Determining adsorbate configuration on alumina surfaces with 13C nuclear magnetic resonance relaxation time analysis

Relative strengths of surface interaction for individual carbon atoms in acyclic and cyclic hydrocarbons adsorbed on alumina surfaces are determined using chemically resolved ¹³C nuclear magnetic resonance (NMR) T₁ relaxation times.

Patterns of admixture and population structure in native populations of Northwest North America

The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas.

We collaborated with six indigenous communities in British Columbia and Southeast Alaska to generate and analyze genome-wide data for over 100 individuals. We then combined this dataset with existing data from populations worldwide, performing an investigation of the genetic structure of indigenous populations of the Pacific Northwest both locally and in relation to continental and worldwide geographic scales. On a regional scale, we identified differences between coastal and interior populations that are likely due to differences both in pre- and post-European contact histories. On a continental scale, we identified differences in genetic structure between populations in the Pacific Northwest and Central and South America, reflecting both differences prior to European contact as well as different post-contact histories of admixture. This study is among the first to analyze genome-wide diversity among indigenous North American populations, and it provides a comparative framework for understanding the effects of European colonization on indigenous communities throughout the Americas.

Risk factors for mediastinitis following cardiac surgery: the importance of managing obesity

BACKGROUND

Mediastinitis is a devastating complication of cardiac surgery. Previous studies have often observed small populations, been retrospective in design, and used a variety of definitions for mediastinitis.

AIM

To identify risk factors for mediastinitis, and strategies to minimize its incidence.

METHODS

A prospective cohort study of 4883 adult patients who underwent cardiac surgery between October 2003 and February 2009, comparing pre- and peri-operative risk factors, microbial aetiology, requirement for re-admission, length of stay and mortality between patients with and without mediastinitis.

FINDINGS

Ninety (1.8%) patients were diagnosed with mediastinitis. Microbial aetiology was defined for 75 patients. Staphlyocococcus aureus was the most common isolate (30 episodes; 15 due to meticillin-resistant S. aureus). Univariate analysis revealed the following pre-operative factors associated with mediastinitis: age; body mass index; diabetes; modified logistic European System for Cardiac Operative Risk Evaluation score; urgent admission; and longer pre-operative stay (P < 0.05). Associated peri-operative factors were: combined coronary artery bypass grafting plus aortic valve replacement; longer aortic cross-clamp time; and longer cardiopulmonary bypass time (P < 0.005). Multi-variate analysis revealed that higher body mass index, combined coronary artery bypass grafting plus aortic valve replacement, and older age were associated with mediastinitis (P < 0.05). Mediastinitis was associated with re-admission to hospital, longer inpatient stay and reduced long-term survival (P < 0.05).

CONCLUSION

Mediastinitis is associated with worse short-term outcomes (re-admission, length of stay) and reduced long-term survival. Obesity is the only modifiable pre-operative risk factor for mediastinitis. It may be possible to reduce risk through pre-operative weight loss programmes before elective surgery.

Visualizing Validation of Protein Surface Classifiers

Many bioinformatics applications construct classifiers that are validated in experiments that compare their results to known ground truth over a corpus. In this paper, we introduce an approach for exploring the results of such classifier validation experiments, focusing on classifiers for regions of molecular surfaces. We provide a tool that allows for examining classification performance patterns over a test corpus. The approach combines a summary view that provides information about an entire corpus of molecules with a detail view that visualizes classifier results directly on protein surfaces. Rather than displaying miniature 3D views of each molecule, the summary provides 2D glyphs of each protein surface arranged in a reorderable, small-multiples grid. Each summary is specifically designed to support visual aggregation to allow the viewer to both get a sense of aggregate properties as well as the details that form them. The detail view provides a 3D visualization of each protein surface coupled with interaction techniques designed to support key tasks, including spatial aggregation and automated camera touring. A prototype implementation of our approach is demonstrated on protein surface classifier experiments.

Separated response function ratios in exclusive, forward π(±) electroproduction

The study of exclusive π(±) electroproduction on the nucleon, including separation of the various structure functions, is of interest for a number of reasons. The ratio RL=σL(π-)/σL(π+) is sensitive to isoscalar contamination to the dominant isovector pion exchange amplitude, which is the basis for the determination of the charged pion form factor from electroproduction data. A change in the value of RT=σT(π-)/σT(π+) from unity at small -t, to 1/4 at large -t, would suggest a transition from coupling to a (virtual) pion to coupling to individual quarks. Furthermore, the mentioned ratios may show an earlier approach to perturbative QCD than the individual cross sections. We have performed the first complete separation of the four unpolarized electromagnetic structure functions above the dominant resonances in forward, exclusive π(±) electroproduction on the deuteron at central Q(2) values of 0.6, 1.0, 1.6  GeV(2) at W=1.95  GeV, and Q(2)=2.45  GeV(2) at W=2.22  GeV. Here, we present the L and T cross sections, with emphasis on RL and RT, and compare them with theoretical calculations. Results for the separated ratio RL indicate dominance of the pion-pole diagram at low -t, while results for RT are consistent with a transition between pion knockout and quark knockout mechanisms.

