Recent Advances in Spaceborne Precipitation Radar Measurement Techniques and Technology

NASA is currently developing advanced instrument concepts and technologies for future spaceborne atmospheric radars, with an over-arching objective of making such instruments more capable in supporting future science needs and more cost effective. Two such examples are the Second- Generation Precipitation Radar (PR-2) and the Nexrad-In- Space (NIS). PR-2 is a 14/35-GHz dual-frequency rain radar with a deployable 5-meter, wide-swath scanned membrane antenna, a dual-polarized/dual-frequency receiver, and a realtime digital signal processor. It is intended for Low Earth Orbit (LEO) operations to provide greatly enhanced rainfall profile retrieval accuracy while consuming only a fraction of the mass of the current TRMM Precipitation Radar (PR). NIS is designed to be a 35-GHz Geostationary Earth Orbiting (GEO) radar for providing hourly monitoring of the life cycle of hurricanes and tropical storms. It uses a 35-m, spherical, lightweight membrane antenna and Doppler processing to acquire 3-dimensional information on the intensity and vertical motion of hurricane rainfall

Direct drug screening and lipid profiling using ambient mass spectrometry

Mass spectrometry (MS) stands in an outstanding position in analysis of biological specimens owing to its abundant structural information, high accuracy, incomparable sensitivity, high speed, and the large variety of its applications. The ion source, an instrumental part for converting the analyte into ions, has played an important role in analyzing biological specimens by MS. However, the performance of conventional spray-based ionization methods always suffers from chemical interferences derived from complex biological matrices. A series of sample extraction, purification, and separation steps is required before the ionization, so as to ensure excellent performance of MS analysis. In order to simplify the MS procedure, ambient mass spectrometry (AMS) was developed, where the analyte can be directly sampled and ionized from complex biological matrices without or with minimal sample preparation. It is beneficial if the developed methods can be appropriately used in wide applications. At the same time, the simple procedure is complicated by declining qualitative and quantitative performance. The goal of the present research is to develop and improve spray-based AMS methods to meet real applications. Three problems need to be solved to meet with the aim: (1) How to collect and process the sample according to its physical and chemical characterizations. (2) How to effectively extract and ionize the target analyte with reduction of matrix effect. (3) How to produce sufficient and accurate structural and quantitative information on the mass spectrum. In this study, paper spray as a new spray-base AMS method has been used for two applications: (1) Direct drug abuse monitoring for forensic and therapeutic use and (2) Quick screening of antibiotics in food for the food safety. In addition to selecting proper paper substrates and solvents, the quantitative performance of paper spray has also been enhanced by treating the paper substrate with oxidation reagent. Moreover, pipette spray was developed as a very sensitive ionization cartridge by integrating the paper-based extraction function with the nano-ESI ion source for direct identification and quantitation of drugs in complex biofluids. Internal standards can be preloaded in accurately confined area on the paper substrate, so that excellent LOQ was achieved for analyzing antimicrobials in milk and abused drug in whole blood. Finally, to the best of the author’s knowledge, the isomeric structures of unsaturated lipids from tissue samples, were first directly determined with systematic structure profiles by the AMS, which was implemented by extraction spray and on-line Paternò-Büchi (PB) reaction. C=C double positions of target unsaturated lipids can be determined according to their unique fingerprint fragments derived from the PB reaction. The small sample consumption of the extraction spray also enables the profiling of spatial distributions of their isomeric ratios in tissues

A database of naturally occurring human urinary peptides and proteins for use in clinical applications

