bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surface Albedo of the Antarctic Sea Ice Zone
Authors: Brandt Richard E. , Warren Stephen G. , Worby Anthony P. , Grenfell Thomas C. 
Published: October 2005

AbstractIn three ship-based field experiments, spectral albedos were measured at ultraviolet, visible, and near-infrared wavelengths for open water, grease ice, nilas, young “grey” ice, young grey-white ice, and first-year ice, both with and without snow cover. From the spectral measurements, broadband albedos are computed for clear and cloudy sky, for the total solar spectrum as well as for visible and near-infrared bands used in climate models, and for Advanced Very High Resolution Radiometer (AVHRR) solar channels. The all-wave albedos vary from 0.07 for open water to 0.87 for thick snow-covered ice under cloud. The frequency distribution of ice types and snow coverage in all seasons is available from the project on Antarctic Sea Ice Processes and Climate (ASPeCt). The ASPeCt dataset contains routine hourly visual observations of sea ice from research and supply ships of several nations using a standard protocol. Ten thousand of these observations, separated by a minimum of 6 nautical miles along voyage tracks, are used together with the measured albedos for each ice type to assign an albedo to each visual observation, resulting in “ice-only” albedos as a function of latitude for each of five longitudinal sectors around Antarctica, for each of the four seasons. These ice albedos are combined with 13 yr of ice concentration estimates from satellite passive microwave measurements to obtain the geographical and seasonal variation of average surface albedo. Most of the Antarctic sea ice is snow covered, even in summer, so the main determinant of area-averaged albedo is the fraction of open water within the pack.
Modeling Bottom Mixed Layer Variability on the Mid-Oregon Shelf during Summer Upwelling
Authors: Kurapov A. L. , Allen J. S. , Egbert G. D. , Miller R. N. 
Published: October 2005

Abstract
Results from a model of wind-driven circulation are analyzed to study spatial and temporal variability in the bottom mixed layer (BML) on the mid-Oregon shelf in summer 2001. The model assimilates acoustic Doppler profiler velocities from two cross-shore lines of moorings 90 km apart to provide improved accuracy of near-bottom velocities and turbulence variables in the area between the mooring lines. Model results suggest that the response of the BML thickness to upwelling- and downwelling-favorable winds differs qualitatively between an area of “simple” bathymetric slope at 45°N and a wider shelf area east of Stonewall Bank (44.5°N). At 45°N, the BML grows in response to downwelling-favorable conditions, in agreement with known theories. East of Stonewall Bank, the BML thickness is increased following upwelling events. In this area, the southward upwelling jet detaches from the coast and flows over a wider part of the Oregon shelf, creating conditions for Ekman pumping near the bottom. Based on computations of bottom stress curl, the vertical pumping velocity in this area may reach 15 m day−1 following periods of intensified upwelling-favorable winds. A column of denser, near-bottom water upwelled over the Ekman flow convergence area is tilted as a result of vertical shear in horizontal velocities, causing unstable stratification and convective overturning. As a result of this process, BML thickness values east of Stonewall Bank can be in excess of 20 m following upwelling, comparable to maximum values at 45°N following downwelling.
Relating River Plume Structure to Vertical Mixing
Authors: Hetland Robert D. 
Published: October 2005

Abstract
The structure of a river plume is related to the vertical mixing using an isohaline-based coordinate system. Salinity coordinates offer the advantage of translating with the plume as it moves or expanding as the plume grows. This coordinate system is used to compare the relative importance of different dynamical processes acting within the plume and to describe the effect each process has on the structure of the plume. Vertical mixing due to inertial shear in the outflow of a narrow estuary and wind mixing are examined using a numerical model of a wind-forced river plume. Vertical mixing, and the corresponding entrainment of background waters, is greatest near the estuary mouth where inertial shear mixing is large. This region is defined as the near field, with the more saline, far-field plume beyond. Wind mixing increases the mixing throughout the plume but has the greatest effect on plume structure at salinity ranges just beyond the near field. Wind mixing is weaker at high salinity classes that have already been mixed to a critical thickness, a point where turbulent mixing of the upper layer by the wind is reduced, protecting these portions of the plume from further wind mixing. The work done by mixing on the plume is of similar magnitude in both the near and far fields.
Boundary Layer Forcing of a Semidiurnal, Cross-Channel Seiche
Authors: Martin Wayne , MacCready Parker , Dewey Richard 
Published: October 2005