Update on transcobalamin deficiency: clinical presentation, treatment and outcome

Transcobalamin (TC) transports cobalamin from blood into cells. TC deficiency is a rare autosomal recessive disorder usually presenting in early infancy with failure to thrive, weakness, diarrhoea, pallor, anemia, and pancytopenia or agammaglobulinemia. It can sometimes resemble neonatal leukemia or severe combined immunodeficiency disease. Diagnosis of TC deficiency is suspected based on megaloblastic anemia, elevation of total plasma homocysteine, and blood or urine methylmalonic acid. It is confirmed by studying the synthesis of TC in cultured fibroblasts, or by molecular analysis of the TCN2 gene. TC deficiency is treatable with supplemental cobalamin, but the optimal type, route and frequency of cobalamin administration and long term patient outcomes are unknown. Here we present a series of 30 patients with TC deficiency, including an update on multiple previously published patients, in order to evaluate the different treatment strategies and provide information about long term outcome. Based on the data presented, current practice appears to favour treatment of individuals with TC deficiency by intramuscular injections of hydroxy- or cyanocobalamin. In most cases presented, at least weekly injections (1 mg IM) were necessary to ensure optimal treatment. Most centres adjusted the treatment regimen based on monitoring CBC, total plasma homocysteine, plasma and urine methylmalonic acid, as well as, clinical status. Finally, continuing IM treatment into adulthood appears to be beneficial.

Interfacial tension measurements using MRI drop shape analysis

Accurate interfacial tension data for fluid systems such as hydrocarbons and water is essential to many applications such as reservoir oil and gas recovery predictions. Conventional interfacial tension measurement techniques typically use optical images to analyze droplet shapes but require that the continuous-phase fluid be optically transparent and that the fluids are not refractive index matched. Magnetic resonance images obtain contrast between fluids using other mechanisms such as magnetic relaxation weighting, so systems that are impossible to measure with optical methods may be analyzed. In this article, we present high-field (9.4 T) MRI images of various droplets analyzed with axisymmetric drop shape analysis. The resultant interfacial tension data show good agreement with literature data. The method is subsequently demonstrated using both opaque continuous phases and refractive-index-matched fluids. We conclude with a brief consideration of the potential to extrapolate the methodology to lower magnetic fields (0.3 T), featuring more accessible hardware; although droplet imaging is possible, resolution and stability do not currently permit accurate interfacial tension measurements.

Low-field permanent magnets for industrial process and quality control

In this review we focus on the technology associated with low-field NMR. We present the current state-of-the-art in low-field NMR hardware and experiments, considering general magnet designs, rf performance, data processing and interpretation. We provide guidance on obtaining the optimum results from these instruments, along with an introduction for those new to low-field NMR. The applications of lowfield NMR are now many and diverse. Furthermore, niche applications have spawned unique magnet designs to accommodate the extremes of operating environment or sample geometry. Trying to capture all the applications, methods, and hardware encompassed by low-field NMR would be a daunting task and likely of little interest to researchers or industrialists working in specific subject areas. Instead we discuss only a few applications to highlight uses of the hardware and experiments in an industrial environment. For details on more particular methods and applications, we provide citations to specialized review articles.

Development of a consumer product ingredient database for chemical exposure screening and prioritization

Consumer products are a primary source of chemical exposures, yet little structured information is available on the chemical ingredients of these products and the concentrations at which ingredients are present. To address this data gap, we created a database of chemicals in consumer products using product Material Safety Data Sheets (MSDSs) publicly provided by a large retailer. The resulting database represents 1797 unique chemicals mapped to 8921 consumer products and a hierarchy of 353 consumer product "use categories" within a total of 15 top-level categories. We examine the utility of this database and discuss ways in which it will support (i) exposure screening and prioritization, (ii) generic or framework formulations for several indoor/consumer product exposure modeling initiatives, (iii) candidate chemical selection for monitoring near field exposure from proximal sources, and (iv) as activity tracers or ubiquitous exposure sources using "chemical space" map analyses. Chemicals present at high concentrations and across multiple consumer products and use categories that hold high exposure potential are identified. Our database is publicly available to serve regulators, retailers, manufacturers, and the public for predictive screening of chemicals in new and existing consumer products on the basis of exposure and risk.

