bluuebunny/crossref_metadata_2025_split huggingface dataset:
Teleconnection between NAO and Climate Downstream of the Tibetan Plateau
Authors: Li Jian , Yu Rucong , Zhou Tianjun 
Published: March 2008

Abstract
Analysis of the monthly NCEP–NCAR reanalysis data and station data reveals a teleconnection pattern (NAULEA) that links climate changes over the North Atlantic and Eurasia. The NAULEA pattern has five action centers. It extends from the North Atlantic to northwestern Europe, and then stretches eastward to the Urals, with its eastern end over North China. Certain climate changes over East Asia, such as the cooling changes in both the upper troposphere and surface in the last few decades of the twentieth century, can be attributed to the NAULEA pattern anomalies and traced upstream to the North Atlantic. The NAULEA pattern is suggested to be another NAO-related teleconnection pattern. Compared with the pattern with the Asian jet waveguide path, which leads to temperature anomalies over northeastern Asia, the NAULEA pattern with a high-latitude path exerts stronger influences on the climate of southwestern China.
A New Sea Surface Temperature and Sea Ice Boundary Dataset for the Community Atmosphere Model
Authors: Hurrell James W. , Hack James J. , Shea Dennis , Caron Julie M. , Rosinski James 
Published: March 2008

Abstract
A new surface boundary forcing dataset for uncoupled simulations with the Community Atmosphere Model is described. It is a merged product based on the monthly mean Hadley Centre sea ice and SST dataset version 1 (HadISST1) and version 2 of the National Oceanic and Atmospheric Administration (NOAA) weekly optimum interpolation (OI) SST analysis. These two source datasets were also used to supply ocean surface information to the 40-yr European Centre for Medium-Range Weather Forecasts Re-Analysis (ERA-40). The merged product provides monthly mean sea surface temperature and sea ice concentration data from 1870 to the present: it is updated monthly, and it is freely available for community use. The merging procedure was designed to take full advantage of the higher-resolution SST information inherent in the NOAA OI.v2 analysis.
A Study on Optimum Tilt Angle for Wind Estimation Using Indian MST Radar
Authors: Anandan V. K. , Rao I. Srinivasa , Reddy P. Narasimha 
Published: March 2008

Abstract
The effect of tilt angle on horizontal wind estimation is studied using Indian mesosphere–stratosphere–troposphere (MST) radar located at Gadanki (13.45°N, 79.18°E). It operates in Doppler beam swinging (DBS) mode with a beamwidth of 3°. Horizontal winds are computed for different tilt angles from 3° to 15° with an increment of 3° from a height range of 3.6–18 km. The effective beam pointing angle (θeff) is calculated to determine the effect of aspect sensitivity on the determination of horizontal wind components. For different tilt angles radar-derived winds are compared with simultaneous GPS sonde wind measurements, which were launched from a nearby site. The first method utilizes direct comparison of radar-derived winds with those of GPS sondes using the actual beam pointing angle; the second method uses the effective beam pointing angle derived from the ratios of two oblique beams. For this study a variety of statistics were explored in terms of standard deviation, correlation coefficient, and percentage error. From the results it is observed that in agreement with previous studies, the effective beam pointing angle deviates from the actual beam pointing angle, which results in the underestimation of horizontal wind components, and also when tilt angle is close to zenith and far from zenith, the estimation of horizontal winds is found to be far from true values at different heights. Radar wind estimation has better agreement with GPS sonde measurement when the off-zenith angle is around 10°. It is also found that correction to the actual beam pointing angle provides 3%–6% improved agreement between the radar and GPS wind measurements.
A Biomechanical Comparison of 2 Technical Variations of Double-Row Rotator Cuff Fixation
Authors: Busfield Benjamin T. , Glousman Ronald E. , McGarry Michelle H. , Tibone James E. , Lee Thay Q. 
Published: March 2008