Abstract
The outer Strait of Juan de Fuca is a stratified, tidal channel about 100 km long, 20 km wide, and 200 m deep. Tidal currents of O(0.5 m s−1) occur at both diurnal and semidiurnal periods and there is a pronounced spring–neap variation in the stratification due to changes in tidal mixing. Vertical isotherm excursions of O(50 m) have previously been observed along the northern side of the channel that appear to be phase locked to the tidal currents. Analyses of recent ADCP and thermistor chain data confirm the isotherm excursions and find that they are accompanied by distinctive baroclinic structures in the horizontal currents that persist across spring–neap cycles, and from year to year. The authors find that the phase of the semidiurnal signal does not vary along the channel, as would be expected of an along-channel internal tide. Instead, comparison of the semidiurnal measurements with two-dimensional analytical and numerical models indicate that much of the baroclinic structure can be explained as a cross-channel, internal seiche that is locally driven by reversing Ekman forcing in the bottom boundary layer. Near the bottom, the vertical motions are kinematic, resulting primarily from cross-channel flow on the side slopes. In the middepths, the seiche appears to explain part but not all of the vertical motions. The seiche appears to persist and to maintain a similar mode shape across large, O(2), changes in stratification. In Juan de Fuca, it is expected that these motions affect the overall salt balance of the system by enhancing mixing between the upper and lower layers of the estuary.
Phylogenetic detection of conserved gene clusters in microbial genomes
Authors: Zheng Yu , Anton Brian P , Roberts Richard J , Kasif Simon 
Published: October 2005

Abstract
Background
Microbial genomes contain an abundance of genes with conserved proximity forming clusters on the chromosome. However, the conservation can be a result of many factors such as vertical inheritance, or functional selection. Thus, identification of conserved gene clusters that are under functional selection provides an effective channel for gene annotation, microarray screening, and pathway reconstruction. The problem of devising a robust method to identify these conserved gene clusters and to evaluate the significance of the conservation in multiple genomes has a number of implications for comparative, evolutionary and functional genomics as well as synthetic biology.

Results
In this paper we describe a new method for detecting conserved gene clusters that incorporates the information captured by a genome phylogenetic tree. We show that our method can overcome the common problem of overestimation of significance due to the bias in the genome database and thereby achieve better accuracy when detecting functionally connected gene clusters. Our results can be accessed at database GeneChords http://genomics10.bu.edu/GeneChords.

Conclusion
The methodology described in this paper gives a scalable framework for discovering conserved gene clusters in microbial genomes. It serves as a platform for many other functional genomic analyses in microorganisms, such as operon prediction, regulatory site prediction, functional annotation of genes, evolutionary origin and development of gene clusters.
High-throughput metal susceptibility testing of microbial biofilms
Authors: Harrison Joe J , Turner Raymond J , Ceri Howard 
Published: October 2005

Abstract

Background
Microbial biofilms exist all over the natural world, a distribution that is paralleled by metal cations and oxyanions. Despite this reality, very few studies have examined how biofilms withstand exposure to these toxic compounds. This article describes a batch culture technique for biofilm and planktonic cell metal susceptibility testing using the MBEC assay. This device is compatible with standard 96-well microtiter plate technology. As part of this method, a two part, metal specific neutralization protocol is summarized. This procedure minimizes residual biological toxicity arising from the carry-over of metals from challenge to recovery media. Neutralization consists of treating cultures with a chemical compound known to react with or to chelate the metal. Treated cultures are plated onto rich agar to allow metal complexes to diffuse into the recovery medium while bacteria remain on top to recover. Two difficulties associated with metal susceptibility testing were the focus of two applications of this technique. First, assays were calibrated to allow comparisons of the susceptibility of different organisms to metals. Second, the effects of exposure time and growth medium composition on the susceptibility of E. coli JM109 biofilms to metals were investigated.

