bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep Cyclonic Circulation in the Gulf of Mexico
Authors: DeHaan Christopher J. , Sturges Wilton 
Published: November 2005

Abstract
The anticyclonic Loop Current dominates the upper-layer flow in the eastern Gulf of Mexico, with a weaker mean anticyclonic pattern in the western gulf. There are reasons, however, to suspect that the deep mean flow should actually be cyclonic. Topographic wave rectification and vortex stretching contribute to this cyclonic tendency, as will the supply of cold incoming deep water at the edges of the basin. The authors find that the deep mean flow is cyclonic both in the eastern and western gulf, with speeds on the order of 1–2 cm s−1 at 2000 m. Historical current-meter mooring data, as well as profiling autonomous Lagrangian circulation explorer (PALACE) floats (at 900 m), suggest that vertical geostrophic shear relative to 1000 m gives a surprisingly accurate result in the interior of the basin. The temperature around the edges of the basin at 2000 m is coldest near the Yucatan Channel, where Caribbean Sea water is colder by ∼0.1°C. The temperature increases steadily with distance in the counterclockwise direction from the Yucatan, consistent with a deep mean cyclonic boundary flow.
Effects of the Pacific Diapycnal Mixing and Wind Stress on the Global and Pacific Meridional Overturning Circulation*
Authors: Furue Ryo , Endoh Masahiro 
Published: November 2005

Abstract
Numerical experiments are conducted using an idealized basin to investigate roles of the deep vertical diffusivity and wind stress of the Pacific Ocean in the global and Pacific meridional overturning circulation. The Pacific middepth diffusivity is found to be enhancing the global meridional overturning circulation; when this part of diffusivity is reduced to the background value, not only is the layered circulation of the Pacific greatly weakened, but also the production of the North Atlantic Deep Water (NADW) and Antarctic Bottom Water (AABW) is significantly reduced. The deeper part of the Pacific diffusivity is found to be enhancing the production of the AABW in the model. When the wind stress is turned off in the Pacific, the deep meridional overturning circulation of the Pacific is reduced and the production of the NADW and AABW is also significantly reduced. This is likely due to the reduction of the wind-enhanced upwelling in the subpolar and equatorial regions. These results suggest the importance of the diapycnal diffusion and sea surface conditions in the Pacific not only to the circulation within the Pacific but also to the global meridional overturning circulation.
Spectral Characteristics of the Response of the Meridional Overturning Circulation to Deep-Water Formation
Authors: Deshayes Julie , Frankignoul Claude 
Published: November 2005

Abstract
The response of the upper limb of the meridional overturning circulation to the variability of deep-water formation is investigated analytically with a linear, reduced-gravity model in basins of simple geometry. The spectral characteristics of the model response are first derived by prescribing white-noise fluctuations in the meridional transport at the northern boundary. Although low-frequency basin modes are solutions to the eigenproblem, they are too dissipative to be significantly excited by the boundary forcing, and the thermocline depth response has a red spectrum with no prevailing time scale other than that of a high-frequency equatorial mode, only flattening at the millennial time scale because of vertical diffusivity. The meridional transport is asymmetric about the equator because the northern part of the basin is directly influenced by the boundary forcing while the southern part is mostly set in motion by long Rossby waves. This results in the equator acting as a low-pass filter for the Southern Hemisphere, which clarifies the so-called buffering effect of the equator. In a basin connected by a southern circumpolar channel, the thermocline depth and the transport spectra are redder than in the forced basin and, when a somewhat more realistic stochastic forcing derived from general circulation model simulations is considered, the variability is strongly reduced at high frequency. The linear model qualitatively explains several features of the low-frequency variability of the meridional overturning circulation in climate models, such as its red spectrum and its larger intensity in the North Atlantic Ocean.
Stratified Tidal Flow over a Bump
Authors: Dewey Richard , Richmond David , Garrett Chris 
Published: November 2005