Modeling two-dimensional magnetic resonance measurements in coupled pore systems

We present numerical simulations of a two-dimensional (2D) nuclear magnetic resonance process, T_{2}-storage-T_{2}, on a simple mixed porosity system, the micrograin consolidation (μGC) model. The results of these calculations are compared with predictions based on the analytic two-site exchange model, for which we have independently established numerical values for all the input parameters. Although there is qualitative and semiquantitative agreement between the two models, we identify specific instances where the two-site model fails to properly describe the combined effects of relaxation and diffusion. Generally, these instances occur when a gradient in magnetization within the large pores of the μGC model is established during the initial phase of the 2D process. The two-site model assumes that the magnetization is spatially uniform within each of its subpore systems and thus cannot describe such effects.

Modeling two-dimensional magnetic resonance measurements in coupled pore systems

We present numerical simulations of a two-dimensional (2D) nuclear magnetic resonance process, T_{2}-storage-T_{2}, on a simple mixed porosity system, the micrograin consolidation (μGC) model. The results of these calculations are compared with predictions based on the analytic two-site exchange model, for which we have independently established numerical values for all the input parameters. Although there is qualitative and semiquantitative agreement between the two models, we identify specific instances where the two-site model fails to properly describe the combined effects of relaxation and diffusion. Generally, these instances occur when a gradient in magnetization within the large pores of the μGC model is established during the initial phase of the 2D process. The two-site model assumes that the magnetization is spatially uniform within each of its subpore systems and thus cannot describe such effects.

Monitoring bacterially induced calcite precipitation in porous media using magnetic resonance imaging and flow measurements

A range of nuclear magnetic resonance (NMR) techniques are employed to provide novel, non-invasive measurements of both the structure and transport properties of porous media following a biologically mediated calcite precipitation reaction. Both a model glass bead pack and a sandstone rock core were considered. Structure was probed using magnetic resonance imaging (MRI) via a combination of quantitative one-dimensional profiles and three-dimensional images, applied before and after the formation of calcite in order to characterise the spatial distribution of the precipitate. It was shown through modification and variations of the calcite precipitation treatment that differences in the calcite fill would occur but all methods were successful in partially blocking the different porous media. Precipitation was seen to occur predominantly at the inlet of the bead pack, whereas precipitation occurred almost uniformly along the sandstone core. Transport properties are quantified using pulse field gradient (PFG) NMR measurements which provide probability distributions of molecular displacement over a set observation time (propagators), supplementing conventional permeability measurements. Propagators quantify the local effect of calcite formation on system hydrodynamics and the extent of stagnant region formation. Collectively, the combination of NMR measurements utilised here provides a toolkit for determining the efficacy of a biological-precipitation reaction for partially blocking porous materials.

Cold injuries in contemporary conflict

OBJECTIVES

To describe the cases of cold injury sustained during the most recent winter operational tour of Afghanistan, Op HERRICK 15.

METHODS

Retrospective review of all notified British military cases of cold injury sustained between 1 Oct 11 and 30 Mar 12 recorded by UK Medical Group Environmental Health Team.

RESULTS

14 patients with 13 Non-freezing Cold Injuries (NFCI) and two hypothermic injuries were identified. Five patients were of African ethnic decent. Eight out of 13 NFCI patients had probably suffered a previous injury, injuries were sustained from December until February and 9/13 NFCI patients had periods of static duties implicated in the injury mechanism. Eight patients were able to remain in operational theatre on restricted duties whilst 6/14 were evacuated home after sustaining their injuries.

CONCLUSIONS

Although awareness and equipment have improved, cold injuries remain an important cause of Disease and Non Battle Injury on current operations within the British Military. Cases of cold injury are probably under reported and often stem from situations where risk would seem predicable. It is hoped this article will assist in enabling greater understanding of contemporary operational cold injuries and continuing the development of preventative strategies.

Assembly of anthrax toxin pore: lethal-factor complexes into lipid nanodiscs

We have devised a procedure to incorporate the anthrax protective antigen (PA) pore complexed with the N-terminal domain of anthrax lethal factor (LFN ) into lipid nanodiscs and analyzed the resulting complexes by negative-stain electron microscopy. Insertion into nanodiscs was performed without relying on primary and secondary detergent screens. The preparations were relatively pure, and the percentage of PA pore inserted into nanodiscs on EM grids was high (∼43%). Three-dimensional analysis of negatively stained single particles revealed the LFN -PA nanodisc complex mirroring the previous unliganded PA pore nanodisc structure, but with additional protein density consistent with multiple bound LFN molecules on the PA cap region. The assembly procedure will facilitate collection of higher resolution cryo-EM LFN -PA nanodisc structures and use of advanced automated particle selection methods.