Results
This high-throughput method generated 96-statistically equivalent biofilms in a single device and thus allowed for comparative and combinatorial experiments of media, microbial strains, exposure times and metals. By adjusting growth conditions, it was possible to examine biofilms of different microorganisms that had similar cell densities. In one example, Pseudomonas aeruginosa ATCC 27853 was up to 80 times more resistant to heavy metalloid oxyanions than Escherichia coli TG1. Further, biofilms were up to 133 times more tolerant to tellurite (TeO3
2-) than corresponding planktonic cultures. Regardless of the growth medium, the tolerance of biofilm and planktonic cell E. coli JM109 to metals was time-dependent.

Conclusion
This method results in accurate, easily reproducible comparisons between the susceptibility of planktonic cells and biofilms to metals. Further, it was possible to make direct comparisons of the ability of different microbial strains to withstand metal toxicity. The data presented here also indicate that exposure time is an important variable in metal susceptibility testing of bacteria.
In-house nucleic acid amplification tests for the detection of Mycobacterium tuberculosis in sputum specimens: meta-analysis and meta-regression
Authors: Flores Laura L , Pai Madhukar , Colford John M , Riley Lee W 
Published: October 2005

Abstract

Background
More than 200 studies related to nucleic acid amplification (NAA) tests to detect Mycobacterium tuberculosis directly from clinical specimens have appeared in the world literature since this technology was first introduced. NAA tests come as either commercial kits or as tests designed by the reporting investigators themselves (in-house tests). In-house tests vary widely in their accuracy, and factors that contribute to heterogeneity in test accuracy are not well characterized. Here, we used meta-analytical methods, including meta-regression, to identify factors related to study design and assay protocols that affect test accuracy in order to identify those factors associated with high estimates of accuracy.

Results
By searching multiple databases and sources, we identified 2520 potentially relevant citations, and analyzed 84 separate studies from 65 publications that dealt with in-house NAA tests to detect M. tuberculosis in sputum samples. Sources of heterogeneity in test accuracy estimates were determined by subgroup and meta-regression analyses. Among 84 studies analyzed, the sensitivity and specificity estimates varied widely; sensitivity varied from 9.4% to 100%, and specificity estimates ranged from 5.6% to 100%. In the meta-regression analysis, the use of IS6110 as a target, and the use of nested PCR methods appeared to be significantly associated with higher diagnostic accuracy.

Conclusion
Estimates of accuracy of in-house NAA tests for tuberculosis are highly heterogeneous. The use of IS6110 as an amplification target, and the use of nested PCR methods appeared to be associated with higher diagnostic accuracy. However, the substantial heterogeneity in both sensitivity and specificity of the in-house NAA tests rendered clinically useful estimates of test accuracy difficult. Future development of NAA-based tests to detect M. tuberculosis from sputum specimens should take into consideration these findings in improving accuracy of in-house NAA tests.
Systematic review and meta-analysis of the diagnostic accuracy of ultrasonography for deep vein thrombosis
Authors: Goodacre Steve , Sampson Fiona , Thomas Steve , van Beek Edwin , Sutton Alex 
Published: October 2005

Abstract

Background
Ultrasound (US) has largely replaced contrast venography as the definitive diagnostic test for deep vein thrombosis (DVT). We aimed to derive a definitive estimate of the diagnostic accuracy of US for clinically suspected DVT and identify study-level factors that might predict accuracy.