Abstract
The interaction of a stratified flow with an isolated topographic feature can introduce numerous disturbances into the flow, including turbulent wakes, internal waves, and eddies. Measurements made near a “bump” east of Race Rocks, Vancouver Island, reveal a wide range of phenomena associated with the variable flow speeds and directions introduced by the local tides. Upstream and downstream flows were observed by placing two acoustic Doppler current profilers (ADCPs) on one flank of the bump. Simultaneous shipboard ADCP surveys corroborated some of the more striking features. Froude number conditions varied from subcritical to supercritical as the tidal velocities varied from 0.2 to 1.5 m s−1. During the strong ebb, when the moored ADCPs were located on the lee side, a persistent full-water-depth lee wave was detected in one of the moored ADCPs and the shipboard ADCP. However, the placement of the moorings would suggest that, by the time it appears in the moored ADCP beams, the lee wave has been swept downstream or has separated from the bump. Raw ADCP beam velocities suggest enhanced turbulence during various phases of the tide. Many of the three-dimensional flow characteristics are in good agreement with laboratory studies, and some characteristics, such as shear in the bottom boundary layer, are not.
Assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteria
Authors: Rey Sébastien , Gardy Jennifer L , Brinkman Fiona SL 
Published: November 2005

Abstract

Background
Identification of a bacterial protein's subcellular localization (SCL) is important for genome annotation, function prediction and drug or vaccine target identification. Subcellular fractionation techniques combined with recent proteomics technology permits the identification of large numbers of proteins from distinct bacterial compartments. However, the fractionation of a complex structure like the cell into several subcellular compartments is not a trivial task. Contamination from other compartments may occur, and some proteins may reside in multiple localizations. New computational methods have been reported over the past few years that now permit much more accurate, genome-wide analysis of the SCL of protein sequences deduced from genomes. There is a need to compare such computational methods with laboratory proteomics approaches to identify the most effective current approach for genome-wide localization characterization and annotation.

Results
In this study, ten subcellular proteome analyses of bacterial compartments were reviewed. PSORTb version 2.0 was used to computationally predict the localization of proteins reported in these publications, and these computational predictions were then compared to the localizations determined by the proteomics study. By using a combined approach, we were able to identify a number of contaminants and proteins with dual localizations, and were able to more accurately identify membrane subproteomes. Our results allowed us to estimate the precision level of laboratory subproteome studies and we show here that, on average, recent high-precision computational methods such as PSORTb now have a lower error rate than laboratory methods.

Conclusion
We have performed the first focused comparison of genome-wide proteomic and computational methods for subcellular localization identification, and show that computational methods have now attained a level of precision that is exceeding that of high-throughput laboratory approaches. We note that analysis of all cellular fractions collectively is required to effectively provide localization information from laboratory studies, and we propose an overall approach to genome-wide subcellular localization characterization that capitalizes on the complementary nature of current laboratory and computational methods.
Evaluation of potential reference genes in real-time RT-PCR studies of Atlantic salmon
Authors: Olsvik Pål A , Lie Kai K , Jordal Ann-Elise O , Nilsen Tom O , Hordvik Ivar 
Published: November 2005

Abstract

Background
Salmonid fishes are among the most widely studied model fish species but reports on systematic evaluation of reference genes in qRT-PCR studies is lacking.

Results
The stability of six potential reference genes was examined in eight tissues of Atlantic salmon (Salmo salar), to determine the most suitable genes to be used in quantitative real-time RT-PCR analyses. The relative transcription levels of genes encoding 18S rRNA, S20 ribosomal protein, β-actin, glyceraldehyde-3P-dehydrogenase (GAPDH), and two paralog genes encoding elongation factor 1A (EF1AA and EF1AB) were quantified in gills, liver, head kidney, spleen, thymus, brain, muscle, and posterior intestine in six untreated adult fish, in addition to a group of individuals that went through smoltification. Based on calculations performed with the geNorm VBA applet, which determines the most stable genes from a set of tested genes in a given cDNA sample, the ranking of the examined genes in adult Atlantic salmon was EF1AB>EF1AA>β-actin>18S rRNA>S20>GAPDH. When the same calculations were done on a total of 24 individuals from four stages in the smoltification process (presmolt, smolt, smoltified seawater and desmoltified freshwater), the gene ranking was EF1AB>EF1AA>S20>β-actin>18S rRNA>GAPDH.

