DNA microarrays used as 'genomic sensors' have great potential in clinical diagnostics. Biases inherent in random PCR-amplification, cross-hybridization effects, and inadequate microarray analysis, ...however, limit detection sensitivity and specificity. Here, we have studied the relationships between viral amplification efficiency, hybridization signal, and target-probe annealing specificity using a customized microarray platform. Novel features of this platform include the development of a robust algorithm that accurately predicts PCR bias during DNA amplification and can be used to improve PCR primer design, as well as a powerful statistical concept for inferring pathogen identity from probe recognition signatures. Compared to real-time PCR, the microarray platform identified pathogens with 94% accuracy (76% sensitivity and 100% specificity) in a panel of 36 patient specimens. Our findings show that microarrays can be used for the robust and accurate diagnosis of pathogens, and further substantiate the use of microarray technology in clinical diagnostics.
The external carotid artery (ECA) anastomoses in many distal territories supplied by the internal carotid artery (ICA) and is an important source of collateral circulation to the brain. Stenosis of ...the ECA in ipsilateral ICA occlusion can produce ischemic sequelae.
To examine the effectiveness of ECA stenting in treating symptomatic ipsilateral ICA occlusion.
We retrospectively reviewed patient databases from 5 academic medical centers to identify all individuals who underwent ECA stenting after 1998. For all discovered cases, coinvestigators used a common submission form to harvest relevant demographic information, clinical data, procedural details, and follow-up results for further analysis.
Twelve patients (median age, 66 years; range, 45-79 years) were identified for our cohort. Vessel disease involvement included severe ECA stenosis >or= 70% in 11 patients and ipsilateral ICA occlusion in all patients. Presenting symptoms included signs of transient ischemic attack, stroke, and amaurosis fugax. ECA stenting was associated with preservation of neurological status in 11 patients and resolution of symptoms in 5 patients at a median follow-up time of 26 months (range, 1-87 months; mean, 29 months). Symptomatic in-stent restenosis did not occur within any patient during the follow-up course.
We found ECA stenting in symptomatic ipsilateral ICA disease to be a potentially effective strategy to preserve neurological function and to relieve ischemic symptoms. Further investigation with larger studies and longer follow-up periods is warranted to elucidate the true indications of this management strategy.
We examine methods for studying polarons in metal oxides with density functional theory (DFT), using the example of cerium dioxide and the functionals, local density approximation + U (LDA+U), ...generalized gradient approximation + U (GGA+U) in the Perdew-Burke-Ernzerhof parametrization (PBE+U), as well as the hybrid functionals B3LYP, Heyd?Scuseria?Ernzerhof (HSE)03, HSE06, and PBE0. We contrast the four polaron energies commonly reported in different parts of the literature: formation energy, localization/relaxation energy, density-of-states level, and polaron-hopping activation barrier. Qualitatively, all these functionals predict "small" (Holstein) polarons on the scale of a single lattice site, although LDA+U and GGA+U are more effective than the hybrids at localizing the Ce 4f electrons. The improvements over pure LDA/GGA appear because of changes in the filled Ce 4f states when using LDA/GGA+U but due to changes in the empty Ce 4f states when using the hybrids. DFT is shown to have sufficient correlation to predict both adiabatic and (approximate) diabatic hopping barriers. Overall, LDA+U = 6 eV provides the best description in comparison to the experiment, followed by GGA+U = 5 eV. The hybrids are worse, tending to overestimate the gap and significantly underestimate the polaron-hopping barriers.
Pathogen detection using DNA microarrays has the potential to become a fast and comprehensive diagnostics tool. However, since pathogen detection chips currently utilize random primers rather than ...specific primers for the RT-PCR step, bias inherent in random PCR amplification becomes a serious problem that causes large inaccuracies in hybridization signals.
In this paper, we study how the efficiency of random PCR amplification affects hybridization signals. We describe a model that predicts the amplification efficiency of a given random primer on a target viral genome. The prediction allows us to filter false-negative probes of the genome that lie in regions of poor random PCR amplification and improves the accuracy of pathogen detection. Subsequently, we propose LOMA, an algorithm to generate random primers that have good amplification efficiency. Wet-lab validation showed that the generated random primers improve the amplification efficiency significantly.
The blind use of a random primer with attached universal tag (random-tagged primer) in a PCR reaction on a pathogen sample may not lead to a successful amplification. Thus, the design of random-tagged primers is an important consideration when performing PCR.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Anton 2 Shaw, David E.; Grossman, J. P.; Bank, Joseph A. ...
Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis,
11/2014
Conference Proceeding
Anton 2 is a second-generation special-purpose supercomputer for molecular dynamics simulations that achieves significant gains in performance, programmability, and capacity compared to its ...predecessor, Anton 1. The architecture of Anton 2 is tailored for fine-grained event-driven operation, which improves performance by increasing the overlap of computation with communication, and also allows a wider range of algorithms to run efficiently, enabling many new software-based optimizations. A 512-node Anton 2 machine, currently in operation, is up to ten times faster than Anton 1 with the same number of nodes, greatly expanding the reach of all-atom biomolecular simulations. Anton 2 is the first platform to achieve simulation rates of multiple microseconds of physical time per day for systems with millions of atoms. Demonstrating strong scaling, the machine simulates a standard 23,558-atom benchmark system at a rate of 85 μs/day---180 times faster than any commodity hardware platform or general-purpose supercomputer.