Background Previous studies have shown comparable biomechanical properties of double-row fixation versus double-row fixation with a knotless lateral row. SutureBridge is a construct that secures the cuff with medial row mattress suture anchors and knotless lateral row fixation of the medial suture ends. Recent completely knotless constructs may lead to lesser clinical outcomes if the construct properties are compromised from lack of suture knots. Hypothesis A completely knotless construct without medial row knots will compromise the biomechanical properties in both cyclic and failure-testing parameters. Study Design Controlled laboratory study. Methods Six matched pairs of cadaveric shoulders were randomized to 2 groups of double row fixation with SutureBridge: group 1 with medial row knots, and group 2 without medial row knots. The specimens were placed in a materials test system at 30° of abduction. Cyclic testing to 180 N at 1 mm/sec for 30 cycles was performed, followed by tensile testing to failure at 1 mm/sec. Results Data included cyclic and failure data from the materials test system and gap data using a video digitizing system. All data from paired specimens were compared using paired Student t tests. Group 1 had a statistically significant difference ( P < .05) for gap formation for the 1st (3.47 vs 5.05 mm) and 30th cycle (4.22 vs 8.10 mm) and at yield load (5.2 vs 9.1 mm). In addition, there was a greater energy absorbed (2805 vs 1648 N-mm), yield load (233 vs 183.1 N), and ultimate load (352.9 vs 253.9 N) for group 1. The mode of failure for the majority (4/6) of group 2 was lateral row failure, whereas all group 1 specimens failed at the clamp. Conclusion Although lateral row knotless fixation has been shown not to sacrifice structural integrity of this construct, the addition of a knotless medial row compromises the construct leading to greater gapping and failure at lower loads. Clinical Relevance This may raise concerns regarding recently marketed completely knotless double row constructs.
Individual Skill Progression on a Virtual Reality Simulator for Shoulder Arthroscopy
Authors: Gomoll Andreas H. , Pappas George , Forsythe Brian , Warner Jon J. P. 
Published: March 2008

Background Previous studies have demonstrated a correlation between surgical experience and performance on a virtual reality arthroscopy simulator but only provided single time point evaluations. Additional longitudinal studies are necessary to confirm the validity of virtual reality simulation before these teaching aids can be more fully recommended for surgical education. Hypothesis Subjects will show improved performance on simulator retesting several years after an initial baseline evaluation, commensurate with their advanced surgical experience. Study Design Controlled laboratory study. Methods After gaining further arthroscopic experience, 10 orthopaedic residents underwent retesting 3 years after initial evaluation on a Procedicus virtual reality arthroscopy simulator. Using a paired t test, simulator parameters were compared in each subject before and after additional arthroscopic experience. Subjects were evaluated for time to completion, number of probe collisions with the tissues, average probe velocity, and distance traveled with the tip of the simulated probe compared to an optimal computer-determined distance. In addition, to evaluate consistency of simulator performance, results were compared to historical controls of equal experience. Results Subjects improved significantly ( P < .02 for all) in the 4 simulator parameters: completion time (−51 %), probe collisions (−29%), average velocity (+122%), and distance traveled (−;32%). With the exception of probe velocity, there were no significant differences between the performance of this group and that of a historical group with equal experience, indicating that groups with similar arthroscopic experience consistently demonstrate equivalent scores on the simulator. Conclusion Subjects significantly improved their performance on simulator retesting 3 years after initial evaluation. Additionally, across independent groups with equivalent surgical experience, similar performance can be expected on simulator parameters; thus it may eventually be possible to establish simulator benchmarks to indicate likely arthroscopic skill. Clinical Relevance These results further validate the use of surgical simulation as an important tool for the evaluation of surgical skills.
The Influence of Soccer-Specific Fatigue on Peak Isokinetic Torque Production of the Knee Flexors and Extensors
Authors: Greig Matt 
Published: March 2008