Conclusion
Overall, this work suggests that the EF1AA and EF1AB genes can be useful as reference genes in qRT-PCR examination of gene expression in the Atlantic salmon.
Membrane testosterone binding sites in prostate carcinoma as a potential new marker and therapeutic target: Study in paraffin tissue sections
Authors: Dambaki Constantina , Kogia Christina , Kampa Marilena , Darivianaki Katherine , Nomikos Michael , Anezinis Ploutarchos , Theodoropoulos Panayiotis A , Castanas Elias , Stathopoulos Efstathios N 
Published: November 2005

Abstract

Background
Steroid action is mediated, in addition to classical intracellular receptors, by recently identified membrane sites, that generate rapid non-genomic effects. We have recently identified a membrane androgen receptor site on prostate carcinoma cells, mediating testosterone rapid effects on the cytoskeleton and secretion within minutes.

Methods
The aim of this study was to investigate whether membrane androgen receptors are differentially expressed in prostate carcinomas, and their relationship to the tumor grade. We examined the expression of membrane androgen receptors in archival material of 109 prostate carcinomas and 103 benign prostate hyperplasias, using fluorescein-labeled BSA-coupled testosterone.

Results
We report that membrane androgen receptors are preferentially expressed in prostate carcinomas, and they correlate to their grade using the Gleason's microscopic grading score system.

Conclusion
We conclude that membrane androgen receptors may represent an index of tumor aggressiveness and possibly specific targets for new therapeutic regimens.
Abnormal expression and processing of the proprotein convertases PC1 and PC2 in human colorectal liver metastases
Authors: Tzimas George N , Chevet Eric , Jenna Sarah , Nguyên Duc Thang , Khatib Abdel M , Marcus Victoria , Zhang Yi , Chrétien Michel , Seidah Nabil , Metrakos Peter 
Published: November 2005

Abstract

Background
The family of proprotein convertases has been recently implicated in tumorigenesis and metastasis in animal models. However, these studies have not yet been completely corroborated in human tumors.

Methods
Using RT PCR, immunoblot and immunohistochemistry we assessed the presence and the processing patterns of the convertases PC1 and PC2 as well as the PC2 specific chaperone 7B2 in human liver metastases originating from colorectal cancer and compared them to unaffected and normal liver. Furthermore, we assessed the presence and processing profiles of PC1, PC2 and 7B2 in primary colon cancers.

Results
mRNA, protein expression, and protein cleavage profiles of proprotein convertases 1 and 2 are altered in liver colorectal metastasis, compared to unaffected and normal liver. Active PC1 protein is overexpressed in tumor, correlating with its mRNA profile. Moreover, the enhanced PC2 processing pattern in tumor correlates with the overexpression of its specific binding protein 7B2. These results were corroborated by immunohistochemistry. The specific and uniform convertase pattern observed in the metastases was present only in a fraction of primary colon cancers.

Conclusion
The uniformly altered proprotein convertase profile in liver metastases is observed only in a fraction of primary colon cancers, suggesting possible selection processes involving PCs during metastasis as well as an active role of PCs in liver metastasis. In addition, the exclusive presence of 7B2 in metastatic tumors may represent a new target for early diagnosis, prognosis and/or treatment.
The International Classification of Functioning as an explanatory model of health after distal radius fracture: A cohort study
Authors: Harris Jocelyn E , MacDermid Joy C , Roth James 
Published: November 2005

Abstract

Background
Distal radius fractures are common injuries that have an increasing impact on health across the lifespan. The purpose of this study was to identify health impacts in body structure/function, activity, and participation at baseline and follow-up, to determine whether they support the ICF model of health.