Owing to its availability, ease of collection and correlation with (patho-) physiology, urine is an attractive source for clinical proteomics. However, the lack of comparable datasets from large cohorts has greatly hindered development in this field. Here we report the establishment of a high resolution proteome database of naturally occurring human urinary peptides and proteins - ranging from 800-17,000 Da - from over 3,600 individual samples using capillary electrophoresis coupled to mass spectrometry, yielding an average of 1,500 peptides per sample. All processed data were deposited in an SQL database, currently containing 5,010 relevant unique urinary peptides that serve as classifiers for diagnosis and monitoring of diseases, including kidney and vascular diseases. Of these, 352 have been sequenced to date. To demonstrate the applicability of this database, two examples of disease diagnosis were provided: For renal damage diagnosis, patients with a specific renal disease were identified with high specificity and sensitivity in a blinded cohort of 131 individuals. We further show definition of biomarkers specific for immunosuppression and complications after transplantation (Kaposi's sarcoma). Due to its high information content, this database will be a powerful tool for the validation of biomarkers for both renal and non-renal diseases

Diagnosis of Multiple Scan-Chain Faults in the Presence of System Logic Defects

We present a combined hardware-software based approach to scan-chain diagnosis, when the outcome of a test may be affected by system faults occurring in the logic outside of the scan chain. For the hardware component we adopt the double-tree scan (DTS) chain architecture, which has previously been shown to be effective in reducing power, volume, and application time of tests for stuck-at and delay faults. We develop a version of flush test which can resolve a multiple fault in a DTS chain to a small number of suspect candidates. Further resolution to a unique multiple fault is enabled by the software component comprising of fault simulation and analysis of the response of the circuit to test patterns produced by ATPG. Experimental results on benchmark circuits show that near-perfect scan-chain diagnosis for multiple faults is possible even when a large number of random system faults are injected in the circuit

Biofluid Analysis with Novel Targeted Mass Spectrometry Methods

Mass spectrometry (MS) provides a high level of sensitivity and specificity to accurately and precisely identify and quantify analytes in a complex matrix. In clinical samples, this instrument is often used to quantify drugs or discover new biomarkers. However, existing workflows routinely use chromatography to separate the components of a sample. These methods lack speed and are expensive, neither of which are ideal characteristics for point of care or high throughput analysis. Paper spray (PS) is an ambient ionization technique that combines the sample preparation and ionization steps, to directly spray a complex sample into a MS. The MS provides the specificity and sensitivity to quantify drugs at low ng/mL levels of detection. Described here are three PS-MS methods demonstrating PS for clinical research. First, a drug is measured for a pharmacokinetic study and demonstrates PS-MS utility for personalized medicine. Then, PS is used to measure whole blood samples collected in a low resource region, demonstrating its compatibility with in-field clinical trial samples. And finally, PS is multiplexed to measure 30 drugs in oral fluid, proving that this methodology can be used for large panels of analytes as traditionally done in the clinical environment. Endogenous metabolites in biofluids can also be measured by MS without prior separation. Multiple reaction monitoring (MRM)- profiling rapidly measures a sample to create a metabolite profile for classifying diseased and healthy samples. This methodology targets biological functional groups in a pooled sample using a library of over 200 precursor (Prec) and neutral loss (NL) scans. All MS signals discovered in these experiments are transformed into ion transitions and are measured in a MRM method. In MRM mode, each transition can be measured on the millisecond time scale allowing for rapid screening of large sample sets. Using univariate and multivariate statistics the sample set can be classified with high accuracy. With diseased sample sets metabolite profiles can be found that classify samples based on signals related to the disease. Since a large variety of functional groups are considered and all signal discovered is collected by MRM, this is considered an unsupervised biomarker discovery methodology. MRM-profiling is described here and demonstrated with over 900 human plasma coronary artery disease samples. First, the metabolite signal was discovered with Prec and NL scans. Then, with a MRM method, the samples were screened in under five days. A metabolite profile was established from this data for the disease. The signals that comprised the MRM-profile were identified and found to be associated with coronary artery disease metabolism. This validates that the methodology generates a useful metabolite profile but is much faster than traditional methodologies. The same methodology is also performed with Parkinson’s disease cerebrospinal fluid samples and discovered signal relevant to the diseased population

The development of an electrochemical sensor for detecting and measuring circulating tumour DNA in human fluids

