Real-time data assimilative modeling on Georges bank

Real-time oceanic forecasts were constructed at sea on Georges Bank during Spring 1999. Ship- and shore-based computations were combined to deliver daily 3-day forecasts to shipboard scientists for interpreting observations and planning operations. Data assimilated included acoustic Doppler current profiler velocities, drifter trajectories, and taxa-specific plankton observations from a Video Plankton Recorder (VPR) system. Services provided included basic 3-D circulation forecasts, forecast positions of drifters, dye and zoo-plankton, and the advective adjustment of observations to produce synoptic maps. The results indicate that real-time, at-sea data assimilative modeling can provide valuable information services and can be deployed routinely, provided that networking among ships, instruments, and shore continues to improve. This paper summarizes the real-time modeling experience. Results of the larger effort including scientific data interpretation are being reported separately

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome

To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events42Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses of 33 women with X mosaicism indicate events preferentially involve the inactive X chromosome. Our results provide further evidence that the sex chromosomes undergo mosaic events more frequently than autosomes, which could have implications for understanding the underlying mechanisms of mosaic events and their possible contribution to risk for chronic diseases

Factors Associated with Revision Surgery after Internal Fixation of Hip Fractures

Background: Femoral neck fractures are associated with high rates of revision surgery after management with internal fixation. Using data from the Fixation using Alternative Implants for the Treatment of Hip fractures (FAITH) trial evaluating methods of internal fixation in patients with femoral neck fractures, we investigated associations between baseline and surgical factors and the need for revision surgery to promote healing, relieve pain, treat infection or improve function over 24 months postsurgery. Additionally, we investigated factors associated with (1) hardware removal and (2) implant exchange from cancellous screws (CS) or sliding hip screw (SHS) to total hip arthroplasty, hemiarthroplasty, or another internal fixation device. Methods: We identified 15 potential factors a priori that may be associated with revision surgery, 7 with hardware removal, and 14 with implant exchange. We used multivariable Cox proportional hazards analyses in our investigation. Results: Factors associated with increased risk of revision surgery included: female sex, [hazard ratio (HR) 1.79, 95% confidence interval (CI) 1.25-2.50; P = 0.001], higher body mass index (fo

The effect of species on lacustrine δ18Odiatom and its implications for palaeoenvironmental reconstructions

The oxygen isotope composition of diatom silica (δ18Odiatom) is increasingly being used to reconstruct climate from marine and lacustrine sedimentary archives. Although diatoms are assumed to precipitate their frustule in isotopic equilibrium with their surrounding water, it is unclear whether internal processes of a given species affect the fractionation of oxygen between the water and the diatom. We present δ18Odiatom data from two diatom size fractions (3–38 and >38 µm) characterized by different species in a sediment core from Heart Lake, Alaska. Differences in δ18Odiatom between the two size fractions varies from 0 to 1.2‰, with a mean offset of 0.01‰ (n = 20). Fourier transform infrared spectroscopy confirms our samples consist of pure biogenic silica (SiO2) and δ18Odiatom trends are not driven by contamination. The maximum offset is outside the range of error, but the mean is within analytical error of the technique (± 1.06‰), demonstrating no discernible species-dependent fractionation in δ18Odiatom. We conclude that lacustrine δ18Odiatom measurements offer a reliable and valuable method for reconstructing δ18Owater. Considering the presence of small offsets in our two records, we advise interpreting shifts in δ18Odiatom only where the magnitude of change is greater than the combined analytical error

Osteoinductive PolyHIPE Foams as Injectable Bone Grafts

We have recently fabricated biodegradable polyHIPEs as injectable bone grafts and characterized the mechanical properties, pore architecture, and cure rates. In this study, calcium phosphate nanoparticles and demineralized bone matrix (DBM) particles were incorporated into injectable polyHIPE foams to promote osteoblastic differentiation of mesenchymal stem cells (MSCs). Upon incorporation of each type of particle, stable monoliths were formed with compressive properties comparable to control polyHIPEs. Pore size quantification indicated a negligible effect of all particles on emulsion stability and resulting pore architecture. Alizarin red calcium staining illustrated the incorporation of calcium phosphate particles at the pore surface, while picrosirius red collagen staining illustrated collagen-rich DBM particles within the monoliths. Osteoinductive particles had a negligible effect on the compressive modulus (∼30 MPa), which remained comparable to human cancellous bone values. All polyHIPE compositions promoted human MSC viability (∼90%) through 2 weeks. Furthermore, gene expression analysis indicated the ability of all polyHIPE compositions to promote osteogenic differentiation through the upregulation of bone-specific markers compared to a time zero control. These findings illustrate the potential for these osteoinductive polyHIPEs to promote osteogenesis and validate future in vivo evaluation. Overall, this work demonstrates the ability to incorporate a range of bioactive components into propylene fumarate dimethacrylate-based injectable polyHIPEs to increase cellular interactions and direct specific behavior without compromising scaffold architecture and resulting properties for various tissue engineering applications