Methods
We undertook a systematic review, meta-analysis and meta-regression of diagnostic cohort studies that compared US to contrast venography in patients with suspected DVT. We searched Medline, EMBASE, CINAHL, Web of Science, Cochrane Database of Systematic Reviews, Cochrane Controlled Trials Register, Database of Reviews of Effectiveness, the ACP Journal Club, and citation lists (1966 to April 2004). Random effects meta-analysis was used to derive pooled estimates of sensitivity and specificity. Random effects meta-regression was used to identify study-level covariates that predicted diagnostic performance.

Results
We identified 100 cohorts comparing US to venography in patients with suspected DVT. Overall sensitivity for proximal DVT (95% confidence interval) was 94.2% (93.2 to 95.0), for distal DVT was 63.5% (59.8 to 67.0), and specificity was 93.8% (93.1 to 94.4). Duplex US had pooled sensitivity of 96.5% (95.1 to 97.6) for proximal DVT, 71.2% (64.6 to 77.2) for distal DVT and specificity of 94.0% (92.8 to 95.1). Triplex US had pooled sensitivity of 96.4% (94.4 to 97.1%) for proximal DVT, 75.2% (67.7 to 81.6) for distal DVT and specificity of 94.3% (92.5 to 95.8). Compression US alone had pooled sensitivity of 93.8 % (92.0 to 95.3%) for proximal DVT, 56.8% (49.0 to 66.4) for distal DVT and specificity of 97.8% (97.0 to 98.4). Sensitivity was higher in more recently published studies and in cohorts with higher prevalence of DVT and more proximal DVT, and was lower in cohorts that reported interpretation by a radiologist. Specificity was higher in cohorts that excluded patients with previous DVT. No studies were identified that compared repeat US to venography in all patients. Repeat US appears to have a positive yield of 1.3%, with 89% of these being confirmed by venography.

Conclusion
Combined colour-doppler US techniques have optimal sensitivity, while compression US has optimal specificity for DVT. However, all estimates are subject to substantial unexplained heterogeneity. The role of repeat scanning is very uncertain and based upon limited data.
Age at onset of Huntington disease is not modulated by the R72P variation in TP53 and the R196K variation in the gene coding for the human caspase activated DNase (hCAD)
Authors: Arning Larissa , Kraus Peter H , Saft Carsten , Andrich Jürgen , Epplen Jörg T 
Published: October 2005

Abstract

Background

TP53 is an attractive candidate for modifying age of onset (AO) in Huntington disease (HD): The amino-terminus of the mutated huntingtin (htt) exon 1 translation product has functional properties which may affect critically the TP53 pathway in HD neurons. The pathogenic domain of mutant htt interacts with nuclear transcription factors, and it potentially modulates TP53-induced transcriptional events. A single nucleotide polymorphism (SNP) resulting in the R72P exchange in TP53 protein might modulate the variation in AO. In addition, also the R196K replacement in human caspase activated DNase (hCAD) may theoretically affect the AO.

Methods
We have genotyped the polymorphisms R72P and R196K in a well established cohort of 167 unrelated HD patients.

Results
The expanded CAG repeat explained 30.8% of the variance in AO. Adding the genotypes of the SNPs investigated did not affect the variance of the AO variance explained.

Conclusion
In this replication study, no association was found explaining a significant amount of the variability in AO of HD thus contradicting a recent report.
Development of abbreviated measures to assess patient trust in a physician, a health insurer, and the medical profession
Authors: Dugan Elizabeth , Trachtenberg Felicia , Hall Mark A 
Published: October 2005

Abstract

Background
Despite the recent proliferation in research on patient trust, it is seldom a primary outcome, and is often a peripheral area of interest. The length of our original scales to measure trust may limit their use because of the practical needs to minimize both respondent burden and research cost. The objective of this study was to develop three abbreviated scales to measure trust in: (1) a physician, (2) a health insurer, and (3) the medical profession.

Methods
Data from two samples were used. The first was a telephone survey of English-speaking adults in the United States (N = 1117) and the second was a telephone survey of English-speaking adults residing in North Carolina who were members of a health maintenance organization (N = 1024). Data were analyzed to examine data completeness, scaling assumptions, internal consistency properties, and factor structure.