The high rates of mortality amongst cancer patients highlights the need for advances in rapid detection and enhanced point of care (PoC) testing. A simple approach tailored towards PoC cancer detection and monitoring using label-free electrochemical biosensors is presented. Screen-Printed Carbon electrodes (SPCEs) have been extensively employed as an economical transducer substrate for electrochemical biosensing applications due to their simplicity, affordability and versatility. In this work, a simple, low-cost DNA biosensor is presented which after initial work with Tp53 was developed specifically to detect mutations in a key oncogene (KRAS). Sensor arrays of SPCEs and carbon-nanotube (CNT) modified SPCEs were used to perform multiplexed measurements of DNA hybridisation. Various amplification techniques for enriching the pool of mutated DNA strands were explored and optimised. Amine-modified ssDNA probes were immobilized by modifying SPCEs and CNT-SPCEs with diazonium and EDC/NHS groups. The sensor performance was characterized using cyclic voltammetry, differential pulse voltammetry, square wave voltammetry and electrochemical impedance spectroscopy all to different extents. The detection principle was evaluated by showing effective on-chip DNA hybridization techniques, discrimination using negative controls, and performing multiple repetitions to ascertain reliability of the system. The developed sensor displayed some sensitivity and selectivity to Tp53, KRAS pG12D, and KRAS pG13D DNA, all of which are important mutations in cancer progression. For the amplified samples, 0.027 ng/µl amplicons were detectable while for the non-amplified samples, 0.85 ng/µl cfDNA concentration was detectable using the assay developed. The importance of these findings lies in the design of future electrochemical assays that are capable of discriminating between circulating tumour DNA in the blood prior to and post cancer therapy. The real-world application of this concept provides not only early diagnostic capability but an avenue for treatment decisions to be guided in such a way that health care providers can initiate, choose, avoid, alter or cease selected therapies when caring for patients that have shown symptoms for cancer or who are at risk of having recurrent cancers.The high rates of mortality amongst cancer patients highlights the need for advances in rapid detection and enhanced point of care (PoC) testing. A simple approach tailored towards PoC cancer detection and monitoring using label-free electrochemical biosensors is presented. Screen-Printed Carbon electrodes (SPCEs) have been extensively employed as an economical transducer substrate for electrochemical biosensing applications due to their simplicity, affordability and versatility. In this work, a simple, low-cost DNA biosensor is presented which after initial work with Tp53 was developed specifically to detect mutations in a key oncogene (KRAS). Sensor arrays of SPCEs and carbon-nanotube (CNT) modified SPCEs were used to perform multiplexed measurements of DNA hybridisation. Various amplification techniques for enriching the pool of mutated DNA strands were explored and optimised. Amine-modified ssDNA probes were immobilized by modifying SPCEs and CNT-SPCEs with diazonium and EDC/NHS groups. The sensor performance was characterized using cyclic voltammetry, differential pulse voltammetry, square wave voltammetry and electrochemical impedance spectroscopy all to different extents. The detection principle was evaluated by showing effective on-chip DNA hybridization techniques, discrimination using negative controls, and performing multiple repetitions to ascertain reliability of the system. The developed sensor displayed some sensitivity and selectivity to Tp53, KRAS pG12D, and KRAS pG13D DNA, all of which are important mutations in cancer progression. For the amplified samples, 0.027 ng/µl amplicons were detectable while for the non-amplified samples, 0.85 ng/µl cfDNA concentration was detectable using the assay developed. The importance of these findings lies in the design of future electrochemical assays that are capable of discriminating between circulating tumour DNA in the blood prior to and post cancer therapy. The real-world application of this concept provides not only early diagnostic capability but an avenue for treatment decisions to be guided in such a way that health care providers can initiate, choose, avoid, alter or cease selected therapies when caring for patients that have shown symptoms for cancer or who are at risk of having recurrent cancers

A Distinct Faecal Microbiota and Metabolite Profile Linked to Bowel Habits in Patients with Irritable Bowel Syndrome

