On Ex Situ NMR: Developing portable low-cost and/or single sided NMR/MRI

Nuclear magnetic resonance spectroscopy (NMR) is of unsurpassed versatility in its ability to non-destructively probe for chemical identity. Portable, low-cost NMR sensors would enable on site identification of potentially hazardous substances, such as signatures from production of nuclear, chemical, and biological weapon agents, narcotics, explosives, toxins, and poisons. There exist however problems that need to be considered in the case of such sensors: (a) small-scale magnets produce inhomogeneous magnetic fields and therefore undesired Larmor frequency distributions that conceal much of the useful spectral information, and (b) sensitivity in most experiments decreases due to the inherently low and strongly inhomogeneous fields associated with portable instruments. Our approach is to: (a) try to improve the field of low cost magnets either with hardware (e.g. magnet design and construction of ''shim coils'') or via special pulse sequences, where the field is ''effectively shimmed'' to appear homogeneous to the sample, and (b) to use microcoils to improve sensitivity and to allow focusing in smaller regions and therefore smaller static field variations. We have been working in setting up a table top, 2-Tesla permanent Halbach magnet system for tabletop NMR. The Spectrometer console is a Tecmag Apollo, controlled by a dell notebook. Currently an external linear chemagnetics rf amplifier is being used, though the power requirements for our system are quite low (a few Watts). The Magnetic Resonance lab in LLNL, has developed several types and sizes of microcoils, which have been proven to perform well for NMR experiments. We have evaluated an rf, 360 {micro}m O.D., microcoil probe that was built previously. We have finished mapping the magnetic field of the magnet. In the optimal position (in terms of field quality), the field inhomogeneity was at 17ppm. Preliminary fluorine spectra with a resolved two peak separation have now been obtained. For the field, as mapped, we have initial designs of first degree shimming, or gradient coils (linear correction to the field). We have calculated ''shim pulses'' to effectively shim the mapped field, for ideal gradient coils. These calculations will be repeated after the coils will be built and evaluated

Railton Community Assessment Project

A collaborative project between Railton Foundation and Stellenbosch University.This booklet is about sharing our process with other people so that they may be able to do the same in other communities. We have realised how valuable this kind of research is in the process of community development and we would like to help share our experiences of collaborative and community participative research. We hope that this handbook will serve as a guideline for any community leader, teacher or researcher who would like to undertake similar research projects. We realise that there are other ways of doing this, but you may find it helpful to see how we went about the community assessment process. In this booklet we will be providing background information that will help to create a context for doing this kind of research, and we will be outlining various steps in the process. To help bring life to this research process, we will give real lived experiences and examples from the Railton Community Assessment Project (CAP) team. Please consult the Railton Community Assessment Project Report for a comprehensive description of the research processes and findings referred to in this booklet. We hope this handbook is helpful to you and your community.Stellenbosch UniversityRailton FoundationPublishers' versio

Portable, Low-cost NMR with Laser-Lathe Lithography Produced

Nuclear Magnetic Resonance (NMR) is unsurpassed in its ability to non-destructively probe chemical identity. Portable, low-cost NMR sensors would enable on-site identification of potentially hazardous substances, as well as the study of samples in a variety of industrial applications. Recent developments in RF microcoil construction (i.e. coils much smaller than the standard 5 mm NMR RF coils), have dramatically increased NMR sensitivity and decreased the limits-of-detection (LOD). We are using advances in laser pantographic microfabrication techniques, unique to LLNL, to produce RF microcoils for field deployable, high sensitivity NMR-based detectors. This same fabrication technique can be used to produce imaging coils for MRI as well as for standard hardware shimming or 'ex-situ' shimming of field inhomogeneities typically associated with inexpensive magnets. This paper describes a portable NMR system based on a laser-fabricated microcoil and homebuilt probe design. For testing this probe, we used a hand-held 2 kg Halbach magnet that can fit into the palm of a hand, and an RF probe with laser-fabricated microcoils. The focus of the paper is on the evaluation of the microcoils, RF probe, and first generation gradient coils. The setup of this system, initial results, sensitivity measurements, and future plans are discussed. The results, even though preliminary, are promising and provide the foundation for developing a portable, inexpensive NMR system for chemical analysis. Such a system will be ideal for chemical identification of trace substances on site

Can agricultural cultivation methods influence the healthfulness of crops for foods

The aim of the current study was to investigate if there are any health effects of long-term consumption of organically grown crops using a rat model. Crops were retrieved over two years from along-term field trial at three different locations in Denmark, using three different cultivation systems(OA, organic based on livestock manure; OB, organic based on green manure; and C, conventional with mineral fertilizers and pesticides)with two field replicates. The cultivation system had an impact on the nutritional quality, affecting γ-tocopherol, some amino acids, and fatty acid composition. Additionally, the nutritional quality was affected by harvest year and location. However, harvest year and location rather than cultivation system affected the measured health biomarkers. In conclusion, the differences in dietary treatments composed of ingredients from different cultivation systems did not lead to significant differences in the measured health biomarkers, except for a significant difference in plasma IgGl evels