Background Epidemiological findings of higher muscular thigh strain injury incidence during the latter stages of soccer match play have been attributed to fatigue. Hypothesis Soccer-specific fatigue will significantly reduce peak isokinetic torque of the knee flexors and extensors. Study Design Descriptive laboratory study. Methods Ten male professional soccer players (mean age, 24.7 ± 4.4 years; body mass, 77.1 ± 8.3 kg; maximum oxygen consumption [VO2 max], 63.0 ± 4.8 mlVkg/min) completed an intermittent treadmill protocol replicating the activity profile of match Play. Before exercise and at 15-minute intervals, each player completed 1 of 2 randomized isokinetic dynamometer protocols. The first protocol quantified peak concentric knee extensor and flexor torque, while the second quantified peak concentric and eccentric knee flexor torque at isokinetic speeds of 180, 300, and 60 deg/s (3.14, 5.25, and 1.05 rad/s) with 5 repetitions at each speed. Results Concentric knee extensor and flexor peak torque were maintained throughout the duration of the exercise protocol, irrespective of movement speed. However, peak eccentric knee flexor torques at the end of the game (T300eccH105 = 127 ± 25 N.m) and at the end of the passive half-time interval (T300eccH60 = 133 ± 32 N.m) were significantly reduced relative to the first 15 minutes (T300eccH00 = 167 ± 35 N·m, P < .01; T300ecoH15 = 161 ± 35 N·m, P = .02). Conclusion Eccentric knee flexor strength decreases as a function of time and after the half-time interval. Clinical Relevance This suggests a greater risk of injuries at these specific times, especially for explosive movements, in accord with epidemiological observations.
Storage and stability of IgG and IgM monoclonal antibodies dried on filter paper and utility in Neisseria meningitidis serotyping by Dot-blot ELISA
Authors: Ferraz Aline S , Belo Elza FT , Coutinho Ligia MCC , Oliveira Ana P , Carmo Andréia MS , Franco Daniele L , Ferreira Tatiane , Yto André Y , Machado Marta SF , Scola Monica CG , De Gaspari Elizabeth 
Published: March 2008

AbstractBackgroundA simple filter paper method was developed for, the transport and storage of monoclonal antibodies (Mabs) at room temperature or -20°C after spotting on filter paper, for subsequent serotyping of outer membrane antigens ofN.meningitidisby dot-blot ELISA.MethodsMonoclonal antibodies (Mabs) were spotted within a 0.5–1 cm diameter area of Whatman grade 903 paper, which were stored individually at room temperature or at -20°C. These MAbs were stored and analyzed after periods of one week, 4 weeks, 12 months, or 13 years in the case of frozen Mab aliquots, or after 4 weeks at -20°C or at room temperature (RT) in the case of Mabs dried on filter paper strips. Assays were performed in parallel using dot-blot ELISA. In addition to the MAbs specific for serotyping class 1, 2 or 3, we used a larger number of Mabs for polysaccharides, lipooligosaccharides (LOS), class 5 and cross-reactive antigens for native outer membrane ofN.meningitidis. The Mabs dried on filter paper were eluted with phosphate-buffered saline (PBS) containing 0.2% gelatin.ResultsMabs of the isotypes IgG and IgM dried on filter papers were not affected by duration of storage. The detection by serotyping Mabs was generally consistent for dried filter paper MAb samples stored frozen for over 1 year at -20°C, and although decreased reactive antibody titers were found after storage, this did not interfere with the specificity of the Mabs used after 13 years as dry spots on filter paper.ConclusionThe use of filter paper is an inexpensive and convenient method for collecting, storing, and transporting Mab samples for serotyping studies. In addition, the samples occupy little space and can be readily transported without freezing. The efficiency of using immunoglobulin G (IgG) or M (IgM) eluted was found to be consistent with measurement of IgG or IgM titers in most corresponding, ascites Mabs stored frozen for over 1 year. The application of meningococcal typing methods and designations depend on the question being asked.
GANDivAWeb: A web server for detecting early folding units ("foldons") from protein 3D structures
Authors: Laborde Thomas , Tomita Masaru , Krishnan Arun 
Published: March 2008

Abstract

Background
It has long been known that small regions of proteins tend to fold independently and are then stabilized by interactions between these distinct subunits or modules. Such units, also known as autonomous folding units (AFUs) or"foldons" play a key role in protein folding. A knowledge of such early folding units has diverse applications in protein engineering as well as in developing an understanding of the protein folding process. Such AFUs can also be used as model systems in order to study the structural organization of proteins.