Methods
This is a prospective cohort study of 790 individuals who were assessed at 1 week, 3 months, and 1 year post injury. The Patient Rated Wrist Evaluation (PRWE), The Wrist Outcome Measure (WOM), and the Medical Outcome Survey Short-Form (SF-36) were used to measure impairment, activity, participation, and health. Multiple regression was used to develop explanatory models of health outcome.

Results
Regression analysis showed that the PRWE explained between 13% (one week) and 33% (three months) of the SF-36 Physical Component Summary Scores with pain, activities and participation subscales showing dominant effects at different stages of recovery. PRWE scores were less related to Mental Component Summary Scores, 10% (three months) and 8% (one year). Wrist impairment scores were less powerful predictors of health status than the PRWE.

Conclusion
The ICF is an informative model for examining distal radius fracture. Difficulty in the domains of activity and participation were able to explain a significant portion of physical health. Post-fracture rehabilitation and outcome assessments should extend beyond physical impairment to insure comprehensive treatment to individuals with distal radius fracture.
Inhibition of HIV derived lentiviral production by TAR RNA binding domain of TAT protein
Authors: Mi Michael Y , Zhang Jiying , He Yukai 
Published: November 2005

Abstract

Background
A critical step in the production of new HIV virions involves the TAT protein binding to the TAR element. The TAT protein contains in close proximity its TAR RNA binding domain and protein transduction domain (PTD). The PTD domain of TAT has been identified as being instrumental in the protein's ability to cross mammalian cell and nuclear membranes. All together, this information led us to form the hypothesis that a protein containing the TAR RNA binding domain could compete with the native full length TAT protein and effectively block the TAR RNA binding site in transduced HIV infected cells.

Results
We synthesized a short peptide named Tat-P, which contained the TAR RNA binding and PTD domains to examine whether the peptide has the potential of inhibiting TAT dependent HIV replication. We investigated the inhibiting effects of Tat-P in vitro using a HIV derived lentiviral vector model. We found that the TAT PTD domain not only efficiently transduced test cells, but also effectively inhibited the production of lentiviral particles in a TAT dependent manner. These results were also supported by data derived from the TAT activated LTR-luciferase expression model and RNA binding assays.

Conclusion
Tat-P may become part of a category of anti-HIV drugs that competes with full length TAT proteins to inhibit HIV replication. In addition, this study indicates that the HIV derived lentiviral vector system is a safe and reliable screening method for anti-HIV drugs, especially for those targeting the interaction of TAT and TAR RNAs.
Memory and selective learning in children with spina bifida-myelomeningocele and shunted hydrocephalus: A preliminary study
Authors: Vachha Behroze , Adams Richard C 
Published: November 2005

AbstractBackgroundSelective learning is the ability to select items of relevance from among less important items. Limited evidence exists regarding the efficiency with which children with spina bifida-myelomeningocele and shunted hydrocephalus (SB/SH) are able to learn information. This report describes initial data related to components of learning and metacognitive skills in children with SB/SH.MethodsTwenty six children with SB/SH and 26 controls (age: 7 – 16 y) with average intelligence, and monolingual English-speaking backgrounds participated in the study. Exclusion criteria for the SB/SH group were: prior history of shunt infection, history of seizure or shunt malfunction within the previous three months, prior diagnoses of attention disorders and/or clinical depression. Children were presented lists of words with equal exemplars each of two distinct semantic categories (e.g. fruits, animals), and told to make as high a score as possible by learning the words. The value of the words was designated by category membership (e.g. animals = low value; fruits = high value). The total number of words learned across three learning trials was used to determine memory span. Selective learning efficiency (SLE) was computed as the efficiency with which items of greater value were selectively learned across three trials.ResultsChildren with SB/SH did worse than controls on memory span (P< 0.05). Although SLE was not significantly different between groups, when asked what strategy was used in the selective learning tasks, 65% of the SB/SH children said they tried to remember all words (inefficient strategy). In contrast, 85% of controls said they tried to remember the higher value words – the more efficient strategy.ConclusionSuccess in school is often dependent on the ability to recall important facts selectively and ignore less important information. Children with SB/SH in our study had a poor memory span and were unable to monitor and report an efficient and workable metacognitive strategy required to remember a list of words. Preliminary findings may begin to explain our previous clinical and research findings wherein children with SB/SH often focus on extraneous details, but demonstrate difficulty remembering the main gist of a story/event.
THR0921, a novel peroxisome proliferator-activated receptor gamma agonist, reduces the severity of collagen-induced arthritis
Authors: Tomita Tetsuya , Kakiuchi Yoshimi , Tsao Philip S 
Published: November 2005

