Gregory A. , Sgaglione Nicholas A. , Cheng Margaret S. , Applegate Gregory R. , Dopirak Ryan M. 
Published: August 2008

Background Osteochondral lesions of the talus are relatively uncommon but may be a cause of significant pain and disability in symptomatic patients. Hypothesis Arthroscopic treatment of osteochondral lesions of the talus will result in good long-term clinical outcomes in the majority of patients. Study Design Case series; Level of evidence, 4. Methods Fifty patients with chronic osteochondral lesions of the talus underwent arthroscopic treatment. Average age was 32 years (range, 12-72 years). Average follow-up was 71 months (range, 24-152 months). Treatment consisted of either drilling of the osteochondral lesions of the talus in situ (n = 4), excision of the osteochondral lesions of the talus and abrasion arthroplasty (n = 6), or excision of the osteochondral lesions of the talus and drilling (n = 40). Preoperative and intraoperative staging of the osteochondral lesions of the talus was performed. Follow-up evaluation included 3 clinical rating systems: Alexander, modified Weber, and American Orthopaedic Foot and Ankle Society Ankle/Hindfoot scores. Results There were 72% excellent/good, 20% fair, and 8% poor results on the Alexander scale. According to the modified Weber scale, there were 64% excellent/good, 30% fair, and 6% poor results. The average American Orthopaedic Foot and Ankle Society Ankle/Hindfoot score was 84 (range, 34-100). We found no correlation between plain radiographs, computed tomography, or magnetic resonance imaging staging and clinical results. However, there was significant correlation between arthroscopic stage and clinical outcome. Seventeen patients had been seen 5 years previously and evaluated using the same criteria; 35% demonstrated a deterioration in their result over time. Conclusion Arthroscopic treatment of chronic symptomatic osteochondral lesions of the talus results in good clinical outcomes in the majority of patients. However, pain and functional limitation may persist in some patients, especially those noted to have unstable osteochondral defects at the time of arthroscopy.
Arthroscopic versus Mini-Open Rotator Cuff Repair
Authors: Morse Kenneth , Davis A. David , Afra Robert , Kaye Elizabeth Krall , Schepsis Anthony , Voloshin Ilya 
Published: August 2008

Background Controversy remains regarding the results of all arthroscopic rotator cuff repairs compared with the mini-open approach. The purpose of this study was to perform a comprehensive literature search and meta-analysis of clinical trials comparing the results of arthroscopic rotator cuff repairs and mini-open rotator cuff repairs. Hypothesis There is no difference between the clinical results obtained from all arthroscopic rotator cuff repairs compared with mini-open repairs. Study Design Meta-analysis. Methods A computerized search of articles published between 1966 and July 2006 was performed using MEDLINE and PubMed. Additionally, a search of abstracts from 4 major annual meetings each held between 2000 and 2005 was performed to identify Level I to III studies comparing the results of arthroscopic rotator cuff repair and mini-open repair. Studies that included follow-up of an average of over 2 years and a minimum of 1 year and included the use of 1 of 4 validated functional outcome scores used to study shoulder injuries were included in the present meta-analysis. All outcome scores were converted to a 100-point scale to allow for outcome comparison. Results Five studies that met the inclusion criteria were identified. There was no difference in functional outcome scores or complications between the arthroscopic and mini-open repair groups. Conclusion Based on current literature, there was no difference in outcomes between the arthroscopic and mini-open rotator cuff repair techniques.
Telomerase activity of HIV-1–specific CD8+ T cells: constitutive up-regulation in controllers and selective increase by blockade of PD ligand 1 in progressors
Authors: Lichterfeld Mathias , Mou Danlei , Cung Thai Duong Hong , Williams Katie L. , Waring Michael T. , Huang Jinghe , Pereyra Florencia , Trocha Alicja , Freeman Gordon J. , Rosenberg Eric S. , Walker Bruce D. , Yu Xu G. 
Published: August 2008

Abstract
Exhaustion of virus-specific T cells may play an important role in the pathophysiology of chronic viral infections. Here, we analyzed telomere length and telomerase activity in HIV-1–specific CD8+ T cells from progressors or controllers to determine underlying molecular pathways of T-cell exhaustion and senescence. Telomere lengths of HIV-1–specific CD8+ T cells from progressors were significantly shorter compared with autologous cytomegalovirus (CMV)/Epstein-Barr virus (EBV)–specific CD8+ T cells or bulk CD8+ T cells, while telomere lengths from controllers significantly exceeded those of autologous bulk CD8+ T cells and reached a similar level as HIV-1–specific CD8+ T cells collected during primary HIV-1 infection. Telomere length stabilization in controllers corresponded to high levels of constitutive telomerase activity, which was associated with preservation of cytotoxic and proliferative properties. Conversely, limited constitutive telomerase activity was observed in HIV-1–specific CD8+ T cells from progressors, although an increase in both telomere length and telomerase activity was achieved in antigenic-peptide–stimulated cells from progressors after blocking the PD-1/PD ligand 1 (PD-L1) pathway. Collectively, these data suggest a causal role of telomere shortening for the functional deficiencies of HIV-1–specific CD8+ T cells in chronic progressive infection, while high constitutive telomerase activities appears to contribute to maintenance of polyfunctional HIV-1–specific CD8+ T cells from HIV-1 controllers.
Alignment of protein structures in the presence of domain motions
Authors: Mosca Roberto , Brannetti Barbara , Schneider Thomas R 
Published: August 2008

Abstract

Background
Structural alignment is an important step in protein comparison. Well-established methods exist for solving this problem under the assumption that the structures under comparison are considered as rigid bodies. However, proteins are flexible entities often undergoing movements that alter the positions of domains or subdomains with respect to each other. Such movements can impede the identification of structural equivalences when rigid aligners are used.