Results
In an earlier work, we had utilized a global network partitioning algorithm to identify modules in proteins. We had shown that these modules correlate well with AFUs. In this work, we have developed a webserver, GANDivAWeb, to identify early folding units or "foldons" in networks using the algorithm described earlier. The website has three functionalities: (a) It is able to display information on the modularity of a database of 1420 proteins used in the original work, (b) It can take as input an uploaded PDB file, identify the modules using the GANDivA algorithm and email the results back to the user and (c) It can take as input an uploaded PDB file and a results file (obtained from functionality (b)) and display the results using the embedded viewer. The results include the module decomposition of the protein, plots of cartoon representations of the protein colored by module identity and connectivity as well as contour plots of the hydrophobicity and relative accessible surface area (RASA) distributions.

Conclusion
We believe that the GANDivAWeb server, will be a useful tool for scientists interested in the phenomena of protein folding as well as in protein engineering. Our tool not only provides a knowledge of the AFUs through a natural graph partitioning approach but is also able to identify residues that are critical during folding. It is our intention to use this tool to study the topological determinants of protein folding by analyzing the topological changes in proteins over the unfolding/folding pathways.
Exceptional molecular and coreceptor-requirement properties of molecular clones isolated from an Human Immunodeficiency Virus Type-1 subtype C infection
Authors: Dash Prasanta K , Siddappa Nagadenahalli B , Mangaiarkarasi Asokan , Mahendarkar Aruna V , Roshan Padmanabhan , Anand Krishnamurthy Kumar , Mahadevan Anita , Satishchandra Parthasarathy , Shankar Susarla K , Prasad Vinayaka R , Ranga Udaykumar 
Published: March 2008

Abstract
Background
The pathogenic significance of coreceptor switch in the viral infection of HIV-1 is not completely understood. This situation is more complex in subtype C infection where coreceptor switch is either absent or extremely rare. To gain insights into the mechanisms that underlie coreceptor requirement of subtype C, we screened several primary viral isolates and identified a clinical sample that demonstrated a potential to grow on standard T-cell lines with no detectable CCR5 expression. The subject was diagnosed with HIV-1 associated dementia in the absence of opportunistic infections of the brain. To isolate molecular clones from this virus, we devised a novel strategy based on anchor primers that target a sequence in the reverse transcriptase, highly conserved among diverse subtypes of HIV-1.

Results
Using this strategy, we isolated 8 full-length molecular clones from the donor. Two of the eight molecular clones, 03In94_D17 and 03In94_D24, (D17 and D24) generated replication-competent viruses. Phylogenetic analysis of the full-length viral sequences revealed that both clones were non-recombinant subtype C viruses. They contain intact open reading frames in all the viral proteins. Both the viral clones are endowed with several unique molecular and biological properties. The viral promoter of the clones is characterized by the presence of four NF-kB binding elements, a feature rarely seen in the subtype C HIV-1 LTR. Interestingly, we identified the coexistence of two different forms of Rev, a truncated form common to subtype C and a full-length form less common for this subtype, in both proviral and plasma virus compartments. An exceptional property of the viruses, atypical of subtype C, is their ability to use a wide range of coreceptors including CCR5, CXCR4, and several others tested. Sequence analysis of Env of D17 and D24 clones identified differences within the variable loops providing important clues for the expanded coreceptor use. The V1, V2 and V4 loops in both of the molecular clones are longer due to the insertion of several amino acid residues that generated potential N-linked glycosylation sites.