The ring-opening of furfuryl alcohol to diol products, including 1,2-pentanediol and 1,5-pentanediol, is investigated over reduced Cu–Co–Al mixed metal oxides in a liquid phase batch reactor under H2 ...pressure. These catalysts are synthesized through the calcination of layered double hydroxides (LDH) to yield well-dispersed, porous mixed metal oxides, which upon reduction displayed activity toward diols, mainly the valuable monomer 1,5-pentanediol. The addition of Cu facilitated the reduction of Co oxide species at lower temperatures, and under optimized conditions, a yield toward 1,5-pentanediol of 44% (total diol yield of 62%) was achieved. Various characterization techniques including temperature-programmed reduction (TPR), X-ray photoelectron spectroscopy (XPS), and X-ray absorption spectroscopy (XAS) are employed to elucidate the structure of the catalysts, suggesting the formation of both metallic (Co and Cu) and oxide (CoO) species after reduction and passivation. Ultimately, this study demonstrates the promising characteristics that nonprecious multimetal catalysts have for the conversion of biomass derived platform molecules to plastic precursors.
Hodi Z, Ellis I O, Elston C W, Pinder S E, Donovan G, Macmillan R D & Lee A H S (2010) Histopathology56, 573–580Comparison of margin assessment by radial and shave sections in wide local excision ...specimens for invasive carcinoma of the breast
Aims: Standard margin assessment of breast carcinoma surgical specimens uses radial sections perpendicular to the margin. Shave sections assess a larger surface area of margin than radial sections. The aim was to assess the value of additional shave sections of the margin.
Methods and results: Both types of section were used to assess 471 wide local excision specimens for invasive carcinoma. One hundred and seventy‐nine specimens had positive margins: only radial margins were involved (tumour within 5 mm of margin) in 76, only shave margins in 45, and both shave and radial margins in 58. Residual carcinoma was found in re‐excision specimens (immediate or later) in 43% when the closest distance to the radial margin was 0–1 mm, 25% for 2–4 mm, 18% for 5–9 mm and 13% for >9 mm. Residual carcinoma was found in 44% of specimens if any shave section was positive and in 9% if all shaves were negative. Residual carcinoma was found in 32% if either radial or shave sections were positive and in 4% if neither was positive.
Conclusions: The combination of radial and shave sections appears to be good at separating patients into two groups with high and low risk of residual carcinoma.
In April 2009, a new influenza A (H1N1 2009) virus emerged that rapidly spread around the world. While current variants of this virus have caused widespread disease, particularly in vulnerable ...groups, there remains the possibility that future variants may cause increased virulence, drug resistance or vaccine escape. Early detection of these virus variants may offer the chance for increased containment and potentially prevention of the virus spread. We have developed and field-tested a resequencing kit that is capable of interrogating all eight segments of the 2009 influenza A(H1N1) virus genome and its variants, with added focus on critical regions such as drug-binding sites, structural components and mutation hotspots. The accompanying base-calling software (EvolSTAR) introduces novel methods that utilize neighbourhood hybridization intensity profiles and substitution bias of probes on the microarray for mutation confirmation and recovery of ambiguous base queries. Our results demonstrate that EvolSTAR is highly accurate and has a much improved call rate. The high throughput and short turn-around time from sample to sequence and analysis results (30 h for 24 samples) makes this kit an efficient large-scale evolutionary biosurveillance tool.
Body image in men with HIV Huang, Jeannie S; Lee, Daniel; Becerra, Karen ...
AIDS patient care and STDs
20, Številka:
10
Journal Article
Recenzirano
To determine body image among HIV-infected men and to determine the relationship of lipodystrophy on body image.
Self-report questionnaires on body image were distributed to HIV-infected men at the ...university-based HIV clinic. Two previously validated instruments, the Body Image Quality of Life (BIQLI) scale and the Situational Inventory of Body Image Dysphoria Short Form (SIBID-S) were used to measure body image effects. The presence of lipodystrophy was determined by both self-report and physician examination. Demographic characteristics, disease stage, health status, and quality of life were also ascertained. Analysis of responses was performed via both group comparisons and linear regression analyses.
One hundred ten men responded. Seventy-one percent identified their sexual orientation as men having sex with men (MSM). Forty-eight reported the presence of lipodystrophic characteristics; 62 reported no lipodystrophic changes. Agreement regarding the presence of lipodystrophy between physician and subject was 0.80 as measured by the kappa coefficient of agreement. Compared to HIV-infected men who denied lipodystrophy, HIV-infected men with self-reported lipodystrophy demonstrated poor body image as measured by BIQLI (p < 0.0001) and SIBID-S scales (p = 0.0001). Similarly, physician rated lipodystrophy was significantly associated with both body image subscale scores.
We demonstrate that lipodystrophy among HIV-infected men is associated with poor body image.
PDF