Results
Abbreviated measures (5-items) were developed for each of the three scales. Cronbach's alpha was 0.87 for trust in a physician (test-retest reliability = 0.71), 0.84 for trust in a health insurer (test-retest reliability = 0.73), and 0.77 for trust in the medical profession.

Conclusion
Assessment of data completeness, scale score dispersion characteristics, reliability and validity test results all provide evidence for the soundness of the abbreviated 5-item scales.
A prototype power assist wheelchair that provides for obstacle detection and avoidance for those with visual impairments
Authors: Simpson Richard , LoPresti Edmund , Hayashi Steve , Guo Songfeng , Ding Dan , Ammer William , Sharma Vinod , Cooper Rory 
Published: October 2005

Abstract

Background
Almost 10% of all individuals who are legally blind also have a mobility impairment. The majority of these individuals are dependent on others for mobility. The Smart Power Assistance Module (SPAM) for manual wheelchairs is being developed to provide independent mobility for this population.

Methods
A prototype of the SPAM has been developed using Yamaha JWII power assist hubs, sonar and infrared rangefinders, and a microprocessor. The prototype limits the user to moving straight forward, straight backward, or turning in place, and increases the resistance of the wheels based on the proximity of obstacles. The result is haptic feedback to the user regarding the environment surrounding the wheelchair.

Results
The prototype has been evaluated with four blindfolded able-bodied users and one individual who is blind but not mobility impaired. For all individuals, the prototype reduced the number of collisions on a simple navigation task.

Conclusion
The prototype demonstrates the feasibility of providing navigation assistance to manual wheelchair users, but several shortcomings of the system were identified to be addressed in a second generation prototype.
Exposure and risks from wearing asbestos mitts
Authors: Cherrie John W , Tindall Matthew , Cowie Hilary 
Published: October 2005

Abstract

Background
Very high fibre inhalation exposure has been measured while people were wearing personal protective equipment manufactured from chrysotile asbestos. However, there is little data that relates specifically to wearing asbestos gloves or mitts, particularly when used in hot environments such as those found in glass manufacturing. The aim of this study was to assess the likely personal exposure to asbestos fibres when asbestos mitts were used.

Results
Three types of work activity were simulated in a small test room with unused mitts and artificially aged mitts. Neither pair of mitts were treated to suppress the dust emission. The measured respirable fibre exposure levels ranged from <0.06 to 0.55 fibres/ml, with no significant difference in fibre exposure between aged and unused mitts. The use of high localised ventilation to simulate convective airflows from a furnace reduced exposure levels by about a factor of five. Differences between tasks were statistically significant, with simulated "rowing" of molten glass lowest and replacement of side seals on the furnace highest. Estimated lifetime cancer risk from 20 years exposure at the upper end of the exposure range measured during the study is less than 22 per 100,000.

Conclusion
People who wore asbestos mitts were likely to have been exposed to relatively low levels of airborne chrysotile asbestos fibres, certainly much lower than the standards that were accepted in the 1960's and 70's. The cancer risks from this type of use are likely to be very low.
No aggression in a 4-year-old boy with an androgen-producing tumour: Case Report
Authors: De la Marche Wouter , Prinsen Karin , Boot Annemieke M , Ferdinand Robert F 
Published: October 2005

Abstract

Background
The androgen testosterone plays a critical role in many aspects of sexual differentiation. Also, it is thought to induce aggressive behaviours or to play a role in social dominance.

Case presentation
In this case report a 4-year-old boy is described whose testosterone and dehydroepiandrosterone sulphate (DHEA-S) levels were raised to pubertal levels due to a testosterone producing testis tumour. This provided the unique opportunity to examine the effects of elevated levels of androgens on levels of aggression or on social dominance before the onset of puberty.

Conclusion
The present case report does not support the hypothesis of a causal relationship between testosterone and aggression or between testosterone and social dominance in young children.