Patients with irritable bowel syndrome (IBS) are suggested to have an altered intestinal microenvironment. We therefore aimed to determine the intestinal microenvironment profile, based on faecal microbiota and metabolites, and the potential link to symptoms in IBS patients. The faecal microbiota was evaluated by the GA-map(TM) dysbiosis test, and tandem mass spectrometry (GC-MS/MS) was used for faecal metabolomic profiling in patients with IBS and healthy subjects. Symptom severity was assessed using the IBS Severity Scoring System and anxiety and depression were assessed using the Hospital Anxiety and Depression Scale. A principal component analysis based on faecal microbiota (n = 54) and metabolites (n = 155) showed a clear separation between IBS patients (n = 40) and healthy subjects (n = 18). Metabolites were the main driver of this separation. Additionally, the intestinal microenvironment profile differed between IBS patients with constipation (n = 15) and diarrhoea (n = 11), while no clustering was detected in subgroups of patients according to symptom severity or anxiety. Furthermore, ingenuity pathway analysis predicted amino acid metabolism and several cellular and molecular functions to be altered in IBS patients. Patients with IBS have a distinct faecal microbiota and metabolite profile linked to bowel habits. Intestinal microenvironment profiling, based on faecal microbiota and metabolites, may be considered as a future non-invasive diagnostic tool, alongside providing valuable insights into the pathophysiology of IBS

RRS Discovery Cruise 381, 28 Aug - 03 Oct 2012. Ocean Surface Mixing, Ocean Submesoscale Interaction Study (OSMOSIS)

Cruise D381 was made in support of NERC's Ocean Surface Boundary Layer theme action programme, OSMOSIS (Ocean Surface Mixing, Ocean Sub-mesoscale Interaction Study). The ocean surface boundary layer (OSBL) deepens in response to convective, wind and surface wave forcing, which produce three-dimensional turbulence that entrains denser water, deepening the layer. The OSBL shoals in response to solar heating and to mesoscale and sub-mesoscale motions that adjust lateral buoyancy gradients into vertical stratification. Recent and ongoing work is revolutionising our view of both the deepening and shoaling processes: new processes are coming into focus that are not currently recognised in model parameterisation schemes. In OSMOSIS we have a project which integrates observations, modelling studies and parameterisation development to deliver a step change in modelling of the OSBL. The OSMOSIS overall aim is to develop new, physically based and observationally supported, parameterisations of processes that deepen and shoal the OSBL, and to implement and evaluate these parameterisations in a state-of-the-art global coupled climate model, facilitating improved weather and climate predictions. Cruise D381 was split into two legs D381A and a process study cruise D381B. D381A partly deployed the OSMOSIS mooring array and two gliders for long term observations near the Porcupine Abyssal Plain Observatory. D381B firstly completed mooring and glider deployment work begun during the preceding D381A cruise. D381B then carried out several days of targetted turbulence profiling looking at changes in turbulent energy dissipation resulting from the interation of upper ocean fluid structures such as eddies, sub-mesoscale filaments and Langmuir cells with surface wind and current shear. Finally D381B conducted two spatial surveys with the towed SeaSoar vehicle to map and diagnose the mesoscale and sub-mesoscale flows, which, unusually, are the `large scale' background in which this study sits

Development of Dendrimer-based Technologies for Phosphoproteomics and Glycoproteomics in Biomarker Discovery

The dynamics of post-translational modifications (PTMs) of proteins keeps cells adapting to the ever-changing microenvironment by regulating protein structure and function in the real-time mode. Of all PTMs, protein phosphorylation and glycosylation are undoubtedly two of the most common and important PTMs and have been demonstrated to be closely linked to the onset and progression of various human diseases. Our lab has been focusing on developing novel and more efficient technologies by taking advantage of the properties of dendrimers – a soluble nanopolymer with chemically well-defined structure and functional surface groups – to facilitate the detection and quantification of PTMs using several biochemical assays and mass spectrometry-based shotgun proteomics