Percolation thresholds in chemical disordered excitable media

The behavior of chemical waves advancing through a disordered excitable medium is investigated in terms of percolation theory and autowave properties in the framework of the light-sensitive Belousov-Zhabotinsky reaction. By controlling the number of sites with a given illumination, different percolation thresholds for propagation are observed, which depend on the relative wave transmittances of the two-state medium considered

Real-Time Fluorescence Loop Mediated Isothermal Amplification for the Diagnosis of Malaria

BACKGROUND: Molecular diagnostic methods can complement existing tools to improve the diagnosis of malaria. However, they require good laboratory infrastructure thereby restricting their use to reference laboratories and research studies. Therefore, adopting molecular tools for routine use in malaria endemic countries will require simpler molecular platforms. The recently developed loop-mediated isothermal amplification (LAMP) method is relatively simple and can be improved for better use in endemic countries. In this study, we attempted to improve this method for malaria diagnosis by using a simple and portable device capable of performing both the amplification and detection (by fluorescence) of LAMP in one platform. We refer to this as the RealAmp method. METHODOLOGY AND SIGNIFICANT FINDINGS: Published genus-specific primers were used to test the utility of this method. DNA derived from different species of malaria parasites was used for the initial characterization. Clinical samples of P. falciparum were used to determine the sensitivity and specificity of this system compared to microscopy and a nested PCR method. Additionally, directly boiled parasite preparations were compared with a conventional DNA isolation method. The RealAmp method was found to be simple and allowed real-time detection of DNA amplification. The time to amplification varied but was generally less than 60 minutes. All human-infecting Plasmodium species were detected. The sensitivity and specificity of RealAmp in detecting P. falciparum was 96.7% and 91.7% respectively, compared to microscopy and 98.9% and 100% respectively, compared to a standard nested PCR method. In addition, this method consistently detected P. falciparum from directly boiled blood samples. CONCLUSION: This RealAmp method has great potential as a field usable molecular tool for diagnosis of malaria. This tool can provide an alternative to conventional PCR based diagnostic methods for field use in clinical and operational programs

A web-based library consult service for evidence-based medicine: Technical development

BACKGROUND: Incorporating evidence based medicine (EBM) into clinical practice requires clinicians to learn to efficiently gain access to clinical evidence and effectively appraise its validity. Even using current electronic systems, selecting literature-based data to solve a single patient-related problem can require more time than practicing physicians or residents can spare. Clinical librarians, as informationists, are uniquely suited to assist physicians in this endeavor. RESULTS: To improve support for evidence-based practice, we have developed a web-based EBM library consult service application (LCS). Librarians use the LCS system to provide full text evidence-based literature with critical appraisal in response to a clinical question asked by a remote physician. LCS uses an entirely Free/Open Source Software platform and will be released under a Free Software license. In the first year of the LCS project, the software was successfully developed and a reference implementation put into active use. Two years of evaluation of the clinical, educational, and attitudinal impact on physician-users and librarian staff are underway, and expected to lead to refinement and wide dissemination of the system. CONCLUSION: A web-based EBM library consult model may provide a useful way for informationists to assist clinicians, and is feasible to implement

Evaluation of cell-free DNA approaches for multi-cancer early detection

In the Circulating Cell-free Genome Atlas (NCT02889978) substudy 1, we evaluate several approaches for a circulating cell-free DNA (cfDNA)-based multi-cancer early detection (MCED) test by defining clinical limit of detection (LOD) based on circulating tumor allele fraction (cTAF), enabling performance comparisons. Among 10 machine-learning classifiers trained on the same samples and independently validated, when evaluated at 98% specificity, those using whole-genome (WG) methylation, single nucleotide variants with paired white blood cell background removal, and combined scores from classifiers evaluated in this study show the highest cancer signal detection sensitivities. Compared with clinical stage and tumor type, cTAF is a more significant predictor of classifier performance and may more closely reflect tumor biology. Clinical LODs mirror relative sensitivities for all approaches. The WG methylation feature best predicts cancer signal origin. WG methylation is the most promising technology for MCED and informs development of a targeted methylation MCED test

Do Fleas Affect Energy Expenditure of Their Free-Living Hosts?

Parasites can cause energetically costly behavioural and immunological responses which potentially can reduce host fitness. However, although most laboratory studies indicate that the metabolic rate of the host increases with parasite infestation, this has never been shown in free-living host populations. In fact, studies thus far have shown no effect of parasitism on field metabolic rate (FMR).We tested the effect of parasites on the energy expenditure of a host by measuring FMR using doubly-labelled water in free-living Baluchistan gerbils (Gerbillus nanus) infested by naturally occurring fleas during winter, spring and summer. We showed for the first time that FMR of free-living G. nanus was significantly and positively correlated with parasite load in spring when parasite load was highest; this relationship approached significance in summer when parasite load was lowest but was insignificant in winter. Among seasons, winter FMRs were highest and summer FMRs were lowest in G. nanus.The lack of parasite effect on FMR in winter could be related to the fact that FMR rates were highest among seasons. In this season, thermoregulatory costs are high which may indicate that less energy could be allocated to defend against parasites or to compensate for other costly activities. The question about the cost of parasitism in nature is now one of the major themes in ecological physiology. Our study supports the hypothesis that parasites can elevate FMR of their hosts, at least under certain conditions. However, the effect is complex and factors such as season and parasite load are involved