Conclusion
The exceptional biological and molecular properties of these clones make them invaluable tools to understand the unique pathogenic characteristics of subtype C.
The evolution of human influenza A viruses from 1999 to 2006: A complete genome study
Authors: Bragstad Karoline , Nielsen Lars P , Fomsgaard Anders 
Published: March 2008

AbstractBackgroundKnowledge about the complete genome constellation of seasonal influenza A viruses from different countries is valuable for monitoring and understanding of the evolution and migration of strains. Few complete genome sequences of influenza A viruses from Europe are publicly available at the present time and there have been few longitudinal genome studies of human influenza A viruses. We have studied the evolution of circulating human H3N2, H1N1 and H1N2 influenza A viruses from 1999 to 2006, we analysed 234 Danish human influenza A viruses and characterised 24 complete genomes.ResultsH3N2 was the prevalent strain in Denmark during the study period, but H1N1 dominated the 2000–2001 season. H1N2 viruses were first observed in Denmark in 2002–2003. After years of little genetic change in the H1N1 viruses the 2005–2006 season presented H1N1 of greater variability than before. This indicates that H1N1 viruses are evolving and that H1N1 soon is likely to be the prevalent strain again. Generally, the influenza A haemagglutinin (HA) of H3N2 viruses formed seasonal phylogenetic clusters. Different lineages co-circulating within the same season were also observed. The evolution has been stochastic, influenced by small "jumps" in genetic distance rather than constant drift, especially with the introduction of the Fujian-like viruses in 2002–2003. Also evolutionary stasis-periods were observed which might indicate well fit viruses. The evolution of H3N2 viruses have also been influenced by gene reassortments between lineages from different seasons. None of the influenza genes were influenced by strong positive selection pressure. The antigenic site B in H3N2 HA was the preferred site for genetic change during the study period probably because the site A has been masked by glycosylations. Substitutions at CTL-epitopes in the genes coding for the neuraminidase (NA), polymerase acidic protein (PA), matrix protein 1 (M1), non-structural protein 1 (NS1) and especially the nucleoprotein (NP) were observed. The N-linked glycosylation pattern varied during the study period and the H3N2 isolates from 2004 to 2006 were highly glycosylated with ten predicted sequons in HA, the highest amount of glycosylations observed in this study period.ConclusionThe present study is the first to our knowledge to characterise the evolution of complete genomes of influenza A H3N2, H1N1 and H1N2 isolates from Europe over a time period of seven years from 1999 to 2006. More precise knowledge about the circulating strains may have implications for predicting the following season strains and thereby better matching the vaccine composition.
Amplification of neural stem cell proliferation by intermediate progenitor cells in Drosophila brain development
Authors: Bello Bruno C , Izergina Natalya , Caussinus Emmanuel , Reichert Heinrich 
Published: March 2008

Abstract
Background
In the mammalian brain, neural stem cells divide asymmetrically and often amplify the number of progeny they generate via symmetrically dividing intermediate progenitors. Here we investigate whether specific neural stem cell-like neuroblasts in the brain of Drosophila might also amplify neuronal proliferation by generating symmetrically dividing intermediate progenitors.

Results
Cell lineage-tracing and genetic marker analysis show that remarkably large neuroblast lineages exist in the dorsomedial larval brain of Drosophila. These lineages are generated by brain neuroblasts that divide asymmetrically to self renew but, unlike other brain neuroblasts, do not segregate the differentiating cell fate determinant Prospero to their smaller daughter cells. These daughter cells continue to express neuroblast-specific molecular markers and divide repeatedly to produce neural progeny, demonstrating that they are proliferating intermediate progenitors. The proliferative divisions of these intermediate progenitors have novel cellular and molecular features; they are morphologically symmetrical, but molecularly asymmetrical in that key differentiating cell fate determinants are segregated into only one of the two daughter cells.

Conclusion
Our findings provide cellular and molecular evidence for a new mode of neurogenesis in the larval brain of Drosophila that involves the amplification of neuroblast proliferation through intermediate progenitors. This type of neurogenesis bears remarkable similarities to neurogenesis in the mammalian brain, where neural stem cells as primary progenitors amplify the number of progeny they generate through generation of secondary progenitors. This suggests that key aspects of neural stem cell biology might be conserved in brain development of insects and mammals.