AbstractTHR0921 is a novel peroxisome proliferator-activated receptor gamma (PPARγ) agonist with potent anti-diabetic properties. Because of the proposed role of PPARγ in inflammation, we investigated the potential of orally active THR0921 to inhibit the pathogenesis of collagen-induced arthritis (CIA). CIA was induced in DBA/1J mice by the injection of bovine type II collagen in complete Freund's adjuvant on days 0 and 21. Mice were treated with THR0921 (50 mg/kg/day) starting on the day of the booster injection and throughout the remaining study period. Both clinical disease activity scores as well as histological scores of joint destruction were significantly reduced in mice treated with THR0921 compared to untreated mice. Proliferation of isolated spleen cells, as well as circulating levels of IgG antibody to type II collagen, was decreased by THR0921. Moreover, spleen cell production of IFN-γ, tumor necrosis factor (TNF)-α and IL-1β in response to exposure to lipopolysaccharide or type II collagen was reduced by in vivo treatment with THR0921. Steady state mRNA levels of TNF-α, IL-1β, monocyte chemotactic protein-1 and receptor activator of nuclear factor κB ligand (RANKL) in isolated joints were all decreased in mice treated with THR0921. Finally, THR0921 inhibited osteoclast differentiation of bone marrow-derived cells stimulated with macrophage colony-stimulating factor and RANKL. In conclusion, THR0921 attenuates collagen-induced arthritis in part by reducing the immune response. As such, PPARγ may be an important therapeutic target for rheumatoid arthritis.
Driver Steering Control and a New Perspective on Car Handling Qualities
Authors: Sharp R S 
Published: November 2005

The article is about steering control of cars by drivers, concentrating on following the lateral profile of the roadway, which is presumed visible ahead of the car. It builds on previously published work, in which it was shown how the driver's preview of the roadway can be combined with the linear dynamics of a simple car to yield a problem of discrete-time optimal-linear-control-theory form. In that work, it was shown how an optimal ‘driver’ of a linear car can convert the path preview sample values, modelled as deriving from a Gaussian white-noise process, into steering wheel displacement commands to cause the car to follow the previewed path with an attractive compromise between precision and ease. Recognizing that real roadway excitation is not so rich in high frequencies as white-noise, a low-pass filter is added to the system. The white-noise sample values are filtered before being seen by the driver. Numerical results are used to show that the optimal preview control is unaltered by the inclusion of the low-pass filter, whereas the feedback control is affected diminishingly as the preview increases. Then, using the established theoretical basis, new results are generated to show time-invariant optimal preview controls for cars and drivers with different layouts and priorities. Tight and loose controls, representing different balances between tracking accuracy and control effort, are calculated and illustrated through simulation. A new performance criterion with handling qualities implications is set up, involving the minimization of the preview distance required. The sensitivities of this distance to variations in the car design parameters are calculated. The influence of additional rear wheel steering is studied from the viewpoint of the preview distance required and the form of the optimal preview gain sequence. Path-following simulations are used to illustrate relatively high-authority and relatively low-authority control strategies, showing manoeuvring well in advance of a turn under appropriate circumstances. The results yield new insights into driver steering control behaviour and vehicle design optimization. The article concludes with a discussion of research in progress aimed at a further improved understanding of how drivers control their vehicles.