Results
We introduce a new method called RAPIDO (R apid A lignment of P roteins i n terms of Do mains) for the three-dimensional alignment of protein structures in the presence of conformational changes. The flexible aligner is coupled to a genetic algorithm for the identification of structurally conserved regions. RAPIDO is capable of aligning protein structures in the presence of large conformational changes. Structurally conserved regions are reliably detected even if they are discontinuous in sequence but continuous in space and can be used for superpositions revealing subtle differences.

Conclusion
RAPIDO is more sensitive than other flexible aligners when applied to cases of closely homologues proteins undergoing large conformational changes. When applied to a set of kinase structures it is able to detect similarities that are missed by other alignment algorithms. The algorithm is sufficiently fast to be applied to the comparison of large sets of protein structures.
Identification and correction of abnormal, incomplete and mispredicted proteins in public databases
Authors: Nagy Alinda , Hegyi Hédi , Farkas Krisztina , Tordai Hedvig , Kozma Evelin , Bányai László , Patthy László 
Published: August 2008

Abstract

Background
Despite significant improvements in computational annotation of genomes, sequences of abnormal, incomplete or incorrectly predicted genes and proteins remain abundant in public databases. Since the majority of incomplete, abnormal or mispredicted entries are not annotated as such, these errors seriously affect the reliability of these databases. Here we describe the MisPred approach that may provide an efficient means for the quality control of databases. The current version of the MisPred approach uses five distinct routines for identifying abnormal, incomplete or mispredicted entries based on the principle that a sequence is likely to be incorrect if some of its features conflict with our current knowledge about protein-coding genes and proteins: (i) conflict between the predicted subcellular localization of proteins and the absence of the corresponding sequence signals; (ii) presence of extracellular and cytoplasmic domains and the absence of transmembrane segments; (iii) co-occurrence of extracellular and nuclear domains; (iv) violation of domain integrity; (v) chimeras encoded by two or more genes located on different chromosomes.

Results
Analyses of predicted EnsEMBL protein sequences of nine deuterostome (Homo sapiens, Mus musculus, Rattus norvegicus, Monodelphis domestica, Gallus gallus, Xenopus tropicalis, Fugu rubripes, Danio rerio and Ciona intestinalis) and two protostome species (Caenorhabditis elegans and Drosophila melanogaster) have revealed that the absence of expected signal peptides and violation of domain integrity account for the majority of mispredictions. Analyses of sequences predicted by NCBI's GNOMON annotation pipeline show that the rates of mispredictions are comparable to those of EnsEMBL. Interestingly, even the manually curated UniProtKB/Swiss-Prot dataset is contaminated with mispredicted or abnormal proteins, although to a much lesser extent than UniProtKB/TrEMBL or the EnsEMBL or GNOMON-predicted entries.

Conclusion
MisPred works efficiently in identifying errors in predictions generated by the most reliable gene prediction tools such as the EnsEMBL and NCBI's GNOMON pipelines and also guides the correction of errors. We suggest that application of the MisPred approach will significantly improve the quality of gene predictions and the associated databases.
A high throughput live transparent animal bioassay to identify non-toxic small molecules or genes that regulate vertebrate fat metabolism for obesity drug development
Authors: Jones Kevin S , Alimov Alexander P , Rilo Horacio L , Jandacek Ronald J , Woollett Laura A , Penberthy W Todd 
Published: August 2008

Abstract

Background
The alarming rise in the obesity epidemic and growing concern for the pathologic consequences of the metabolic syndrome warrant great need for development of obesity-related pharmacotherapeutics. The search for such therapeutics is severely limited by the slow throughput of animal models of obesity. Amenable to placement into a 96 well plate, zebrafish larvae have emerged as one of the highest throughput vertebrate model organisms for performing small molecule screens. A method for visually identifying non-toxic molecular effectors of fat metabolism using a live transparent vertebrate was developed. Given that increased levels of nicotinamide adenine dinucleotide (NAD) via deletion of CD38 have been shown to prevent high fat diet induced obesity in mice in a SIRT-1 dependent fashion we explored the possibility of directly applying NAD to zebrafish.

Methods
Zebrafish larvae were incubated with daily refreshing of nile red containing media starting from a developmental stage of equivalent fat content among siblings (3 days post-fertilization, dpf) and continuing with daily refreshing until 7 dpf.

Results
PPAR activators, beta-adrenergic agonists, SIRT-1 activators, and nicotinic acid treatment all caused predicted changes in fat, cholesterol, and gene expression consistent with a high degree of evolutionary conservation of fat metabolism signal transduction extending from man to zebrafish larvae. All changes in fat content were visually quantifiable in a relative fashion using live zebrafish larvae nile red fluorescence microscopy. Resveratrol treatment caused the greatest and most consistent loss of fat content. The resveratrol tetramer Vaticanol B caused loss of fat equivalent in potency to resveratrol alone. Significantly, the direct administration of NAD decreased fat content in zebrafish. Results from knockdown of a zebrafish G-PCR ortholog previously determined to decrease fat content in C. elegans support that future GPR142 antagonists may be effective non-toxic anti-obesity therapeutics.

Conclusion
Owing to the apparently high level of evolutionary conservation of signal transduction pathways regulating lipid metabolism, the zebrafish can be useful for identifying non-toxic small molecules or pharmacological target gene products for developing molecular therapeutics for treating clinical obesity. Our results support the promising potential in applying NAD or resveratrol where the underlying target protein likely involves Sirtuin family member proteins. Furthermore data supports future studies focused on determining whether there is a high concentration window for resveratrol that is effective and non-toxic in high fat obesity murine models.